diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
index 4172c33e14352d92fffbcd540394c76e396246d5..ad9344e672f706de5d43a3b456c92b32d007ed60 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
@@ -401,7 +401,11 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
}
if (result != null) {
MeSH mesh = meshParser.getMeSH(result.getChemicalId());
+ if (mesh!=null) {
result.addSynonyms(mesh.getSynonyms());
+ } else {
+ logger.warn("Problematic mesh id: "+result.getChemicalId());
+ }
}
} catch (IOException e) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
index a8b5d0184f95f048d3079058c796845288a244bc..18f3df2848899d4b6d2701a3c1157f7c0ecd3544 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
@@ -237,17 +237,17 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
}
}
- }
- }
- }
- }
- } catch (WrongResponseCodeIOException e) {
- logger.warn(prefix + "Cannot find information for element.");
- } catch (Exception e) {
- throw new AnnotatorException(e);
- }
- }
- }
+ }
+ }
+ }
+ }
+ } catch (WrongResponseCodeIOException e) {
+ logger.warn(prefix + "Cannot find information for element.");
+ } catch (Exception e) {
+ throw new AnnotatorException(e);
+ }
+ }
+ }
/**
* Creates query url for given {@link MiriamType#HGNC} identifier.
@@ -265,10 +265,12 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
*
* @param name
* {@link MiriamType#HGNC_SYMBOL}
- * @return url to restful api webpage for given hgnc symbol
+ * @return url to restful API web page for given HGNC symbol
*/
private String getHgncNameUrl(String name) {
- return REST_API_URL + "symbol/" + name;
+ String hgncSymbol = "" + name;
+ hgncSymbol = hgncSymbol.split("\\s+")[0];
+ return REST_API_URL + "symbol/" + hgncSymbol;
}
/**
@@ -304,34 +306,34 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
} else {
Node entry = getNode("doc", resultNode.getChildNodes());
- NodeList list = entry.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("arr")) {
- String type = getNodeAttr("name", node);
- if (type.equals("uniprot_ids")) {
- NodeList uniprotList = node.getChildNodes();
- for (int j = 0; j < uniprotList.getLength(); j++) {
- Node uniprotNode = uniprotList.item(j);
- if (uniprotNode.getNodeType() == Node.ELEMENT_NODE) {
- if (uniprotNode.getNodeName().equals("str")) {
- result.add(createMiriamData(MiriamType.UNIPROT, uniprotNode.getTextContent()));
- }
- }
- }
- }
- }
- }
- }
- }
- return result;
- } catch (WrongResponseCodeIOException e) {
- logger.warn("No HGNC data found for id: "+miriamData);
- return new ArrayList<>();
- } catch (Exception e) {
- throw new AnnotatorException(e);
- }
+ NodeList list = entry.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("arr")) {
+ String type = getNodeAttr("name", node);
+ if (type.equals("uniprot_ids")) {
+ NodeList uniprotList = node.getChildNodes();
+ for (int j = 0; j < uniprotList.getLength(); j++) {
+ Node uniprotNode = uniprotList.item(j);
+ if (uniprotNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (uniprotNode.getNodeName().equals("str")) {
+ result.add(createMiriamData(MiriamType.UNIPROT, uniprotNode.getTextContent()));
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return result;
+ } catch (WrongResponseCodeIOException e) {
+ logger.warn("No HGNC data found for id: " + miriamData);
+ return new ArrayList<>();
+ } catch (Exception e) {
+ throw new AnnotatorException(e);
+ }
}
/**
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java
index fbfb32622f483212e0043813cfd430b83fe40fa5..33d279d3158acc2d6eee1494ef039f7c8cee3e90 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java
@@ -127,7 +127,7 @@ public interface ReferenceGenomeConnector {
* @param version
* version of the reference genome
* @throws IOException
- * thrown when there is a problem with removeing file
+ * thrown when there is a problem with removing file
*/
void removeGenomeVersion(MiriamData organism, String version) throws IOException;
@@ -135,7 +135,7 @@ public interface ReferenceGenomeConnector {
* Returns url to the file that describes reference genome.
*
* @param organism
- * organism of redference genome
+ * organism of reference genome
* @param version
* version of the reference genome
* @return url to the file that describes reference genome
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java
index d32370f0633f02eccd0bdb9b5a5d3920cb363318..d95d98b5c9dfe2889bb81014c9b241807a5e65d6 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java
@@ -42,429 +42,433 @@ import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
*/
public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnector implements ReferenceGenomeConnector {
- /**
- * Server domain name.
- */
- private static final String SERVER = "hgdownload.cse.ucsc.edu";
-
- /**
- * Prefix string used for marking queries in cache database that identifies
- * list of reference genome versions by organism id.
- */
- static final String FILENAME_BY_ORGANISM_VERSION_PREFIX = "ORGANISM_VERSION_FILE:";
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(UcscReferenceGenomeConnector.class);
-
- /**
- * Regex pattern that helps to find out organism names in source file.
- */
- private Pattern organismNamePattern = Pattern.compile("<!--([A-Za-z\\-\\.\\ ]+)Downloads [=]+ -->");
-
- /**
- * Regex pattern that helps to find out reference genome versions.
- */
- private Pattern organismDataUrlPattern = Pattern.compile("\\/goldenPath\\/([A-Za-z0-9\\-\\.]+)\\/bigZips\\/");
-
- /**
- * Access point to taxonomy information.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
-
- /**
- * Default constructor.
- */
- public UcscReferenceGenomeConnector() {
- super(UcscReferenceGenomeConnector.class);
- }
-
- @Override
- public List<String> getDownloadedGenomeVersions(MiriamData organism) {
- List<String> results = new ArrayList<>();
-
- List<ReferenceGenome> genomes = getReferenceGenomeDao().getByType(ReferenceGenomeType.UCSC);
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getOrganism().equals(organism)) {
- results.add(referenceGenome.getVersion());
- }
- }
- return results;
- }
-
- @Override
- public List<String> getAvailableGenomeVersion(MiriamData organism) throws ReferenceGenomeConnectorException {
- Set<String> ids = new HashSet<>();
- try {
- String content = getWebPageContent("http://hgdownload.cse.ucsc.edu/downloads.html");
- Integer start = null;
- Integer end = content.length();
- Matcher matcher = organismNamePattern.matcher(content);
- while (matcher.find()) {
- String name = matcher.group(1).trim();
- if (start != null) {
- end = matcher.start();
- break;
- }
-
- if (name.equalsIgnoreCase("Shared Data")) {
- continue;
- }
- if (name.equalsIgnoreCase("liftOver File")) {
- continue;
- }
- MiriamData taxonomy = taxonomyBackend.getByName(name);
- if (organism.equals(taxonomy)) {
- start = matcher.end();
- }
- }
- // we haven't found a start point for our organism (organism couldn't be
- // found in the list of available organisms)
- if (start != null) {
- String organismContent = content.substring(start, end);
-
- matcher = organismDataUrlPattern.matcher(organismContent);
- while (matcher.find()) {
- String name = matcher.group(1).trim();
- ids.add(name);
- }
- }
-
- } catch (IOException | TaxonomySearchException e) {
- throw new ReferenceGenomeConnectorException("Problem with accessing UCSC database", e);
- }
- List<String> result = new ArrayList<>();
- result.addAll(ids);
- Collections.sort(result, new Comparator<String>() {
- public int compare(String o1, String o2) {
- return extractInt(o2) - extractInt(o1);
- }
-
- });
- return result;
- }
-
- @Override
- public List<MiriamData> getAvailableOrganisms() throws ReferenceGenomeConnectorException {
- try {
- List<MiriamData> result = new ArrayList<>();
- String content = getWebPageContent("http://hgdownload.cse.ucsc.edu/downloads.html");
-
- Matcher matcher = organismNamePattern.matcher(content);
- while (matcher.find()) {
- String name = matcher.group(1).trim();
- if (name.equalsIgnoreCase("Shared Data")) {
- continue;
- }
- if (name.equalsIgnoreCase("liftOver File")) {
- continue;
- }
- MiriamData taxonomy = taxonomyBackend.getByName(name);
- if (taxonomy != null) {
- result.add(taxonomy);
- }
- }
-
- return result;
- } catch (IOException | TaxonomySearchException e) {
- throw new ReferenceGenomeConnectorException("Problem with accessing UCSC database", e);
- }
- }
-
- @Override
- public void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async)
- throws FileNotAvailableException, IOException, ReferenceGenomeConnectorException {
- try {
- downloadGenomeVersion(organism, version, updater, async, getGenomeVersionFile(organism, version));
- } catch (URISyntaxException e) {
- throw new InvalidStateException(e);
- }
- }
-
- @Override
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith("http")) {
- result = getWebPageContent(name);
- } else if (name.startsWith(FILENAME_BY_ORGANISM_VERSION_PREFIX)) {
- String[] tmp = name.substring(FILENAME_BY_ORGANISM_VERSION_PREFIX.length()).split("\n");
- result = getGenomeVersionFile(new MiriamData(MiriamType.TAXONOMY, tmp[0]), tmp[1]);
- } else {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (FileNotAvailableException e) {
- throw new SourceNotAvailable("Cannot find file for the query: " + query, e);
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- @Override
- public void removeGenomeVersion(MiriamData organism, String version) throws IOException {
- List<ReferenceGenome> genomes = getReferenceGenomeDao().getByType(ReferenceGenomeType.UCSC);
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getOrganism().equals(organism) && referenceGenome.getVersion().equals(version)) {
- // removing file from big file cache might not be the best idea here
- if (getBigFileCache().isCached(referenceGenome.getSourceUrl())) {
- getBigFileCache().removeFile(referenceGenome.getSourceUrl());
- }
- for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
- if (getBigFileCache().isCached(mapping.getSourceUrl())) {
- getBigFileCache().removeFile(mapping.getSourceUrl());
- }
- }
- getReferenceGenomeDao().delete(referenceGenome);
- }
- }
- }
-
- /**
- * @return the taxonomyBackend
- * @see #taxonomyBackend
- */
- public TaxonomyBackend getTaxonomyBackend() {
- return taxonomyBackend;
- }
-
- /**
- * @param taxonomyBackend
- * the taxonomyBackend to set
- * @see #taxonomyBackend
- */
- public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
- this.taxonomyBackend = taxonomyBackend;
- }
-
- /**
- * Task that will be able to fetch genome file from ftp server.
- *
- * @author Piotr Gawron
- *
- */
- private final class DownloadGenomeVersionTask implements Callable<Void> {
-
- /**
- * Url to the file that we want to download.
- *
- */
- private String url;
-
- /**
- * Callback listener that will receive information about upload progress.
- *
- */
- private IProgressUpdater updater;
-
- /**
- * Organism for which we want to fetch genome.
- */
- private MiriamData organism;
-
- /**
- * Version of the genome.
- */
- private String version;
-
- /**
- * Default constructor.
- *
- * @param url
- * {@link #url}
- * @param updater
- * {@link #updater}
- * @param organism
- * {@link #organism}
- * @param version
- * {@link #version}
- */
- private DownloadGenomeVersionTask(MiriamData organism, String version, String url, IProgressUpdater updater) {
- this.url = url;
- this.organism = organism;
- this.version = version;
- if (updater != null) {
- this.updater = updater;
- } else {
- this.updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- };
- }
- }
-
- @Override
- public Void call() throws Exception {
- getDbUtils().createSessionForCurrentThread();
- try {
- ReferenceGenome referenceGenome = new ReferenceGenome();
- referenceGenome.setOrganism(organism);
- referenceGenome.setType(ReferenceGenomeType.UCSC);
- referenceGenome.setVersion(version);
- referenceGenome.setSourceUrl(url);
- getReferenceGenomeDao().add(referenceGenome);
- getReferenceGenomeDao().flush();
- getReferenceGenomeDao().commit();
- getDbUtils().closeSessionForCurrentThread();
-
- getBigFileCache().downloadFile(url, false, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- if (updater != null) {
- updater.setProgress(progress);
- }
- // we have to get the object because it's in separate thred
- ReferenceGenome temp = getReferenceGenomeDao().getById(referenceGenome.getId());
- temp.setDownloadProgress(progress);
- getReferenceGenomeDao().update(temp);
- getReferenceGenomeDao().commit();
- }
- });
- return null;
- } finally {
- getDbUtils().closeSessionForCurrentThread();
- }
- }
-
- }
-
- @Override
- public void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async, String customUrl)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
- Callable<Void> computations = new DownloadGenomeVersionTask(organism, version, customUrl, updater);
- if (async) {
- getAsyncExecutorService().submit(computations);
- } else {
- Future<Void> task = getSyncExecutorService().submit(computations);
- executeTask(task);
- }
- }
-
- /**
- * Returns local path on ftp server to folder with data about given organism
- * and version.
- *
- * @param organism
- * organism of reference genome
- * @param version
- * of reference genome
- * @return local path on ftp server to folder with data about reference genome
- */
- private String getGenomePath(MiriamData organism, String version) {
- return "/goldenPath/" + version + "/bigZips/";
- }
-
- @Override
- public String getGenomeVersionFile(MiriamData organism, String version) throws FileNotAvailableException {
- String filename = super.getCacheValue(FILENAME_BY_ORGANISM_VERSION_PREFIX + organism.getResource() + "\n" + version);
- if (filename != null) {
- return filename;
- }
- FTPClient ftp = createFtpClient();
- try {
- ftp.connect(SERVER);
- // After connection attempt, you should check the reply code to verify
- // success.
- int reply = ftp.getReplyCode();
-
- if (!FTPReply.isPositiveCompletion(reply)) {
- throw new FileNotAvailableException("Cannot find file with genome for: " + organism + "; " + version + ". FTP server refused connection.");
- } else {
- ftp.enterLocalPassiveMode();
- ftp.login("anonymous", "");
- ftp.setFileType(FTP.BINARY_FILE_TYPE);
-
- String remotePath = getGenomePath(organism, version);
- FTPFile[] files = ftp.listFiles(remotePath);
- for (FTPFile ftpFile : files) {
- if (ftpFile.getName().endsWith(".2bit")) {
- if (filename != null) {
- logger.warn("More than one 2bit file found in a folder: " + remotePath + ". Using first: " + filename);
- } else {
- filename = ftpFile.getName();
- }
- }
- }
- ftp.logout();
- }
- } catch (IOException e) {
- throw new FileNotAvailableException(e);
- } finally {
- if (ftp.isConnected()) {
- try {
- ftp.disconnect();
- } catch (IOException ioe) {
- throw new FileNotAvailableException("Cannot find file with genome for: " + organism + "; " + version + ". Problem with ftp connection.", ioe);
- }
- }
- }
- if (filename == null) {
- throw new FileNotAvailableException("Cannot find file with genome for: " + organism + "; " + version);
- }
- String result = "ftp://" + SERVER + getGenomePath(organism, version) + filename;
- super.setCacheValue(FILENAME_BY_ORGANISM_VERSION_PREFIX + organism.getResource() + "\n" + version, result);
- return result;
- }
-
- /**
- * Creates new instance of {@link FTPClient}.
- *
- * @return new instance of {@link FTPClient}
- */
- FTPClient createFtpClient() {
- FTPClient ftp = new FTPClient();
- return ftp;
- }
-
- /**
- * Extracts int from the version of the genome. The genome version look like
- * follow: xxxx011.
- *
- * @param s
- * genome version where suffix part is integer number that informs
- * about version
- * @return {@link Integer} representing version of the genome from string that
- * describes genome version (it contains also some letters characters}
- */
- int extractInt(String s) {
- int startIndex = 0;
- int endIndex = s.length() - 2;
- for (int i = 0; i < s.length(); i++) {
- startIndex = i;
- if (s.charAt(i) >= '0' && s.charAt(i) <= '9') {
- break;
- }
- }
- for (int i = startIndex; i < s.length(); i++) {
- if (s.charAt(i) < '0' || s.charAt(i) > '9') {
- break;
- }
- endIndex = i;
- }
- endIndex++;
- if (startIndex >= endIndex) {
- return 0;
- } else {
- return Integer.parseInt(s.substring(startIndex, endIndex));
- }
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
+ /**
+ * Server domain name.
+ */
+ private static final String SERVER = "hgdownload.cse.ucsc.edu";
+
+ /**
+ * Prefix string used for marking queries in cache database that identifies list
+ * of reference genome versions by organism id.
+ */
+ static final String FILENAME_BY_ORGANISM_VERSION_PREFIX = "ORGANISM_VERSION_FILE:";
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(UcscReferenceGenomeConnector.class);
+
+ /**
+ * Regex pattern that helps to find out organism names in source file.
+ */
+ private Pattern organismNamePattern = Pattern.compile("<!--([A-Za-z\\-\\.\\ ]+)Downloads [=]*[\\ ]*-->");
+
+ /**
+ * Regex pattern that helps to find out reference genome versions.
+ */
+ private Pattern organismDataUrlPattern = Pattern.compile("\\/goldenPath\\/([A-Za-z0-9\\-\\.]+)\\/bigZips\\/");
+
+ /**
+ * Access point to taxonomy information.
+ */
+ @Autowired
+ private TaxonomyBackend taxonomyBackend;
+
+ /**
+ * Default constructor.
+ */
+ public UcscReferenceGenomeConnector() {
+ super(UcscReferenceGenomeConnector.class);
+ }
+
+ @Override
+ public List<String> getDownloadedGenomeVersions(MiriamData organism) {
+ List<String> results = new ArrayList<>();
+
+ List<ReferenceGenome> genomes = getReferenceGenomeDao().getByType(ReferenceGenomeType.UCSC);
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getOrganism().equals(organism)) {
+ results.add(referenceGenome.getVersion());
+ }
+ }
+ return results;
+ }
+
+ @Override
+ public List<String> getAvailableGenomeVersion(MiriamData organism) throws ReferenceGenomeConnectorException {
+ Set<String> ids = new HashSet<>();
+ try {
+ String content = getWebPageContent("http://hgdownload.cse.ucsc.edu/downloads.html");
+ Integer start = null;
+ Integer end = content.length();
+ Matcher matcher = organismNamePattern.matcher(content);
+ while (matcher.find()) {
+ String name = matcher.group(1).trim();
+ if (start != null) {
+ end = matcher.start();
+ break;
+ }
+
+ if (name.equalsIgnoreCase("Shared Data")) {
+ continue;
+ }
+ if (name.equalsIgnoreCase("liftOver File")) {
+ continue;
+ }
+ MiriamData taxonomy = taxonomyBackend.getByName(name);
+ if (organism.equals(taxonomy)) {
+ start = matcher.end();
+ }
+ }
+ // we haven't found a start point for our organism (organism couldn't be
+ // found in the list of available organisms)
+ if (start != null) {
+ String organismContent = content.substring(start, end);
+
+ matcher = organismDataUrlPattern.matcher(organismContent);
+ while (matcher.find()) {
+ String name = matcher.group(1).trim();
+ ids.add(name);
+ }
+ }
+
+ } catch (IOException | TaxonomySearchException e) {
+ throw new ReferenceGenomeConnectorException("Problem with accessing UCSC database", e);
+ }
+ List<String> result = new ArrayList<>();
+ result.addAll(ids);
+ Collections.sort(result, new Comparator<String>() {
+ public int compare(String o1, String o2) {
+ return extractInt(o2) - extractInt(o1);
+ }
+
+ });
+ return result;
+ }
+
+ @Override
+ public List<MiriamData> getAvailableOrganisms() throws ReferenceGenomeConnectorException {
+ try {
+ List<MiriamData> result = new ArrayList<>();
+ String content = getWebPageContent("http://hgdownload.cse.ucsc.edu/downloads.html");
+
+ Matcher matcher = organismNamePattern.matcher(content);
+ while (matcher.find()) {
+ String name = matcher.group(1).trim();
+ if (name.equalsIgnoreCase("Shared Data")) {
+ continue;
+ }
+ if (name.equalsIgnoreCase("liftOver File")) {
+ continue;
+ }
+ MiriamData taxonomy = taxonomyBackend.getByName(name);
+ if (taxonomy != null) {
+ result.add(taxonomy);
+ }
+ }
+
+ return result;
+ } catch (IOException | TaxonomySearchException e) {
+ throw new ReferenceGenomeConnectorException("Problem with accessing UCSC database", e);
+ }
+ }
+
+ @Override
+ public void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async)
+ throws FileNotAvailableException, IOException, ReferenceGenomeConnectorException {
+ try {
+ downloadGenomeVersion(organism, version, updater, async, getGenomeVersionFile(organism, version));
+ } catch (URISyntaxException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith("http")) {
+ result = getWebPageContent(name);
+ } else if (name.startsWith(FILENAME_BY_ORGANISM_VERSION_PREFIX)) {
+ String[] tmp = name.substring(FILENAME_BY_ORGANISM_VERSION_PREFIX.length()).split("\n");
+ result = getGenomeVersionFile(new MiriamData(MiriamType.TAXONOMY, tmp[0]), tmp[1]);
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (FileNotAvailableException e) {
+ throw new SourceNotAvailable("Cannot find file for the query: " + query, e);
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ @Override
+ public void removeGenomeVersion(MiriamData organism, String version) throws IOException {
+ List<ReferenceGenome> genomes = getReferenceGenomeDao().getByType(ReferenceGenomeType.UCSC);
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getOrganism().equals(organism) && referenceGenome.getVersion().equals(version)) {
+ // removing file from big file cache might not be the best idea here
+ if (getBigFileCache().isCached(referenceGenome.getSourceUrl())) {
+ getBigFileCache().removeFile(referenceGenome.getSourceUrl());
+ }
+ for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
+ if (getBigFileCache().isCached(mapping.getSourceUrl())) {
+ getBigFileCache().removeFile(mapping.getSourceUrl());
+ }
+ }
+ getReferenceGenomeDao().delete(referenceGenome);
+ }
+ }
+ }
+
+ /**
+ * @return the taxonomyBackend
+ * @see #taxonomyBackend
+ */
+ public TaxonomyBackend getTaxonomyBackend() {
+ return taxonomyBackend;
+ }
+
+ /**
+ * @param taxonomyBackend
+ * the taxonomyBackend to set
+ * @see #taxonomyBackend
+ */
+ public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
+ this.taxonomyBackend = taxonomyBackend;
+ }
+
+ /**
+ * Task that will be able to fetch genome file from ftp server.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class DownloadGenomeVersionTask implements Callable<Void> {
+
+ /**
+ * Url to the file that we want to download.
+ *
+ */
+ private String url;
+
+ /**
+ * Callback listener that will receive information about upload progress.
+ *
+ */
+ private IProgressUpdater updater;
+
+ /**
+ * Organism for which we want to fetch genome.
+ */
+ private MiriamData organism;
+
+ /**
+ * Version of the genome.
+ */
+ private String version;
+
+ /**
+ * Default constructor.
+ *
+ * @param url
+ * {@link #url}
+ * @param updater
+ * {@link #updater}
+ * @param organism
+ * {@link #organism}
+ * @param version
+ * {@link #version}
+ */
+ private DownloadGenomeVersionTask(MiriamData organism, String version, String url, IProgressUpdater updater) {
+ this.url = url;
+ this.organism = organism;
+ this.version = version;
+ if (updater != null) {
+ this.updater = updater;
+ } else {
+ this.updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ };
+ }
+ }
+
+ @Override
+ public Void call() throws Exception {
+ getDbUtils().createSessionForCurrentThread();
+ try {
+ ReferenceGenome referenceGenome = new ReferenceGenome();
+ referenceGenome.setOrganism(organism);
+ referenceGenome.setType(ReferenceGenomeType.UCSC);
+ referenceGenome.setVersion(version);
+ referenceGenome.setSourceUrl(url);
+ getReferenceGenomeDao().add(referenceGenome);
+ getReferenceGenomeDao().flush();
+ getReferenceGenomeDao().commit();
+ getDbUtils().closeSessionForCurrentThread();
+
+ getBigFileCache().downloadFile(url, false, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ if (updater != null) {
+ updater.setProgress(progress);
+ }
+ // we have to get the object because it's in separate thred
+ ReferenceGenome temp = getReferenceGenomeDao().getById(referenceGenome.getId());
+ temp.setDownloadProgress(progress);
+ getReferenceGenomeDao().update(temp);
+ getReferenceGenomeDao().commit();
+ }
+ });
+ return null;
+ } finally {
+ getDbUtils().closeSessionForCurrentThread();
+ }
+ }
+
+ }
+
+ @Override
+ public void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async,
+ String customUrl) throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
+ Callable<Void> computations = new DownloadGenomeVersionTask(organism, version, customUrl, updater);
+ if (async) {
+ getAsyncExecutorService().submit(computations);
+ } else {
+ Future<Void> task = getSyncExecutorService().submit(computations);
+ executeTask(task);
+ }
+ }
+
+ /**
+ * Returns local path on ftp server to folder with data about given organism and
+ * version.
+ *
+ * @param organism
+ * organism of reference genome
+ * @param version
+ * of reference genome
+ * @return local path on ftp server to folder with data about reference genome
+ */
+ private String getGenomePath(MiriamData organism, String version) {
+ return "/goldenPath/" + version + "/bigZips/";
+ }
+
+ @Override
+ public String getGenomeVersionFile(MiriamData organism, String version) throws FileNotAvailableException {
+ String filename = super.getCacheValue(
+ FILENAME_BY_ORGANISM_VERSION_PREFIX + organism.getResource() + "\n" + version);
+ if (filename != null) {
+ return filename;
+ }
+ FTPClient ftp = createFtpClient();
+ try {
+ ftp.connect(SERVER);
+ // After connection attempt, you should check the reply code to verify
+ // success.
+ int reply = ftp.getReplyCode();
+
+ if (!FTPReply.isPositiveCompletion(reply)) {
+ throw new FileNotAvailableException(
+ "Cannot find file with genome for: " + organism + "; " + version + ". FTP server refused connection.");
+ } else {
+ ftp.enterLocalPassiveMode();
+ ftp.login("anonymous", "");
+ ftp.setFileType(FTP.BINARY_FILE_TYPE);
+
+ String remotePath = getGenomePath(organism, version);
+ FTPFile[] files = ftp.listFiles(remotePath);
+ for (FTPFile ftpFile : files) {
+ logger.debug(ftpFile.getName());
+ if (ftpFile.getName().endsWith(".2bit")) {
+ if (filename != null) {
+ logger.warn("More than one 2bit file found in a folder: " + remotePath + ". Using first: " + filename);
+ } else {
+ filename = ftpFile.getName();
+ }
+ }
+ }
+ ftp.logout();
+ }
+ } catch (IOException e) {
+ throw new FileNotAvailableException(e);
+ } finally {
+ if (ftp.isConnected()) {
+ try {
+ ftp.disconnect();
+ } catch (IOException ioe) {
+ throw new FileNotAvailableException(
+ "Cannot find file with genome for: " + organism + "; " + version + ". Problem with ftp connection.", ioe);
+ }
+ }
+ }
+ if (filename == null) {
+ throw new FileNotAvailableException("Cannot find file with genome for: " + organism + "; " + version);
+ }
+ String result = "ftp://" + SERVER + getGenomePath(organism, version) + filename;
+ super.setCacheValue(FILENAME_BY_ORGANISM_VERSION_PREFIX + organism.getResource() + "\n" + version, result);
+ return result;
+ }
+
+ /**
+ * Creates new instance of {@link FTPClient}.
+ *
+ * @return new instance of {@link FTPClient}
+ */
+ FTPClient createFtpClient() {
+ FTPClient ftp = new FTPClient();
+ return ftp;
+ }
+
+ /**
+ * Extracts int from the version of the genome. The genome version look like
+ * follow: xxxx011.
+ *
+ * @param s
+ * genome version where suffix part is integer number that informs
+ * about version
+ * @return {@link Integer} representing version of the genome from string that
+ * describes genome version (it contains also some letters characters}
+ */
+ int extractInt(String s) {
+ int startIndex = 0;
+ int endIndex = s.length() - 2;
+ for (int i = 0; i < s.length(); i++) {
+ startIndex = i;
+ if (s.charAt(i) >= '0' && s.charAt(i) <= '9') {
+ break;
+ }
+ }
+ for (int i = startIndex; i < s.length(); i++) {
+ if (s.charAt(i) < '0' || s.charAt(i) > '9') {
+ break;
+ }
+ endIndex = i;
+ }
+ endIndex++;
+ if (startIndex >= endIndex) {
+ return 0;
+ } else {
+ return Integer.parseInt(s.substring(startIndex, endIndex));
+ }
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
index 71347a9620d10f39b0269c9f292b835750eef416..5dc32a4bd5510019c15bb6e27a7a4e08b3b025aa 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
@@ -32,514 +32,538 @@ import lcsb.mapviewer.model.map.species.Species;
public class HgncAnnotatorTest extends AnnotationTestFunctions {
- final Logger logger = Logger.getLogger(HgncAnnotatorTest.class);
-
- @Autowired
- private HgncAnnotator hgncAnnotator;
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetAnnotationsForSNCA() throws Exception {
- try {
- MiriamData snca = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(snca);
- hgncAnnotator.annotateElement(proteinAlias);
- assertNotNull(proteinAlias.getSymbol());
- assertTrue(proteinAlias.getFormerSymbols().size() > 0);
- assertNotNull(proteinAlias.getFullName());
- assertTrue(proteinAlias.getMiriamData().size() > 1);
- assertTrue(proteinAlias.getSynonyms().size() > 0);
-
- boolean ensemble = false;
- boolean hgncId = false;
- boolean hgncSymbol = false;
- boolean refseq = false;
- boolean entrez = false;
- boolean uniprot = false;
- for (MiriamData md : proteinAlias.getMiriamData()) {
- if (MiriamType.ENSEMBL.equals(md.getDataType())) {
- ensemble = true;
- } else if (MiriamType.HGNC.equals(md.getDataType())) {
- assertEquals("Invalid HGNC id", "11138", md.getResource());
- hgncId = true;
- } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- hgncSymbol = true;
- } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
- refseq = true;
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- entrez = true;
- } else if (MiriamType.UNIPROT.equals(md.getDataType())) {
- uniprot = true;
- }
- }
-
- assertTrue("Ensemble symbol cannot be found", ensemble);
- assertTrue("Hgnc id cannot be found", hgncId);
- assertTrue("Hgnc symbol cannot be found", hgncSymbol);
- assertTrue("RefSeq cannot be found", refseq);
- assertTrue("Entrez cannot be found", entrez);
- assertTrue("Uniprot cannot be found", uniprot);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForElementWithMultiHGNC() throws Exception {
- try {
- MiriamData snca = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- MiriamData park7 = new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(snca);
- proteinAlias.addMiriamData(park7);
- hgncAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForHGNC_ID() throws Exception {
- try {
- MiriamData nsmf = new MiriamData(MiriamType.HGNC, "11138");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(nsmf);
- hgncAnnotator.annotateElement(proteinAlias);
- assertNotNull(proteinAlias.getSymbol());
- assertTrue(proteinAlias.getFormerSymbols().size() > 0);
- assertNotNull(proteinAlias.getFullName());
- assertTrue(proteinAlias.getMiriamData().size() > 1);
- assertTrue(proteinAlias.getSynonyms().size() > 0);
-
- boolean ensemble = false;
- boolean hgncId = false;
- boolean hgncSymbol = false;
- boolean refseq = false;
- boolean entrez = false;
- for (MiriamData md : proteinAlias.getMiriamData()) {
- if (MiriamType.ENSEMBL.equals(md.getDataType())) {
- ensemble = true;
- } else if (MiriamType.HGNC.equals(md.getDataType())) {
- hgncId = true;
- } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- hgncSymbol = true;
- } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
- refseq = true;
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- entrez = true;
- }
- }
-
- assertTrue("Ensemble symbol cannot be found", ensemble);
- assertTrue("Hgnc id cannot be found", hgncId);
- assertTrue("Hgnc symbol cannot be found", hgncSymbol);
- assertTrue("RefSeq cannot be found", refseq);
- assertTrue("Entrez cannot be found", entrez);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForSNCA2() throws Exception {
- try {
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.setName("SNCA");
- hgncAnnotator.annotateElement(proteinAlias);
- assertNotNull(proteinAlias.getSymbol());
- assertNotNull(proteinAlias.getName());
- assertTrue(proteinAlias.getFormerSymbols().size() > 0);
- assertNotNull(proteinAlias.getFullName());
- assertTrue(proteinAlias.getMiriamData().size() > 1);
- assertTrue(proteinAlias.getSynonyms().size() > 0);
-
- boolean ensemble = false;
- boolean hgncId = false;
- boolean hgncSymbol = false;
- boolean refseq = false;
- boolean entrez = false;
- for (MiriamData md : proteinAlias.getMiriamData()) {
- if (MiriamType.ENSEMBL.equals(md.getDataType())) {
- ensemble = true;
- } else if (MiriamType.HGNC.equals(md.getDataType())) {
- hgncId = true;
- } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- hgncSymbol = true;
- } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
- refseq = true;
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- entrez = true;
- }
- }
-
- assertTrue("Ensemble symbol cannot be found", ensemble);
- assertTrue("Hgnc id cannot be found", hgncId);
- assertTrue("Hgnc symbol cannot be found", hgncSymbol);
- assertTrue("RefSeq cannot be found", refseq);
- assertTrue("Entrez cannot be found", entrez);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForInvalid() throws Exception {
- try {
- Species proteinAlias = new GenericProtein("id");
- proteinAlias.setName("UNKNNOWNASD asd");
- hgncAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForInvalid2() throws Exception {
- try {
- Species proteinAlias = new GenericProtein("id");
- proteinAlias.setName("cAMP/cGMP-dependent protein kinase");
- hgncAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceInvalidate() throws Exception {
- String query = "http://google.pl/";
- try {
- String newRes = "hello";
-
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, hgncAnnotator.getCacheType(), newRes);
- String res = cache.getStringByQuery(query, hgncAnnotator.getCacheType());
- assertEquals(newRes, res);
- cache.invalidateByQuery(query, hgncAnnotator.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- res = cache.getStringByQuery(query, hgncAnnotator.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, hgncAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForInvalidMiriamSet() throws Exception {
- try {
- MiriamData md1 = new MiriamData(MiriamType.HGNC, "11138");
- MiriamData md2 = new MiriamData(MiriamType.HGNC, "111382");
- Species proteinAlias = new GenericProtein("");
- proteinAlias.addMiriamData(md1);
- proteinAlias.addMiriamData(md2);
- hgncAnnotator.annotateElement(proteinAlias);
- assertEquals(1, getWarnings().size());
- assertEquals("SNCA", proteinAlias.getName());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncIdToUniprot() throws Exception {
- try {
- List<MiriamData> result = hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "11138"));
- assertEquals(1, result.size());
- assertEquals(new MiriamData(MiriamType.UNIPROT, "P37840", HgncAnnotator.class), result.get(0));
- assertEquals(0, hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "1", HgncAnnotator.class)).size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncIdToName() throws Exception {
- try {
- assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "FSD2", HgncAnnotator.class), hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "18024")));
- assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "LMOD1", HgncAnnotator.class), hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "6647")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUnknownHgncIdToName() throws Exception {
- try {
- assertNull(hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "asd")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncToUniProt1() throws Exception {
- try {
- List<MiriamData> list = hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8"));
- assertEquals(1, list.size());
- assertEquals("Q14790", list.get(0).getResource());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncToUniProtWithInvalidArg() throws Exception {
- try {
- hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.CAS, "CASP8"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testHgncToEntrezWithInvalidArg() throws Exception {
- try {
- hgncAnnotator.hgncToEntrez(new MiriamData(MiriamType.CAS, "CASP8"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsValidHgnc() throws Exception {
- try {
- assertFalse(hgncAnnotator.isValidHgncMiriam(new MiriamData(MiriamType.CAS, "CASP8")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsValidHgnc2() throws Exception {
- try {
- assertTrue(hgncAnnotator.isValidHgncMiriam(new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testHgncIdToNameWithInvalidArg() throws Exception {
- try {
- hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.CAS, "CASP8"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncToUniProt2() throws Exception {
- try {
-
- MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8");
- MiriamData data2 = new MiriamData(MiriamType.HGNC_SYMBOL, "CASP10");
-
- List<MiriamData> list = hgncAnnotator.hgncToUniprot(data1);
- assertEquals(1, list.size());
- assertEquals("Q14790", list.get(0).getResource());
-
- list = hgncAnnotator.hgncToUniprot(data2);
- assertEquals(1, list.size());
- assertEquals("Q92851", list.get(0).getResource());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncToUniProt3() throws Exception {
- try {
- MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "blablabla invalid name");
- List<MiriamData> list = hgncAnnotator.hgncToUniprot(data1);
- assertNotNull(list);
- assertEquals(0, list.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncToEntrez() throws Exception {
- try {
- // check by symbol
- MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "PTGS1");
- MiriamData entrez = hgncAnnotator.hgncToEntrez(data1);
- assertNotNull(entrez);
- assertTrue(new MiriamData(MiriamType.ENTREZ, "5742", HgncAnnotator.class).equals(entrez));
-
- // check by id
- data1 = new MiriamData(MiriamType.HGNC, "11138");
- entrez = hgncAnnotator.hgncToEntrez(data1);
- assertNotNull(entrez);
- assertTrue(new MiriamData(MiriamType.ENTREZ, "6622", HgncAnnotator.class).equals(entrez));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidHgncToEntrez() throws Exception {
- try {
- MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "xxxxxsd");
- MiriamData entrez = hgncAnnotator.hgncToEntrez(data1);
- assertNull(entrez);
-
- data1 = new MiriamData(MiriamType.HGNC, "xxxxxsd");
- entrez = hgncAnnotator.hgncToEntrez(data1);
- assertNull(entrez);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- hgncAnnotator.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- hgncAnnotator.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = hgncAnnotator.getCache();
- try {
- // exclude first cached value
- hgncAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- hgncAnnotator.setWebPageDownloader(mockDownloader);
- hgncAnnotator.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- hgncAnnotator.setWebPageDownloader(downloader);
- hgncAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- hgncAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, hgncAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- hgncAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus() throws Exception {
- WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<response><result/></response>");
- hgncAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, hgncAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- hgncAnnotator.setWebPageDownloader(downloader);
- }
- }
+ final Logger logger = Logger.getLogger(HgncAnnotatorTest.class);
+
+ @Autowired
+ private HgncAnnotator hgncAnnotator;
+
+ @Before
+ public void setUp() {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetAnnotationsForSNCA() throws Exception {
+ try {
+ MiriamData snca = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(snca);
+ hgncAnnotator.annotateElement(proteinAlias);
+ assertNotNull(proteinAlias.getSymbol());
+ assertTrue(proteinAlias.getFormerSymbols().size() > 0);
+ assertNotNull(proteinAlias.getFullName());
+ assertTrue(proteinAlias.getMiriamData().size() > 1);
+ assertTrue(proteinAlias.getSynonyms().size() > 0);
+
+ boolean ensemble = false;
+ boolean hgncId = false;
+ boolean hgncSymbol = false;
+ boolean refseq = false;
+ boolean entrez = false;
+ boolean uniprot = false;
+ for (MiriamData md : proteinAlias.getMiriamData()) {
+ if (MiriamType.ENSEMBL.equals(md.getDataType())) {
+ ensemble = true;
+ } else if (MiriamType.HGNC.equals(md.getDataType())) {
+ assertEquals("Invalid HGNC id", "11138", md.getResource());
+ hgncId = true;
+ } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ hgncSymbol = true;
+ } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
+ refseq = true;
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ entrez = true;
+ } else if (MiriamType.UNIPROT.equals(md.getDataType())) {
+ uniprot = true;
+ }
+ }
+
+ assertTrue("Ensemble symbol cannot be found", ensemble);
+ assertTrue("Hgnc id cannot be found", hgncId);
+ assertTrue("Hgnc symbol cannot be found", hgncSymbol);
+ assertTrue("RefSeq cannot be found", refseq);
+ assertTrue("Entrez cannot be found", entrez);
+ assertTrue("Uniprot cannot be found", uniprot);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForElementWithMultiHGNC() throws Exception {
+ try {
+ MiriamData snca = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ MiriamData park7 = new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(snca);
+ proteinAlias.addMiriamData(park7);
+ hgncAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForHGNC_ID() throws Exception {
+ try {
+ MiriamData nsmf = new MiriamData(MiriamType.HGNC, "11138");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(nsmf);
+ hgncAnnotator.annotateElement(proteinAlias);
+ assertNotNull(proteinAlias.getSymbol());
+ assertTrue(proteinAlias.getFormerSymbols().size() > 0);
+ assertNotNull(proteinAlias.getFullName());
+ assertTrue(proteinAlias.getMiriamData().size() > 1);
+ assertTrue(proteinAlias.getSynonyms().size() > 0);
+
+ boolean ensemble = false;
+ boolean hgncId = false;
+ boolean hgncSymbol = false;
+ boolean refseq = false;
+ boolean entrez = false;
+ for (MiriamData md : proteinAlias.getMiriamData()) {
+ if (MiriamType.ENSEMBL.equals(md.getDataType())) {
+ ensemble = true;
+ } else if (MiriamType.HGNC.equals(md.getDataType())) {
+ hgncId = true;
+ } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ hgncSymbol = true;
+ } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
+ refseq = true;
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ entrez = true;
+ }
+ }
+
+ assertTrue("Ensemble symbol cannot be found", ensemble);
+ assertTrue("Hgnc id cannot be found", hgncId);
+ assertTrue("Hgnc symbol cannot be found", hgncSymbol);
+ assertTrue("RefSeq cannot be found", refseq);
+ assertTrue("Entrez cannot be found", entrez);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForSNCA2() throws Exception {
+ try {
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.setName("SNCA");
+ hgncAnnotator.annotateElement(proteinAlias);
+ assertNotNull(proteinAlias.getSymbol());
+ assertNotNull(proteinAlias.getName());
+ assertTrue(proteinAlias.getFormerSymbols().size() > 0);
+ assertNotNull(proteinAlias.getFullName());
+ assertTrue(proteinAlias.getMiriamData().size() > 1);
+ assertTrue(proteinAlias.getSynonyms().size() > 0);
+
+ boolean ensemble = false;
+ boolean hgncId = false;
+ boolean hgncSymbol = false;
+ boolean refseq = false;
+ boolean entrez = false;
+ for (MiriamData md : proteinAlias.getMiriamData()) {
+ if (MiriamType.ENSEMBL.equals(md.getDataType())) {
+ ensemble = true;
+ } else if (MiriamType.HGNC.equals(md.getDataType())) {
+ hgncId = true;
+ } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ hgncSymbol = true;
+ } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
+ refseq = true;
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ entrez = true;
+ }
+ }
+
+ assertTrue("Ensemble symbol cannot be found", ensemble);
+ assertTrue("Hgnc id cannot be found", hgncId);
+ assertTrue("Hgnc symbol cannot be found", hgncSymbol);
+ assertTrue("RefSeq cannot be found", refseq);
+ assertTrue("Entrez cannot be found", entrez);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForBID() throws Exception {
+ try {
+ GenericProtein bidProtein = new GenericProtein("id");
+ bidProtein.setName("BID");
+ hgncAnnotator.annotateElement(bidProtein);
+
+ GenericProtein bidMutationProtein = new GenericProtein("id2");
+ bidMutationProtein.setName("BID (p15)");
+ hgncAnnotator.annotateElement(bidMutationProtein);
+
+ assertEquals(bidProtein.getSymbol(),bidMutationProtein.getSymbol());
+ assertEquals(bidProtein.getFormerSymbols(),bidMutationProtein.getFormerSymbols());
+ assertEquals(bidProtein.getFullName(),bidMutationProtein.getFullName());
+ assertEquals(bidProtein.getMiriamData(),bidMutationProtein.getMiriamData());
+ assertEquals(bidProtein.getSynonyms(),bidMutationProtein.getSynonyms());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForInvalid() throws Exception {
+ try {
+ Species proteinAlias = new GenericProtein("id");
+ proteinAlias.setName("UNKNNOWNASD asd");
+ hgncAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForInvalid2() throws Exception {
+ try {
+ Species proteinAlias = new GenericProtein("id");
+ proteinAlias.setName("cAMP/cGMP-dependent protein kinase");
+ hgncAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterfaceInvalidate() throws Exception {
+ String query = "http://google.pl/";
+ try {
+ String newRes = "hello";
+
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, hgncAnnotator.getCacheType(), newRes);
+ String res = cache.getStringByQuery(query, hgncAnnotator.getCacheType());
+ assertEquals(newRes, res);
+ cache.invalidateByQuery(query, hgncAnnotator.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ res = cache.getStringByQuery(query, hgncAnnotator.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, hgncAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForInvalidMiriamSet() throws Exception {
+ try {
+ MiriamData md1 = new MiriamData(MiriamType.HGNC, "11138");
+ MiriamData md2 = new MiriamData(MiriamType.HGNC, "111382");
+ Species proteinAlias = new GenericProtein("");
+ proteinAlias.addMiriamData(md1);
+ proteinAlias.addMiriamData(md2);
+ hgncAnnotator.annotateElement(proteinAlias);
+ assertEquals(1, getWarnings().size());
+ assertEquals("SNCA", proteinAlias.getName());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncIdToUniprot() throws Exception {
+ try {
+ List<MiriamData> result = hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "11138"));
+ assertEquals(1, result.size());
+ assertEquals(new MiriamData(MiriamType.UNIPROT, "P37840", HgncAnnotator.class), result.get(0));
+ assertEquals(0, hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "1", HgncAnnotator.class)).size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncIdToName() throws Exception {
+ try {
+ assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "FSD2", HgncAnnotator.class),
+ hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "18024")));
+ assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "LMOD1", HgncAnnotator.class),
+ hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "6647")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUnknownHgncIdToName() throws Exception {
+ try {
+ assertNull(hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "asd")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToUniProt1() throws Exception {
+ try {
+ List<MiriamData> list = hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8"));
+ assertEquals(1, list.size());
+ assertEquals("Q14790", list.get(0).getResource());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToUniProtWithInvalidArg() throws Exception {
+ try {
+ hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.CAS, "CASP8"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToEntrezWithInvalidArg() throws Exception {
+ try {
+ hgncAnnotator.hgncToEntrez(new MiriamData(MiriamType.CAS, "CASP8"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsValidHgnc() throws Exception {
+ try {
+ assertFalse(hgncAnnotator.isValidHgncMiriam(new MiriamData(MiriamType.CAS, "CASP8")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsValidHgnc2() throws Exception {
+ try {
+ assertTrue(hgncAnnotator.isValidHgncMiriam(new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncIdToNameWithInvalidArg() throws Exception {
+ try {
+ hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.CAS, "CASP8"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToUniProt2() throws Exception {
+ try {
+
+ MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8");
+ MiriamData data2 = new MiriamData(MiriamType.HGNC_SYMBOL, "CASP10");
+
+ List<MiriamData> list = hgncAnnotator.hgncToUniprot(data1);
+ assertEquals(1, list.size());
+ assertEquals("Q14790", list.get(0).getResource());
+
+ list = hgncAnnotator.hgncToUniprot(data2);
+ assertEquals(1, list.size());
+ assertEquals("Q92851", list.get(0).getResource());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToUniProt3() throws Exception {
+ try {
+ MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "blablabla invalid name");
+ List<MiriamData> list = hgncAnnotator.hgncToUniprot(data1);
+ assertNotNull(list);
+ assertEquals(0, list.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToEntrez() throws Exception {
+ try {
+ // check by symbol
+ MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "PTGS1");
+ MiriamData entrez = hgncAnnotator.hgncToEntrez(data1);
+ assertNotNull(entrez);
+ assertTrue(new MiriamData(MiriamType.ENTREZ, "5742", HgncAnnotator.class).equals(entrez));
+
+ // check by id
+ data1 = new MiriamData(MiriamType.HGNC, "11138");
+ entrez = hgncAnnotator.hgncToEntrez(data1);
+ assertNotNull(entrez);
+ assertTrue(new MiriamData(MiriamType.ENTREZ, "6622", HgncAnnotator.class).equals(entrez));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidHgncToEntrez() throws Exception {
+ try {
+ MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "xxxxxsd");
+ MiriamData entrez = hgncAnnotator.hgncToEntrez(data1);
+ assertNull(entrez);
+
+ data1 = new MiriamData(MiriamType.HGNC, "xxxxxsd");
+ entrez = hgncAnnotator.hgncToEntrez(data1);
+ assertNull(entrez);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ hgncAnnotator.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ hgncAnnotator.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = hgncAnnotator.getCache();
+ try {
+ // exclude first cached value
+ hgncAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ hgncAnnotator.setWebPageDownloader(mockDownloader);
+ hgncAnnotator.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ hgncAnnotator.setWebPageDownloader(downloader);
+ hgncAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ hgncAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, hgncAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ hgncAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenReturn("<response><result/></response>");
+ hgncAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, hgncAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ hgncAnnotator.setWebPageDownloader(downloader);
+ }
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
index 5ff31b7460e125167a6e4df0574204fe723c3de1..0ae6336559f94305885ac9491bc3dbeda41e05a1 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
@@ -49,921 +49,926 @@ import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
public class UcscReferenceGenomeConnectorTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(UcscReferenceGenomeConnectorTest.class);
-
- @Autowired
- UcscReferenceGenomeConnector connector;
-
- @Autowired
- ReferenceGenomeDao referenceGenomeDao;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testRefreshCacheQuery() throws Exception {
- try {
- assertNotNull(connector.refreshCacheQuery("http://google.pl/"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableGenomeVersion() throws Exception {
- MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
- try {
- List<String> list = connector.getAvailableGenomeVersion(human);
- assertTrue(list.size() >= 17);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableGenomeVersionWhenProblemWithTaxonomyServer() throws Exception {
- MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
- TaxonomyBackend taxonomyBackend = connector.getTaxonomyBackend();
- try {
- // simulate problems with taxonomy server
- TaxonomyBackend taxonomyMock = Mockito.mock(TaxonomyBackend.class);
- when(taxonomyMock.getByName(anyString())).thenThrow(new TaxonomySearchException(null, null));
- connector.setTaxonomyBackend(taxonomyMock);
-
- connector.getAvailableGenomeVersion(human);
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setTaxonomyBackend(taxonomyBackend);
- }
- }
-
- @Test
- public void testGetAvailableGenomeVersionForInvalidTaxonomy() throws Exception {
- MiriamData unknown = new MiriamData(MiriamType.TAXONOMY, "10101010101");
- try {
- List<String> list = connector.getAvailableGenomeVersion(unknown);
- assertEquals(0, list.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableOrganisms() throws Exception {
- try {
- MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
- MiriamData chicken = new MiriamData(MiriamType.TAXONOMY, "9031");
- List<MiriamData> list = connector.getAvailableOrganisms();
- assertTrue(list.size() > 40);
-
- assertTrue(list.contains(human));
- assertTrue(list.contains(chicken));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableOrganismsWhenUcscWebpageDown() throws Exception {
- WebPageDownloader downloader = connector.getWebPageDownloader();
- GeneralCacheInterface originalCache = connector.getCache();
- try {
- // exclude first cached value
- connector.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- connector.setWebPageDownloader(mockDownloader);
- connector.getAvailableOrganisms();
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- assertTrue(e.getMessage().contains("Problem with accessing UCSC database"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setWebPageDownloader(downloader);
- connector.setCache(originalCache);
- }
- }
-
- @Test
- public void testDownloadGenomeVersion() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
- String version = "eboVir3";
-
- try {
- dbUtils.createSessionForCurrentThread();
- List<String> list = connector.getDownloadedGenomeVersions(yeast);
- if (list.contains(version)) {
- connector.removeGenomeVersion(yeast, version);
- }
- dbUtils.closeSessionForCurrentThread();
- list = connector.getDownloadedGenomeVersions(yeast);
-
- assertFalse(list.contains(version));
-
- connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false);
-
- list = connector.getDownloadedGenomeVersions(yeast);
- assertTrue(list.contains(version));
-
- List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- ReferenceGenome genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
- connector.downloadGeneMappingGenomeVersion(genome, "test", null, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- dbUtils.createSessionForCurrentThread();
- genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
- assertEquals(1, genome.getGeneMapping().size());
- dbUtils.closeSessionForCurrentThread();
-
- try {
- // try to download the same thing for the second time
- connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- assertTrue(e.getMessage().contains("already exists"));
- }
-
- try {
- // try to download something that is not big bed
- connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.txt");
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- assertTrue(e.getMessage().contains("Only big bed format files are supported"));
- }
-
-// connector.removeGeneMapping(genome.getGeneMapping().get(0));
-
- int warningCount = getWarnings().size();
-
- // try to remove invalid mapping
- connector.removeGeneMapping(new ReferenceGenomeGeneMapping());
-
- assertEquals(warningCount + 1, getWarnings().size());
-
- dbUtils.createSessionForCurrentThread();
- connector.removeGenomeVersion(yeast, version);
- dbUtils.closeSessionForCurrentThread();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @SuppressWarnings("unchecked")
- @Test
- public void testDownloadGenomeVersionWhenInternalUrlIsInvalid() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
- String version = "eboVir3";
-
- ExecutorService originalExecutorService = connector.getSyncExecutorService();
- try {
- ExecutorService executorService = Mockito.mock(ExecutorService.class);
- connector.setSyncExecutorService(executorService);
- Future<?> task = Mockito.mock(Future.class);
- when(task.get()).thenThrow(new ExecutionException(new URISyntaxException("", "")));
- when(executorService.submit(any(Callable.class))).thenReturn(task);
-
- connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false);
- fail("Exception expected");
-
- } catch (InvalidStateException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setSyncExecutorService(originalExecutorService);
- }
- }
-
- @Test
- public void testDownloadGenomeVersionAsync() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
- String version = "eboVir3";
-
- BigFileCache bigFileCache = connector.getBigFileCache();
- try {
- dbUtils.createSessionForCurrentThread();
- List<String> list = connector.getDownloadedGenomeVersions(yeast);
- if (list.contains(version)) {
- connector.removeGenomeVersion(yeast, version);
- }
- list = connector.getDownloadedGenomeVersions(yeast);
-
- dbUtils.closeSessionForCurrentThread();
-
- // create a mock for ftp connections (so we speed up tests), the real
- // connection is tested elsewhere
- BigFileCache mockCache = Mockito.mock(BigFileCache.class);
- Mockito.doAnswer(new Answer<Void>() {
-
- @Override
- public Void answer(InvocationOnMock invocation) throws Throwable {
- IProgressUpdater updater = (IProgressUpdater) invocation.getArguments()[2];
- updater.setProgress(100);
- return null;
- }
- }).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
-
- connector.setBigFileCache(mockCache);
-
- assertFalse(list.contains(version));
-
- connector.downloadGenomeVersion(yeast, version, null, true);
-
- waitForDownload();
-
- dbUtils.createSessionForCurrentThread();
- list = connector.getDownloadedGenomeVersions(yeast);
- assertTrue(list.contains(version));
-
- List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- ReferenceGenome genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- dbUtils.closeSessionForCurrentThread();
- assertNotNull(genome);
- connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- waitForDownload();
-
- genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
- referenceGenomeDao.refresh(genome);
- assertEquals(1, genome.getGeneMapping().size());
-
- try {
- // try to download the same thing for the second time
- connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- assertTrue(e.getMessage().contains("already exists"));
- }
-
- try {
- // try to download something that is not big bed
- connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.txt");
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- assertTrue(e.getMessage().contains("Only big bed format files are supported"));
- }
-
- connector.removeGeneMapping(genome.getGeneMapping().get(0));
-
- int warningCount = getWarnings().size();
-
- // try to remove invalid mapping
- connector.removeGeneMapping(new ReferenceGenomeGeneMapping());
-
- assertEquals(warningCount + 1, getWarnings().size());
-
- connector.removeGenomeVersion(yeast, version);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setBigFileCache(bigFileCache);
- }
- }
-
- @Test
- public void testDownloadGenomeVersionAsyncWithException() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
- String version = "eboVir3";
-
- BigFileCache bigFileCache = connector.getBigFileCache();
- try {
- dbUtils.createSessionForCurrentThread();
- List<String> list = connector.getDownloadedGenomeVersions(yeast);
- if (list.contains(version)) {
- connector.removeGenomeVersion(yeast, version);
- }
- list = connector.getDownloadedGenomeVersions(yeast);
-
- dbUtils.closeSessionForCurrentThread();
-
- // create a mock for ftp connections (so we speed up tests), the real
- // connection is tested elsewhere
- BigFileCache mockCache = Mockito.mock(BigFileCache.class);
-
- connector.setBigFileCache(mockCache);
-
- assertFalse(list.contains(version));
-
- connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true);
-
- waitForDownload();
-
- dbUtils.createSessionForCurrentThread();
- list = connector.getDownloadedGenomeVersions(yeast);
- assertTrue(list.contains(version));
-
- List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- ReferenceGenome genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- dbUtils.closeSessionForCurrentThread();
- assertNotNull(genome);
-
- Mockito.doThrow(new IOException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
- assertEquals(0, getErrors().size());
- connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- waitForDownload();
-
- logger.debug(getErrors());
- // during this downlad we expect exception thrown by downloader
- assertEquals(1, getErrors().size());
-
- Mockito.doThrow(new OutOfMemoryError()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
- connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- waitForDownload();
- // during this downlad we expect error, this shouldn't change list of
- // errors
- assertEquals(1, getErrors().size());
-
- Mockito.doThrow(new URISyntaxException("", "")).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
- connector.downloadGeneMappingGenomeVersion(genome, "test3", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- waitForDownload();
-
- // during this downlad we expect error (exception thrown by downloader)
- assertEquals(2, getErrors().size());
-
- genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
- referenceGenomeDao.refresh(genome);
- assertEquals(3, genome.getGeneMapping().size());
-
- connector.removeGeneMapping(genome.getGeneMapping().get(2));
- connector.removeGeneMapping(genome.getGeneMapping().get(1));
- connector.removeGeneMapping(genome.getGeneMapping().get(0));
- connector.removeGenomeVersion(yeast, version);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setBigFileCache(bigFileCache);
- }
- }
-
- @Test
- public void testDownloadGenomeVersionWithException() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
- String version = "eboVir3";
-
- BigFileCache bigFileCache = connector.getBigFileCache();
- try {
- List<String> list = connector.getDownloadedGenomeVersions(yeast);
- if (list.contains(version)) {
- connector.removeGenomeVersion(yeast, version);
- }
- list = connector.getDownloadedGenomeVersions(yeast);
-
- // create a mock for ftp connections (so we speed up tests), the real
- // connection is tested elsewhere
- BigFileCache mockCache = Mockito.mock(BigFileCache.class);
-
- connector.setBigFileCache(mockCache);
-
- assertFalse(list.contains(version));
-
- connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false);
-
- list = connector.getDownloadedGenomeVersions(yeast);
- assertTrue(list.contains(version));
-
- List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- ReferenceGenome genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
-
- Mockito.doThrow(new IOException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
- assertEquals(0, getErrors().size());
- try {
- connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
- fail("Exception expected");
- } catch (IOException e) {
-
- }
-
- Mockito.doThrow(new RuntimeException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
- try {
- connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- fail("Exception expected");
- } catch (InvalidStateException e) {
-
- }
-
- Mockito.doThrow(new URISyntaxException("", "")).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
-
- try {
- connector.downloadGeneMappingGenomeVersion(genome, "test3", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
- fail("Exception expected");
- } catch (URISyntaxException e) {
-
- }
-
- genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
- referenceGenomeDao.refresh(genome);
- assertEquals(3, genome.getGeneMapping().size());
-
- connector.removeGeneMapping(genome.getGeneMapping().get(2));
- connector.removeGeneMapping(genome.getGeneMapping().get(1));
- connector.removeGeneMapping(genome.getGeneMapping().get(0));
- connector.removeGenomeVersion(yeast, version);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setBigFileCache(bigFileCache);
- }
- }
-
- @Test
- public void testGetGenomeVersionFile() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
- try {
- String url = connector.getGenomeVersionFile(yeast, version);
- assertNotNull(url);
- url.contains("sacCer3.2bit");
- url.contains("ftp");
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUnknownGenomeVersionFile() {
- MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
- String version = "hg8";
- try {
- connector.getGenomeVersionFile(human, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalid() throws Exception {
- try {
- connector.refreshCacheQuery("invalid query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalid2() throws Exception {
- try {
- connector.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefresh() throws Exception {
- try {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- String query = UcscReferenceGenomeConnector.FILENAME_BY_ORGANISM_VERSION_PREFIX + yeast.getResource() + "\n" + version;
- Object res = connector.refreshCacheQuery(query);
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshUnknownFile() throws Exception {
- try {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "unkVer";
-
- String query = UcscReferenceGenomeConnector.FILENAME_BY_ORGANISM_VERSION_PREFIX + yeast.getResource() + "\n" + version;
- connector.refreshCacheQuery(query);
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector();
- connectorUnderTest.setBigFileCache(connector.getBigFileCache());
- connectorUnderTest.setDbUtils(connector.getDbUtils());
- connectorUnderTest.setReferenceGenomeDao(connector.getReferenceGenomeDao());
- connectorUnderTest.setReferenceGenomeGeneMappingDao(connector.getReferenceGenomeGeneMappingDao());
-
- assertEquals(connector.getBigFileCache(), connectorUnderTest.getBigFileCache());
- assertEquals(connector.getDbUtils(), connectorUnderTest.getDbUtils());
- assertEquals(connector.getReferenceGenomeDao(), connectorUnderTest.getReferenceGenomeDao());
- assertEquals(connector.getReferenceGenomeGeneMappingDao(), connectorUnderTest.getReferenceGenomeGeneMappingDao());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGenomeVersionExtractorForInvalidGenome() throws Exception {
- try {
- int version = connector.extractInt("");
- assertEquals(0, version);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGenomeVersionExtractorForInvalidGenome2() throws Exception {
- try {
- int version = connector.extractInt("x");
- assertEquals(0, version);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGenomeVersionExtractorForValid() throws Exception {
- try {
- int version = connector.extractInt("x1");
- assertEquals(1, version);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGenomeVersionExtractorForValid2() throws Exception {
- try {
- int version = connector.extractInt("xy12z");
- assertEquals(12, version);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = connector.getWebPageDownloader();
- GeneralCacheInterface originalCache = connector.getCache();
- try {
- // exclude first cached value
- connector.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- connector.setWebPageDownloader(mockDownloader);
- connector.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setWebPageDownloader(downloader);
- connector.setCache(originalCache);
- }
- }
-
- @Test
- public void testRefreshCacheQueryWhenFtpConnectionFails() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- Mockito.doReturn(FTPReply.REQUEST_DENIED).when(mockClient).getReplyCode();
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- connectorUnderTest.getGenomeVersionFile(yeast, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- assertTrue(e.getMessage().contains("FTP server refused connection"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetGenomeVersionFileWhenFtpConnectionFails2() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- try {
- Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
- Mockito.doReturn(false).when(mockClient).isConnected();
- } catch (Exception e) {
- fail();
- }
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- connectorUnderTest.getGenomeVersionFile(yeast, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetGenomeVersionFileWhenFtpConnectionFails() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- try {
- Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
- Mockito.doReturn(true).when(mockClient).isConnected();
- } catch (Exception e) {
- fail();
- }
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- connectorUnderTest.getGenomeVersionFile(yeast, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetGenomeVersionFileWhenFtpConnectionFails3() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- try {
- Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
- Mockito.doReturn(true).when(mockClient).isConnected();
- Mockito.doThrow(new IOException()).when(mockClient).disconnect();
- } catch (Exception e) {
- fail();
- }
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- connectorUnderTest.getGenomeVersionFile(yeast, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetGenomeVersionFileWhenFtpDisconnectConnectionFails() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- try {
- Mockito.doThrow(new IOException()).when(mockClient).disconnect();
- Mockito.doReturn(new FTPFile[] {}).when(mockClient).listFiles(anyString());
- Mockito.doReturn(FTPReply.COMMAND_OK).when(mockClient).getReplyCode();
- Mockito.doReturn(true).when(mockClient).isConnected();
- } catch (Exception e) {
- fail();
- }
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- connectorUnderTest.getGenomeVersionFile(yeast, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- assertTrue(e.getMessage().contains("Problem with ftp connection"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetGenomeVersionFileWithMore2bitFiles() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- try {
- FTPFile file1 = new FTPFile();
- file1.setName("1.2bit");
- FTPFile file2 = new FTPFile();
- file2.setName("2.2bit");
- FTPFile[] files = new FTPFile[] { file1, file2 };
-
- Mockito.doReturn(files).when(mockClient).listFiles(anyString());
- Mockito.doReturn(FTPReply.COMMAND_OK).when(mockClient).getReplyCode();
- } catch (Exception e) {
- fail();
- }
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- String url = connectorUnderTest.getGenomeVersionFile(yeast, version);
- assertEquals(1, getWarnings().size());
- assertTrue(url.endsWith("1.2bit"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private void waitForDownload() throws InterruptedException {
- while (connector.getDownloadThreadCount() > 0) {
- logger.debug("Waiting for download to finish");
- Thread.sleep(100);
- }
- }
+ Logger logger = Logger.getLogger(UcscReferenceGenomeConnectorTest.class);
+
+ @Autowired
+ UcscReferenceGenomeConnector connector;
+
+ @Autowired
+ ReferenceGenomeDao referenceGenomeDao;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testRefreshCacheQuery() throws Exception {
+ try {
+ assertNotNull(connector.refreshCacheQuery("http://google.pl/"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableGenomeVersion() throws Exception {
+ MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
+ try {
+ List<String> list = connector.getAvailableGenomeVersion(human);
+ logger.debug(list);
+ assertTrue(list.size() >= 17);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableGenomeVersionWhenProblemWithTaxonomyServer() throws Exception {
+ MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
+ TaxonomyBackend taxonomyBackend = connector.getTaxonomyBackend();
+ try {
+ // simulate problems with taxonomy server
+ TaxonomyBackend taxonomyMock = Mockito.mock(TaxonomyBackend.class);
+ when(taxonomyMock.getByName(anyString())).thenThrow(new TaxonomySearchException(null, null));
+ connector.setTaxonomyBackend(taxonomyMock);
+
+ connector.getAvailableGenomeVersion(human);
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setTaxonomyBackend(taxonomyBackend);
+ }
+ }
+
+ @Test
+ public void testGetAvailableGenomeVersionForInvalidTaxonomy() throws Exception {
+ MiriamData unknown = new MiriamData(MiriamType.TAXONOMY, "10101010101");
+ try {
+ List<String> list = connector.getAvailableGenomeVersion(unknown);
+ assertEquals(0, list.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableOrganisms() throws Exception {
+ try {
+ MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
+ MiriamData chicken = new MiriamData(MiriamType.TAXONOMY, "9031");
+ List<MiriamData> list = connector.getAvailableOrganisms();
+ logger.debug(list);
+ assertTrue(list.size() > 40);
+
+ assertTrue(list.contains(human));
+ assertTrue(list.contains(chicken));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableOrganismsWhenUcscWebpageDown() throws Exception {
+ WebPageDownloader downloader = connector.getWebPageDownloader();
+ GeneralCacheInterface originalCache = connector.getCache();
+ try {
+ // exclude first cached value
+ connector.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ connector.setWebPageDownloader(mockDownloader);
+ connector.getAvailableOrganisms();
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ assertTrue(e.getMessage().contains("Problem with accessing UCSC database"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setWebPageDownloader(downloader);
+ connector.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testDownloadGenomeVersion() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ String version = "eboVir3";
+
+ try {
+ dbUtils.createSessionForCurrentThread();
+ List<String> list = connector.getDownloadedGenomeVersions(yeast);
+ if (list.contains(version)) {
+ connector.removeGenomeVersion(yeast, version);
+ }
+ dbUtils.closeSessionForCurrentThread();
+ list = connector.getDownloadedGenomeVersions(yeast);
+
+ assertFalse(list.contains(version));
+
+ connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false);
+
+ list = connector.getDownloadedGenomeVersions(yeast);
+ assertTrue(list.contains(version));
+
+ List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ ReferenceGenome genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+ connector.downloadGeneMappingGenomeVersion(genome, "test", null, false,
+ "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ dbUtils.createSessionForCurrentThread();
+ genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+ assertEquals(1, genome.getGeneMapping().size());
+ dbUtils.closeSessionForCurrentThread();
+
+ try {
+ // try to download the same thing for the second time
+ connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ assertTrue(e.getMessage().contains("already exists"));
+ }
+
+ try {
+ // try to download something that is not big bed
+ connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.txt");
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ assertTrue(e.getMessage().contains("Only big bed format files are supported"));
+ }
+
+ // connector.removeGeneMapping(genome.getGeneMapping().get(0));
+
+ int warningCount = getWarnings().size();
+
+ // try to remove invalid mapping
+ connector.removeGeneMapping(new ReferenceGenomeGeneMapping());
+
+ assertEquals(warningCount + 1, getWarnings().size());
+
+ dbUtils.createSessionForCurrentThread();
+ connector.removeGenomeVersion(yeast, version);
+ dbUtils.closeSessionForCurrentThread();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ @Test
+ public void testDownloadGenomeVersionWhenInternalUrlIsInvalid() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ String version = "eboVir3";
+
+ ExecutorService originalExecutorService = connector.getSyncExecutorService();
+ try {
+ ExecutorService executorService = Mockito.mock(ExecutorService.class);
+ connector.setSyncExecutorService(executorService);
+ Future<?> task = Mockito.mock(Future.class);
+ when(task.get()).thenThrow(new ExecutionException(new URISyntaxException("", "")));
+ when(executorService.submit(any(Callable.class))).thenReturn(task);
+
+ connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false);
+ fail("Exception expected");
+
+ } catch (InvalidStateException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setSyncExecutorService(originalExecutorService);
+ }
+ }
+
+ @Test
+ public void testDownloadGenomeVersionAsync() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ String version = "eboVir3";
+
+ BigFileCache bigFileCache = connector.getBigFileCache();
+ try {
+ dbUtils.createSessionForCurrentThread();
+ List<String> list = connector.getDownloadedGenomeVersions(yeast);
+ if (list.contains(version)) {
+ connector.removeGenomeVersion(yeast, version);
+ }
+ list = connector.getDownloadedGenomeVersions(yeast);
+
+ dbUtils.closeSessionForCurrentThread();
+
+ // create a mock for ftp connections (so we speed up tests), the real
+ // connection is tested elsewhere
+ BigFileCache mockCache = Mockito.mock(BigFileCache.class);
+ Mockito.doAnswer(new Answer<Void>() {
+
+ @Override
+ public Void answer(InvocationOnMock invocation) throws Throwable {
+ IProgressUpdater updater = (IProgressUpdater) invocation.getArguments()[2];
+ updater.setProgress(100);
+ return null;
+ }
+ }).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+
+ connector.setBigFileCache(mockCache);
+
+ assertFalse(list.contains(version));
+
+ connector.downloadGenomeVersion(yeast, version, null, true);
+
+ waitForDownload();
+
+ dbUtils.createSessionForCurrentThread();
+ list = connector.getDownloadedGenomeVersions(yeast);
+ assertTrue(list.contains(version));
+
+ List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ ReferenceGenome genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ dbUtils.closeSessionForCurrentThread();
+ assertNotNull(genome);
+ connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ waitForDownload();
+
+ genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+ referenceGenomeDao.refresh(genome);
+ assertEquals(1, genome.getGeneMapping().size());
+
+ try {
+ // try to download the same thing for the second time
+ connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ assertTrue(e.getMessage().contains("already exists"));
+ }
+
+ try {
+ // try to download something that is not big bed
+ connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.txt");
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ assertTrue(e.getMessage().contains("Only big bed format files are supported"));
+ }
+
+ connector.removeGeneMapping(genome.getGeneMapping().get(0));
+
+ int warningCount = getWarnings().size();
+
+ // try to remove invalid mapping
+ connector.removeGeneMapping(new ReferenceGenomeGeneMapping());
+
+ assertEquals(warningCount + 1, getWarnings().size());
+
+ connector.removeGenomeVersion(yeast, version);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setBigFileCache(bigFileCache);
+ }
+ }
+
+ @Test
+ public void testDownloadGenomeVersionAsyncWithException() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ String version = "eboVir3";
+
+ BigFileCache bigFileCache = connector.getBigFileCache();
+ try {
+ dbUtils.createSessionForCurrentThread();
+ List<String> list = connector.getDownloadedGenomeVersions(yeast);
+ if (list.contains(version)) {
+ connector.removeGenomeVersion(yeast, version);
+ }
+ list = connector.getDownloadedGenomeVersions(yeast);
+
+ dbUtils.closeSessionForCurrentThread();
+
+ // create a mock for ftp connections (so we speed up tests), the real
+ // connection is tested elsewhere
+ BigFileCache mockCache = Mockito.mock(BigFileCache.class);
+
+ connector.setBigFileCache(mockCache);
+
+ assertFalse(list.contains(version));
+
+ connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true);
+
+ waitForDownload();
+
+ dbUtils.createSessionForCurrentThread();
+ list = connector.getDownloadedGenomeVersions(yeast);
+ assertTrue(list.contains(version));
+
+ List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ ReferenceGenome genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ dbUtils.closeSessionForCurrentThread();
+ assertNotNull(genome);
+
+ Mockito.doThrow(new IOException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+ assertEquals(0, getErrors().size());
+ connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ waitForDownload();
+
+ logger.debug(getErrors());
+ // during this downlad we expect exception thrown by downloader
+ assertEquals(1, getErrors().size());
+
+ Mockito.doThrow(new OutOfMemoryError()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+ connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ waitForDownload();
+ // during this downlad we expect error, this shouldn't change list of
+ // errors
+ assertEquals(1, getErrors().size());
+
+ Mockito.doThrow(new URISyntaxException("", "")).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+ connector.downloadGeneMappingGenomeVersion(genome, "test3", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ waitForDownload();
+
+ // during this downlad we expect error (exception thrown by downloader)
+ assertEquals(2, getErrors().size());
+
+ genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+ referenceGenomeDao.refresh(genome);
+ assertEquals(3, genome.getGeneMapping().size());
+
+ connector.removeGeneMapping(genome.getGeneMapping().get(2));
+ connector.removeGeneMapping(genome.getGeneMapping().get(1));
+ connector.removeGeneMapping(genome.getGeneMapping().get(0));
+ connector.removeGenomeVersion(yeast, version);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setBigFileCache(bigFileCache);
+ }
+ }
+
+ @Test
+ public void testDownloadGenomeVersionWithException() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ String version = "eboVir3";
+
+ BigFileCache bigFileCache = connector.getBigFileCache();
+ try {
+ List<String> list = connector.getDownloadedGenomeVersions(yeast);
+ if (list.contains(version)) {
+ connector.removeGenomeVersion(yeast, version);
+ }
+ list = connector.getDownloadedGenomeVersions(yeast);
+
+ // create a mock for ftp connections (so we speed up tests), the real
+ // connection is tested elsewhere
+ BigFileCache mockCache = Mockito.mock(BigFileCache.class);
+
+ connector.setBigFileCache(mockCache);
+
+ assertFalse(list.contains(version));
+
+ connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false);
+
+ list = connector.getDownloadedGenomeVersions(yeast);
+ assertTrue(list.contains(version));
+
+ List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ ReferenceGenome genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+
+ Mockito.doThrow(new IOException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+ assertEquals(0, getErrors().size());
+ try {
+ connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
+ fail("Exception expected");
+ } catch (IOException e) {
+
+ }
+
+ Mockito.doThrow(new RuntimeException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+ try {
+ connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ fail("Exception expected");
+ } catch (InvalidStateException e) {
+
+ }
+
+ Mockito.doThrow(new URISyntaxException("", "")).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+
+ try {
+ connector.downloadGeneMappingGenomeVersion(genome, "test3", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
+ fail("Exception expected");
+ } catch (URISyntaxException e) {
+
+ }
+
+ genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+ referenceGenomeDao.refresh(genome);
+ assertEquals(3, genome.getGeneMapping().size());
+
+ connector.removeGeneMapping(genome.getGeneMapping().get(2));
+ connector.removeGeneMapping(genome.getGeneMapping().get(1));
+ connector.removeGeneMapping(genome.getGeneMapping().get(0));
+ connector.removeGenomeVersion(yeast, version);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setBigFileCache(bigFileCache);
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFile() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+ try {
+ String url = connector.getGenomeVersionFile(yeast, version);
+ assertNotNull(url);
+ url.contains("sacCer3.2bit");
+ url.contains("ftp");
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUnknownGenomeVersionFile() {
+ MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
+ String version = "hg8";
+ try {
+ connector.getGenomeVersionFile(human, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalid() throws Exception {
+ try {
+ connector.refreshCacheQuery("invalid query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalid2() throws Exception {
+ try {
+ connector.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefresh() throws Exception {
+ try {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ String query = UcscReferenceGenomeConnector.FILENAME_BY_ORGANISM_VERSION_PREFIX + yeast.getResource() + "\n"
+ + version;
+ Object res = connector.refreshCacheQuery(query);
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshUnknownFile() throws Exception {
+ try {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "unkVer";
+
+ String query = UcscReferenceGenomeConnector.FILENAME_BY_ORGANISM_VERSION_PREFIX + yeast.getResource() + "\n"
+ + version;
+ connector.refreshCacheQuery(query);
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ try {
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector();
+ connectorUnderTest.setBigFileCache(connector.getBigFileCache());
+ connectorUnderTest.setDbUtils(connector.getDbUtils());
+ connectorUnderTest.setReferenceGenomeDao(connector.getReferenceGenomeDao());
+ connectorUnderTest.setReferenceGenomeGeneMappingDao(connector.getReferenceGenomeGeneMappingDao());
+
+ assertEquals(connector.getBigFileCache(), connectorUnderTest.getBigFileCache());
+ assertEquals(connector.getDbUtils(), connectorUnderTest.getDbUtils());
+ assertEquals(connector.getReferenceGenomeDao(), connectorUnderTest.getReferenceGenomeDao());
+ assertEquals(connector.getReferenceGenomeGeneMappingDao(), connectorUnderTest.getReferenceGenomeGeneMappingDao());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGenomeVersionExtractorForInvalidGenome() throws Exception {
+ try {
+ int version = connector.extractInt("");
+ assertEquals(0, version);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGenomeVersionExtractorForInvalidGenome2() throws Exception {
+ try {
+ int version = connector.extractInt("x");
+ assertEquals(0, version);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGenomeVersionExtractorForValid() throws Exception {
+ try {
+ int version = connector.extractInt("x1");
+ assertEquals(1, version);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGenomeVersionExtractorForValid2() throws Exception {
+ try {
+ int version = connector.extractInt("xy12z");
+ assertEquals(12, version);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = connector.getWebPageDownloader();
+ GeneralCacheInterface originalCache = connector.getCache();
+ try {
+ // exclude first cached value
+ connector.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ connector.setWebPageDownloader(mockDownloader);
+ connector.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setWebPageDownloader(downloader);
+ connector.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryWhenFtpConnectionFails() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ Mockito.doReturn(FTPReply.REQUEST_DENIED).when(mockClient).getReplyCode();
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ connectorUnderTest.getGenomeVersionFile(yeast, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ assertTrue(e.getMessage().contains("FTP server refused connection"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFileWhenFtpConnectionFails2() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ try {
+ Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
+ Mockito.doReturn(false).when(mockClient).isConnected();
+ } catch (Exception e) {
+ fail();
+ }
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ connectorUnderTest.getGenomeVersionFile(yeast, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFileWhenFtpConnectionFails() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ try {
+ Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
+ Mockito.doReturn(true).when(mockClient).isConnected();
+ } catch (Exception e) {
+ fail();
+ }
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ connectorUnderTest.getGenomeVersionFile(yeast, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFileWhenFtpConnectionFails3() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ try {
+ Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
+ Mockito.doReturn(true).when(mockClient).isConnected();
+ Mockito.doThrow(new IOException()).when(mockClient).disconnect();
+ } catch (Exception e) {
+ fail();
+ }
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ connectorUnderTest.getGenomeVersionFile(yeast, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFileWhenFtpDisconnectConnectionFails() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ try {
+ Mockito.doThrow(new IOException()).when(mockClient).disconnect();
+ Mockito.doReturn(new FTPFile[] {}).when(mockClient).listFiles(anyString());
+ Mockito.doReturn(FTPReply.COMMAND_OK).when(mockClient).getReplyCode();
+ Mockito.doReturn(true).when(mockClient).isConnected();
+ } catch (Exception e) {
+ fail();
+ }
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ connectorUnderTest.getGenomeVersionFile(yeast, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ assertTrue(e.getMessage().contains("Problem with ftp connection"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFileWithMore2bitFiles() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ try {
+ FTPFile file1 = new FTPFile();
+ file1.setName("1.2bit");
+ FTPFile file2 = new FTPFile();
+ file2.setName("2.2bit");
+ FTPFile[] files = new FTPFile[] { file1, file2 };
+
+ Mockito.doReturn(files).when(mockClient).listFiles(anyString());
+ Mockito.doReturn(FTPReply.COMMAND_OK).when(mockClient).getReplyCode();
+ } catch (Exception e) {
+ fail();
+ }
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ String url = connectorUnderTest.getGenomeVersionFile(yeast, version);
+ assertEquals(1, getWarnings().size());
+ assertTrue(url.endsWith("1.2bit"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private void waitForDownload() throws InterruptedException {
+ while (connector.getDownloadThreadCount() > 0) {
+ logger.debug("Waiting for download to finish");
+ Thread.sleep(100);
+ }
+ }
}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringSetComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringSetComparator.java
index 201874c8bd606faaa39472d6bbbfc73f1bca8737..1e3c4759d40fdc9747cb2cd3a22a9d2f62b4c7df 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringSetComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringSetComparator.java
@@ -1,48 +1,48 @@
-package lcsb.mapviewer.common.comparator;
-
-import java.util.Comparator;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-/**
- * Comparator used for comparing sets of strings.
- *
- * @author Piotr Gawron
- *
- */
-public class StringSetComparator implements Comparator<Set<String>> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(StringSetComparator.class);
-
- @Override
- public int compare(Set<String> arg0, Set<String> arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- for (String string : arg1) {
- if (!arg0.contains(string)) {
- logger.debug(string + " couldn't be found in " + arg0);
- return 1;
- }
- }
-
- for (String string : arg0) {
- if (!arg1.contains(string)) {
- logger.debug(string + " couldn't be found in " + arg1);
- return -1;
- }
- }
- return 0;
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import java.util.Comparator;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Comparator used for comparing sets of strings.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class StringSetComparator implements Comparator<Set<String>> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(StringSetComparator.class);
+
+ @Override
+ public int compare(Set<String> arg0, Set<String> arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ for (String string : arg1) {
+ if (!arg0.contains(string)) {
+ logger.debug(string + " couldn't be found in " + arg0);
+ return 1;
+ }
+ }
+
+ for (String string : arg0) {
+ if (!arg1.contains(string)) {
+ logger.debug(string + " couldn't be found in " + arg1);
+ return -1;
+ }
+ }
+ return 0;
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/LineTransformation.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/LineTransformation.java
index 89dc7109f73ea3e44caede6c204294c2d2c3a0de..85025057e118337ea06839372e38649379e3acb9 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/LineTransformation.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/LineTransformation.java
@@ -1,199 +1,199 @@
-package lcsb.mapviewer.common.geometry;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.Configuration;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class with basic operators on lines.
- *
- * @author Piotr Gawron
- *
- */
-public class LineTransformation {
-
- /**
- * Which value in the PathIterartor segment information array corrsepond to X
- * coordinate in the cubicTo type.
- */
- private static final int SEG_CUBICTO_END_Y_COORDINATE_INDEX = 5;
- /**
- * Which value in the PathIterartor segment information array corrsepond to Y
- * coordinate in the cubicTo type.
- */
- private static final int SEG_CUBICTO_END_X_COORDINATE_INDEX = 4;
- /**
- * Length of the PathIterartor segment information array.
- */
- private static final int PATH_ITERATOR_COORDINATES_STRUCT_SIZE = 6;
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LineTransformation.class.getName());
-
- /**
- * Returns a cross point between path and a line.
- *
- * @param line
- * line for which we are looking for the intersection
- * @param pi
- * PathIterator for which we are looking for the intersection
- * @return point of intersection beteewn path and line if the points doesn't
- * exist then null is returned
- */
- public Point2D getIntersectionWithPathIterator(final Line2D line, final PathIterator pi) {
- if (pi == null) {
- return null;
- }
- double[] coordinates = new double[PATH_ITERATOR_COORDINATES_STRUCT_SIZE];
- Point2D first = null;
- Point2D last = null;
- Point2D actual = null;
- while (!pi.isDone()) {
- int type = pi.currentSegment(coordinates);
- last = actual;
- actual = new Point2D.Double(coordinates[0], coordinates[1]);
- switch (type) {
- case PathIterator.SEG_MOVETO:
- break;
- case PathIterator.SEG_LINETO:
- break;
- case PathIterator.SEG_QUADTO:
- break;
- case PathIterator.SEG_CUBICTO:
-
- // in case when there is an arc we define only end points of the arc
- // as a border
- actual = new Point2D.Double(coordinates[SEG_CUBICTO_END_X_COORDINATE_INDEX], coordinates[SEG_CUBICTO_END_Y_COORDINATE_INDEX]);
- break;
- case PathIterator.SEG_CLOSE:
- actual = first;
- break;
- default:
- break;
- }
- if (first == null) {
- first = actual;
-
- // check if the two following points are not the same (this could cause
- // NaN values)
- } else if (last.distance(actual) > Configuration.EPSILON) {
- double x1 = last.getX();
- double y1 = last.getY();
- double x2 = actual.getX();
- double y2 = actual.getY();
- double x3 = line.getX1();
- double y3 = line.getY1();
- double x4 = line.getX2();
- double y4 = line.getY2();
- if (Line2D.linesIntersect(x1, y1, x2, y2, x3, y3, x4, y4)) {
- double d = (x1 - x2) * (y3 - y4) - (y1 - y2) * (x3 - x4);
- double xi = ((x3 - x4) * (x1 * y2 - y1 * x2) - (x1 - x2) * (x3 * y4 - y3 * x4)) / d;
- double yi = ((y3 - y4) * (x1 * y2 - y1 * x2) - (y1 - y2) * (x3 * y4 - y3 * x4)) / d;
- return new Point2D.Double(xi, yi);
- }
- }
-
- pi.next();
- }
- return null;
- }
-
- /**
- * Returns a distance between line segment and a point.
- *
- * @param line
- * line segment to which we are looking the shortest distance
- * @param point
- * point from which are looking the shortest distance
- * @return distance between line and a point
- */
- public double distBetweenPointAndLineSegment(final Line2D line, final Point2D point) {
- return distBetweenPointAndLineSegment(line.getP1(), line.getP2(), point);
- }
-
- /**
- * Returns a distance between line segment (defined by v and w points) and a
- * point.
- *
- * @param v
- * start point of the line
- * @param w
- * end point of the line
- * @param point
- * point from which we want to find a distance
- * @return distance between point and line segment
- */
- public double distBetweenPointAndLineSegment(final Point2D v, final Point2D w, final Point2D point) {
- // Return minimum distance between line segment vw and point p
- double l2 = v.distanceSq(w); // i.e. |w-v|^2 - avoid a sqrt
- if (l2 == 0.0) {
- return point.distance(v); // v == w case
- }
- // Consider the line extending the segment, parameterized as v + t (w - v).
- // We find projection of point p onto the line.
- // It falls where t = [(p-v) . (w-v)] / |w-v|^2
- double t = ((point.getX() - v.getX()) * (w.getX() - v.getX()) + (point.getY() - v.getY()) * (w.getY() - v.getY())) / l2;
- if (t < 0.0) {
- return point.distance(v); // Beyond the 'v' end of the segment
- } else if (t > 1.0) {
- return point.distance(w); // Beyond the 'w' end of the segment
- }
- // Projection falls on the segment
- return point.distance(v.getX() + t * (w.getX() - v.getX()), v.getY() + t * (w.getY() - v.getY()));
- }
-
- /**
- * Returns a point that is on the line and is as close as possible to the
- * point.
- *
- * @param line
- * line on which the point should be found
- * @param point
- * point to which the result should be as close as possible
- * @return point on the line that is as close as possible to the parameter
- * point
- */
- public Point2D closestPointOnSegmentLineToPoint(final Line2D line, final Point2D point) {
- Point2D result = closestPointOnSegmentLineToPoint(line.getP1(), line.getP2(), point);
- return result;
- }
-
- /**
- * Returns a point that is on the line (v-w) and is as close as possible to
- * the point.
- *
- * @param v
- * start of the line segment
- * @param w
- * end of the line segment
- * @param p
- * point to which the result should be as close as possible
- * @return point on the line (v-w) that is as close as possible to the
- * parameter point
- */
- public Point2D closestPointOnSegmentLineToPoint(final Point2D v, final Point2D w, final Point2D p) {
- // Return minimum distance between line segment vw and point p
- double l2 = v.distanceSq(w); // i.e. |w-v|^2 - avoid a sqrt
- if (l2 == 0.0) {
- return v; // v == w case
- }
- // Consider the line extending the segment, parameterized as v + t (w - v).
- // We find projection of point p onto the line.
- // It falls where t = [(p-v) . (w-v)] / |w-v|^2
- double t = ((p.getX() - v.getX()) * (w.getX() - v.getX()) + (p.getY() - v.getY()) * (w.getY() - v.getY())) / l2;
- if (t < 0.0) {
- return v; // Beyond the 'v' end of the segment
- } else if (t > 1.0) {
- return w; // Beyond the 'w' end of the segment
- }
- // Projection falls on the segment
- return new Point2D.Double(v.getX() + t * (w.getX() - v.getX()), v.getY() + t * (w.getY() - v.getY()));
- }
-
-}
+package lcsb.mapviewer.common.geometry;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Class with basic operators on lines.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LineTransformation {
+
+ /**
+ * Which value in the PathIterartor segment information array corrsepond to X
+ * coordinate in the cubicTo type.
+ */
+ private static final int SEG_CUBICTO_END_Y_COORDINATE_INDEX = 5;
+ /**
+ * Which value in the PathIterartor segment information array corrsepond to Y
+ * coordinate in the cubicTo type.
+ */
+ private static final int SEG_CUBICTO_END_X_COORDINATE_INDEX = 4;
+ /**
+ * Length of the PathIterartor segment information array.
+ */
+ private static final int PATH_ITERATOR_COORDINATES_STRUCT_SIZE = 6;
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LineTransformation.class.getName());
+
+ /**
+ * Returns a cross point between path and a line.
+ *
+ * @param line
+ * line for which we are looking for the intersection
+ * @param pi
+ * PathIterator for which we are looking for the intersection
+ * @return point of intersection between path and line if the points doesn't
+ * exist then null is returned
+ */
+ public Point2D getIntersectionWithPathIterator(final Line2D line, final PathIterator pi) {
+ if (pi == null) {
+ return null;
+ }
+ double[] coordinates = new double[PATH_ITERATOR_COORDINATES_STRUCT_SIZE];
+ Point2D first = null;
+ Point2D last = null;
+ Point2D actual = null;
+ while (!pi.isDone()) {
+ int type = pi.currentSegment(coordinates);
+ last = actual;
+ actual = new Point2D.Double(coordinates[0], coordinates[1]);
+ switch (type) {
+ case PathIterator.SEG_MOVETO:
+ break;
+ case PathIterator.SEG_LINETO:
+ break;
+ case PathIterator.SEG_QUADTO:
+ break;
+ case PathIterator.SEG_CUBICTO:
+
+ // in case when there is an arc we define only end points of the arc
+ // as a border
+ actual = new Point2D.Double(coordinates[SEG_CUBICTO_END_X_COORDINATE_INDEX],
+ coordinates[SEG_CUBICTO_END_Y_COORDINATE_INDEX]);
+ break;
+ case PathIterator.SEG_CLOSE:
+ actual = first;
+ break;
+ default:
+ break;
+ }
+ if (first == null) {
+ first = actual;
+
+ // check if the two following points are not the same (this could cause
+ // NaN values)
+ } else if (last.distance(actual) > Configuration.EPSILON) {
+ double x1 = last.getX();
+ double y1 = last.getY();
+ double x2 = actual.getX();
+ double y2 = actual.getY();
+ double x3 = line.getX1();
+ double y3 = line.getY1();
+ double x4 = line.getX2();
+ double y4 = line.getY2();
+ if (Line2D.linesIntersect(x1, y1, x2, y2, x3, y3, x4, y4)) {
+ double d = (x1 - x2) * (y3 - y4) - (y1 - y2) * (x3 - x4);
+ double xi = ((x3 - x4) * (x1 * y2 - y1 * x2) - (x1 - x2) * (x3 * y4 - y3 * x4)) / d;
+ double yi = ((y3 - y4) * (x1 * y2 - y1 * x2) - (y1 - y2) * (x3 * y4 - y3 * x4)) / d;
+ return new Point2D.Double(xi, yi);
+ }
+ }
+
+ pi.next();
+ }
+ return null;
+ }
+
+ /**
+ * Returns a distance between line segment and a point.
+ *
+ * @param line
+ * line segment to which we are looking the shortest distance
+ * @param point
+ * point from which are looking the shortest distance
+ * @return distance between line and a point
+ */
+ public double distBetweenPointAndLineSegment(final Line2D line, final Point2D point) {
+ return distBetweenPointAndLineSegment(line.getP1(), line.getP2(), point);
+ }
+
+ /**
+ * Returns a distance between line segment (defined by v and w points) and a
+ * point.
+ *
+ * @param v
+ * start point of the line
+ * @param w
+ * end point of the line
+ * @param point
+ * point from which we want to find a distance
+ * @return distance between point and line segment
+ */
+ public double distBetweenPointAndLineSegment(final Point2D v, final Point2D w, final Point2D point) {
+ // Return minimum distance between line segment vw and point p
+ double l2 = v.distanceSq(w); // i.e. |w-v|^2 - avoid a sqrt
+ if (l2 == 0.0) {
+ return point.distance(v); // v == w case
+ }
+ // Consider the line extending the segment, parameterized as v + t (w - v).
+ // We find projection of point p onto the line.
+ // It falls where t = [(p-v) . (w-v)] / |w-v|^2
+ double t = ((point.getX() - v.getX()) * (w.getX() - v.getX()) + (point.getY() - v.getY()) * (w.getY() - v.getY()))
+ / l2;
+ if (t < 0.0) {
+ return point.distance(v); // Beyond the 'v' end of the segment
+ } else if (t > 1.0) {
+ return point.distance(w); // Beyond the 'w' end of the segment
+ }
+ // Projection falls on the segment
+ return point.distance(v.getX() + t * (w.getX() - v.getX()), v.getY() + t * (w.getY() - v.getY()));
+ }
+
+ /**
+ * Returns a point that is on the line and is as close as possible to the point.
+ *
+ * @param line
+ * line on which the point should be found
+ * @param point
+ * point to which the result should be as close as possible
+ * @return point on the line that is as close as possible to the parameter point
+ */
+ public Point2D closestPointOnSegmentLineToPoint(final Line2D line, final Point2D point) {
+ Point2D result = closestPointOnSegmentLineToPoint(line.getP1(), line.getP2(), point);
+ return result;
+ }
+
+ /**
+ * Returns a point that is on the line (v-w) and is as close as possible to the
+ * point.
+ *
+ * @param v
+ * start of the line segment
+ * @param w
+ * end of the line segment
+ * @param p
+ * point to which the result should be as close as possible
+ * @return point on the line (v-w) that is as close as possible to the parameter
+ * point
+ */
+ public Point2D closestPointOnSegmentLineToPoint(final Point2D v, final Point2D w, final Point2D p) {
+ // Return minimum distance between line segment vw and point p
+ double l2 = v.distanceSq(w); // i.e. |w-v|^2 - avoid a sqrt
+ if (l2 == 0.0) {
+ return v; // v == w case
+ }
+ // Consider the line extending the segment, parameterized as v + t (w - v).
+ // We find projection of point p onto the line.
+ // It falls where t = [(p-v) . (w-v)] / |w-v|^2
+ double t = ((p.getX() - v.getX()) * (w.getX() - v.getX()) + (p.getY() - v.getY()) * (w.getY() - v.getY())) / l2;
+ if (t < 0.0) {
+ return v; // Beyond the 'v' end of the segment
+ } else if (t > 1.0) {
+ return w; // Beyond the 'w' end of the segment
+ }
+ // Projection falls on the segment
+ return new Point2D.Double(v.getX() + t * (w.getX() - v.getX()), v.getY() + t * (w.getY() - v.getY()));
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
index 685768126502bce1aac27fae0f11a2adb1a8c303..477a446ee6c97c1994c57505e4f0eecc82caa0ac 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
@@ -17,9 +17,8 @@ import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
/**
* This structure contains information about {@link CellDesignerElement
@@ -28,216 +27,215 @@ import lcsb.mapviewer.model.map.species.field.RnaRegion;
*/
public class CellDesignerElementCollection {
- /**
- * Element by element identifier (it's CellDesigner identifier).
- */
- private Map<String, CellDesignerElement<?>> elementById = new HashMap<>();
-
- /**
- * Returns element by given identifier.
- *
- * @param speciesId
- * element identifier
- * @return element by given identifier
- *
- * @param <T>
- * type of returned object
- */
- @SuppressWarnings("unchecked")
- public <T extends CellDesignerElement<?>> T getElementByElementId(String speciesId) {
- return (T) elementById.get(speciesId);
- }
-
- /**
- *
- */
- private Map<String, String> sbmlIdByElement = new HashMap<>();
-
- /**
- * Returns element identifier that should be used for model element when
- * creating cell designer xml file.
- *
- * @param modelElement
- * model element for which we want to obtain identifier
- * @return identifier of cell designer element that will be exported
- */
- public String getElementId(Element modelElement) {
- if ("default".equals(modelElement.getElementId())) {
- return modelElement.getElementId();
- } else {
- String sbmlId = getSbmlId(modelElement, true);
- if (sbmlIdByElement.get(sbmlId) == null) {
- String id = "s_id_" + modelElement.getElementId();
- if (sbmlIdByElement.values().contains(id)) {
- throw new InvalidArgumentException("id duplicates");
- }
- sbmlIdByElement.put(sbmlId, id);
- }
- return sbmlIdByElement.get(sbmlId);
-
- }
- }
-
- /**
- * Creates a String that identifies element as distinct SBML entity.
- *
- * @param modelElement
- * element that we want to identify
- * @param useComplex
- * should we use identifier of a complex. This should be used by
- * default (because if the complex is different then element should
- * have different identifier). However, when element asks complex for
- * id, complex will try to resolve ids of children (because this is
- * what defines complex identity), and in such situation it should
- * disable resolving complex, because there will by infinity cyclic
- * calls and stack overflow error will be thrown.
- * @return unique String for SBML entity
- */
- private String getSbmlId(Element modelElement, boolean useComplex) {
- String compartmenName = "default";
- if (modelElement.getCompartment() != null) {
- compartmenName = modelElement.getCompartment().getName();
- }
-
- String modifications = "";
- if (modelElement instanceof AntisenseRna) {
- AntisenseRna asAntisenseRna = ((AntisenseRna) modelElement);
- for (AntisenseRnaRegion region : asAntisenseRna.getRegions()) {
- modifications += region.getState();
- }
- } else if (modelElement instanceof Gene) {
- Gene asGene = ((Gene) modelElement);
- for (ModificationResidue region : asGene.getModificationResidues()) {
- modifications += region.getState();
- }
- } else if (modelElement instanceof Protein) {
- Protein asProtein = ((Protein) modelElement);
- modifications = asProtein.getStructuralState();
- for (ModificationResidue region : asProtein.getModificationResidues()) {
- modifications += region.getState();
- }
- } else if (modelElement instanceof Rna) {
- Rna asRna = ((Rna) modelElement);
- for (RnaRegion region : asRna.getRegions()) {
- modifications += region.getState();
- }
- } else if (modelElement instanceof Complex) {
- Complex asComplex = ((Complex) modelElement);
- modifications = asComplex.getStructuralState();
- }
-
- String complexId = "";
- String homodimer = "";
- if (modelElement instanceof Species) {
- homodimer = ((Species) modelElement).getHomodimer() + "";
- if (((Species) modelElement).getComplex() != null) {
- if (useComplex) {
- if (!isCyclicNesting(((Species) modelElement).getComplex())) {
- complexId = getElementId(((Species) modelElement).getComplex());
- } else {
- throw new InvalidArgumentException("Cycling nested structure found in element: " + modelElement.getElementId());
- }
- } else {
- complexId = ((Species) modelElement).getComplex().getName();
- }
- }
- }
- String childrenId = "";
- if (modelElement instanceof Complex) {
- Complex asComplex = (Complex) modelElement;
- List<String> childIds = new ArrayList<>();
- for (Species child : asComplex.getAllChildren()) {
- childIds.add(getSbmlId(child, false));
- }
- Collections.sort(childIds);
- for (String string : childIds) {
- childrenId += string + "\n";
- }
- }
-
- // identifier that distinguish elements in SBML depends only on type,
- // name, compartment, modifications, homodimer, state, complex where it's
- // located,
- // children of the complex
- String sbmlId = compartmenName + "\n" + modelElement.getName() + "\n" + modelElement.getStringType() + "\n" + modifications + "\n" + complexId + "\n"
- + homodimer + "\n" + childrenId;
-
- return sbmlId;
- }
-
- /**
- * Checks if complex parenting is cyclic.
- *
- * @param complex
- * complex for which data is checked
- * @return true if parent of the complex is also a (grand)child of this
- * complex, false otherwise
- */
- private boolean isCyclicNesting(Complex complex) {
- Set<Complex> foundComplexes = new HashSet<>();
- while (complex != null) {
- if (foundComplexes.contains(complex)) {
- return true;
- }
- foundComplexes.add(complex);
- complex = complex.getComplex();
- }
- return false;
- }
-
- /**
- * Adds cell designer structures.
- *
- * @param elements
- * list of objects to add
- */
- public void addElements(List<? extends CellDesignerElement<?>> elements) {
- for (CellDesignerElement<?> element : elements) {
- addElement(element);
- }
- }
-
- /**
- * Adds cell designer object.
- *
- * @param element
- * object to add
- */
- public void addElement(CellDesignerElement<?> element) {
- addElement(element, element.getElementId());
- }
-
- /**
- * Adds CellDesigner element with custom id (instead the one obtained from
- * CellDesigner structure).
- *
- * @param element
- * element to be add
- * @param id
- * id that should be used for identifying element
- */
- public void addElement(CellDesignerElement<?> element, String id) {
- if (elementById.get(id) != null) {
- throw new InvalidArgumentException(
- "[" + element.getClass().getSimpleName() + " " + element.getElementId() + "]\t" + "Element with given id alread exists. ID: " + id);
- }
- elementById.put(id, element);
- }
-
- /**
- * Adds CellDesigner structure in a way that it would be accessed via
- * identifier for model structure. Method used only for unit test.
- *
- * @param modelElement
- * model element that will create identifier
- * @param element
- * element to be added
- */
- public void addModelElement(Element modelElement, CellDesignerElement<?> element) {
- addElement(element, getElementId(modelElement));
- if (getElementByElementId(element.getElementId()) == null) {
- addElement(element);
- }
- }
+ /**
+ * Element by element identifier (it's CellDesigner identifier).
+ */
+ private Map<String, CellDesignerElement<?>> elementById = new HashMap<>();
+
+ /**
+ * Returns element by given identifier.
+ *
+ * @param speciesId
+ * element identifier
+ * @return element by given identifier
+ *
+ * @param <T>
+ * type of returned object
+ */
+ @SuppressWarnings("unchecked")
+ public <T extends CellDesignerElement<?>> T getElementByElementId(String speciesId) {
+ return (T) elementById.get(speciesId);
+ }
+
+ /**
+ *
+ */
+ private Map<String, String> sbmlIdByElement = new HashMap<>();
+
+ /**
+ * Returns element identifier that should be used for model element when
+ * creating cell designer xml file.
+ *
+ * @param modelElement
+ * model element for which we want to obtain identifier
+ * @return identifier of cell designer element that will be exported
+ */
+ public String getElementId(Element modelElement) {
+ if ("default".equals(modelElement.getElementId())) {
+ return modelElement.getElementId();
+ } else {
+ String sbmlId = getSbmlId(modelElement, true);
+ if (sbmlIdByElement.get(sbmlId) == null) {
+ String id = "s_id_" + modelElement.getElementId();
+ if (sbmlIdByElement.values().contains(id)) {
+ throw new InvalidArgumentException("id duplicates");
+ }
+ sbmlIdByElement.put(sbmlId, id);
+ }
+ return sbmlIdByElement.get(sbmlId);
+
+ }
+ }
+
+ /**
+ * Creates a String that identifies element as distinct SBML entity.
+ *
+ * @param modelElement
+ * element that we want to identify
+ * @param useComplex
+ * should we use identifier of a complex. This should be used by
+ * default (because if the complex is different then element should
+ * have different identifier). However, when element asks complex for
+ * id, complex will try to resolve ids of children (because this is
+ * what defines complex identity), and in such situation it should
+ * disable resolving complex, because there will by infinity cyclic
+ * calls and stack overflow error will be thrown.
+ * @return unique String for SBML entity
+ */
+ private String getSbmlId(Element modelElement, boolean useComplex) {
+ String compartmenName = "default";
+ if (modelElement.getCompartment() != null) {
+ compartmenName = modelElement.getCompartment().getName();
+ }
+
+ String modifications = "";
+ List<ModificationResidue> regions = new ArrayList<>();
+ if (modelElement instanceof AntisenseRna) {
+ AntisenseRna asAntisenseRna = ((AntisenseRna) modelElement);
+ regions.addAll(asAntisenseRna.getRegions());
+ } else if (modelElement instanceof Gene) {
+ Gene asGene = ((Gene) modelElement);
+ regions.addAll(asGene.getModificationResidues());
+ } else if (modelElement instanceof Protein) {
+ Protein asProtein = ((Protein) modelElement);
+ modifications = asProtein.getStructuralState();
+ regions.addAll(asProtein.getModificationResidues());
+ } else if (modelElement instanceof Rna) {
+ Rna asRna = ((Rna) modelElement);
+ regions.addAll(asRna.getRegions());
+ } else if (modelElement instanceof Complex) {
+ Complex asComplex = ((Complex) modelElement);
+ modifications = asComplex.getStructuralState();
+ }
+ for (ModificationResidue region : regions) {
+ if (region instanceof AbstractSiteModification) {
+ modifications += ((AbstractSiteModification) region).getState();
+ }
+ }
+
+ String complexId = "";
+ String homodimer = "";
+ if (modelElement instanceof Species) {
+ homodimer = ((Species) modelElement).getHomodimer() + "";
+ if (((Species) modelElement).getComplex() != null) {
+ if (useComplex) {
+ if (!isCyclicNesting(((Species) modelElement).getComplex())) {
+ complexId = getElementId(((Species) modelElement).getComplex());
+ } else {
+ throw new InvalidArgumentException(
+ "Cycling nested structure found in element: " + modelElement.getElementId());
+ }
+ } else {
+ complexId = ((Species) modelElement).getComplex().getName();
+ }
+ }
+ }
+ String childrenId = "";
+ if (modelElement instanceof Complex) {
+ Complex asComplex = (Complex) modelElement;
+ List<String> childIds = new ArrayList<>();
+ for (Species child : asComplex.getAllChildren()) {
+ childIds.add(getSbmlId(child, false));
+ }
+ Collections.sort(childIds);
+ for (String string : childIds) {
+ childrenId += string + "\n";
+ }
+ }
+
+ // identifier that distinguish elements in SBML depends only on type,
+ // name, compartment, modifications, homodimer, state, complex where it's
+ // located,
+ // children of the complex
+ String sbmlId = compartmenName + "\n" + modelElement.getName() + "\n" + modelElement.getStringType() + "\n"
+ + modifications + "\n" + complexId + "\n" + homodimer + "\n" + childrenId;
+
+ return sbmlId;
+ }
+
+ /**
+ * Checks if complex parenting is cyclic.
+ *
+ * @param complex
+ * complex for which data is checked
+ * @return true if parent of the complex is also a (grand)child of this complex,
+ * false otherwise
+ */
+ private boolean isCyclicNesting(Complex complex) {
+ Set<Complex> foundComplexes = new HashSet<>();
+ while (complex != null) {
+ if (foundComplexes.contains(complex)) {
+ return true;
+ }
+ foundComplexes.add(complex);
+ complex = complex.getComplex();
+ }
+ return false;
+ }
+
+ /**
+ * Adds cell designer structures.
+ *
+ * @param elements
+ * list of objects to add
+ */
+ public void addElements(List<? extends CellDesignerElement<?>> elements) {
+ for (CellDesignerElement<?> element : elements) {
+ addElement(element);
+ }
+ }
+
+ /**
+ * Adds cell designer object.
+ *
+ * @param element
+ * object to add
+ */
+ public void addElement(CellDesignerElement<?> element) {
+ addElement(element, element.getElementId());
+ }
+
+ /**
+ * Adds CellDesigner element with custom id (instead the one obtained from
+ * CellDesigner structure).
+ *
+ * @param element
+ * element to be add
+ * @param id
+ * id that should be used for identifying element
+ */
+ public void addElement(CellDesignerElement<?> element, String id) {
+ if (elementById.get(id) != null) {
+ throw new InvalidArgumentException("[" + element.getClass().getSimpleName() + " " + element.getElementId() + "]\t"
+ + "Element with given id alread exists. ID: " + id);
+ }
+ elementById.put(id, element);
+ }
+
+ /**
+ * Adds CellDesigner structure in a way that it would be accessed via identifier
+ * for model structure. Method used only for unit test.
+ *
+ * @param modelElement
+ * model element that will create identifier
+ * @param element
+ * element to be added
+ */
+ public void addModelElement(Element modelElement, CellDesignerElement<?> element) {
+ addElement(element, getElementId(modelElement));
+ if (getElementByElementId(element.getElementId()) == null) {
+ addElement(element);
+ }
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
index c92137511e64402519dcbd6714373403b9a57589..30ab81753601fb2038ed17e7c881db0dc4b95766 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
@@ -1,252 +1,255 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Parser of CellDesigner xml used for parsing SpeciesAlias.
- *
- * @author Piotr Gawron
- *
- * @see Complex
- */
-public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class.getName());
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed from
- * xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Model for which we parse elements.
- */
- private Model model;
-
- /**
- * Default constructor with model object for which we parse data.
- *
- * @param model
- * model for which we parse elements
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public SpeciesAliasXmlParser(CellDesignerElementCollection elements, Model model) {
- this.elements = elements;
- this.model = model;
- }
-
- @Override
- Species parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
-
- String speciesId = getNodeAttr("species", aliasNode);
- String aliasId = getNodeAttr("id", aliasNode);
- CellDesignerSpecies<?> species = elements.getElementByElementId(speciesId);
- if (species == null) {
- throw new InvalidXmlSchemaException("Unknown species for alias (speciesId: " + speciesId + ")");
- }
- if (species instanceof CellDesignerComplexSpecies) {
- logger.warn("[" + speciesId + "," + aliasId
- + "]\tSpecies is defined as a complex, but alias is not a complex. Changing alias to complex.");
- }
-
- elements.addElement(species, aliasId);
- Species result = species.createModelElement(aliasId);
-
- String state = "usual";
- NodeList nodes = aliasNode.getChildNodes();
- View usualView = null;
- View briefView = null;
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:activity")) {
- result.setActivity(getNodeValue(node).equalsIgnoreCase("active"));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
- result.setX(getNodeAttr("X", node));
- result.setY(getNodeAttr("Y", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
- result.setFontSize(getNodeAttr("size", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:view")) {
- state = getNodeAttr("state", node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:usualView")) {
- usualView = getCommonParser().getView(node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:briefView")) {
- briefView = getCommonParser().getView(node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
- processAliasState(node, result);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
- // not handled
- continue;
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
- }
- }
- }
-
- View view = null;
- if (state.equalsIgnoreCase("usual")) {
- view = usualView;
- } else if (state.equalsIgnoreCase("brief")) {
- view = briefView;
- }
-
- if (view != null) {
- // inner position defines the position in compartment
- // result.moveBy(view.innerPosition);
- result.setWidth(view.getBoxSize().width);
- result.setHeight(view.getBoxSize().height);
- result.setLineWidth(view.getSingleLine().getWidth());
- result.setColor(view.getColor());
- } else {
- throw new InvalidXmlSchemaException("No view in Alias");
- }
- result.setState(state);
- String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
- if (!compartmentAliasId.isEmpty()) {
- Compartment compartment = model.getElementByElementId(compartmentAliasId);
- if (compartment == null) {
- throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
- } else {
- result.setCompartment(compartment);
- compartment.addElement(result);
- }
- }
- String complexAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
- if (!complexAliasId.isEmpty()) {
- Complex complex = model.getElementByElementId(complexAliasId);
- if (complex == null) {
- throw new InvalidXmlSchemaException(
- "ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
- } else {
- result.setComplex(complex);
- complex.addSpecies(result);
- }
- }
- return result;
- }
-
- /**
- * Process node with information about alias state and puts data into alias.
- *
- * @param node
- * node where information about alias state is stored
- * @param alias
- * alias object to be modified if necessary
- */
- private void processAliasState(Node node, Species alias) {
- String state = getNodeAttr("state", node);
- if ("open".equalsIgnoreCase(state)) {
- String prefix = getNodeAttr("prefix", node);
- String label = getNodeAttr("label", node);
- alias.setStatePrefix(prefix);
- alias.setStateLabel(label);
- } else if ("empty".equalsIgnoreCase(state)) {
- return;
- } else if (state == null || state.isEmpty()) {
- return;
- } else {
- throw new NotImplementedException("[Alias: " + alias.getElementId() + "] Unkown alias state: " + state);
- }
-
- }
-
- @Override
- public String toXml(Species species) {
- Compartment ca = null;
- // artificial compartment aliases should be excluded
- if (species.getCompartment() != null && !(species.getCompartment() instanceof PathwayCompartment)) {
- ca = (Compartment) species.getCompartment();
- } else if (species.getComplex() == null) {
- ModelData model = species.getModelData();
- if (model != null) {
- for (Compartment cAlias : model.getModel().getCompartments()) {
- if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(species)) {
- if (ca == null) {
- ca = cAlias;
- } else if (ca.getSize() > cAlias.getSize()) {
- ca = cAlias;
- }
- }
- }
- }
- }
-
- Complex complex = species.getComplex();
-
- String compartmentAliasId = null;
- if (ca != null) {
- compartmentAliasId = ca.getElementId();
- }
- StringBuilder sb = new StringBuilder("");
- sb.append("<celldesigner:speciesAlias ");
- sb.append("id=\"" + species.getElementId() + "\" ");
- sb.append("species=\"" + elements.getElementId(species) + "\" ");
- if (compartmentAliasId != null) {
- sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
- }
-
- if (complex != null) {
- sb.append("complexSpeciesAlias=\"" + complex.getElementId() + "\" ");
- }
- sb.append(">\n");
-
- if (species.getActivity() != null) {
- if (species.getActivity()) {
- sb.append("<celldesigner:activity>active</celldesigner:activity>\n");
- } else {
- sb.append("<celldesigner:activity>inactive</celldesigner:activity>\n");
- }
- }
-
- sb.append("<celldesigner:bounds ");
- sb.append("x=\"" + species.getX() + "\" ");
- sb.append("y=\"" + species.getY() + "\" ");
- sb.append("w=\"" + species.getWidth() + "\" ");
- sb.append("h=\"" + species.getHeight() + "\" ");
- sb.append("/>\n");
-
- sb.append("<celldesigner:font size=\"" + species.getFontSize() + "\"/>\n");
-
- // TODO to be improved
- sb.append("<celldesigner:view state=\"usual\"/>\n");
- sb.append("<celldesigner:usualView>");
- sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
- sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
- sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
- sb.append("</celldesigner:usualView>\n");
- sb.append("<celldesigner:briefView>");
- sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
- sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
- sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
- sb.append("</celldesigner:briefView>\n");
- if (species.getStateLabel() != null || species.getStatePrefix() != null) {
- sb.append("<celldesigner:info state=\"open\" prefix=\"" + species.getStatePrefix() + "\" label=\""
- + species.getStateLabel() + "\"/>\n");
- }
- sb.append("</celldesigner:speciesAlias>\n");
- return sb.toString();
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Parser of CellDesigner xml used for parsing SpeciesAlias.
+ *
+ * @author Piotr Gawron
+ *
+ * @see Complex
+ */
+public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class.getName());
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Model for which we parse elements.
+ */
+ private Model model;
+
+ /**
+ * Default constructor with model object for which we parse data.
+ *
+ * @param model
+ * model for which we parse elements
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public SpeciesAliasXmlParser(CellDesignerElementCollection elements, Model model) {
+ this.elements = elements;
+ this.model = model;
+ }
+
+ @Override
+ Species parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
+
+ String speciesId = getNodeAttr("species", aliasNode);
+ String aliasId = getNodeAttr("id", aliasNode);
+ CellDesignerSpecies<?> species = elements.getElementByElementId(speciesId);
+ if (species == null) {
+ throw new InvalidXmlSchemaException("Unknown species for alias (speciesId: " + speciesId + ")");
+ }
+ if (species instanceof CellDesignerComplexSpecies) {
+ logger.warn("[" + speciesId + "," + aliasId
+ + "]\tSpecies is defined as a complex, but alias is not a complex. Changing alias to complex.");
+ }
+
+ elements.addElement(species, aliasId);
+ Species result = species.createModelElement(aliasId);
+
+ String state = "usual";
+ NodeList nodes = aliasNode.getChildNodes();
+ View usualView = null;
+ View briefView = null;
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:activity")) {
+ result.setActivity(getNodeValue(node).equalsIgnoreCase("active"));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+ result.setX(getNodeAttr("X", node));
+ result.setY(getNodeAttr("Y", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
+ result.setFontSize(getNodeAttr("size", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:view")) {
+ state = getNodeAttr("state", node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:usualView")) {
+ usualView = getCommonParser().getView(node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:briefView")) {
+ briefView = getCommonParser().getView(node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
+ processAliasState(node, result);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
+ // not handled
+ continue;
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
+ }
+ }
+ }
+
+ View view = null;
+ if (state.equalsIgnoreCase("usual")) {
+ view = usualView;
+ } else if (state.equalsIgnoreCase("brief")) {
+ view = briefView;
+ }
+
+ if (view != null) {
+ // inner position defines the position in compartment
+ // result.moveBy(view.innerPosition);
+ result.setWidth(view.getBoxSize().width);
+ result.setHeight(view.getBoxSize().height);
+ result.setLineWidth(view.getSingleLine().getWidth());
+ result.setColor(view.getColor());
+ } else {
+ throw new InvalidXmlSchemaException("No view in Alias");
+ }
+ result.setState(state);
+ String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
+ if (!compartmentAliasId.isEmpty()) {
+ Compartment compartment = model.getElementByElementId(compartmentAliasId);
+ if (compartment == null) {
+ throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
+ } else {
+ result.setCompartment(compartment);
+ compartment.addElement(result);
+ }
+ }
+ String complexAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
+ if (!complexAliasId.isEmpty()) {
+ Complex complex = model.getElementByElementId(complexAliasId);
+ if (complex == null) {
+ throw new InvalidXmlSchemaException(
+ "ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
+ } else {
+ result.setComplex(complex);
+ complex.addSpecies(result);
+ }
+ }
+
+
+ species.updateModelElementAfterLayoutAdded(result);
+ return result;
+ }
+
+ /**
+ * Process node with information about alias state and puts data into alias.
+ *
+ * @param node
+ * node where information about alias state is stored
+ * @param alias
+ * alias object to be modified if necessary
+ */
+ private void processAliasState(Node node, Species alias) {
+ String state = getNodeAttr("state", node);
+ if ("open".equalsIgnoreCase(state)) {
+ String prefix = getNodeAttr("prefix", node);
+ String label = getNodeAttr("label", node);
+ alias.setStatePrefix(prefix);
+ alias.setStateLabel(label);
+ } else if ("empty".equalsIgnoreCase(state)) {
+ return;
+ } else if (state == null || state.isEmpty()) {
+ return;
+ } else {
+ throw new NotImplementedException("[Alias: " + alias.getElementId() + "] Unkown alias state: " + state);
+ }
+
+ }
+
+ @Override
+ public String toXml(Species species) {
+ Compartment ca = null;
+ // artificial compartment aliases should be excluded
+ if (species.getCompartment() != null && !(species.getCompartment() instanceof PathwayCompartment)) {
+ ca = (Compartment) species.getCompartment();
+ } else if (species.getComplex() == null) {
+ ModelData model = species.getModelData();
+ if (model != null) {
+ for (Compartment cAlias : model.getModel().getCompartments()) {
+ if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(species)) {
+ if (ca == null) {
+ ca = cAlias;
+ } else if (ca.getSize() > cAlias.getSize()) {
+ ca = cAlias;
+ }
+ }
+ }
+ }
+ }
+
+ Complex complex = species.getComplex();
+
+ String compartmentAliasId = null;
+ if (ca != null) {
+ compartmentAliasId = ca.getElementId();
+ }
+ StringBuilder sb = new StringBuilder("");
+ sb.append("<celldesigner:speciesAlias ");
+ sb.append("id=\"" + species.getElementId() + "\" ");
+ sb.append("species=\"" + elements.getElementId(species) + "\" ");
+ if (compartmentAliasId != null) {
+ sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
+ }
+
+ if (complex != null) {
+ sb.append("complexSpeciesAlias=\"" + complex.getElementId() + "\" ");
+ }
+ sb.append(">\n");
+
+ if (species.getActivity() != null) {
+ if (species.getActivity()) {
+ sb.append("<celldesigner:activity>active</celldesigner:activity>\n");
+ } else {
+ sb.append("<celldesigner:activity>inactive</celldesigner:activity>\n");
+ }
+ }
+
+ sb.append("<celldesigner:bounds ");
+ sb.append("x=\"" + species.getX() + "\" ");
+ sb.append("y=\"" + species.getY() + "\" ");
+ sb.append("w=\"" + species.getWidth() + "\" ");
+ sb.append("h=\"" + species.getHeight() + "\" ");
+ sb.append("/>\n");
+
+ sb.append("<celldesigner:font size=\"" + species.getFontSize() + "\"/>\n");
+
+ // TODO to be improved
+ sb.append("<celldesigner:view state=\"usual\"/>\n");
+ sb.append("<celldesigner:usualView>");
+ sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
+ sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
+ sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
+ sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("</celldesigner:usualView>\n");
+ sb.append("<celldesigner:briefView>");
+ sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
+ sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
+ sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
+ sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("</celldesigner:briefView>\n");
+ if (species.getStateLabel() != null || species.getStatePrefix() != null) {
+ sb.append("<celldesigner:info state=\"open\" prefix=\"" + species.getStatePrefix() + "\" label=\""
+ + species.getStateLabel() + "\"/>\n");
+ }
+ sb.append("</celldesigner:speciesAlias>\n");
+ return sb.toString();
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
index 6742baaafabf2462881b1dac6dfca6943aa871c3..172182d4c2297b28e480a927a17c29b7526b71fe 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
@@ -1,235 +1,425 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.geometry.LineTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerEllipseTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPolygonTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerRectangleTransformation;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This abstract class is an interface for setting up graphical data for alias
- * from CellDesigner specific format into standard layout.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- */
-public abstract class AbstractCellDesignerAliasConverter<T extends Element> implements ICellDesignerAliasConverter<T> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(AbstractCellDesignerAliasConverter.class);
-
- /**
- * CellDesigner graphical helper with polygon transformation functions.
- */
- private CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
-
- /**
- * CellDesigner graphical helper with lin transformation functions.
- */
- private LineTransformation lineTransformation = new LineTransformation();
-
- /**
- * CellDesigner graphical helper with ellipse transformation functions.
- */
- private CellDesignerEllipseTransformation ellipseTransformation = new CellDesignerEllipseTransformation();
-
- /**
- * CellDesigner graphical helper with rectangle transformation functions.
- */
- private CellDesignerRectangleTransformation rectangleTransformation = new CellDesignerRectangleTransformation();
-
- /**
- * What is the distance between homodimer aliases when homodimer>1.
- */
- public static final int HOMODIMER_OFFSET = 6;
-
- /**
- * Should the converter use sbgn standard.
- */
- private boolean sbgn;
-
- /**
- * Default constructor that prevents from instatiation of the class.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected AbstractCellDesignerAliasConverter(boolean sbgn) {
- this.sbgn = sbgn;
- };
-
- @Override
- public CellDesignerAnchor getAnchorForCoordinates(T alias, Point2D point) {
- double dist = Double.MAX_VALUE;
- CellDesignerAnchor result = null;
- for (CellDesignerAnchor anchor : CellDesignerAnchor.values()) {
- double newDist = getPointCoordinates(alias, anchor).distance(point);
- if (newDist < dist) {
- dist = newDist;
- result = anchor;
- }
- }
- // if the distance to all known anchors is too big then assume center
- if (dist > 1) {
- return null;
- }
- return result;
- }
-
- @Override
- public abstract Point2D getPointCoordinates(T alias, CellDesignerAnchor anchor);
-
- @Override
- public Point2D getAnchorPointCoordinates(T alias, CellDesignerAnchor anchor, PolylineData ld) {
- if (anchor != null && anchor.getAngle() != null) {
- return getPointCoordinates(alias, anchor);
- } else {
- Point2D p1 = ld.getPoints().get(1);
- Point2D p2 = ld.getPoints().get(0);
- double dx = p2.getX() - p1.getX();
- double dy = p2.getY() - p1.getY();
- double angle = Math.atan2(dy, dx);
- return getAnchorPointCoordinates(alias, angle);
- }
- }
-
- /**
- * This method computes coordinates that should be associated with the angle
- * on the border of the alias.
- *
- * @param alias
- * alias to be investigated
- * @param angle
- * angle on the border of the alias
- * @return coordinates on the border of the alias described by the angle
- */
- protected Point2D getAnchorPointCoordinates(T alias, double angle) {
- Point2D result = null;
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
- result = alias.getCenter();
- } else {
- double dist = Math.max(alias.getWidth(), alias.getHeight()) * 2;
- Point2D startPoint = alias.getCenter();
- double x = startPoint.getX() - Math.cos(angle) * dist;
- double y = startPoint.getY() - Math.sin(angle) * dist;
- Point2D endPoint = new Point2D.Double(x, y);
- Line2D line = new Line2D.Double(startPoint, endPoint);
- result = lineTransformation.getIntersectionWithPathIterator(line, getBoundPathIterator(alias));
- if (result == null) {
- logger.warn("Unknown crossing point: " + line.getP1() + "; " + line.getP2());
- result = alias.getCenter();
- }
- }
- return result;
- }
-
- /**
- * This method returns border of the alias as a PathIterator.
- *
- * @param alias
- * object for which we want to find a border
- * @return border of the alias
- */
- protected abstract PathIterator getBoundPathIterator(T alias);
-
- /**
- * Checks if anchor is valid for the alias to find a point on the border.
- *
- * @param alias
- * object to be checked
- * @param anchor
- * anchor point
- * @return true if the conditions are ok (alias size >0 and angle != null)
- */
- protected boolean invalidAnchorPosition(T alias, CellDesignerAnchor anchor) {
- if (anchor == null || anchor.getAngle() == null) {
- return true;
- }
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
- return true;
- }
- // TODO handle with one of params equal to 0
-
- return false;
- }
-
- /**
- * @return the polygonTransformation
- */
- protected CellDesignerPolygonTransformation getPolygonTransformation() {
- return polygonTransformation;
- }
-
- /**
- * @param polygonTransformation
- * the polygonTransformation to set
- */
- protected void setPolygonTransformation(CellDesignerPolygonTransformation polygonTransformation) {
- this.polygonTransformation = polygonTransformation;
- }
-
- /**
- * @return the lineTransformation
- */
- protected LineTransformation getLineTransformation() {
- return lineTransformation;
- }
-
- /**
- * @param lineTransformation
- * the lineTransformation to set
- */
- protected void setLineTransformation(LineTransformation lineTransformation) {
- this.lineTransformation = lineTransformation;
- }
-
- /**
- * @return the ellipseTransformation
- */
- protected CellDesignerEllipseTransformation getEllipseTransformation() {
- return ellipseTransformation;
- }
-
- /**
- * @param ellipseTransformation
- * the ellipseTransformation to set
- */
- protected void setEllipseTransformation(CellDesignerEllipseTransformation ellipseTransformation) {
- this.ellipseTransformation = ellipseTransformation;
- }
-
- /**
- * @return the rectangleTransformation
- */
- protected CellDesignerRectangleTransformation getRectangleTransformation() {
- return rectangleTransformation;
- }
-
- /**
- * @param rectangleTransformation
- * the rectangleTransformation to set
- */
- protected void setRectangleTransformation(CellDesignerRectangleTransformation rectangleTransformation) {
- this.rectangleTransformation = rectangleTransformation;
- }
-
- /**
- * @return the sbgn
- * @see #sbgn
- */
- protected boolean isSbgn() {
- return sbgn;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.geometry.LineTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerEllipseTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPolygonTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerRectangleTransformation;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * This abstract class is an interface for setting up graphical data for alias
+ * from CellDesigner specific format into standard layout.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ */
+public abstract class AbstractCellDesignerAliasConverter<T extends Element> implements ICellDesignerAliasConverter<T> {
+
+ /**
+ * PI value.
+ */
+ private static final double PI = Math.PI;
+
+ /**
+ * Constant determining angle of the top right corner.
+ */
+ protected static final double RIGHT_TOP_RESIDUE_MAX_ANGLE = 0.25 * PI;
+
+ /**
+ * Constant determining angle of the top left corner.
+ */
+ protected static final double TOP_RESIDUE_MAX_ANGLE = 0.75 * PI;
+
+ /**
+ * Constant determining angle of the bottom left corner.
+ */
+ protected static final double LEFT_RESIDUE_MAX_ANGLE = 1.25 * PI;
+
+ /**
+ * Constant determining angle of the bottom right corner.
+ */
+ protected static final double BOTTOM_RESIDUE_MAX_ANGLE = 1.75 * PI;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(AbstractCellDesignerAliasConverter.class);
+
+ /**
+ * CellDesigner graphical helper with polygon transformation functions.
+ */
+ private CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
+
+ /**
+ * CellDesigner graphical helper with line transformation functions.
+ */
+ private LineTransformation lineTransformation = new LineTransformation();
+
+ /**
+ * CellDesigner graphical helper with ellipse transformation functions.
+ */
+ private CellDesignerEllipseTransformation ellipseTransformation = new CellDesignerEllipseTransformation();
+
+ /**
+ * CellDesigner graphical helper with rectangle transformation functions.
+ */
+ private CellDesignerRectangleTransformation rectangleTransformation = new CellDesignerRectangleTransformation();
+
+ /**
+ * What is the distance between homodimer aliases when homodimer>1.
+ */
+ public static final int HOMODIMER_OFFSET = 6;
+
+ /**
+ * Should the converter use SBGN standard.
+ */
+ private boolean sbgn;
+
+ /**
+ * Default constructor that prevents from instantiation of the class.
+ *
+ * @param sbgn
+ * Should the converter use SBGN standard
+ */
+ protected AbstractCellDesignerAliasConverter(boolean sbgn) {
+ this.sbgn = sbgn;
+ };
+
+ @Override
+ public CellDesignerAnchor getAnchorForCoordinates(T alias, Point2D point) {
+ double dist = Double.MAX_VALUE;
+ CellDesignerAnchor result = null;
+ for (CellDesignerAnchor anchor : CellDesignerAnchor.values()) {
+ double newDist = getPointCoordinates(alias, anchor).distance(point);
+ if (newDist < dist) {
+ dist = newDist;
+ result = anchor;
+ }
+ }
+ // if the distance to all known anchors is too big then assume center
+ if (dist > 1) {
+ return null;
+ }
+ return result;
+ }
+
+ @Override
+ public abstract Point2D getPointCoordinates(T alias, CellDesignerAnchor anchor);
+
+ @Override
+ public Point2D getAnchorPointCoordinates(T alias, CellDesignerAnchor anchor, PolylineData ld) {
+ if (anchor != null && anchor.getAngle() != null) {
+ return getPointCoordinates(alias, anchor);
+ } else {
+ Point2D p1 = ld.getPoints().get(1);
+ Point2D p2 = ld.getPoints().get(0);
+ double dx = p2.getX() - p1.getX();
+ double dy = p2.getY() - p1.getY();
+ double angle = Math.atan2(dy, dx);
+ return getAnchorPointCoordinates(alias, angle);
+ }
+ }
+
+ /**
+ * This method computes coordinates that should be associated with the angle on
+ * the border of the alias.
+ *
+ * @param alias
+ * alias to be investigated
+ * @param angle
+ * angle on the border of the alias
+ * @return coordinates on the border of the alias described by the angle
+ */
+ protected Point2D getAnchorPointCoordinates(T alias, double angle) {
+ Point2D result = null;
+ if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ result = alias.getCenter();
+ } else {
+ double dist = Math.max(alias.getWidth(), alias.getHeight()) * 2;
+ Point2D startPoint = alias.getCenter();
+ double x = startPoint.getX() - Math.cos(angle) * dist;
+ double y = startPoint.getY() - Math.sin(angle) * dist;
+ Point2D endPoint = new Point2D.Double(x, y);
+ Line2D line = new Line2D.Double(startPoint, endPoint);
+ result = lineTransformation.getIntersectionWithPathIterator(line, getBoundPathIterator(alias));
+ if (result == null) {
+ logger.warn("Unknown crossing point: " + line.getP1() + "; " + line.getP2());
+ result = alias.getCenter();
+ }
+ }
+ return result;
+ }
+
+ /**
+ * This method returns border of the alias as a PathIterator.
+ *
+ * @param alias
+ * object for which we want to find a border
+ * @return border of the alias
+ */
+ protected abstract PathIterator getBoundPathIterator(T alias);
+
+ /**
+ * Checks if anchor is valid for the alias to find a point on the border.
+ *
+ * @param alias
+ * object to be checked
+ * @param anchor
+ * anchor point
+ * @return true if the conditions are ok (alias size >0 and angle != null)
+ */
+ protected boolean invalidAnchorPosition(T alias, CellDesignerAnchor anchor) {
+ if (anchor == null || anchor.getAngle() == null) {
+ return true;
+ }
+ if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ return true;
+ }
+ // TODO handle with one of params equal to 0
+
+ return false;
+ }
+
+ /**
+ * @return the polygonTransformation
+ */
+ protected CellDesignerPolygonTransformation getPolygonTransformation() {
+ return polygonTransformation;
+ }
+
+ /**
+ * @param polygonTransformation
+ * the polygonTransformation to set
+ */
+ protected void setPolygonTransformation(CellDesignerPolygonTransformation polygonTransformation) {
+ this.polygonTransformation = polygonTransformation;
+ }
+
+ /**
+ * @return the lineTransformation
+ */
+ protected LineTransformation getLineTransformation() {
+ return lineTransformation;
+ }
+
+ /**
+ * @param lineTransformation
+ * the lineTransformation to set
+ */
+ protected void setLineTransformation(LineTransformation lineTransformation) {
+ this.lineTransformation = lineTransformation;
+ }
+
+ /**
+ * @return the ellipseTransformation
+ */
+ protected CellDesignerEllipseTransformation getEllipseTransformation() {
+ return ellipseTransformation;
+ }
+
+ /**
+ * @param ellipseTransformation
+ * the ellipseTransformation to set
+ */
+ protected void setEllipseTransformation(CellDesignerEllipseTransformation ellipseTransformation) {
+ this.ellipseTransformation = ellipseTransformation;
+ }
+
+ /**
+ * @return the rectangleTransformation
+ */
+ protected CellDesignerRectangleTransformation getRectangleTransformation() {
+ return rectangleTransformation;
+ }
+
+ /**
+ * @param rectangleTransformation
+ * the rectangleTransformation to set
+ */
+ protected void setRectangleTransformation(CellDesignerRectangleTransformation rectangleTransformation) {
+ this.rectangleTransformation = rectangleTransformation;
+ }
+
+ /**
+ * @return the sbgn
+ * @see #sbgn
+ */
+ protected boolean isSbgn() {
+ return sbgn;
+ }
+
+ /**
+ * Returns coordinates on the {@link Species} border for given angle for
+ * residues.
+ *
+ * @param species
+ * object on border which the point is looked for
+ * @param angle
+ * CellDEsigner specific angle defining coordinates (;/)
+ * @return coordinates on the alias border that correspond to the angle
+ */
+ @Override
+ public Point2D getResidueCoordinates(final T species, double angle) {
+ Point2D result = null;
+ if (species.getWidth() == 0 && species.getHeight() == 0) {
+ result = species.getCenter();
+ } else {
+ double x = 0;
+ double y = 0;
+ while (angle > 2 * PI) {
+ angle -= 2 * PI;
+ }
+ while (angle < 0) {
+ angle += 2 * PI;
+ }
+ if (angle < RIGHT_TOP_RESIDUE_MAX_ANGLE) {
+ // CHECKSTYLE:OFF 0.5 is much readable than any other suggestion
+ double ratio = 0.5 + angle / (PI / 2);
+ // CHECKSTYLE:ON
+ x = species.getX() + species.getWidth();
+ y = species.getY() + species.getHeight() * (1 - ratio);
+ } else if (angle < TOP_RESIDUE_MAX_ANGLE) {
+ double ratio = (angle - RIGHT_TOP_RESIDUE_MAX_ANGLE) / (PI / 2);
+ y = species.getY();
+ x = species.getX() + species.getWidth() * (1 - ratio);
+ } else if (angle < LEFT_RESIDUE_MAX_ANGLE) {
+ double ratio = (angle - TOP_RESIDUE_MAX_ANGLE) / (PI / 2);
+ y = species.getY() + species.getHeight() * (ratio);
+ x = species.getX();
+ } else if (angle < BOTTOM_RESIDUE_MAX_ANGLE) {
+ double ratio = (angle - LEFT_RESIDUE_MAX_ANGLE) / (PI / 2);
+ y = species.getY() + species.getHeight();
+ x = species.getX() + species.getWidth() * ratio;
+ } else if (angle <= 2 * PI + Configuration.EPSILON) {
+ double ratio = (angle - BOTTOM_RESIDUE_MAX_ANGLE) / (PI / 2);
+ y = species.getY() + species.getHeight() * (1 - ratio);
+ x = species.getX() + species.getWidth();
+ } else {
+ throw new InvalidStateException();
+ }
+ Point2D center = species.getCenter();
+ double correctedAngle = -Math.atan2((y - center.getY()), (x - center.getX()));
+ result = getPointCoordinatesOnBorder(species, correctedAngle);
+ }
+ return result;
+
+ }
+
+ /**
+ * Returns coordinates on the {@link Element} border for given angle.
+ *
+ * @param elemnt
+ * {@link Element} on border which the point is looked for
+ * @param angle
+ * angle between X axis center point of {@link Species} and point that
+ * we are looking for
+ * @return coordinates on the {@link Species} border that correspond to the
+ * angle
+ */
+ protected Point2D getPointCoordinatesOnBorder(final T elemnt, final double angle) {
+ Point2D result = null;
+ if (elemnt.getWidth() == 0 && elemnt.getHeight() == 0) {
+ result = elemnt.getCenter();
+ } else {
+ double dist = Math.max(elemnt.getWidth(), elemnt.getHeight()) * 2;
+ Point2D startPoint = elemnt.getCenter();
+ double x = startPoint.getX() + Math.cos(angle) * dist;
+ double y = startPoint.getY() - Math.sin(angle) * dist;
+ Point2D endPoint = new Point2D.Double(x, y);
+ Line2D line = new Line2D.Double(startPoint, endPoint);
+ result = lineTransformation.getIntersectionWithPathIterator(line, getBoundPathIterator(elemnt));
+ }
+ return result;
+
+ }
+
+ @Override
+ public Double getAngleForPoint(T element, Point2D position) {
+ double result = -1;
+ double correctedAngle = -Math.atan2((position.getY() - element.getCenterY()),
+ (position.getX() - element.getCenterX()));
+
+ double dist = Math.max(element.getWidth(), element.getHeight()) * 2;
+ Point2D startPoint = element.getCenter();
+ double x = startPoint.getX() + Math.cos(correctedAngle) * dist;
+ double y = startPoint.getY() - Math.sin(correctedAngle) * dist;
+ Point2D endPoint = new Point2D.Double(x, y);
+ Line2D line = new Line2D.Double(startPoint, endPoint);
+
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
+
+ path.moveTo(element.getX(), element.getY());
+ path.lineTo(element.getX(), element.getY() + element.getHeight());
+ path.lineTo(element.getX() + element.getWidth(), element.getY() + element.getHeight());
+ path.lineTo(element.getX() + element.getWidth(), element.getY());
+ path.closePath();
+
+ Point2D pointOnBorder = lineTransformation.getIntersectionWithPathIterator(line,
+ path.getPathIterator(new AffineTransform()));
+
+ if (Math.abs(pointOnBorder.getX() - element.getX() - element.getWidth()) < Configuration.EPSILON && //
+ pointOnBorder.getY() - element.getY() - element.getHeight() / 2 < Configuration.EPSILON) {
+ double ratio = 1 - (pointOnBorder.getY() - element.getY()) / element.getHeight();
+ result = (ratio - 0.5) * (PI / 2);
+ } else if (Math.abs(pointOnBorder.getY() - element.getY()) < Configuration.EPSILON) {
+ double ratio = 1 - (pointOnBorder.getX() - element.getX()) / element.getWidth();
+ result = ratio * (PI / 2) + RIGHT_TOP_RESIDUE_MAX_ANGLE;
+ } else if (Math.abs(pointOnBorder.getX() - element.getX()) < Configuration.EPSILON) {
+ double ratio = (pointOnBorder.getY() - element.getY()) / element.getHeight();
+ result = ratio * (PI / 2) + TOP_RESIDUE_MAX_ANGLE;
+ } else if (Math.abs(pointOnBorder.getY() - element.getY() - element.getHeight()) < Configuration.EPSILON) {
+ double ratio = (pointOnBorder.getX() - element.getX()) / element.getWidth();
+ result = ratio * (PI / 2) + LEFT_RESIDUE_MAX_ANGLE;
+ } else if (Math.abs(pointOnBorder.getX() - element.getX() - element.getWidth()) < Configuration.EPSILON && //
+ pointOnBorder.getY() - element.getY() - element.getHeight() < Configuration.EPSILON) {
+ double ratio = 1 - (pointOnBorder.getY() - element.getY()) / element.getHeight();
+ result = ratio * (PI / 2) + BOTTOM_RESIDUE_MAX_ANGLE;
+ } else {
+ logger.warn("Problem with finding angle. Using default 0");
+ result = 0;
+ }
+ return result;
+ }
+
+ @Override
+ public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
+ return null;
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos) {
+ return this.getCoordinatesByPosition(element, pos, 0.0);
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos, Double width) {
+ throw new NotImplementedException("Not implemented for: " + this.getClass());
+ }
+
+ @Override
+ public Double getCellDesignerSize(ModificationResidue mr) {
+ throw new NotImplementedException("Not implemented for: " + this.getClass());
+ }
+
+ @Override
+ public Double getWidthBySize(Element element, Double size) {
+ throw new NotImplementedException("Not implemented for: " + this.getClass());
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
index f558c3d7f1ead56135c366f2a461978a2fa981ae..613c3b51b2199bb16f5d73f2872e593a6f65f5ba 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
@@ -1,115 +1,146 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class that provides CellDesigner specific graphical information for
- * AntisenseRna. It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected AntisenseRnaCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- /**
- * How big should be the arc in rectangle for nucleic acid feature
- * representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- if (isSbgn()) {
- return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- }
- ArrayList<Point2D> points = getPoints(alias);
- return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
- }
-
- @Override
- protected PathIterator getBoundPathIterator(Species alias) {
- return getAntisebseRnaPath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns shape of the AntisenseRna as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getPoints(Element alias) {
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
- ArrayList<Point2D> points = new ArrayList<Point2D>();
-
- // CHECKSTYLE:OFF
- points.add(new Point2D.Double(x + width / 8, y + height / 2));
- points.add(new Point2D.Double(x, y));
- points.add(new Point2D.Double(x + width * 3 / 8, y));
- points.add(new Point2D.Double(x + width * 3 / 4, y));
- points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
- points.add(new Point2D.Double(x + width, y + height));
- points.add(new Point2D.Double(x + width * 5 / 8, y + height));
- points.add(new Point2D.Double(x + width / 4, y + height));
- // CHECKSTYLE:ON
- return points;
- }
-
- /**
- * Returns shape of the AntisenseRna as a GeneralPath object.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return GeneralPath object defining border of the given alias
- */
- private GeneralPath getAntisebseRnaPath(Element alias) {
- // CHECKSTYLE:OFF
- GeneralPath path;
- if (!isSbgn()) {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
- path.moveTo(alias.getX(), alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + alias.getWidth() / 4, alias.getY() + alias.getHeight());
- path.closePath();
- } else {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
- double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
-
- path.moveTo(x, y);
- path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.lineTo(x + width, y);
- path.closePath();
- }
- // CHECKSTYLE:ON
- return path;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AbstractRegionModification;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Class that provides CellDesigner specific graphical information for
+ * AntisenseRna. It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected AntisenseRnaCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature
+ * representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ if (isSbgn()) {
+ return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(),
+ alias.getHeight(), anchor);
+ }
+ ArrayList<Point2D> points = getPoints(alias);
+ return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
+ }
+
+ @Override
+ protected PathIterator getBoundPathIterator(Species alias) {
+ return getAntisebseRnaPath(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns shape of the AntisenseRna as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getPoints(Element alias) {
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+ ArrayList<Point2D> points = new ArrayList<Point2D>();
+
+ // CHECKSTYLE:OFF
+ points.add(new Point2D.Double(x + width / 8, y + height / 2));
+ points.add(new Point2D.Double(x, y));
+ points.add(new Point2D.Double(x + width * 3 / 8, y));
+ points.add(new Point2D.Double(x + width * 3 / 4, y));
+ points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
+ points.add(new Point2D.Double(x + width, y + height));
+ points.add(new Point2D.Double(x + width * 5 / 8, y + height));
+ points.add(new Point2D.Double(x + width / 4, y + height));
+ // CHECKSTYLE:ON
+ return points;
+ }
+
+ /**
+ * Returns shape of the AntisenseRna as a GeneralPath object.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return GeneralPath object defining border of the given alias
+ */
+ private GeneralPath getAntisebseRnaPath(Element alias) {
+ // CHECKSTYLE:OFF
+ GeneralPath path;
+ if (!isSbgn()) {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
+ path.moveTo(alias.getX(), alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX() + alias.getWidth() / 4, alias.getY() + alias.getHeight());
+ path.closePath();
+ } else {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
+ double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
+
+ path.moveTo(x, y);
+ path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width,
+ y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.lineTo(x + width, y);
+ path.closePath();
+ }
+ // CHECKSTYLE:ON
+ return path;
+ }
+
+ @Override
+ public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
+ return (mr.getPosition().getX() - mr.getSpecies().getX()) / (mr.getSpecies().getWidth() * 3.0 / 4.0);
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos, Double width) {
+ double x = element.getX() + element.getWidth() * 3.0 / 4.0 * pos;
+ x = Math.max(element.getX() + width / 2, x);
+ x = Math.min(element.getX() + element.getWidth() * 3.0 / 4.0 - width / 2, x);
+ return new Point2D.Double(x, element.getY());
+ }
+
+ @Override
+ public Double getCellDesignerSize(ModificationResidue mr) {
+ if (mr instanceof AbstractRegionModification) {
+ return ((AbstractRegionModification) mr).getWidth() / (mr.getSpecies().getWidth() * 3.0 / 4.0);
+ }
+ throw new NotImplementedException("Not implemented for: " + this.getClass() + ", " + mr.getClass());
+ }
+
+ @Override
+ public Double getWidthBySize(Element element, Double size) {
+ return size * (element.getWidth() * 3.0 / 4.0);
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
index 5e0364e6f7e83784d7235803566b5782f5fd505e..272366e5235cbb35a1c659af5e50d575cbce2b02 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
@@ -1,114 +1,153 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Unknown;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * This class is designed to obtain CellDesigner specific data from
- * {@link Element}.
- *
- * @author Piotr Gawron
- *
- */
-
-public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<Element> {
-
- /**
- * Class helping with transforming objectcs into meaningfull identifiers.
- */
- private static ElementUtils eu = new ElementUtils();
-
- /**
- * Returns a converter for given {@link Element}. If converter doesn't exist
- * exception is thrown.
- *
- * @param element
- * element for which we are loooking for a converter
- * @param sbgn
- * Should the converter use sbgn standard
- * @return converter that can be applied for the given element
- */
- private ICellDesignerAliasConverter<? extends Element> getConverterForAlias(Element element, boolean sbgn) {
- if (element == null) {
- throw new InvalidArgumentException("element cannot be null");
- }
- if (element instanceof Protein) {
- return new ProteinCellDesignerAliasConverter(sbgn);
- } else if (element instanceof Degraded) {
- return new DegradedCellDesignerAliasConverter(sbgn);
- } else if (element instanceof Complex) {
- return new ComplexCellDesignerAliasConverter(sbgn);
- } else if (element instanceof SimpleMolecule) {
- return new SimpleMoleculeCellDesignerAliasConverter(sbgn);
- } else if (element instanceof Drug) {
- return new DrugCellDesignerAliasConverter(sbgn);
- } else if (element instanceof Ion) {
- return new IonCellDesignerAliasConverter(sbgn);
- } else if (element instanceof Phenotype) {
- return new PhenotypeCellDesignerAliasConverter(sbgn);
- } else if (element instanceof Rna) {
- return new RnaCellDesignerAliasConverter(sbgn);
- } else if (element instanceof AntisenseRna) {
- return new AntisenseRnaCellDesignerAliasConverter(sbgn);
- } else if (element instanceof Gene) {
- return new GeneCellDesignerAliasConverter(sbgn);
- } else if (element instanceof Unknown) {
- return new UnknownCellDesignerAliasConverter(sbgn);
- } else {
- throw new NotImplementedException(eu.getElementTag(element) + "Unknown converter for class");
- }
- }
-
- /**
- * Converter used for operations on the {@link Element} given in constructor.
- */
- @SuppressWarnings("rawtypes")
- private ICellDesignerAliasConverter converter = null;
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- * @param element
- * element for which this converter will be used
- */
- public CellDesignerAliasConverter(Element element, boolean sbgn) {
- converter = getConverterForAlias(element, sbgn);
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public CellDesignerAnchor getAnchorForCoordinates(Element element, Point2D point) {
- return converter.getAnchorForCoordinates(element, point);
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public Point2D getPointCoordinates(Element element, CellDesignerAnchor anchor) {
- return converter.getPointCoordinates(element, anchor);
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public Point2D getAnchorPointCoordinates(Element element, CellDesignerAnchor anchor, PolylineData line) {
- return converter.getAnchorPointCoordinates(element, anchor, line);
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * This class is designed to obtain CellDesigner specific data from
+ * {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<Element> {
+
+ /**
+ * Class helping with transforming objects into meaningful identifiers.
+ */
+ private static ElementUtils eu = new ElementUtils();
+
+ /**
+ * Returns a converter for given {@link Element}. If converter doesn't exist
+ * exception is thrown.
+ *
+ * @param element
+ * element for which we are looking for a converter
+ * @param sbgn
+ * Should the converter use SBGN standard
+ * @return converter that can be applied for the given element
+ */
+ private ICellDesignerAliasConverter<? extends Element> getConverterForAlias(Element element, boolean sbgn) {
+ if (element == null) {
+ throw new InvalidArgumentException("element cannot be null");
+ }
+ if (element instanceof Protein) {
+ return new ProteinCellDesignerAliasConverter(sbgn);
+ } else if (element instanceof Degraded) {
+ return new DegradedCellDesignerAliasConverter(sbgn);
+ } else if (element instanceof Complex) {
+ return new ComplexCellDesignerAliasConverter(sbgn);
+ } else if (element instanceof SimpleMolecule) {
+ return new SimpleMoleculeCellDesignerAliasConverter(sbgn);
+ } else if (element instanceof Drug) {
+ return new DrugCellDesignerAliasConverter(sbgn);
+ } else if (element instanceof Ion) {
+ return new IonCellDesignerAliasConverter(sbgn);
+ } else if (element instanceof Phenotype) {
+ return new PhenotypeCellDesignerAliasConverter(sbgn);
+ } else if (element instanceof Rna) {
+ return new RnaCellDesignerAliasConverter(sbgn);
+ } else if (element instanceof AntisenseRna) {
+ return new AntisenseRnaCellDesignerAliasConverter(sbgn);
+ } else if (element instanceof Gene) {
+ return new GeneCellDesignerAliasConverter(sbgn);
+ } else if (element instanceof Unknown) {
+ return new UnknownCellDesignerAliasConverter(sbgn);
+ } else {
+ throw new NotImplementedException(eu.getElementTag(element) + "Unknown converter for class");
+ }
+ }
+
+ /**
+ * Converter used for operations on the {@link Element} given in constructor.
+ */
+ @SuppressWarnings("rawtypes")
+ private ICellDesignerAliasConverter converter = null;
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use SBGN standard
+ * @param element
+ * element for which this converter will be used
+ */
+ public CellDesignerAliasConverter(Element element, boolean sbgn) {
+ converter = getConverterForAlias(element, sbgn);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public CellDesignerAnchor getAnchorForCoordinates(Element element, Point2D point) {
+ return converter.getAnchorForCoordinates(element, point);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public Point2D getPointCoordinates(Element element, CellDesignerAnchor anchor) {
+ return converter.getPointCoordinates(element, anchor);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public Point2D getAnchorPointCoordinates(Element element, CellDesignerAnchor anchor, PolylineData line) {
+ return converter.getAnchorPointCoordinates(element, anchor, line);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public Double getAngleForPoint(Element element, Point2D position) {
+ return converter.getAngleForPoint(element, position);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public Point2D getResidueCoordinates(Element species, double angle) {
+ return converter.getResidueCoordinates(species, angle);
+ }
+
+ @Override
+ public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
+ return converter.getCellDesignerPositionByCoordinates(mr);
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos) {
+ return converter.getCoordinatesByPosition(element, pos);
+ }
+
+ @Override
+ public Double getCellDesignerSize(ModificationResidue mr) {
+ return converter.getCellDesignerSize(mr);
+ }
+
+ @Override
+ public Double getWidthBySize(Element element, Double size) {
+ return converter.getWidthBySize(element, size);
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos, Double width) {
+ return converter.getCoordinatesByPosition(element, pos, width);
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java
index 5a26c2bc169c3060fa19aa41b66e3fe0240c293c..e09ff00182661df44f68ddf28c40d997e8534ae5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java
@@ -1,81 +1,120 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.Rectangle;
-import java.awt.Shape;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class that provides CellDesigner specific graphical information for Gene.
- * It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected GeneCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- /**
- * How big should be the arc in rectangle for nucleic acid feature representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- }
-
- /**
- * Shape representation of the gene alias.
- *
- * @param alias
- * alias for which we are looking for a Shape
- * @return Shape object that represents alias
- */
- private Shape getGeneShape(Element alias) {
- if (!isSbgn()) {
- Shape shape;
- shape = new Rectangle(alias.getX().intValue(), alias.getY().intValue(), alias.getWidth().intValue(), alias.getHeight().intValue());
- return shape;
- } else {
- GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
- double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
-
- path.moveTo(x, y);
- path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.curveTo(x, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.curveTo(x + width, y + height,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.lineTo(x + width, y);
- path.closePath();
- return path;
- }
- }
-
- @Override
- public PathIterator getBoundPathIterator(Species alias) {
- return getGeneShape(alias).getPathIterator(new AffineTransform());
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.Rectangle;
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.field.AbstractRegionModification;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Gene.
+ * It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Gene> {
+
+ Logger logger = Logger.getLogger(GeneCellDesignerAliasConverter.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use SBGN standard
+ */
+ protected GeneCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature
+ * representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+
+ @Override
+ public Point2D getPointCoordinates(Gene alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(),
+ alias.getHeight(), anchor);
+ }
+
+ /**
+ * Shape representation of the gene alias.
+ *
+ * @param alias
+ * alias for which we are looking for a Shape
+ * @return Shape object that represents alias
+ */
+ private Shape getGeneShape(Element alias) {
+ if (!isSbgn()) {
+ Shape shape;
+ shape = new Rectangle(alias.getX().intValue(), alias.getY().intValue(), alias.getWidth().intValue(),
+ alias.getHeight().intValue());
+ return shape;
+ } else {
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
+ double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
+
+ path.moveTo(x, y);
+ path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width,
+ y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.lineTo(x + width, y);
+ path.closePath();
+ return path;
+ }
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Gene alias) {
+ return getGeneShape(alias).getPathIterator(new AffineTransform());
+ }
+
+ @Override
+ public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
+ Double result = (mr.getPosition().getX() - mr.getSpecies().getX()) / mr.getSpecies().getWidth();
+ result = Math.min(result, 1.0);
+ result = Math.max(result, 0.0);
+ return result;
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos, Double modificationWidth) {
+ double x = element.getX() + element.getWidth() * pos;
+ x = Math.max(element.getX() + modificationWidth/2, x);
+ x = Math.min(element.getX() + element.getWidth() - modificationWidth/2, x);
+
+ Point2D result = new Point2D.Double(x, element.getY());
+ return result;
+ }
+
+ @Override
+ public Double getCellDesignerSize(ModificationResidue mr) {
+ if (mr instanceof AbstractRegionModification) {
+ return ((AbstractRegionModification) mr).getWidth() / mr.getSpecies().getWidth();
+ }
+ throw new NotImplementedException("Not implemented for: " + this.getClass() + ", " + mr.getClass());
+ }
+
+ @Override
+ public Double getWidthBySize(Element element, Double size) {
+ return size * element.getWidth();
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ICellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ICellDesignerAliasConverter.java
index a42fa6d4b6ff3245e52fb8e0189c30cc997c34c4..21de988f8c52418e8b59b56e71157538192e4b75 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ICellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ICellDesignerAliasConverter.java
@@ -1,61 +1,96 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * Interface that defines functions usefull in transforming graphical
- * information from objects retrieved from CellDesigner xml into abslote values.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- */
-public interface ICellDesignerAliasConverter<T extends Element> {
- /**
- * This method computes which anchor is the most probable for describing the
- * point on the border of alias. There are 16 possible anchors on the border
- * of every alias and one undefined point that will be used if no point can be
- * found (see {@link CellDesignerAnchor} to find information about anchors).
- *
- * @param alias
- * object for which we try to find anchor
- * @param point
- * point on the border of alias for which we try to find anchor
- * @return CellDesigner anchor point that describe the best point on the
- * border
- */
- CellDesignerAnchor getAnchorForCoordinates(T alias, Point2D point);
-
- /**
- * This method transform CellDesigner anchor point on the alias into x,y
- * coordinates.
- *
- * @param alias
- * we want to find coordinates on this alias border
- * @param anchor
- * CelDesigner anchor that defines point on the border
- * @return point on the border that is defined by the anchor point
- */
- Point2D getPointCoordinates(T alias, CellDesignerAnchor anchor);
-
- /**
- * This method transform CellDesigner anchor point on the alias into x,y
- * coordinates. If the anchor point doesn't define point then the line
- * parameter is used to find the right angle on the alias border and point on
- * the border with this angle is used as a result.
- *
- * @param alias
- * we want to find coordinates on this alias border
- * @param anchor
- * CelDesigner anchor that defines point on the border
- * @param line
- * line that starts in the alias
- * @return point on the border that is defined by the anchor point
- */
- Point2D getAnchorPointCoordinates(T alias, CellDesignerAnchor anchor, PolylineData line);
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Interface that defines functions useful in transforming graphical information
+ * from objects retrieved from CellDesigner xml into absolute values.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ */
+public interface ICellDesignerAliasConverter<T extends Element> {
+ /**
+ * This method computes which anchor is the most probable for describing the
+ * point on the border of alias. There are 16 possible anchors on the border of
+ * every alias and one undefined point that will be used if no point can be
+ * found (see {@link CellDesignerAnchor} to find information about anchors).
+ *
+ * @param alias
+ * object for which we try to find anchor
+ * @param point
+ * point on the border of alias for which we try to find anchor
+ * @return CellDesigner anchor point that describe the best point on the border
+ */
+ CellDesignerAnchor getAnchorForCoordinates(T alias, Point2D point);
+
+ /**
+ * This method transform CellDesigner anchor point on the alias into x,y
+ * coordinates.
+ *
+ * @param alias
+ * we want to find coordinates on this alias border
+ * @param anchor
+ * CelDesigner anchor that defines point on the border
+ * @return point on the border that is defined by the anchor point
+ */
+ Point2D getPointCoordinates(T alias, CellDesignerAnchor anchor);
+
+ /**
+ * This method transform CellDesigner anchor point on the alias into x,y
+ * coordinates. If the anchor point doesn't define point then the line parameter
+ * is used to find the right angle on the alias border and point on the border
+ * with this angle is used as a result.
+ *
+ * @param alias
+ * we want to find coordinates on this alias border
+ * @param anchor
+ * CelDesigner anchor that defines point on the border
+ * @param line
+ * line that starts in the alias
+ * @return point on the border that is defined by the anchor point
+ */
+ Point2D getAnchorPointCoordinates(T alias, CellDesignerAnchor anchor, PolylineData line);
+
+ Point2D getResidueCoordinates(final T species, double angle);
+
+ Double getAngleForPoint(T alias, Point2D position);
+
+ public Double getCellDesignerPositionByCoordinates(ModificationResidue mr);
+
+ /**
+ * Gets coordinates on element based on CellDesigner position
+ *
+ * @param element
+ * element on which we want to find coordinates
+ * @param pos
+ * CellDesigner position (value between 0-1)
+ * @return coordinates on the element
+ */
+ public Point2D getCoordinatesByPosition(Element element, Double pos);
+
+ /**
+ * Gets coordinates on element based on CellDesigner position taking into
+ * account width of the {@link ModificationResidue} that we want to place.
+ *
+ * @param element
+ * element on which we want to find coordinates
+ * @param pos
+ * CellDesigner position (value between 0-1)
+ * @param modificationWidth
+ * width of the {@link ModificationResidue}
+ * @return coordinates on the element
+ */
+ public Point2D getCoordinatesByPosition(Element element, Double pos, Double modificationWidth);
+
+ public Double getCellDesignerSize(ModificationResidue mr);
+
+ public Double getWidthBySize(Element element, Double size);
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java
index 1b1fbd6efe3e581f63203a1a1a131fbc9439afdd..5b8e000b5062070ba9f4db784de1e266afa7e821 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java
@@ -3,9 +3,12 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry;
import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.Species;
/**
@@ -15,86 +18,102 @@ import lcsb.mapviewer.model.map.species.Species;
* @author Piotr Gawron
*
*/
-public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected IonCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
-
- return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, diameter, diameter, anchor);
- }
-
- /**
- * Returns transformed y coordinate for the ion alias.
- *
- * @param alias
- * object alias to to which we are looking for y coordinate
- * @return y coordinate of the alias
- */
- private double getYCoord(Element alias) {
- double y = alias.getY();
- return y;
- }
-
- /**
- * Returns transformed x coordinate for the ion alias.
- *
- * @param alias
- * object alias to to which we are looking for x coordinate
- * @param diameter
- * diameter of the circle representing alias
- * @return x coordinate of the alias
- */
- private double getXCoord(Element alias, double diameter) {
- double x = alias.getX() + (alias.getWidth() - diameter) / 2;
- return x;
- }
-
- /**
- * Returns diameter of the ion alias.
- *
- * @param alias
- * object alias to to which we are looking for diameter.
- * @return diameter of the alias
- */
- private double getDiameter(Element alias) {
- double diameter = Math.min(alias.getWidth(), alias.getHeight());
- if (diameter < 0) {
- diameter = 0;
- }
- return diameter;
- }
-
- @Override
- public Point2D getAnchorPointCoordinates(Species alias, double angle) {
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
- return alias.getCenter();
- }
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
- Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
- return result;
-
- }
-
- @Override
- protected PathIterator getBoundPathIterator(Species alias) {
- throw new NotImplementedException("This class doesn't have bound");
- }
+public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Ion> {
+
+ Logger logger = Logger.getLogger(IonCellDesignerAliasConverter.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use SBGN standard
+ */
+ protected IonCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ @Override
+ public Point2D getPointCoordinates(Ion alias, CellDesignerAnchor anchor) {
+ double diameter = getDiameter(alias);
+ double x = getXCoord(alias, diameter);
+ double y = getYCoord(alias);
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+
+ return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, diameter, diameter, anchor);
+ }
+
+ /**
+ * Returns transformed y coordinate for the ion alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for y coordinate
+ * @return y coordinate of the alias
+ */
+ private double getYCoord(Element alias) {
+ double y = alias.getY();
+ return y;
+ }
+
+ /**
+ * Returns transformed x coordinate for the ion alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for x coordinate
+ * @param diameter
+ * diameter of the circle representing alias
+ * @return x coordinate of the alias
+ */
+ private double getXCoord(Element alias, double diameter) {
+ double x = alias.getX() + (alias.getWidth() - diameter) / 2;
+ return x;
+ }
+
+ /**
+ * Returns diameter of the ion alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for diameter.
+ * @return diameter of the alias
+ */
+ private double getDiameter(Element alias) {
+ double diameter = Math.min(alias.getWidth(), alias.getHeight());
+ if (diameter < 0) {
+ diameter = 0;
+ }
+ return diameter;
+ }
+
+ @Override
+ public Point2D getAnchorPointCoordinates(Ion alias, double angle) {
+ if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ return alias.getCenter();
+ }
+ double diameter = getDiameter(alias);
+ double x = getXCoord(alias, diameter);
+ double y = getYCoord(alias);
+ Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
+ return result;
+
+ }
+
+ @Override
+ protected PathIterator getBoundPathIterator(Ion alias) {
+ throw new NotImplementedException("This class doesn't have bound");
+ }
+
+ @Override
+ public Point2D getPointCoordinatesOnBorder(Ion ion, final double angle) {
+ if (ion.getWidth() == 0 && ion.getHeight() == 0) {
+ logger.warn("Looking for coordinates for the alias with 0 size");
+ return ion.getCenter();
+ }
+ double diameter = getDiameter(ion);
+ double x = getXCoord(ion, diameter);
+ double y = getYCoord(ion);
+ Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
+ return result;
+
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
index 0cee48a0e63f19509fc0dc46c7ea5b004cea319d..e48e6caea925d4f626e17389745624220d7250bf 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
@@ -1,118 +1,150 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class that provides CellDesigner specific graphical information for Rna.
- * It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected RnaCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- /**
- * How big should be the arc in rectangle for nucleic acid feature representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- if (isSbgn()) {
- return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(),
- alias.getWidth(), alias.getHeight(), anchor);
- }
- ArrayList<Point2D> points = getPoints(alias);
- return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
- }
-
- @Override
- public PathIterator getBoundPathIterator(Species alias) {
- return getRnaPath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns shape of the Rna as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getPoints(Element alias) {
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
- ArrayList<Point2D> points = new ArrayList<Point2D>();
- // CHECKSTYLE:OFF
- points.add(new Point2D.Double(x + width / 8, y + height / 2));
- points.add(new Point2D.Double(x + width / 4, y));
- points.add(new Point2D.Double(x + width * 5 / 8, y));
- points.add(new Point2D.Double(x + width, y));
- points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
- points.add(new Point2D.Double(x + width * 3 / 4, y + height));
- points.add(new Point2D.Double(x + width * 3 / 8, y + height));
- // CHECKSTYLE:ON
- points.add(new Point2D.Double(x, y + height));
- return points;
- }
-
- /**
- * Returns shape of the Rna as a GeneralPath object.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return GeneralPath object defining border of the given alias
- */
- private GeneralPath getRnaPath(Element alias) {
- // CHECKSTYLE:OFF
- GeneralPath path;
- if (!isSbgn()) {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
- path.moveTo(alias.getX() + alias.getWidth() / 4, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX(), alias.getY() + alias.getHeight());
- path.closePath();
- } else {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
- double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
-
- path.moveTo(x, y);
- path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.curveTo(x, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.curveTo(x + width, y + height,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.lineTo(x + width, y);
- path.closePath();
- }
- // CHECKSTYLE:ON
- return path;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AbstractRegionModification;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Rna. It's
+ * used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+ Logger logger = Logger.getLogger(RnaCellDesignerAliasConverter.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected RnaCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature
+ * representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ if (isSbgn()) {
+ return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(),
+ alias.getHeight(), anchor);
+ }
+ ArrayList<Point2D> points = getPoints(alias);
+ return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Species alias) {
+ return getRnaPath(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns shape of the Rna as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getPoints(Element alias) {
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+ ArrayList<Point2D> points = new ArrayList<Point2D>();
+ // CHECKSTYLE:OFF
+ points.add(new Point2D.Double(x + width / 8, y + height / 2));
+ points.add(new Point2D.Double(x + width / 4, y));
+ points.add(new Point2D.Double(x + width * 5 / 8, y));
+ points.add(new Point2D.Double(x + width, y));
+ points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
+ points.add(new Point2D.Double(x + width * 3 / 4, y + height));
+ points.add(new Point2D.Double(x + width * 3 / 8, y + height));
+ // CHECKSTYLE:ON
+ points.add(new Point2D.Double(x, y + height));
+ return points;
+ }
+
+ /**
+ * Returns shape of the Rna as a GeneralPath object.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return GeneralPath object defining border of the given alias
+ */
+ private GeneralPath getRnaPath(Element alias) {
+ // CHECKSTYLE:OFF
+ GeneralPath path;
+ if (!isSbgn()) {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
+ path.moveTo(alias.getX() + alias.getWidth() / 4, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX(), alias.getY() + alias.getHeight());
+ path.closePath();
+ } else {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
+ double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
+
+ path.moveTo(x, y);
+ path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width,
+ y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.lineTo(x + width, y);
+ path.closePath();
+ }
+ // CHECKSTYLE:ON
+ return path;
+ }
+
+ @Override
+ public Double getCellDesignerPositionByCoordinates(ModificationResidue mr) {
+ return (mr.getPosition().getX() - mr.getSpecies().getX() - mr.getSpecies().getWidth() / 4.0)
+ / (mr.getSpecies().getWidth() * 3.0 / 4.0);
+ }
+
+ @Override
+ public Point2D getCoordinatesByPosition(Element element, Double pos, Double modificationWidth) {
+ double x = element.getX() + element.getWidth() / 4.0 + element.getWidth() * 3.0 / 4.0 * pos;
+ x = Math.max(element.getX() + modificationWidth / 2, x);
+ x = Math.min(element.getX() + element.getWidth() - modificationWidth / 2, x);
+
+ return new Point2D.Double(x, element.getY());
+ }
+
+ @Override
+ public Double getCellDesignerSize(ModificationResidue mr) {
+ if (mr instanceof AbstractRegionModification) {
+ return ((AbstractRegionModification) mr).getWidth() / (mr.getSpecies().getWidth() * 3.0 / 4.0);
+ }
+ throw new NotImplementedException("Not implemented for: " + this.getClass() + ", " + mr.getClass());
+ }
+
+ @Override
+ public Double getWidthBySize(Element element, Double size) {
+ return size * (element.getWidth() * 3.0 / 4.0);
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java
index 858fea5cdb7e39849900ca9d3e3fc7cd7e640405..20a2e974e2f43a7c7e2057016045fe912044bcf9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java
@@ -3,9 +3,11 @@ package lcsb.mapviewer.converter.model.celldesigner.geometry;
import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
/**
* Class that provides CellDesigner specific graphical information for
@@ -14,52 +16,69 @@ import lcsb.mapviewer.model.map.species.Species;
* @author Piotr Gawron
*
*/
-public class SimpleMoleculeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+public class SimpleMoleculeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SimpleMolecule> {
+
+ Logger logger = Logger.getLogger(SimpleMoleculeCellDesignerAliasConverter.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected SimpleMoleculeCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ @Override
+ public Point2D getPointCoordinates(SimpleMolecule alias, CellDesignerAnchor anchor) {
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = Math.max(alias.getWidth(), 1);
+ double height = Math.max(alias.getHeight(), 1);
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ if (isSbgn()) {
+ return getEllipseTransformation().getPointOnEllipseByAnchor(x + (width - height) / 2, y, height, height, anchor);
+ }
+ return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, width, height, anchor);
+ }
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected SimpleMoleculeCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
+ @Override
+ public Point2D getAnchorPointCoordinates(SimpleMolecule alias, double angle) {
+ if (alias.getWidth().equals(0.0) && alias.getHeight().equals(0.0)) {
+ return alias.getCenter();
+ }
+ Point2D result;
+ if (!isSbgn()) {
+ result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(),
+ alias.getHeight(), angle);
+ } else {
+ result = getEllipseTransformation().getPointOnEllipseByRadian(
+ alias.getX() + (alias.getWidth() - alias.getHeight()) / 2, alias.getY(), alias.getHeight(), alias.getHeight(),
+ angle);
+ }
+ return result;
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- double x = alias.getX();
- double y = alias.getY();
- double width = Math.max(alias.getWidth(), 1);
- double height = Math.max(alias.getHeight(), 1);
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- if (isSbgn()) {
- return getEllipseTransformation().getPointOnEllipseByAnchor(x + (width - height) / 2, y, height, height, anchor);
- }
- return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, width, height, anchor);
- }
+ }
- @Override
- public Point2D getAnchorPointCoordinates(Species alias, double angle) {
- if (alias.getWidth().equals(0.0) && alias.getHeight().equals(0.0)) {
- return alias.getCenter();
- }
- Point2D result;
- if (!isSbgn()) {
- result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), angle);
- } else {
- result = getEllipseTransformation()
- .getPointOnEllipseByRadian(alias.getX() + (alias.getWidth() - alias.getHeight()) / 2, alias.getY(), alias.getHeight(), alias.getHeight(), angle);
- }
- return result;
+ @Override
+ public PathIterator getBoundPathIterator(SimpleMolecule alias) {
+ throw new NotImplementedException("This class doesn't provide boundPath");
+ }
- }
+ @Override
+ public Point2D getPointCoordinatesOnBorder(final SimpleMolecule simpleMolecule, final double angle) {
+ if (simpleMolecule.getWidth() == 0 && simpleMolecule.getHeight() == 0) {
+ logger.warn("Looking for coordinates on border of alias of size 0");
+ return simpleMolecule.getCenter();
+ }
+ Point2D result;
+ result = getEllipseTransformation().getPointOnEllipseByRadian(simpleMolecule.getX(), simpleMolecule.getY(),
+ simpleMolecule.getWidth(), simpleMolecule.getHeight(), angle);
+ return result;
- @Override
- public PathIterator getBoundPathIterator(Species alias) {
- throw new NotImplementedException("This class doesn't provide boundPath");
- }
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java
index 0d54efec3d264b791b1955358f4fb0db027ebd76..70ac03254ba23e788bb2ea297636a495db6acc17 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java
@@ -1,54 +1,73 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class that provides CellDesigner specific graphical information for
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown.model.map.species.Unknown
- * Unknown}. It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected UnknownCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- return getEllipseTransformation().getPointOnEllipseByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- }
-
- @Override
- public PathIterator getBoundPathIterator(Species alias) {
- throw new NotImplementedException("This class doesn't provide boundPath");
- }
-
- @Override
- public Point2D getAnchorPointCoordinates(Species alias, double angle) {
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
- return alias.getCenter();
- }
- Point2D result;
- result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), angle);
- return result;
-
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Class that provides CellDesigner specific graphical information for
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown.model.map.species.Unknown
+ * Unknown}. It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Unknown> {
+
+ Logger logger = Logger.getLogger(UnknownCellDesignerAliasConverter.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected UnknownCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ @Override
+ public Point2D getPointCoordinates(Unknown alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ return getEllipseTransformation().getPointOnEllipseByAnchor(alias.getX(), alias.getY(), alias.getWidth(),
+ alias.getHeight(), anchor);
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Unknown alias) {
+ throw new NotImplementedException("This class doesn't provide boundPath");
+ }
+
+ @Override
+ public Point2D getAnchorPointCoordinates(Unknown alias, double angle) {
+ if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ return alias.getCenter();
+ }
+ Point2D result;
+ result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(),
+ alias.getHeight(), angle);
+ return result;
+
+ }
+
+ @Override
+ public Point2D getPointCoordinatesOnBorder(Unknown unknown, final double angle) {
+ if (unknown.getWidth() == 0 && unknown.getHeight() == 0) {
+ logger.warn("Looking for coordinates for unknown of 0 size");
+ return unknown.getCenter();
+ }
+ Point2D result;
+ result = getEllipseTransformation().getPointOnEllipseByRadian(unknown.getX(), unknown.getY(), unknown.getWidth(),
+ unknown.getHeight(), angle);
+ return result;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
index 1213df96ac1b3cb495499cfb166636eb1a3ee052..2db1d9e5e3ea02f845d68116bb05730abfcf0028 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
@@ -5,15 +5,19 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
/**
* Class that performs parsing of the CellDesigner xml for AntisenseRna object.
@@ -23,151 +27,163 @@ import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
*/
public class AntisenseRnaXmlParser extends AbstractElementXmlParser<CellDesignerAntisenseRna, AntisenseRna> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(AntisenseRnaXmlParser.class.getName());
-
- /**
- * List of {@link CellDesignerElement celldesigner elements} obtained during
- * parsing process.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Default constructor.
- *
- * @param elements
- * list of {@link CellDesignerElement celldesigner elements} obtained
- * during parsing process
- */
- public AntisenseRnaXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
- }
-
- @Override
- public Pair<String, CellDesignerAntisenseRna> parseXmlElement(Node antisenseRnaNode) throws InvalidXmlSchemaException {
- CellDesignerAntisenseRna antisenseRna = new CellDesignerAntisenseRna();
- String identifier = getNodeAttr("id", antisenseRnaNode);
- antisenseRna.setName(decodeName(getNodeAttr("name", antisenseRnaNode)));
- NodeList list = antisenseRnaNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("celldesigner:notes")) {
- antisenseRna.setNotes(getRap().getNotes(node));
- } else if (node.getNodeName().equals("celldesigner:listOfRegions")) {
- NodeList residueList = node.getChildNodes();
- for (int j = 0; j < residueList.getLength(); j++) {
- Node residueNode = residueList.item(j);
- if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
- if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:region")) {
- antisenseRna.addRegion(getAntisenseRnaRegion(residueNode));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfRegions " + residueNode.getNodeName());
- }
- }
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:antisenseRna " + node.getNodeName());
- }
- }
- }
- Pair<String, CellDesignerAntisenseRna> result = new Pair<String, CellDesignerAntisenseRna>(identifier, antisenseRna);
- return result;
- }
-
- @Override
- public String toXml(AntisenseRna antisenseRna) {
- String attributes = "";
- String result = "";
- attributes += " id=\"ar_" + elements.getElementId(antisenseRna) + "\"";
- if (!antisenseRna.getName().equals("")) {
- attributes += " name=\"" + escapeXml(encodeName(antisenseRna.getName())) + "\"";
- }
- result += "<celldesigner:AntisenseRNA" + attributes + ">";
- result += "<celldesigner:notes>";
- result += "<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>";
-
- RestAnnotationParser rap = new RestAnnotationParser();
- result += rap.createAnnotationString(antisenseRna);
- result += antisenseRna.getNotes();
- result += "</body></html>";
- result += "</celldesigner:notes>";
- if (antisenseRna.getRegions().size() > 0) {
- result += "<celldesigner:listOfRegions>";
- for (AntisenseRnaRegion region : antisenseRna.getRegions()) {
- result += toXml(region);
- }
- result += "</celldesigner:listOfRegions>";
- }
- result += "</celldesigner:AntisenseRNA>";
- return result;
- }
-
- /**
- * Transforms AntisenseRnaRegion into CellDEsigner xml representation.
- *
- * @param region
- * object to be transformed
- * @return xml representation of the given region
- */
- private String toXml(AntisenseRnaRegion region) {
- String result = "";
- String attributes = "";
- if (!region.getIdAntisenseRnaRegion().equals("")) {
- attributes += " id=\"" + region.getIdAntisenseRnaRegion() + "\"";
- }
- if (!region.getName().equals("")) {
- attributes += " name=\"" + escapeXml(region.getName()) + "\"";
- }
- if (region.getSize() != 0) {
- attributes += " size=\"" + region.getSize() + "\"";
- }
- if (region.getPos() != 0) {
- attributes += " pos=\"" + region.getPos() + "\"";
- }
- if (region.getType() != null) {
- attributes += " type=\"" + region.getType().getName() + "\"";
- }
- result += "<celldesigner:region " + attributes + ">";
- result += "</celldesigner:region>";
-
- return result;
- }
-
- /**
- * Method that parse xml node into AntisenseRnaRegion element.
- *
- * @param regionNode
- * xml node to parse
- * @return AntisenseRnaRegion object from xml node
- * @throws InvalidXmlSchemaException
- * thrown when input xml node doesn't follow defined schema
- */
- private CellDesignerAntisenseRnaRegion getAntisenseRnaRegion(Node regionNode) throws InvalidXmlSchemaException {
- CellDesignerAntisenseRnaRegion residue = new CellDesignerAntisenseRnaRegion();
- residue.setIdAntisenseRnaRegion(getNodeAttr("id", regionNode));
- residue.setName(getNodeAttr("name", regionNode));
- residue.setSize(getNodeAttr("size", regionNode));
- residue.setPos(getNodeAttr("pos", regionNode));
- String typeString = getNodeAttr("type", regionNode);
- if (typeString != null) {
- AntisenseRnaRegionType type = AntisenseRnaRegionType.getTypeByString(typeString);
- if (type == null) {
- throw new InvalidXmlSchemaException("Unknown antisense rna region type: " + typeString);
- }
- residue.setType(type);
- }
- NodeList list = regionNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:region " + node.getNodeName());
- }
- }
- return residue;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(AntisenseRnaXmlParser.class.getName());
+
+ /**
+ * List of {@link CellDesignerElement celldesigner elements} obtained during
+ * parsing process.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Default constructor.
+ *
+ * @param elements
+ * list of {@link CellDesignerElement celldesigner elements} obtained
+ * during parsing process
+ */
+ public AntisenseRnaXmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ }
+
+ @Override
+ public Pair<String, CellDesignerAntisenseRna> parseXmlElement(Node antisenseRnaNode)
+ throws InvalidXmlSchemaException {
+ CellDesignerAntisenseRna antisenseRna = new CellDesignerAntisenseRna();
+ String identifier = getNodeAttr("id", antisenseRnaNode);
+ antisenseRna.setName(decodeName(getNodeAttr("name", antisenseRnaNode)));
+ NodeList list = antisenseRnaNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("celldesigner:notes")) {
+ antisenseRna.setNotes(getRap().getNotes(node));
+ } else if (node.getNodeName().equals("celldesigner:listOfRegions")) {
+ NodeList residueList = node.getChildNodes();
+ for (int j = 0; j < residueList.getLength(); j++) {
+ Node residueNode = residueList.item(j);
+ if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:region")) {
+ antisenseRna.addRegion(getAntisenseRnaRegion(residueNode));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfRegions " + residueNode.getNodeName());
+ }
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:antisenseRna " + node.getNodeName());
+ }
+ }
+ }
+ Pair<String, CellDesignerAntisenseRna> result = new Pair<String, CellDesignerAntisenseRna>(identifier,
+ antisenseRna);
+ return result;
+ }
+
+ @Override
+ public String toXml(AntisenseRna antisenseRna) {
+ String attributes = "";
+ String result = "";
+ attributes += " id=\"ar_" + elements.getElementId(antisenseRna) + "\"";
+ if (!antisenseRna.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(encodeName(antisenseRna.getName())) + "\"";
+ }
+ result += "<celldesigner:AntisenseRNA" + attributes + ">";
+ result += "<celldesigner:notes>";
+ result += "<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>";
+
+ RestAnnotationParser rap = new RestAnnotationParser();
+ result += rap.createAnnotationString(antisenseRna);
+ result += antisenseRna.getNotes();
+ result += "</body></html>";
+ result += "</celldesigner:notes>";
+ if (antisenseRna.getRegions().size() > 0) {
+ result += "<celldesigner:listOfRegions>";
+ for (ModificationResidue region : antisenseRna.getRegions()) {
+ result += toXml(region);
+ }
+ result += "</celldesigner:listOfRegions>";
+ }
+ result += "</celldesigner:AntisenseRNA>";
+ return result;
+ }
+
+ /**
+ * Transforms AntisenseRnaRegion into CellDEsigner xml representation.
+ *
+ * @param region
+ * object to be transformed
+ * @return xml representation of the given region
+ */
+ private String toXml(ModificationResidue region) {
+ CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(region);
+
+ String result = "";
+ String attributes = "";
+ if (!region.getIdModificationResidue().equals("")) {
+ attributes += " id=\"" + region.getIdModificationResidue() + "\"";
+ }
+ if (!region.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(region.getName()) + "\"";
+ }
+ String type = null;
+ if (region instanceof CodingRegion) {
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ type = "CodingRegion";
+ } else if (region instanceof ModificationSite) {
+ type = "Modification Site";
+ } else if (region instanceof ProteinBindingDomain) {
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ type = "proteinBindingDomain";
+ } else {
+ throw new InvalidArgumentException("Unknown modificatin type: " + region.getClass());
+ }
+
+ attributes += " pos=\"" + cellDesignerModificationResidue.getPos() + "\"";
+ attributes += " type=\"" + type + "\"";
+ result += "<celldesigner:region " + attributes + ">";
+ result += "</celldesigner:region>";
+
+ return result;
+ }
+
+ /**
+ * Method that parse xml node into AntisenseRnaRegion element.
+ *
+ * @param regionNode
+ * xml node to parse
+ * @return AntisenseRnaRegion object from xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when input xml node doesn't follow defined schema
+ */
+ private CellDesignerModificationResidue getAntisenseRnaRegion(Node regionNode) throws InvalidXmlSchemaException {
+ CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
+ residue.setIdModificationResidue(getNodeAttr("id", regionNode));
+ residue.setName(getNodeAttr("name", regionNode));
+ residue.setSize(getNodeAttr("size", regionNode));
+ residue.setPos(getNodeAttr("pos", regionNode));
+ String typeString = getNodeAttr("type", regionNode);
+ if (typeString != null) {
+ try {
+ residue.setModificationType(ModificationType.getByCellDesignerName(typeString));
+ } catch (InvalidArgumentException e) {
+ throw new InvalidXmlSchemaException(e);
+ }
+ }
+
+ NodeList list = regionNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:region " + node.getNodeName());
+ }
+ }
+ return residue;
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
index 3813032e290fcb0a5a8632fe27ec6c362aba596e..7e041680e5843dd51d8387cdb9998218cb368ea9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
@@ -5,158 +5,194 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
/**
- * Class that performs parsing of the CellDesigner xml for {@link CellDesignerGene} object.
+ * Class that performs parsing of the CellDesigner xml for
+ * {@link CellDesignerGene} object.
*
* @author Piotr Gawron
*
*/
public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Gene> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(GeneXmlParser.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(GeneXmlParser.class.getName());
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
- /**
- * Default constructor. Model is required because some nodes require access to
- * other parts of the model.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public GeneXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
- }
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public GeneXmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ }
- @Override
- public Pair<String, CellDesignerGene> parseXmlElement(Node geneNode) throws InvalidXmlSchemaException {
- CellDesignerGene gene = new CellDesignerGene();
- String identifier = getNodeAttr("id", geneNode);
- gene.setName(decodeName(getNodeAttr("name", geneNode)));
- NodeList list = geneNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("celldesigner:notes")) {
- gene.setNotes(getRap().getNotes(node));
- } else if (node.getNodeName().equals("celldesigner:listOfRegions")) {
- NodeList residueList = node.getChildNodes();
- for (int j = 0; j < residueList.getLength(); j++) {
- Node residueNode = residueList.item(j);
- if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
- if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:region")) {
- gene.addModificationResidue(getModificationResidue(residueNode));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfRegions " + residueNode.getNodeName());
- }
- }
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:gene " + node.getNodeName());
- }
- }
- }
- return new Pair<String, CellDesignerGene>(identifier, gene);
- }
+ @Override
+ public Pair<String, CellDesignerGene> parseXmlElement(Node geneNode) throws InvalidXmlSchemaException {
+ CellDesignerGene gene = new CellDesignerGene();
+ String identifier = getNodeAttr("id", geneNode);
+ gene.setName(decodeName(getNodeAttr("name", geneNode)));
+ NodeList list = geneNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("celldesigner:notes")) {
+ gene.setNotes(getRap().getNotes(node));
+ } else if (node.getNodeName().equals("celldesigner:listOfRegions")) {
+ NodeList residueList = node.getChildNodes();
+ for (int j = 0; j < residueList.getLength(); j++) {
+ Node residueNode = residueList.item(j);
+ if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:region")) {
+ gene.addModificationResidue(getModificationResidue(residueNode));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfRegions " + residueNode.getNodeName());
+ }
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:gene " + node.getNodeName());
+ }
+ }
+ }
+ return new Pair<String, CellDesignerGene>(identifier, gene);
+ }
- /**
- * Parse modification for a gene.
- *
- * @param residueNode
- * source xml node
- * @return object representing modification
- * @throws InvalidXmlSchemaException
- * thrown when input xml node doesn't follow defined schema
- */
- CellDesignerModificationResidue getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
- CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
- residue.setIdModificationResidue(getNodeAttr("id", residueNode));
- residue.setName(getNodeAttr("name", residueNode));
- residue.setSide(getNodeAttr("side", residueNode));
- residue.setAngle(getNodeAttr("pos", residueNode));
- NodeList list = residueNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:region " + node.getNodeName());
- }
- }
- return residue;
- }
+ /**
+ * Parse modification for a gene.
+ *
+ * @param residueNode
+ * source xml node
+ * @return object representing modification
+ * @throws InvalidXmlSchemaException
+ * thrown when input xml node doesn't follow defined schema
+ */
+ CellDesignerModificationResidue getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
+ CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
+ residue.setIdModificationResidue(getNodeAttr("id", residueNode));
+ residue.setName(getNodeAttr("name", residueNode));
+ residue.setSide(getNodeAttr("side", residueNode));
+ residue.setSize(getNodeAttr("size", residueNode));
+ residue.setActive(getNodeAttr("active", residueNode));
+ residue.setAngle(getNodeAttr("pos", residueNode));
+ String type = getNodeAttr("type", residueNode);
+ try {
+ residue.setModificationType(ModificationType.getByCellDesignerName(type));
+ } catch (InvalidArgumentException e) {
+ throw new InvalidXmlSchemaException(e);
+ }
+ NodeList list = residueNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:region " + node.getNodeName());
+ }
+ }
+ return residue;
+ }
- @Override
- public String toXml(Gene gene) {
- String attributes = "";
- String result = "";
- attributes += " id=\"g_" + elements.getElementId(gene) + "\"";
- if (!gene.getName().equals("")) {
- attributes += " name=\"" + escapeXml(encodeName(gene.getName())) + "\"";
- }
- result += "<celldesigner:gene" + attributes + ">";
- result += "<celldesigner:notes>";
- result += "<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>";
- RestAnnotationParser rap = new RestAnnotationParser();
- result += rap.createAnnotationString(gene);
- result += gene.getNotes();
- result += "</body></html>";
- result += "</celldesigner:notes>";
+ @Override
+ public String toXml(Gene gene) {
+ String attributes = "";
+ String result = "";
+ attributes += " id=\"g_" + elements.getElementId(gene) + "\"";
+ if (!gene.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(encodeName(gene.getName())) + "\"";
+ }
+ result += "<celldesigner:gene" + attributes + ">";
+ result += "<celldesigner:notes>";
+ result += "<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>";
+ RestAnnotationParser rap = new RestAnnotationParser();
+ result += rap.createAnnotationString(gene);
+ result += gene.getNotes();
+ result += "</body></html>";
+ result += "</celldesigner:notes>";
- if (gene.getModificationResidues().size() > 0) {
- result += "<celldesigner:listOfRegions>\n";
- for (ModificationResidue mr : gene.getModificationResidues()) {
- result += toXml(mr);
- }
- result += "</celldesigner:listOfRegions>\n";
- }
+ if (gene.getModificationResidues().size() > 0) {
+ result += "<celldesigner:listOfRegions>\n";
+ for (ModificationResidue mr : gene.getModificationResidues()) {
+ result += toXml(mr);
+ }
+ result += "</celldesigner:listOfRegions>\n";
+ }
- result += "</celldesigner:gene>";
- return result;
- }
+ result += "</celldesigner:gene>";
+ return result;
+ }
- /**
- * Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
- *
- * @param mr
- * object to transform into xml
- * @return CellDesigner xml for {@link CellDesignerModificationResidue}
- */
- String toXml(ModificationResidue mr) {
- String result = "";
- String attributes = "";
- if (!mr.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
- }
- if (!mr.getName().equals("")) {
- attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
- }
- if (!mr.getSide().equals("")) {
- attributes += " side=\"" + mr.getSide() + "\"";
- }
- if (mr.getAngle() != null) {
- attributes += " pos=\"" + mr.getAngle() + "\"";
- }
- result += "<celldesigner:region " + attributes + ">";
- result += "</celldesigner:region>\n";
+ /**
+ * Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
+ *
+ * @param mr
+ * object to transform into xml
+ * @return CellDesigner xml for {@link CellDesignerModificationResidue}
+ */
+ String toXml(ModificationResidue mr) {
+ CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
- return result;
- }
+ String result = "";
+ String attributes = "";
+ if (!mr.getIdModificationResidue().equals("")) {
+ attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
+ }
+ if (!mr.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
+ }
+ String type = null;
+ if (mr instanceof ModificationSite) {
+ type = ModificationType.MODIFICATION_SITE.getCellDesignerName();
+ } else if (mr instanceof RegulatoryRegion) {
+ type = ModificationType.REGULATORY_REGION.getCellDesignerName();
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ } else if (mr instanceof CodingRegion) {
+ type = ModificationType.CODING_REGION.getCellDesignerName();
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ } else if (mr instanceof TranscriptionSite) {
+ TranscriptionSite transcriptionSite = (TranscriptionSite) mr;
+ if (transcriptionSite.getDirection().equals("RIGHT")) {
+ type = ModificationType.TRANSCRIPTION_SITE_RIGHT.getCellDesignerName();
+ } else {
+ type = ModificationType.TRANSCRIPTION_SITE_LEFT.getCellDesignerName();
+ }
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ attributes += " active=\"" + transcriptionSite.getActive() + "\"";
+ } else {
+ throw new InvalidArgumentException("Don't know how to handle: " + mr.getClass());
+ }
+ attributes += " type=\"" + type + "\"";
+ attributes += " pos=\"" + cellDesignerModificationResidue.getPos() + "\"";
+ result += "<celldesigner:region " + attributes + ">";
+ result += "</celldesigner:region>\n";
+
+ return result;
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
index 68cd9af32aa18bae5cbbf1832c54febe80d4fef1..4f1e6d4cdc3a317b8f505dffdda898c45d3717c7 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
@@ -1,5 +1,8 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
+import java.util.ArrayList;
+import java.util.List;
+
import org.apache.log4j.Logger;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@@ -8,15 +11,19 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.Residue;
/**
- * Class that performs parsing of the CellDesigner xml for {@link CellDesignerProtein}
- * object.
+ * Class that performs parsing of the CellDesigner xml for
+ * {@link CellDesignerProtein} object.
*
* @author Piotr Gawron
*
@@ -24,152 +31,237 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
public class ProteinXmlParser extends AbstractElementXmlParser<CellDesignerProtein<?>, Protein> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ProteinXmlParser.class.getName());
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Default constructor. Model is required because some nodes require access to
- * other parts of the model.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public ProteinXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
- }
-
- @Override
- public Pair<String, CellDesignerProtein<?>> parseXmlElement(Node proteinNode) throws InvalidXmlSchemaException {
- CellDesignerProtein<?> protein = null;
- String value = getNodeAttr("type", proteinNode);
- ProteinMapping mapping = ProteinMapping.getMappingByString(value);
- if (mapping != null) {
- protein = mapping.createProtein();
- } else {
- throw new InvalidXmlSchemaException("Protein node in Sbml model is of unknown type: " + value);
- }
-
- String identifier = getNodeAttr("id", proteinNode);
- protein.setName(decodeName(getNodeAttr("name", proteinNode)));
- NodeList list = proteinNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("celldesigner:listOfModificationResidues")) {
- NodeList residueList = node.getChildNodes();
- for (int j = 0; j < residueList.getLength(); j++) {
- Node residueNode = residueList.item(j);
- if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
- if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:modificationResidue")) {
- protein.addModificationResidue(getModificationResidue(residueNode));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfModificationResidues " + residueNode.getNodeName());
- }
- }
- }
- } else if (node.getNodeName().equals("celldesigner:notes")) {
- protein.setNotes(getRap().getNotes(node));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:protein " + node.getNodeName());
- }
- }
- }
-
- return new Pair<String, CellDesignerProtein<?>>(identifier, protein);
- }
-
- @Override
- public String toXml(Protein protein) {
- String attributes = "";
- String result = "";
- attributes += " id=\"p_" + elements.getElementId(protein) + "\"";
- if (protein.getName() != null && !protein.getName().equals("")) {
- attributes += " name=\"" + escapeXml(encodeName(protein.getName())) + "\"";
- }
- String type = null;
- ProteinMapping mapping = ProteinMapping.getMappingByClass(protein.getClass());
- if (mapping != null) {
- type = mapping.getCellDesignerString();
- } else {
- throw new InvalidArgumentException("Invalid protein class type: " + protein.getClass().getName());
- }
- attributes += " type=\"" + type + "\"";
- result += "<celldesigner:protein" + attributes + ">\n";
- if (protein.getModificationResidues().size() > 0) {
- result += "<celldesigner:listOfModificationResidues>";
- for (ModificationResidue mr : protein.getModificationResidues()) {
- result += toXml(mr);
- }
- result += "</celldesigner:listOfModificationResidues>\n";
- }
- // ignore notes - all notes will be stored in species
- // result +=
- // "<celldesigner:notes>"+protein.getNotes()+"</celldesigner:notes>";
- result += "</celldesigner:protein>\n";
- return result;
- }
-
- /**
- * Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
- *
- * @param mr
- * object to transform into xml
- * @return CellDesigner xml for {@link CellDesignerModificationResidue}
- */
- private String toXml(ModificationResidue mr) {
- String result = "";
- String attributes = "";
- if (!mr.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
- }
- if (!mr.getName().equals("")) {
- attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
- }
- if (!mr.getSide().equals("")) {
- attributes += " side=\"" + mr.getSide() + "\"";
- }
- if (mr.getAngle() != null) {
- attributes += " angle=\"" + mr.getAngle() + "\"";
- }
- result += "<celldesigner:modificationResidue " + attributes + ">";
- result += "</celldesigner:modificationResidue>";
-
- return result;
- }
-
- /**
- * Parses CellDesigner xml node for ModificationResidue.
- *
- * @param residueNode
- * xml node to parse
- * @return {@link CellDesignerModificationResidue} object created from the node
- * @throws InvalidXmlSchemaException
- * thrown when input xml node doesn't follow defined schema
- */
- private CellDesignerModificationResidue getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
- CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
- residue.setIdModificationResidue(getNodeAttr("id", residueNode));
- residue.setName(getNodeAttr("name", residueNode));
- residue.setSide(getNodeAttr("side", residueNode));
- residue.setAngle(getNodeAttr("angle", residueNode));
- NodeList list = residueNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:modificationResidue " + node.getNodeName());
- }
- }
- return residue;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ProteinXmlParser.class.getName());
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public ProteinXmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ }
+
+ @Override
+ public Pair<String, CellDesignerProtein<?>> parseXmlElement(Node proteinNode) throws InvalidXmlSchemaException {
+ CellDesignerProtein<?> protein = null;
+ String value = getNodeAttr("type", proteinNode);
+ ProteinMapping mapping = ProteinMapping.getMappingByString(value);
+ if (mapping != null) {
+ protein = mapping.createProtein();
+ } else {
+ throw new InvalidXmlSchemaException("Protein node in Sbml model is of unknown type: " + value);
+ }
+
+ String identifier = getNodeAttr("id", proteinNode);
+ protein.setName(decodeName(getNodeAttr("name", proteinNode)));
+ NodeList list = proteinNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("celldesigner:listOfModificationResidues")) {
+ NodeList residueList = node.getChildNodes();
+ for (int j = 0; j < residueList.getLength(); j++) {
+ Node residueNode = residueList.item(j);
+ if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:modificationResidue")) {
+ protein.addModificationResidue(getModificationResidue(residueNode));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfModificationResidues " + residueNode.getNodeName());
+ }
+ }
+ }
+ } else if (node.getNodeName().equals("celldesigner:listOfBindingRegions")) {
+ NodeList residueList = node.getChildNodes();
+ for (int j = 0; j < residueList.getLength(); j++) {
+ Node residueNode = residueList.item(j);
+ if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:bindingRegion")) {
+ protein.addModificationResidue(getBindingRegion(residueNode));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfModificationResidues " + residueNode.getNodeName());
+ }
+ }
+ }
+ } else if (node.getNodeName().equals("celldesigner:notes")) {
+ protein.setNotes(getRap().getNotes(node));
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:protein " + node.getNodeName());
+ }
+ }
+ }
+
+ return new Pair<String, CellDesignerProtein<?>>(identifier, protein);
+ }
+
+ @Override
+ public String toXml(Protein protein) {
+ String attributes = "";
+ String result = "";
+ attributes += " id=\"p_" + elements.getElementId(protein) + "\"";
+ if (protein.getName() != null && !protein.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(encodeName(protein.getName())) + "\"";
+ }
+ String type = null;
+ ProteinMapping mapping = ProteinMapping.getMappingByClass(protein.getClass());
+ if (mapping != null) {
+ type = mapping.getCellDesignerString();
+ } else {
+ throw new InvalidArgumentException("Invalid protein class type: " + protein.getClass().getName());
+ }
+ attributes += " type=\"" + type + "\"";
+ result += "<celldesigner:protein" + attributes + ">\n";
+
+ List<Residue> residues = new ArrayList<>();
+ List<BindingRegion> bindingRegions = new ArrayList<>();
+ for (ModificationResidue mr : protein.getModificationResidues()) {
+ if (mr instanceof Residue) {
+ residues.add((Residue) mr);
+ } else if (mr instanceof BindingRegion) {
+ bindingRegions.add((BindingRegion) mr);
+ } else {
+ throw new InvalidArgumentException("Don't know how to handle: " + mr.getClass());
+ }
+ }
+ if (residues.size() > 0) {
+ result += "<celldesigner:listOfModificationResidues>";
+ for (Residue mr : residues) {
+ result += toXml(mr);
+ }
+ result += "</celldesigner:listOfModificationResidues>\n";
+ }
+ if (bindingRegions.size() > 0) {
+ result += "<celldesigner:listOfBindingRegions>";
+ for (BindingRegion mr : bindingRegions) {
+ result += toXml(mr);
+ }
+ result += "</celldesigner:listOfBindingRegions>\n";
+ }
+ // ignore notes - all notes will be stored in species
+ // result +=
+ // "<celldesigner:notes>"+protein.getNotes()+"</celldesigner:notes>";
+ result += "</celldesigner:protein>\n";
+ return result;
+ }
+
+ /**
+ * Generates CellDesigner xml for {@link Residue}.
+ *
+ * @param mr
+ * object to transform into xml
+ * @return CellDesigner xml for {@link Residue}
+ */
+ private String toXml(Residue mr) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(mr.getSpecies(), false);
+
+ String result = "";
+ String attributes = "";
+ if (!mr.getIdModificationResidue().equals("")) {
+ attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
+ }
+ if (!mr.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
+ }
+ attributes += " angle=\"" + converter.getAngleForPoint(mr.getSpecies(), mr.getPosition()) + "\"";
+ result += "<celldesigner:modificationResidue " + attributes + ">";
+ result += "</celldesigner:modificationResidue>";
+
+ return result;
+ }
+
+ /**
+ * Generates CellDesigner xml for {@link BindingRegion}.
+ *
+ * @param mr
+ * object to transform into xml
+ * @return CellDesigner xml for {@link BindingRegion}
+ */
+ private String toXml(BindingRegion mr) {
+
+ CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
+ String result = "";
+ String attributes = "";
+ if (!mr.getIdModificationResidue().equals("")) {
+ attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
+ }
+ if (!mr.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
+ }
+ attributes += " angle=\"" + cellDesignerModificationResidue.getAngle() + "\"";
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ result += "<celldesigner:bindingRegion " + attributes + ">";
+ result += "</celldesigner:bindingRegion>";
+
+ return result;
+ }
+
+ /**
+ * Parses CellDesigner xml node for ModificationResidue.
+ *
+ * @param residueNode
+ * xml node to parse
+ * @return {@link CellDesignerModificationResidue} object created from the node
+ * @throws InvalidXmlSchemaException
+ * thrown when input xml node doesn't follow defined schema
+ */
+ private CellDesignerModificationResidue getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
+ CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
+ residue.setIdModificationResidue(getNodeAttr("id", residueNode));
+ residue.setName(getNodeAttr("name", residueNode));
+ residue.setSide(getNodeAttr("side", residueNode));
+ residue.setAngle(getNodeAttr("angle", residueNode));
+ residue.setModificationType(ModificationType.RESIDUE);
+ NodeList list = residueNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:modificationResidue " + node.getNodeName());
+ }
+ }
+ return residue;
+ }
+
+ /**
+ * Parses CellDesigner xml node for ModificationResidue.
+ *
+ * @param residueNode
+ * xml node to parse
+ * @return {@link CellDesignerModificationResidue} object created from the node
+ * @throws InvalidXmlSchemaException
+ * thrown when input xml node doesn't follow defined schema
+ */
+ private CellDesignerModificationResidue getBindingRegion(Node residueNode) throws InvalidXmlSchemaException {
+ CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
+ residue.setIdModificationResidue(getNodeAttr("id", residueNode));
+ residue.setName(getNodeAttr("name", residueNode));
+ residue.setSize(getNodeAttr("size", residueNode));
+ residue.setAngle(getNodeAttr("angle", residueNode));
+ residue.setModificationType(ModificationType.BINDING_REGION);
+ NodeList list = residueNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:modificationResidue " + node.getNodeName());
+ }
+ }
+ return residue;
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
index 2febc38cc9615cff4420b7e0665521d27fe14817..1a8561939784facaba3ff978804574de184934e5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
@@ -5,16 +5,24 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerRnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
/**
- * Class that performs parsing of the CellDesigner xml for {@link CellDesignerRna} object.
+ * Class that performs parsing of the CellDesigner xml for
+ * {@link CellDesignerRna} object.
*
* @author Piotr Gawron
*
@@ -22,105 +30,155 @@ import lcsb.mapviewer.model.map.species.Rna;
public class RnaXmlParser extends AbstractElementXmlParser<CellDesignerRna, Rna> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(RnaXmlParser.class.getName());
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Default constructor. Model is required because some nodes require access to
- * other parts of the model.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public RnaXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
- }
-
- @Override
- public Pair<String, CellDesignerRna> parseXmlElement(Node rnaNode) throws InvalidXmlSchemaException {
- CellDesignerRna rna = new CellDesignerRna();
- String identifier = getNodeAttr("id", rnaNode);
- rna.setName(decodeName(getNodeAttr("name", rnaNode)));
- NodeList list = rnaNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("celldesigner:notes")) {
- rna.setNotes(getRap().getNotes(node));
- } else if (node.getNodeName().equals("celldesigner:listOfRegions")) {
- NodeList residueList = node.getChildNodes();
- for (int j = 0; j < residueList.getLength(); j++) {
- Node residueNode = residueList.item(j);
- if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
- if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:region")) {
- rna.addRegion(getRnaRegion(residueNode));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfRegions " + residueNode.getNodeName());
- }
- }
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:rna " + node.getNodeName());
- }
- }
- }
- return new Pair<String, CellDesignerRna>(identifier, rna);
- }
-
- /**
- * Parses CellDesigner xml node for RnaRegion.
- *
- * @param residueNode
- * xml node to parse
- * @return {@link CellDesignerRnaRegion} object created from the node
- * @throws InvalidXmlSchemaException
- * thrown when input xml node doesn't follow defined schema
- */
- private CellDesignerRnaRegion getRnaRegion(Node residueNode) throws InvalidXmlSchemaException {
- CellDesignerRnaRegion residue = new CellDesignerRnaRegion();
- residue.setIdRnaRegion(getNodeAttr("id", residueNode));
- residue.setSize(getNodeAttr("size", residueNode));
- residue.setPos(getNodeAttr("pos", residueNode));
- residue.setType(getNodeAttr("type", residueNode));
- NodeList list = residueNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:region " + node.getNodeName());
- }
- }
- return residue;
- }
-
- @Override
- public String toXml(Rna rna) {
- String attributes = "";
- String result = "";
- attributes += " id=\"r_" + elements.getElementId(rna) + "\"";
- if (!rna.getName().equals("")) {
- attributes += " name=\"" + escapeXml(encodeName(rna.getName())) + "\"";
- }
- result += "<celldesigner:RNA" + attributes + ">";
- result += "<celldesigner:notes>";
- result += "<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>";
- RestAnnotationParser rap = new RestAnnotationParser();
- result += rap.createAnnotationString(rna);
- result += rna.getNotes();
- result += "</body></html>";
- result += "</celldesigner:notes>";
-
- result += "</celldesigner:RNA>";
- return result;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(RnaXmlParser.class.getName());
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public RnaXmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ }
+
+ @Override
+ public Pair<String, CellDesignerRna> parseXmlElement(Node rnaNode) throws InvalidXmlSchemaException {
+ CellDesignerRna rna = new CellDesignerRna();
+ String identifier = getNodeAttr("id", rnaNode);
+ rna.setName(decodeName(getNodeAttr("name", rnaNode)));
+ NodeList list = rnaNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("celldesigner:notes")) {
+ rna.setNotes(getRap().getNotes(node));
+ } else if (node.getNodeName().equals("celldesigner:listOfRegions")) {
+ NodeList residueList = node.getChildNodes();
+ for (int j = 0; j < residueList.getLength(); j++) {
+ Node residueNode = residueList.item(j);
+ if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:region")) {
+ rna.addRegion(getRnaRegion(residueNode));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfRegions " + residueNode.getNodeName());
+ }
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:rna " + node.getNodeName());
+ }
+ }
+ }
+ return new Pair<String, CellDesignerRna>(identifier, rna);
+ }
+
+ /**
+ * Parses CellDesigner xml node for RnaRegion.
+ *
+ * @param residueNode
+ * xml node to parse
+ * @return {@link CellDesignerRnaRegion} object created from the node
+ * @throws InvalidXmlSchemaException
+ * thrown when input xml node doesn't follow defined schema
+ */
+ private CellDesignerModificationResidue getRnaRegion(Node residueNode) throws InvalidXmlSchemaException {
+ CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
+ residue.setIdModificationResidue(getNodeAttr("id", residueNode));
+ residue.setSize(getNodeAttr("size", residueNode));
+ residue.setPos(getNodeAttr("pos", residueNode));
+ String typeString = getNodeAttr("type", residueNode);
+ if (typeString != null) {
+ residue.setModificationType(ModificationType.getByCellDesignerName(typeString));
+ }
+ NodeList list = residueNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:region " + node.getNodeName());
+ }
+ }
+ return residue;
+ }
+
+ @Override
+ public String toXml(Rna rna) {
+ String attributes = "";
+ String result = "";
+ attributes += " id=\"r_" + elements.getElementId(rna) + "\"";
+ if (!rna.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(encodeName(rna.getName())) + "\"";
+ }
+ result += "<celldesigner:RNA" + attributes + ">";
+ result += "<celldesigner:notes>";
+ result += "<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>";
+ RestAnnotationParser rap = new RestAnnotationParser();
+ result += rap.createAnnotationString(rna);
+ result += rna.getNotes();
+ result += "</body></html>";
+ result += "</celldesigner:notes>";
+
+ if (rna.getRegions().size() > 0) {
+ result += "<celldesigner:listOfRegions>";
+ for (ModificationResidue mr : rna.getRegions()) {
+ result += toXml(mr);
+ }
+ result += "</celldesigner:listOfRegions>";
+ }
+
+ result += "</celldesigner:RNA>";
+ return result;
+ }
+
+ /**
+ * Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
+ *
+ * @param mr
+ * object to transform into xml
+ * @return CellDesigner xml for {@link CellDesignerModificationResidue}
+ */
+ String toXml(ModificationResidue mr) {
+ CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
+
+ String result = "";
+ String attributes = "";
+ if (!mr.getIdModificationResidue().equals("")) {
+ attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
+ }
+ if (!mr.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
+ }
+ String type = null;
+ if (mr instanceof ModificationSite) {
+ type = ModificationType.MODIFICATION_SITE.getCellDesignerName();
+ } else if (mr instanceof CodingRegion) {
+ type = ModificationType.CODING_REGION.getCellDesignerName();
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ } else if (mr instanceof ProteinBindingDomain) {
+ type = ModificationType.PROTEIN_BINDING_DOMAIN.getCellDesignerName();
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ } else {
+ throw new InvalidArgumentException("Don't know how to handle: " + mr.getClass());
+ }
+ attributes += " type=\"" + type + "\"";
+ attributes += " pos=\"" + cellDesignerModificationResidue.getPos() + "\"";
+ result += "<celldesigner:region " + attributes + ">";
+ result += "</celldesigner:region>\n";
+
+ return result;
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
index c573707a2035ec14a6983048947b976a95f07799..a38a634c097cc21692fe90c3fa9b70cc4781bc78 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
@@ -20,9 +20,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerRnaRegion;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
@@ -211,7 +209,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
attributesBuilder.append(" constant=\"" + species.getConstant().toString().toLowerCase() + "\"");
}
if (species.getBoundaryCondition() != null) {
- attributesBuilder.append(" boundaryCondition=\"" + species.getBoundaryCondition().toString().toLowerCase() + "\"");
+ attributesBuilder
+ .append(" boundaryCondition=\"" + species.getBoundaryCondition().toString().toLowerCase() + "\"");
}
Compartment comp = null;
@@ -459,7 +458,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
}
for (CellDesignerModificationResidue mr : state.getModifications()) {
- rna.addRegion(createRnaRegion(mr));
+ rna.addRegion(mr);
}
} else if (species instanceof CellDesignerSimpleMolecule) {
if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
@@ -476,8 +475,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
}
for (CellDesignerModificationResidue mr : state.getModifications()) {
- CellDesignerAntisenseRnaRegion region = createAntisenseRnaRegion(mr);
- antisenseRna.addRegion(region);
+ antisenseRna.addRegion(mr);
}
} else {
if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
@@ -549,7 +547,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
}
/**
- * Creates {@link CellDesignerModificationResidue} from the apropriate xml node.
+ * Creates {@link CellDesignerModificationResidue} from the appropriate xml
+ * node.
*
* @param rootNode
* xml node
@@ -603,49 +602,4 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
return "<celldesigner:modification residue=\"" + mr.getIdModificationResidue() + "\" state=\"" + state
+ "\"> </celldesigner:modification>\n";
}
-
- /**
- * Creates {@link CellDesignerAntisenseRnaRegion} from
- * {@link CellDesignerModificationResidue} description.
- *
- * @param mr
- * object from which we create {@link CellDesignerAntisenseRnaRegion}
- * @return {@link CellDesignerAntisenseRnaRegion} object created from param
- */
- CellDesignerAntisenseRnaRegion createAntisenseRnaRegion(CellDesignerModificationResidue mr) {
- CellDesignerAntisenseRnaRegion region = new CellDesignerAntisenseRnaRegion();
- region.setIdAntisenseRnaRegion(mr.getIdModificationResidue());
- if (mr.getSize() != null) {
- region.setSize(mr.getSize());
- }
- region.setState(mr.getState());
- region.setName(mr.getName());
- if (mr.getAngle() != null) {
- region.setPos(mr.getAngle());
- }
- return region;
- }
-
- /**
- * Creates {@link CellDesignerRnaRegion} from
- * {@link CellDesignerModificationResidue} description.
- *
- * @param mr
- * object from which we create {@link CellDesignerRnaRegion}
- * @return {@link CellDesignerRnaRegion} object created from param
- */
- public CellDesignerRnaRegion createRnaRegion(CellDesignerModificationResidue mr) {
- CellDesignerRnaRegion result = new CellDesignerRnaRegion();
- result.setIdRnaRegion(mr.getIdModificationResidue());
- if (mr.getSize() != null) {
- result.setSize(mr.getSize());
- }
- result.setState(mr.getState());
- result.setName(mr.getName());
- if (mr.getAngle() != null) {
- result.setPos(mr.getAngle());
- }
- return result;
- }
-
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
index e3456b1c883be2e35b467ce847c334b709a798fa..9ad77efd72744ef067410592b646760e63baed5d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
@@ -1,150 +1,149 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-
-/**
- * Class representing CellDesigner {@link AntisenseRna}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerAntisenseRna.class);
-
- /**
- * List of antisense rna regions (some rna sequences) in this object.
- */
- private List<CellDesignerAntisenseRnaRegion> regions = new ArrayList<CellDesignerAntisenseRnaRegion>();
-
- /**
- * Constructor that copies the data from species given in the argument.
- *
- * @param species
- * parent species from which we want to copy data
- */
- public CellDesignerAntisenseRna(CellDesignerSpecies<?> species) {
- super(species);
- if (species instanceof CellDesignerAntisenseRna) {
- CellDesignerAntisenseRna asRna = (CellDesignerAntisenseRna) species;
- for (CellDesignerAntisenseRnaRegion region : asRna.getRegions()) {
- addRegion(new CellDesignerAntisenseRnaRegion(region));
- }
- }
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerAntisenseRna() {
- super();
- }
-
- @Override
- public CellDesignerAntisenseRna copy() {
- if (this.getClass() == CellDesignerAntisenseRna.class) {
- return new CellDesignerAntisenseRna(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * Addd antisense rna region (part of rna sequence that has some meaning) to
- * the object. If the region with given id exists then the data of this region
- * is copied to the one that is already in the
- * {@link CellDesignerAntisenseRna}.
- *
- *
- * @param region
- * region to add
- */
- public void addRegion(CellDesignerAntisenseRnaRegion region) {
- for (CellDesignerAntisenseRnaRegion region2 : regions) {
- if (region2.getIdAntisenseRnaRegion().equals(region.getIdAntisenseRnaRegion())) {
- region2.update(region);
- return;
- }
- }
-
- regions.add(region);
- region.setSpecies(this);
- }
-
- @Override
- public void update(CellDesignerSpecies<?> sp) {
- super.update(sp);
- if (sp instanceof CellDesignerAntisenseRna) {
- CellDesignerAntisenseRna rna = (CellDesignerAntisenseRna) sp;
- for (CellDesignerAntisenseRnaRegion mr : getRegions()) {
- mr.setState(null);
- }
-
- for (CellDesignerAntisenseRnaRegion region : rna.getRegions()) {
- updateRegion(region);
- }
- }
- }
-
- /**
- * Method update antisense rna region from the object in params (if the object
- * with the same id already exists). If there is no object with given id then
- * new object is added to antisense rna.
- *
- * @param param
- * - object with new data from where update should be performed
- */
- private void updateRegion(CellDesignerAntisenseRnaRegion param) {
- for (CellDesignerAntisenseRnaRegion region : regions) {
- if (region.getIdAntisenseRnaRegion().equals(param.getIdAntisenseRnaRegion())) {
- region.update(param);
- return;
- }
- }
- regions.add(param);
- }
-
- /**
- * @return the regions
- * @see #regions
- */
- public List<CellDesignerAntisenseRnaRegion> getRegions() {
- return regions;
- }
-
- /**
- * @param regions
- * the regions to set
- * @see #regions
- */
- public void setRegions(List<CellDesignerAntisenseRnaRegion> regions) {
- this.regions = regions;
- }
-
- @Override
- public AntisenseRna createModelElement(String aliasId) {
- AntisenseRna result = new AntisenseRna(aliasId);
- super.setModelObjectFields(result);
- for (CellDesignerAntisenseRnaRegion region : regions) {
- result.addRegion(region.createAntisenseRegionAlias());
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class representing CellDesigner {@link AntisenseRna}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerAntisenseRna.class);
+
+ /**
+ * List of antisense rna regions (some rna sequences) in this object.
+ */
+ private List<CellDesignerModificationResidue> regions = new ArrayList<>();
+
+ /**
+ * Constructor that copies the data from species given in the argument.
+ *
+ * @param species
+ * parent species from which we want to copy data
+ */
+ public CellDesignerAntisenseRna(CellDesignerSpecies<?> species) {
+ super(species);
+ if (species instanceof CellDesignerAntisenseRna) {
+ CellDesignerAntisenseRna asRna = (CellDesignerAntisenseRna) species;
+ for (CellDesignerModificationResidue region : asRna.getRegions()) {
+ addRegion(new CellDesignerModificationResidue(region));
+ }
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerAntisenseRna() {
+ super();
+ }
+
+ @Override
+ public CellDesignerAntisenseRna copy() {
+ if (this.getClass() == CellDesignerAntisenseRna.class) {
+ return new CellDesignerAntisenseRna(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * Add antisense rna region (part of rna sequence that has some meaning) to the
+ * object. If the region with given id exists then the data of this region is
+ * copied to the one that is already in the {@link CellDesignerAntisenseRna}.
+ *
+ *
+ * @param region
+ * region to add
+ */
+ public void addRegion(CellDesignerModificationResidue region) {
+ for (CellDesignerModificationResidue region2 : regions) {
+ if (region2.getIdModificationResidue().equals(region.getIdModificationResidue())) {
+ region2.update(region);
+ return;
+ }
+ }
+ regions.add(region);
+ region.setSpecies(this);
+ }
+
+ @Override
+ public void update(CellDesignerSpecies<?> sp) {
+ super.update(sp);
+ if (sp instanceof CellDesignerAntisenseRna) {
+ CellDesignerAntisenseRna rna = (CellDesignerAntisenseRna) sp;
+ for (CellDesignerModificationResidue region : rna.getRegions()) {
+ updateRegion(region);
+ }
+ }
+ }
+
+ /**
+ * Method update antisense rna region from the object in params (if the object
+ * with the same id already exists). If there is no object with given id then
+ * new object is added to antisense rna.
+ *
+ * @param param
+ * - object with new data from where update should be performed
+ */
+ private void updateRegion(CellDesignerModificationResidue param) {
+ for (CellDesignerModificationResidue region : regions) {
+ if (region.getIdModificationResidue().equals(param.getIdModificationResidue())) {
+ region.update(param);
+ return;
+ }
+ }
+ regions.add(param);
+ }
+
+ /**
+ * @return the regions
+ * @see #regions
+ */
+ public List<CellDesignerModificationResidue> getRegions() {
+ return regions;
+ }
+
+ /**
+ * @param regions
+ * the regions to set
+ * @see #regions
+ */
+ public void setRegions(List<CellDesignerModificationResidue> regions) {
+ this.regions = regions;
+ }
+
+ @Override
+ public AntisenseRna createModelElement(String aliasId) {
+ AntisenseRna result = new AntisenseRna(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species element) {
+ for (CellDesignerModificationResidue region : regions) {
+ ((AntisenseRna) element).addRegion(region.createModificationResidue(element));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
index e66ed1ca142def7e6f248a4a2a776e5b623132b9..c502500383a2e016d7c102f3d5e0467cfa6a07ab 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
@@ -1,152 +1,156 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-
-/**
- * Class representing CellDesigner {@link Compartment}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerCompartment extends CellDesignerElement<Compartment> implements Comparable<CellDesignerCompartment> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerCompartment.class);
-
- /**
- * Identifier of the compartment. Unique in the model
- */
- private String compartmentId = "";
-
- /**
- * List of agregated elements.
- */
- private Set<CellDesignerElement<?>> elements = new HashSet<>();
-
- /**
- * Default constructor with identifier given as a parameter.
- *
- * @param id
- * identifier of the compartment
- */
- public CellDesignerCompartment(String id) {
- compartmentId = id;
- setName(id);
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerCompartment() {
- super();
- }
-
- /**
- * Constructor that initialize the data using compartment given as a
- * parameter.
- *
- * @param compartment
- * object which is used for data intialization
- */
- public CellDesignerCompartment(CellDesignerCompartment compartment) {
- super(compartment);
- setElementId(compartment.getElementId());
- for (CellDesignerElement<?> element : compartment.getElements()) {
- addElement(element.copy());
- }
- }
-
- @Override
- public int compareTo(CellDesignerCompartment param) {
- if (param == null) {
- return -1;
- }
- if (!compartmentId.equals(param.getElementId())) {
- return compartmentId.compareTo(param.getElementId());
- }
- if (!getName().equals(param.getName())) {
- return getName().compareTo(param.getName());
- }
- return 0;
- }
-
- @Override
- public boolean equals(Object param) {
- if (this == param) {
- return true;
- }
- if (!(param instanceof CellDesignerCompartment)) {
- return false;
- }
-
- return compareTo((CellDesignerCompartment) param) == 0;
- }
-
- @Override
- public int hashCode() {
- String result = compartmentId + "_" + getName();
- return result.hashCode();
- }
-
- @Override
- public CellDesignerCompartment copy() {
- if (this.getClass() != CellDesignerCompartment.class) {
- throw new NotImplementedException("this method should be overloaded");
- }
- return new CellDesignerCompartment(this);
- }
-
- @Override
- public String getElementId() {
- return compartmentId;
- }
-
- @Override
- public void setElementId(String id) {
- this.compartmentId = id;
- }
-
- /**
- * Adds element.
- *
- * @param element
- * element to add
- */
- public void addElement(CellDesignerElement<?> element) {
- elements.add(element);
- element.setParent(this);
- }
-
- /**
- *
- * @return {@link #elements}
- */
- public Set<CellDesignerElement<?>> getElements() {
- return elements;
- }
-
- @Override
- public Compartment createModelElement(String aliasId) {
- Compartment result = new Compartment(aliasId);
- super.setModelObjectFields(result);
- if (elements.size() > 0) {
- throw new NotImplementedException();
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+
+/**
+ * Class representing CellDesigner {@link Compartment}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerCompartment extends CellDesignerElement<Compartment>
+ implements Comparable<CellDesignerCompartment> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerCompartment.class);
+
+ /**
+ * Identifier of the compartment. Unique in the model
+ */
+ private String compartmentId = "";
+
+ /**
+ * List of aggregated elements.
+ */
+ private Set<CellDesignerElement<?>> elements = new HashSet<>();
+
+ /**
+ * Default constructor with identifier given as a parameter.
+ *
+ * @param id
+ * identifier of the compartment
+ */
+ public CellDesignerCompartment(String id) {
+ compartmentId = id;
+ setName(id);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerCompartment() {
+ super();
+ }
+
+ /**
+ * Constructor that initialize the data using compartment given as a parameter.
+ *
+ * @param compartment
+ * object which is used for data initialization
+ */
+ public CellDesignerCompartment(CellDesignerCompartment compartment) {
+ super(compartment);
+ setElementId(compartment.getElementId());
+ for (CellDesignerElement<?> element : compartment.getElements()) {
+ addElement(element.copy());
+ }
+ }
+
+ @Override
+ public int compareTo(CellDesignerCompartment param) {
+ if (param == null) {
+ return -1;
+ }
+ if (!compartmentId.equals(param.getElementId())) {
+ return compartmentId.compareTo(param.getElementId());
+ }
+ if (!getName().equals(param.getName())) {
+ return getName().compareTo(param.getName());
+ }
+ return 0;
+ }
+
+ @Override
+ public boolean equals(Object param) {
+ if (this == param) {
+ return true;
+ }
+ if (!(param instanceof CellDesignerCompartment)) {
+ return false;
+ }
+
+ return compareTo((CellDesignerCompartment) param) == 0;
+ }
+
+ @Override
+ public int hashCode() {
+ String result = compartmentId + "_" + getName();
+ return result.hashCode();
+ }
+
+ @Override
+ public CellDesignerCompartment copy() {
+ if (this.getClass() != CellDesignerCompartment.class) {
+ throw new NotImplementedException("this method should be overloaded");
+ }
+ return new CellDesignerCompartment(this);
+ }
+
+ @Override
+ public String getElementId() {
+ return compartmentId;
+ }
+
+ @Override
+ public void setElementId(String id) {
+ this.compartmentId = id;
+ }
+
+ /**
+ * Adds element.
+ *
+ * @param element
+ * element to add
+ */
+ public void addElement(CellDesignerElement<?> element) {
+ elements.add(element);
+ element.setParent(this);
+ }
+
+ /**
+ *
+ * @return {@link #elements}
+ */
+ public Set<CellDesignerElement<?>> getElements() {
+ return elements;
+ }
+
+ @Override
+ public Compartment createModelElement(String aliasId) {
+ Compartment result = new Compartment(aliasId);
+ super.setModelObjectFields(result);
+ if (elements.size() > 0) {
+ throw new NotImplementedException();
+ }
+ return result;
+ }
+
+ @Override
+ public void updateModelElementAfterLayoutAdded(Compartment element) {
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
index 577844e96537028f07da499799ffbc5f63e5d6d1..5f2bf1910863679b298741261a0a5815d317322d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
@@ -14,9 +14,9 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.species.Element;
/**
- * Generic CellDesigner element map. It is a root object in inheritance three for
- * every element ({@link CellDesignerSpecies} or {@link CellDesignerCompartment}
- * ).
+ * Generic CellDesigner element map. It is a root object in inheritance three
+ * for every element ({@link CellDesignerSpecies} or
+ * {@link CellDesignerCompartment} ).
*
* @param <T>
* type of the {@link Element} in the model that is describe by this
@@ -26,423 +26,426 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public abstract class CellDesignerElement<T extends Element> implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Maximum length of the valid synonym name.
- */
- private static final int MAX_SYNONYM_LENGTH = 255;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CellDesignerElement.class);
-
- /**
- * Notes describing this element.
- */
- private String notes;
-
- /**
- * Symbol of the element.
- */
- private String symbol;
-
- /**
- * Full name of the element.
- */
- private String fullName;
-
- /**
- * Abbreviation associated with the element.
- */
- private String abbreviation;
-
- /**
- * Formula associated with the element.
- */
- private String formula;
-
- /**
- * Short name of the element.
- */
- private String name = "";
-
- /**
- * Lists of all synonyms used for describing this element.
- */
- private List<String> synonyms = new ArrayList<>();
-
- /**
- * List of former symbols used to describe this element.
- */
- private List<String> formerSymbols = new ArrayList<>();
-
- /**
- * Where this element lies on.
- */
- private CellDesignerCompartment parent;
-
- /**
- * In which complex this element is located.
- */
- private CellDesignerComplexSpecies complex;
-
- /**
- * Set of miriam annotations for this element.
- */
- private Set<MiriamData> miriamData = new HashSet<>();
-
- /**
- * Default constructor that initialize the data with the information given in
- * the parameter.
- *
- * @param element
- * original object from which data should be initialized
- */
- protected CellDesignerElement(CellDesignerElement<?> element) {
- this.parent = element.parent;
- this.complex = element.complex;
- this.notes = element.notes;
- this.symbol = element.symbol;
- this.fullName = element.fullName;
- this.name = element.getName();
- this.getSynonyms().addAll(element.getSynonyms());
- this.getFormerSymbols().addAll(element.getFormerSymbols());
-
- for (MiriamData md : element.getMiriamData()) {
- addMiriamData(new MiriamData(md));
- }
- this.abbreviation = element.getAbbreviation();
- this.formula = element.getFormula();
- }
-
- /**
- * Default constructor.
- */
- protected CellDesignerElement() {
- this.notes = "";
- }
-
- /**
- * Adds set of {@link MiriamData} to the object.
- *
- * @param miriamData
- * objects to be added
- */
- public void addMiriamData(Collection<MiriamData> miriamData) {
- for (MiriamData md : miriamData) {
- addMiriamData(md);
- }
- }
-
- /**
- * Returns identifier of the species.
- *
- * @return identifier of the species
- */
- public abstract String getElementId();
-
- /**
- * Adds {@link MiriamData} to the element.
- *
- * @param md
- * object to be added
- */
- public void addMiriamData(MiriamData md) {
- if (this.miriamData.contains(md)) {
- logger.warn("Miriam data (" + md.getDataType() + ": " + md.getResource() + ") for " + getElementId() + " already exists. Ignoring...");
- } else {
- this.miriamData.add(md);
- }
-
- }
-
- /**
- * Sets notes about the object.
- *
- * @param notes
- * new notes
- */
- public void setNotes(String notes) {
- if (notes != null) {
- if (notes.contains("</html>")) {
- throw new InvalidArgumentException("Notes cannot contain html tags...");
- }
- }
- this.notes = notes;
- }
-
- /**
- * Makes a copy of the element.
- *
- * @return copy of the object
- */
- public abstract CellDesignerElement<T> copy();
-
- /**
- * Adds synonyms to the element.
- *
- * @param synonyms
- * list of synonyms to be added
- */
- public void addSynonyms(List<String> synonyms) {
- for (String string : synonyms) {
- if (string.length() > MAX_SYNONYM_LENGTH) {
- String message = " <Synonym too long. Only " + MAX_SYNONYM_LENGTH + " characters are allowed>";
- this.getSynonyms().add(string.substring(0, MAX_SYNONYM_LENGTH - message.length()) + message);
- } else {
- this.getSynonyms().add(string);
- }
- }
-
- }
-
- /**
- * Returns notes about the object.
- *
- * @return notes about the object
- */
- public String getNotes() {
- return notes;
- }
-
- /**
- * Returns the symbol of the element.
- *
- * @return the symbol of the element
- */
- public String getSymbol() {
- return symbol;
- }
-
- /**
- * Sets symbol of the element.
- *
- * @param symbol
- * new symbol
- */
- public void setSymbol(String symbol) {
- this.symbol = symbol;
- }
-
- /**
- * @return the fullName
- * @see #fullName
- */
- public String getFullName() {
- return fullName;
- }
-
- /**
- * @param fullName
- * the fullName to set
- * @see #fullName
- */
- public void setFullName(String fullName) {
- this.fullName = fullName;
- }
-
- /**
- * Returns the name of the object.
- *
- * @return name of the object
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * Get list of synonyms.
- *
- * @return list of synonyms
- */
- public List<String> getSynonyms() {
- return synonyms;
- }
-
- /**
- * Sets list of synonyms to the element.
- *
- * @param synonyms
- * new list
- */
- public void setSynonyms(List<String> synonyms) {
- this.synonyms = synonyms;
- }
-
- /**
- * @return the formerSymbols
- * @see #formerSymbols
- */
- public List<String> getFormerSymbols() {
- return formerSymbols;
- }
-
- /**
- * @param formerSymbols
- * the formerSymbols to set
- * @see #formerSymbols
- */
- public void setFormerSymbols(List<String> formerSymbols) {
- this.formerSymbols = formerSymbols;
- }
-
- /**
- * @return the parent
- * @see #parent
- */
- public CellDesignerCompartment getParent() {
- return parent;
- }
-
- /**
- * @param parent
- * the parent to set
- * @see #parent
- */
- public void setParent(CellDesignerCompartment parent) {
- this.parent = parent;
- }
-
- /**
- * @return the complex
- * @see #complex
- */
- public CellDesignerComplexSpecies getComplex() {
- return complex;
- }
-
- /**
- * @param complex
- * the complex to set
- * @see #complex
- */
- public void setComplex(CellDesignerComplexSpecies complex) {
- this.complex = complex;
- }
-
- /**
- * Returns list of {@link MiriamData annotations} for the object.
- *
- * @return list of {@link MiriamData annotations} for the object
- */
- public Set<MiriamData> getMiriamData() {
- return miriamData;
- }
-
- /**
- * Returns the abbreviation.
- *
- * @return the abbreviation
- */
- public String getAbbreviation() {
- return abbreviation;
- }
-
- /**
- * Sets abbreviation.
- *
- * @param abbreviation
- * new abbreviation
- */
- public void setAbbreviation(String abbreviation) {
- this.abbreviation = abbreviation;
- }
-
- /**
- * Returns the formula.
- *
- * @return the formula
- */
- public String getFormula() {
- return formula;
- }
-
- /**
- * Sets formula.
- *
- * @param formula
- * new formula
- */
- public void setFormula(String formula) {
- this.formula = formula;
- }
-
- /**
- * Adds synonym.
- *
- * @param synonym
- * synonym to add
- */
- public void addSynonym(String synonym) {
- this.synonyms.add(synonym);
- }
-
- /**
- * Adds former symbol.
- *
- * @param formerSymbol
- * former symbol to add
- */
- public void addFormerSymbol(String formerSymbol) {
- this.formerSymbols.add(formerSymbol);
- }
-
- /**
- * Sets element identifier.
- *
- * @param elementId
- * element identifier
- */
- public abstract void setElementId(String elementId);
-
- /**
- * Creates model object from this celldesigner structure.
- *
- * @return model object from this celldesigner structure
- */
- public T createModelElement() {
- return createModelElement(null);
- }
-
- /**
- * Creates model object from this celldesigner structure.
- *
- * @param modelElementId
- * identifier of new model object
- * @return model object from this celldesigner structure
- */
- public abstract T createModelElement(String modelElementId);
-
- /**
- * Sets values from this cell designer structure into model object.
- *
- * @param result
- * object to which values should be assigned
- */
- protected void setModelObjectFields(T result) {
- result.setNotes(notes);
- result.setSymbol(symbol);
- result.setFullName(fullName);
- result.setAbbreviation(abbreviation);
- result.setFormula(formula);
- result.setName(name);
- result.addSynonyms(synonyms);
- result.addFormerSymbols(formerSymbols);
- result.addMiriamData(miriamData);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Maximum length of the valid synonym name.
+ */
+ private static final int MAX_SYNONYM_LENGTH = 255;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerElement.class);
+
+ /**
+ * Notes describing this element.
+ */
+ private String notes;
+
+ /**
+ * Symbol of the element.
+ */
+ private String symbol;
+
+ /**
+ * Full name of the element.
+ */
+ private String fullName;
+
+ /**
+ * Abbreviation associated with the element.
+ */
+ private String abbreviation;
+
+ /**
+ * Formula associated with the element.
+ */
+ private String formula;
+
+ /**
+ * Short name of the element.
+ */
+ private String name = "";
+
+ /**
+ * Lists of all synonyms used for describing this element.
+ */
+ private List<String> synonyms = new ArrayList<>();
+
+ /**
+ * List of former symbols used to describe this element.
+ */
+ private List<String> formerSymbols = new ArrayList<>();
+
+ /**
+ * Where this element lies on.
+ */
+ private CellDesignerCompartment parent;
+
+ /**
+ * In which complex this element is located.
+ */
+ private CellDesignerComplexSpecies complex;
+
+ /**
+ * Set of miriam annotations for this element.
+ */
+ private Set<MiriamData> miriamData = new HashSet<>();
+
+ /**
+ * Default constructor that initialize the data with the information given in
+ * the parameter.
+ *
+ * @param element
+ * original object from which data should be initialized
+ */
+ protected CellDesignerElement(CellDesignerElement<?> element) {
+ this.parent = element.parent;
+ this.complex = element.complex;
+ this.notes = element.notes;
+ this.symbol = element.symbol;
+ this.fullName = element.fullName;
+ this.name = element.getName();
+ this.getSynonyms().addAll(element.getSynonyms());
+ this.getFormerSymbols().addAll(element.getFormerSymbols());
+
+ for (MiriamData md : element.getMiriamData()) {
+ addMiriamData(new MiriamData(md));
+ }
+ this.abbreviation = element.getAbbreviation();
+ this.formula = element.getFormula();
+ }
+
+ /**
+ * Default constructor.
+ */
+ protected CellDesignerElement() {
+ this.notes = "";
+ }
+
+ /**
+ * Adds set of {@link MiriamData} to the object.
+ *
+ * @param miriamData
+ * objects to be added
+ */
+ public void addMiriamData(Collection<MiriamData> miriamData) {
+ for (MiriamData md : miriamData) {
+ addMiriamData(md);
+ }
+ }
+
+ /**
+ * Returns identifier of the species.
+ *
+ * @return identifier of the species
+ */
+ public abstract String getElementId();
+
+ /**
+ * Adds {@link MiriamData} to the element.
+ *
+ * @param md
+ * object to be added
+ */
+ public void addMiriamData(MiriamData md) {
+ if (this.miriamData.contains(md)) {
+ logger.warn("Miriam data (" + md.getDataType() + ": " + md.getResource() + ") for " + getElementId()
+ + " already exists. Ignoring...");
+ } else {
+ this.miriamData.add(md);
+ }
+
+ }
+
+ /**
+ * Sets notes about the object.
+ *
+ * @param notes
+ * new notes
+ */
+ public void setNotes(String notes) {
+ if (notes != null) {
+ if (notes.contains("</html>")) {
+ throw new InvalidArgumentException("Notes cannot contain html tags...");
+ }
+ }
+ this.notes = notes;
+ }
+
+ /**
+ * Makes a copy of the element.
+ *
+ * @return copy of the object
+ */
+ public abstract CellDesignerElement<T> copy();
+
+ /**
+ * Adds synonyms to the element.
+ *
+ * @param synonyms
+ * list of synonyms to be added
+ */
+ public void addSynonyms(List<String> synonyms) {
+ for (String string : synonyms) {
+ if (string.length() > MAX_SYNONYM_LENGTH) {
+ String message = " <Synonym too long. Only " + MAX_SYNONYM_LENGTH + " characters are allowed>";
+ this.getSynonyms().add(string.substring(0, MAX_SYNONYM_LENGTH - message.length()) + message);
+ } else {
+ this.getSynonyms().add(string);
+ }
+ }
+
+ }
+
+ /**
+ * Returns notes about the object.
+ *
+ * @return notes about the object
+ */
+ public String getNotes() {
+ return notes;
+ }
+
+ /**
+ * Returns the symbol of the element.
+ *
+ * @return the symbol of the element
+ */
+ public String getSymbol() {
+ return symbol;
+ }
+
+ /**
+ * Sets symbol of the element.
+ *
+ * @param symbol
+ * new symbol
+ */
+ public void setSymbol(String symbol) {
+ this.symbol = symbol;
+ }
+
+ /**
+ * @return the fullName
+ * @see #fullName
+ */
+ public String getFullName() {
+ return fullName;
+ }
+
+ /**
+ * @param fullName
+ * the fullName to set
+ * @see #fullName
+ */
+ public void setFullName(String fullName) {
+ this.fullName = fullName;
+ }
+
+ /**
+ * Returns the name of the object.
+ *
+ * @return name of the object
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * Get list of synonyms.
+ *
+ * @return list of synonyms
+ */
+ public List<String> getSynonyms() {
+ return synonyms;
+ }
+
+ /**
+ * Sets list of synonyms to the element.
+ *
+ * @param synonyms
+ * new list
+ */
+ public void setSynonyms(List<String> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ /**
+ * @return the formerSymbols
+ * @see #formerSymbols
+ */
+ public List<String> getFormerSymbols() {
+ return formerSymbols;
+ }
+
+ /**
+ * @param formerSymbols
+ * the formerSymbols to set
+ * @see #formerSymbols
+ */
+ public void setFormerSymbols(List<String> formerSymbols) {
+ this.formerSymbols = formerSymbols;
+ }
+
+ /**
+ * @return the parent
+ * @see #parent
+ */
+ public CellDesignerCompartment getParent() {
+ return parent;
+ }
+
+ /**
+ * @param parent
+ * the parent to set
+ * @see #parent
+ */
+ public void setParent(CellDesignerCompartment parent) {
+ this.parent = parent;
+ }
+
+ /**
+ * @return the complex
+ * @see #complex
+ */
+ public CellDesignerComplexSpecies getComplex() {
+ return complex;
+ }
+
+ /**
+ * @param complex
+ * the complex to set
+ * @see #complex
+ */
+ public void setComplex(CellDesignerComplexSpecies complex) {
+ this.complex = complex;
+ }
+
+ /**
+ * Returns list of {@link MiriamData annotations} for the object.
+ *
+ * @return list of {@link MiriamData annotations} for the object
+ */
+ public Set<MiriamData> getMiriamData() {
+ return miriamData;
+ }
+
+ /**
+ * Returns the abbreviation.
+ *
+ * @return the abbreviation
+ */
+ public String getAbbreviation() {
+ return abbreviation;
+ }
+
+ /**
+ * Sets abbreviation.
+ *
+ * @param abbreviation
+ * new abbreviation
+ */
+ public void setAbbreviation(String abbreviation) {
+ this.abbreviation = abbreviation;
+ }
+
+ /**
+ * Returns the formula.
+ *
+ * @return the formula
+ */
+ public String getFormula() {
+ return formula;
+ }
+
+ /**
+ * Sets formula.
+ *
+ * @param formula
+ * new formula
+ */
+ public void setFormula(String formula) {
+ this.formula = formula;
+ }
+
+ /**
+ * Adds synonym.
+ *
+ * @param synonym
+ * synonym to add
+ */
+ public void addSynonym(String synonym) {
+ this.synonyms.add(synonym);
+ }
+
+ /**
+ * Adds former symbol.
+ *
+ * @param formerSymbol
+ * former symbol to add
+ */
+ public void addFormerSymbol(String formerSymbol) {
+ this.formerSymbols.add(formerSymbol);
+ }
+
+ /**
+ * Sets element identifier.
+ *
+ * @param elementId
+ * element identifier
+ */
+ public abstract void setElementId(String elementId);
+
+ /**
+ * Creates model object from this CellDesigner structure.
+ *
+ * @return model object from this CellDesigner structure
+ */
+ public T createModelElement() {
+ return createModelElement(null);
+ }
+
+ /**
+ * Creates model object from this CellDesigner structure.
+ *
+ * @param modelElementId
+ * identifier of new model object
+ * @return model object from this CellDesigner structure
+ */
+ public abstract T createModelElement(String modelElementId);
+
+ public abstract void updateModelElementAfterLayoutAdded(T element);
+
+ /**
+ * Sets values from this cell designer structure into model object.
+ *
+ * @param result
+ * object to which values should be assigned
+ */
+ protected void setModelObjectFields(T result) {
+ result.setNotes(notes);
+ result.setSymbol(symbol);
+ result.setFullName(fullName);
+ result.setAbbreviation(abbreviation);
+ result.setFormula(formula);
+ result.setName(name);
+ result.addSynonyms(synonyms);
+ result.addFormerSymbols(formerSymbols);
+ result.addMiriamData(miriamData);
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
index efc960c93ecf0b71b58863567529b7646be24847..7e485de81648c9a341e7c26f21983230751d4d40 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
@@ -6,6 +6,7 @@ import java.util.List;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Class representing CellDesigner {@link Gene}.
@@ -15,103 +16,107 @@ import lcsb.mapviewer.model.map.species.Gene;
*/
public class CellDesignerGene extends CellDesignerSpecies<Gene> {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of modifications for the Gene.
- */
- private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
-
- /**
- * Constructor that initializes gene with the data passed in the argument.
- *
- * @param species
- * original species used for data initialization
- */
- public CellDesignerGene(CellDesignerSpecies<?> species) {
- super(species);
- if (species instanceof CellDesignerGene) {
- CellDesignerGene gene = (CellDesignerGene) species;
- for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
- addModificationResidue(new CellDesignerModificationResidue(mr));
- }
- }
- }
-
- @Override
- public void update(CellDesignerSpecies<?> species) {
- super.update(species);
- if (species instanceof CellDesignerGene) {
- CellDesignerGene gene = (CellDesignerGene) species;
-
- for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
- addModificationResidue(mr);
- }
- }
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerGene() {
- super();
- }
-
- @Override
- public CellDesignerGene copy() {
- if (this.getClass() == CellDesignerGene.class) {
- return new CellDesignerGene(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * Adds modification to the gene.
- *
- * @param modificationResidue
- * modifiaction to add
- */
- public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
- for (CellDesignerModificationResidue mr : modificationResidues) {
- if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
- mr.update(modificationResidue);
- return;
- }
- }
- modificationResidues.add(modificationResidue);
- modificationResidue.setSpecies(this);
-
- }
-
- /**
- * @return the modificationResidues
- * @see #modificationResidues
- */
- public List<CellDesignerModificationResidue> getModificationResidues() {
- return modificationResidues;
- }
-
- /**
- * @param modificationResidues
- * the modificationResidues to set
- * @see #modificationResidues
- */
- public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
- this.modificationResidues = modificationResidues;
- }
-
- @Override
- public Gene createModelElement(String aliasId) {
- Gene result = new Gene(aliasId);
- super.setModelObjectFields(result);
- for (CellDesignerModificationResidue mr : modificationResidues) {
- result.addModificationResidue(mr.createModificationResidueAlias());
- }
- return result;
-
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * List of modifications for the Gene.
+ */
+ private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
+
+ /**
+ * Constructor that initializes gene with the data passed in the argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public CellDesignerGene(CellDesignerSpecies<?> species) {
+ super(species);
+ if (species instanceof CellDesignerGene) {
+ CellDesignerGene gene = (CellDesignerGene) species;
+ for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
+ addModificationResidue(new CellDesignerModificationResidue(mr));
+ }
+ }
+ }
+
+ @Override
+ public void update(CellDesignerSpecies<?> species) {
+ super.update(species);
+ if (species instanceof CellDesignerGene) {
+ CellDesignerGene gene = (CellDesignerGene) species;
+
+ for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
+ addModificationResidue(mr);
+ }
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerGene() {
+ super();
+ }
+
+ @Override
+ public CellDesignerGene copy() {
+ if (this.getClass() == CellDesignerGene.class) {
+ return new CellDesignerGene(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * Adds modification to the gene.
+ *
+ * @param modificationResidue
+ * modification to add
+ */
+ public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
+ for (CellDesignerModificationResidue mr : modificationResidues) {
+ if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
+ mr.update(modificationResidue);
+ return;
+ }
+ }
+ modificationResidues.add(modificationResidue);
+ modificationResidue.setSpecies(this);
+
+ }
+
+ /**
+ * @return the modificationResidues
+ * @see #modificationResidues
+ */
+ public List<CellDesignerModificationResidue> getModificationResidues() {
+ return modificationResidues;
+ }
+
+ /**
+ * @param modificationResidues
+ * the modificationResidues to set
+ * @see #modificationResidues
+ */
+ public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
+ this.modificationResidues = modificationResidues;
+ }
+
+ @Override
+ public Gene createModelElement(String aliasId) {
+ Gene result = new Gene(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species element) {
+ for (CellDesignerModificationResidue region : modificationResidues) {
+ ((Gene) element).addModificationResidue(region.createModificationResidue(element));
+ }
+ }
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java
index 31eb0cf621a5d2d86a08bdfd244facf0ad683196..cfd15dbf01463562f80203cffe7ff53d5c1cf62a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java
@@ -1,52 +1,51 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Ion;
-
-/**
- * Class representing CellDesigner {@link Ion}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerIon extends CellDesignerChemical<Ion> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructor that initializes ion with the data passed in the argument.
- *
- * @param species
- * original species used for data initialization
- */
- public CellDesignerIon(CellDesignerSpecies<?> species) {
- super(species);
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerIon() {
- super();
- }
-
- @Override
- public CellDesignerIon copy() {
- if (this.getClass() == CellDesignerIon.class) {
- return new CellDesignerIon(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public Ion createModelElement(String aliasId) {
- Ion result = new Ion(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Ion;
+
+/**
+ * Class representing CellDesigner {@link Ion}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerIon extends CellDesignerChemical<Ion> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructor that initializes ion with the data passed in the argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public CellDesignerIon(CellDesignerSpecies<?> species) {
+ super(species);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerIon() {
+ super();
+ }
+
+ @Override
+ public CellDesignerIon copy() {
+ if (this.getClass() == CellDesignerIon.class) {
+ return new CellDesignerIon(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public Ion createModelElement(String aliasId) {
+ Ion result = new Ion(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
index ae3677e954e3caf411d5af7276fedbabf42cfaf8..9fa15ca0dff3c18c82d4db90de02094f23bda405 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
@@ -1,153 +1,159 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.model.map.species.Protein;
-
-/**
- * Class representing CellDesigner {@link Protein} object.
- *
- * @param <T>
- * type of a {@link Protein} modeled by this class
- * @author Piotr Gawron
- *
- */
-public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<T> {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CellDesignerProtein.class.getName());
-
- /**
- * State of the protein.
- */
- private String structuralState = null;
-
- /**
- * List of modifications for the Protein.
- */
- private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<CellDesignerModificationResidue>();
-
- /**
- * Constructor that initializes protein with the data passed in the argument.
- *
- * @param species
- * original species used for data initialization
- */
- public CellDesignerProtein(CellDesignerSpecies<?> species) {
- super(species);
- if (species instanceof CellDesignerProtein) {
- CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
- if (protein.getStructuralState() != null) {
- setStructuralState(new String(protein.getStructuralState()));
- }
- for (CellDesignerModificationResidue mr : protein.getModificationResidues()) {
- addModificationResidue(new CellDesignerModificationResidue(mr));
- }
- }
- }
-
- @Override
- public void update(CellDesignerSpecies<?> species) {
- super.update(species);
- if (species instanceof CellDesignerProtein) {
- CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
- if (getStructuralState() == null || getStructuralState().equals("")) {
- setStructuralState(protein.getStructuralState());
- }
- for (CellDesignerModificationResidue mr : protein.getModificationResidues()) {
- addModificationResidue(mr);
- }
- }
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerProtein() {
- super();
- }
-
- @Override
- public CellDesignerProtein<T> copy() {
- if (this.getClass().equals(CellDesignerProtein.class)) {
- return new CellDesignerProtein<T>(this);
- } else {
- throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
- }
- }
-
- /**
- * Adds modification to the protein.
- *
- * @param modificationResidue
- * modification to add
- */
- public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
- for (CellDesignerModificationResidue mr : modificationResidues) {
- if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
- mr.update(modificationResidue);
- return;
- }
- }
- modificationResidues.add(modificationResidue);
- modificationResidue.setSpecies(this);
- }
-
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState
- * the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- if (this.structuralState != null && !this.structuralState.equals("")
- && !this.structuralState.equals(structuralState)) {
- logger.warn("replacing structural state, Old: " + this.structuralState + " into new: " + structuralState);
- }
- this.structuralState = structuralState;
- }
-
- /**
- * @return the modificationResidues
- * @see #modificationResidues
- */
- public List<CellDesignerModificationResidue> getModificationResidues() {
- return modificationResidues;
- }
-
- /**
- * @param modificationResidues
- * the modificationResidues to set
- * @see #modificationResidues
- */
- public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
- this.modificationResidues = modificationResidues;
- }
-
- @Override
- protected void setModelObjectFields(T result) {
- super.setModelObjectFields(result);
- result.setStructuralState(structuralState);
- for (CellDesignerModificationResidue mr : modificationResidues) {
- result.addModificationResidue(mr.createModificationResidueAlias());
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class representing CellDesigner {@link Protein} object.
+ *
+ * @param <T>
+ * type of a {@link Protein} modeled by this class
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<T> {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerProtein.class.getName());
+
+ /**
+ * State of the protein.
+ */
+ private String structuralState = null;
+
+ /**
+ * List of modifications for the Protein.
+ */
+ private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<CellDesignerModificationResidue>();
+
+ /**
+ * Constructor that initializes protein with the data passed in the argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public CellDesignerProtein(CellDesignerSpecies<?> species) {
+ super(species);
+ if (species instanceof CellDesignerProtein) {
+ CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
+ if (protein.getStructuralState() != null) {
+ setStructuralState(new String(protein.getStructuralState()));
+ }
+ for (CellDesignerModificationResidue mr : protein.getModificationResidues()) {
+ addModificationResidue(new CellDesignerModificationResidue(mr));
+ }
+ }
+ }
+
+ @Override
+ public void update(CellDesignerSpecies<?> species) {
+ super.update(species);
+ if (species instanceof CellDesignerProtein) {
+ CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
+ if (getStructuralState() == null || getStructuralState().equals("")) {
+ setStructuralState(protein.getStructuralState());
+ }
+ for (CellDesignerModificationResidue mr : protein.getModificationResidues()) {
+ addModificationResidue(mr);
+ }
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerProtein() {
+ super();
+ }
+
+ @Override
+ public CellDesignerProtein<T> copy() {
+ if (this.getClass().equals(CellDesignerProtein.class)) {
+ return new CellDesignerProtein<T>(this);
+ } else {
+ throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
+ }
+ }
+
+ /**
+ * Adds modification to the protein.
+ *
+ * @param modificationResidue
+ * modification to add
+ */
+ public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
+ for (CellDesignerModificationResidue mr : modificationResidues) {
+ if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
+ mr.update(modificationResidue);
+ return;
+ }
+ }
+ modificationResidues.add(modificationResidue);
+ modificationResidue.setSpecies(this);
+ }
+
+ /**
+ * @return the structuralState
+ * @see #structuralState
+ */
+ public String getStructuralState() {
+ return structuralState;
+ }
+
+ /**
+ * @param structuralState
+ * the structuralState to set
+ * @see #structuralState
+ */
+ public void setStructuralState(String structuralState) {
+ if (this.structuralState != null && !this.structuralState.equals("")
+ && !this.structuralState.equals(structuralState)) {
+ logger.warn("replacing structural state, Old: " + this.structuralState + " into new: " + structuralState);
+ }
+ this.structuralState = structuralState;
+ }
+
+ /**
+ * @return the modificationResidues
+ * @see #modificationResidues
+ */
+ public List<CellDesignerModificationResidue> getModificationResidues() {
+ return modificationResidues;
+ }
+
+ /**
+ * @param modificationResidues
+ * the modificationResidues to set
+ * @see #modificationResidues
+ */
+ public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
+ this.modificationResidues = modificationResidues;
+ }
+
+ @Override
+ protected void setModelObjectFields(T result) {
+ super.setModelObjectFields(result);
+ result.setStructuralState(structuralState);
+ }
+
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species element) {
+ for (CellDesignerModificationResidue mr : modificationResidues) {
+ ((Protein) element).addModificationResidue(mr.createModificationResidue(element));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
index a1d476c3f02c9681fed20b53cf0bbd62b8d869ef..64e121ad9a3dd26675334a8e62feb267e7a1b0a2 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
@@ -1,147 +1,149 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerRnaRegion;
-import lcsb.mapviewer.model.map.species.Rna;
-
-/**
- * Class representing CellDesigner {@link Rna}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerRna extends CellDesignerSpecies<Rna> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerRna.class.getName());
-
- /**
- * List of rna regions (some rna sequences) in this object.
- */
- private List<CellDesignerRnaRegion> regions = new ArrayList<>();
-
- /**
- * Constructor that initializes rna with the data passed in the argument.
- *
- * @param species
- * original species used for data initialization
- */
- public CellDesignerRna(CellDesignerSpecies<?> species) {
- super(species);
- if (species instanceof CellDesignerRna) {
- CellDesignerRna rna = (CellDesignerRna) species;
- for (CellDesignerRnaRegion region : rna.getRegions()) {
- addRegion(new CellDesignerRnaRegion(region));
- }
- }
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerRna() {
- super();
- }
-
- @Override
- public CellDesignerRna copy() {
- if (this.getClass() == CellDesignerRna.class) {
- return new CellDesignerRna(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public void update(CellDesignerSpecies<?> species) {
- super.update(species);
- if (species instanceof CellDesignerRna) {
- CellDesignerRna rna = (CellDesignerRna) species;
- for (CellDesignerRnaRegion mr : getRegions()) {
- mr.setState(null);
- }
-
- for (CellDesignerRnaRegion region : rna.getRegions()) {
- updateRegion(region);
- }
- }
- }
-
- /**
- * Updates region in the rna. If region doesn't exist then it is added.
- *
- * @param param
- * region that with the data to update
- */
- private void updateRegion(CellDesignerRnaRegion param) {
- for (CellDesignerRnaRegion region : regions) {
- if (region.getIdRnaRegion().equals(param.getIdRnaRegion())) {
- region.update(param);
- return;
- }
- }
- addRegion(new CellDesignerRnaRegion(param));
- }
-
- /**
- * Adds region. If the region with given id exists then the data of this
- * region is copied to the one that is already in the {@link CellDesignerRna}.
- *
- * @param rnaRegion
- * region to add
- */
- public void addRegion(CellDesignerRnaRegion rnaRegion) {
- for (CellDesignerRnaRegion region2 : regions) {
- if (region2.getIdRnaRegion().equals(rnaRegion.getIdRnaRegion())) {
- region2.update(rnaRegion);
- return;
- }
- }
-
- regions.add(rnaRegion);
- rnaRegion.setSpecies(this);
-
- }
-
- /**
- * @return the regions
- * @see #regions
- */
- public List<CellDesignerRnaRegion> getRegions() {
- return regions;
- }
-
- /**
- * @param regions
- * the regions to set
- * @see #regions
- */
- public void setRegions(List<CellDesignerRnaRegion> regions) {
- this.regions = regions;
- }
-
- @Override
- public Rna createModelElement(String aliasId) {
- Rna result = new Rna(aliasId);
- super.setModelObjectFields(result);
- for (CellDesignerRnaRegion region : regions) {
- result.addRegion(region.createRnaRegionAlias());
- }
-
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class representing CellDesigner {@link Rna}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerRna extends CellDesignerSpecies<Rna> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerRna.class.getName());
+
+ /**
+ * List of rna regions (some rna sequences) in this object.
+ */
+ private List<CellDesignerModificationResidue> regions = new ArrayList<>();
+
+ /**
+ * Constructor that initializes rna with the data passed in the argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public CellDesignerRna(CellDesignerSpecies<?> species) {
+ super(species);
+ if (species instanceof CellDesignerRna) {
+ CellDesignerRna rna = (CellDesignerRna) species;
+ for (CellDesignerModificationResidue region : rna.getRegions()) {
+ addRegion(new CellDesignerModificationResidue(region));
+ }
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerRna() {
+ super();
+ }
+
+ @Override
+ public CellDesignerRna copy() {
+ if (this.getClass() == CellDesignerRna.class) {
+ return new CellDesignerRna(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public void update(CellDesignerSpecies<?> species) {
+ super.update(species);
+ if (species instanceof CellDesignerRna) {
+ CellDesignerRna rna = (CellDesignerRna) species;
+
+ for (CellDesignerModificationResidue region : rna.getRegions()) {
+ updateRegion(region);
+ }
+ }
+ }
+
+ /**
+ * Updates region in the rna. If region doesn't exist then it is added.
+ *
+ * @param param
+ * region that with the data to update
+ */
+ private void updateRegion(CellDesignerModificationResidue param) {
+ for (CellDesignerModificationResidue region : regions) {
+ if (region.getIdModificationResidue().equals(param.getIdModificationResidue())) {
+ region.update(param);
+ return;
+ }
+ }
+ addRegion(new CellDesignerModificationResidue(param));
+ }
+
+ /**
+ * Adds region. If the region with given id exists then the data of this region
+ * is copied to the one that is already in the {@link CellDesignerRna}.
+ *
+ * @param rnaRegion
+ * region to add
+ */
+ public void addRegion(CellDesignerModificationResidue rnaRegion) {
+ for (CellDesignerModificationResidue region2 : regions) {
+ if (region2.getIdModificationResidue().equals(rnaRegion.getIdModificationResidue())) {
+ region2.update(rnaRegion);
+ return;
+ }
+ }
+
+ regions.add(rnaRegion);
+ rnaRegion.setSpecies(this);
+
+ }
+
+ /**
+ * @return the regions
+ * @see #regions
+ */
+ public List<CellDesignerModificationResidue> getRegions() {
+ return regions;
+ }
+
+ /**
+ * @param regions
+ * the regions to set
+ * @see #regions
+ */
+ public void setRegions(List<CellDesignerModificationResidue> regions) {
+ this.regions = regions;
+ }
+
+ @Override
+ public Rna createModelElement(String aliasId) {
+ Rna result = new Rna(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species element) {
+ for (CellDesignerModificationResidue region : regions) {
+ Rna rna = (Rna) element;
+ rna.addRegion(region.createModificationResidue(rna));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
index 4acada56476e594330adb6de81d9af2b2feccb49..189df358e98ebb9b6e05b3ea8c80cc22613e6950 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
@@ -540,4 +540,8 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
this.constant = constant;
}
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species element) {
+ }
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
deleted file mode 100644
index 36decddc98a49f81ef86a92f4431a0349825d4c2..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
+++ /dev/null
@@ -1,334 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import java.io.Serializable;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-/**
- * This structure contains information about antisense rna region (rna fragment
- * of interest) for a specific
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna
- * AntisenseRna}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerAntisenseRnaRegion implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default size of the object (in graphical representation).
- */
- private static final double DEFAULT_SIZE = 0.1;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerAntisenseRnaRegion.class.getName());
-
- /**
- * Unique identifier in the database.
- */
- private int id;
-
- /**
- * String identifier of the element. Unique in the model.
- */
- private String idAntisenseRnaRegion = "";
-
- /**
- * Name of the region.
- */
- private String name = "";
-
- /**
- * Defines a state of the region (for instance ubiquitinated etc).
- *
- * @see ModificationState
- */
- private ModificationState state = null;
-
- /**
- * Type of the region in the rna. There are three possible values:
- * <ul>
- * <li>Coding region,</li>
- * <li>Protein binding domain,</li>
- * <li>Modification site.</li>
- * </ul>
- */
- private AntisenseRnaRegionType type;
-
- /**
- * Size of the region in the graphic representation.
- */
- private double size = DEFAULT_SIZE;
-
- /**
- * Position on the species in graphic representation.
- */
- private Double pos;
-
- /**
- * Defines a species where the region belongs to.
- */
- private CellDesignerAntisenseRna species;
-
- /**
- * Default constructor.
- */
- public CellDesignerAntisenseRnaRegion() {
-
- }
-
- /**
- * Constructor that initialize object with the data from the parameter.
- *
- * @param original
- * object from which we initialize data
- */
- public CellDesignerAntisenseRnaRegion(CellDesignerAntisenseRnaRegion original) {
- this.idAntisenseRnaRegion = original.idAntisenseRnaRegion;
- this.name = original.name;
- this.size = original.size;
- this.pos = original.pos;
- this.type = original.type;
- }
-
- /**
- * Creates a copy of current object.
- *
- * @return copy of the object
- */
- public CellDesignerAntisenseRnaRegion copy() {
- if (this.getClass() == CellDesignerAntisenseRnaRegion.class) {
- return new CellDesignerAntisenseRnaRegion(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
-
- }
-
- /**
- * Sets size from the string.
- *
- * @param text
- * size to parse and set
- * @see #size
- */
- public void setSize(String text) {
- try {
- size = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
- }
-
- /**
- * Sets position from the string.
- *
- * @param text
- * position to parse and set
- * @see #pos
- */
- public void setPos(String text) {
- try {
- pos = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid pos: " + text, e);
- }
- }
-
- /**
- * Update data in this object from parameter (only if values in parameter
- * object are valid).
- *
- * @param mr
- * object from which we are updating data
- */
- public void update(CellDesignerAntisenseRnaRegion mr) {
- if (this.idAntisenseRnaRegion != null && !this.idAntisenseRnaRegion.equals("") && !this.idAntisenseRnaRegion.equals(mr.getIdAntisenseRnaRegion())) {
- throw new InvalidArgumentException("Cannot update from mr with different id");
- }
- this.size = mr.getSize();
- if (mr.getState() != null) {
- this.state = mr.getState();
- }
- if (mr.getName() != null) {
- this.name = mr.getName();
- }
- if (mr.getPos() != null) {
- this.setPos(mr.getPos());
- }
-
- }
-
- @Override
- public String toString() {
- String result = getIdAntisenseRnaRegion() + "," + getName() + "," + getType() + "," + getPos() + "," + getSize() + ",";
- return result;
- }
-
- /**
- * @return the idAntisenseRnaRegion
- * @see #idAntisenseRnaRegion
- */
- public String getIdAntisenseRnaRegion() {
- return idAntisenseRnaRegion;
- }
-
- /**
- * @param idAntisenseRnaRegion
- * the id to set
- * @see #idAntisenseRnaRegion
- */
- public void setIdAntisenseRnaRegion(String idAntisenseRnaRegion) {
- this.idAntisenseRnaRegion = idAntisenseRnaRegion;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the state
- * @see #state
- */
- public ModificationState getState() {
- return state;
- }
-
- /**
- * @param state
- * the state to set
- * @see #state
- */
- public void setState(ModificationState state) {
- this.state = state;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public AntisenseRnaRegionType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(AntisenseRnaRegionType type) {
- this.type = type;
- }
-
- /**
- * @return the size
- * @see #size
- */
- public double getSize() {
- return size;
- }
-
- /**
- * @param size
- * the size to set
- * @see #size
- */
- public void setSize(double size) {
- this.size = size;
- }
-
- /**
- * @return the pos
- * @see #pos
- */
- public Double getPos() {
- return pos;
- }
-
- /**
- * @param pos
- * the pos to set
- * @see #pos
- */
- public void setPos(Double pos) {
- this.pos = pos;
- }
-
- /**
- * @return the species
- * @see #species
- */
- public CellDesignerAntisenseRna getSpecies() {
- return species;
- }
-
- /**
- * @param species
- * the species to set
- * @see #species
- */
- public void setSpecies(CellDesignerAntisenseRna species) {
- this.species = species;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * Creates model representation of {@link AntisenseRnaRegion}.
- *
- * @return {@link AntisenseRnaRegion} representing this object in a model
- */
- public AntisenseRnaRegion createAntisenseRegionAlias() {
- AntisenseRnaRegion result = new AntisenseRnaRegion();
- result.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
- result.setName(name);
- result.setSize(size);
- result.setPos(pos);
- result.setType(type);
- return result;
- }
-
-}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
index 34bf5b75c4e47f0f21bb0c55b5f543b628dfa951..10789b0b509f5559600096ece698857338bec02f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
@@ -1,333 +1,557 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import java.io.Serializable;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-/**
- * This class represent modification residue in protein and gene. However, it is
- * sometimes also used for storing information about AntisenseRna/Rna regions...
- * (due to CellDesigner xml strange structure).
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerModificationResidue implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerModificationResidue.class.getName());
-
- /**
- * Identifier of the modification. Must be unique in single map model.
- */
- private String idModificationResidue = "";
-
- /**
- * Name of the modification.
- */
- private String name = "";
-
- /**
- * Some strange param in CellDesigner. No idea what is it for.
- */
- private String side = "";
-
- /**
- * State in which this modification is.
- */
- private ModificationState state = null;
-
- /**
- * Where this modification is located (on which side of the border).
- */
- private Double angle = null;
-
- /**
- * How big is this modification (used only for some types of the
- * modification).
- */
- private Double size = null;
-
- /**
- * Species to which this modification belong to.
- */
- private CellDesignerSpecies<?> species;
-
- /**
- * Default constructor.
- */
- public CellDesignerModificationResidue() {
- }
-
- /**
- * Constructor that initaize object with the data taken from the parameter.
- *
- * @param mr
- * original object from which data is taken
- */
- public CellDesignerModificationResidue(CellDesignerModificationResidue mr) {
- this.idModificationResidue = mr.idModificationResidue;
- this.name = mr.name;
- this.angle = mr.angle;
- this.size = mr.size;
- this.side = mr.side;
- this.state = mr.state;
- }
-
- /**
- * Constructor that creates object from model representation of modification.
- *
- * @param mr
- * model represnation of {@link ModificationResidue}
- */
- public CellDesignerModificationResidue(ModificationResidue mr) {
- this.idModificationResidue = mr.getIdModificationResidue();
- this.name = mr.getName();
- this.angle = mr.getAngle();
- this.size = mr.getSize();
- this.side = mr.getSide();
- this.state = mr.getState();
- }
-
- /**
- * Default constructor.
- *
- * @param id
- * identifier of the modificationr esidue
- */
- public CellDesignerModificationResidue(String id) {
- this.idModificationResidue = id;
- }
-
- /**
- * Updates fields in the object with the data given in the parameter
- * modification.
- *
- * @param mr
- * modification residue from which data will be used to update
- */
- public void update(CellDesignerModificationResidue mr) {
- if (mr.getName() != null && !mr.getName().equals("")) {
- this.name = mr.name;
- }
- if (mr.getAngle() != null) {
- this.angle = mr.angle;
- }
- if (mr.getSize() != null) {
- this.size = mr.size;
- }
- if (mr.getSide() != null && !mr.getSide().equals("")) {
- this.side = mr.side;
- }
- if (mr.getState() != null) {
- this.state = mr.state;
- }
- }
-
- @Override
- public String toString() {
- String result = getIdModificationResidue() + "," + getName() + "," + getState() + "," + getAngle() + "," + getSize() + "," + getSide() + ",";
- return result;
- }
-
- /**
- * Creates copy of the object.
- *
- * @return copy of the object.
- */
- public CellDesignerModificationResidue copy() {
- if (this.getClass() == CellDesignerModificationResidue.class) {
- return new CellDesignerModificationResidue(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * Sets {@link #angle} .
- *
- * @param text
- * angle in text format
- */
- public void setAngle(String text) {
- try {
- if (text != null && !text.equals("")) {
- angle = Double.parseDouble(text);
- } else {
- angle = null;
- }
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
-
- }
-
- /**
- * Sets {@link #size}.
- *
- * @param text
- * size in text format.
- */
- public void setSize(String text) {
- try {
- if (text != null && !text.equals("")) {
- size = Double.parseDouble(text);
- } else {
- size = null;
- }
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid size: " + text, e);
- }
- }
-
- /**
- * @return the id
- * @see #idModificationResidue
- */
- public String getIdModificationResidue() {
- return idModificationResidue;
- }
-
- /**
- * @param idModificationResidue
- * the id to set
- * @see #idModificationResidue
- */
- public void setIdModificationResidue(String idModificationResidue) {
- this.idModificationResidue = idModificationResidue;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the side
- * @see #side
- */
- public String getSide() {
- return side;
- }
-
- /**
- * @param side
- * the side to set
- * @see #side
- */
- public void setSide(String side) {
- this.side = side;
- }
-
- /**
- * @return the state
- * @see #state
- */
- public ModificationState getState() {
- return state;
- }
-
- /**
- * @param state
- * the state to set
- * @see #state
- */
- public void setState(ModificationState state) {
- this.state = state;
- }
-
- /**
- * @return the angle
- * @see #angle
- */
- public Double getAngle() {
- return angle;
- }
-
- /**
- * @param angle
- * the angle to set
- * @see #angle
- */
- public void setAngle(Double angle) {
- this.angle = angle;
- }
-
- /**
- * @return the size
- * @see #size
- */
- public Double getSize() {
- return size;
- }
-
- /**
- * @param size
- * the size to set
- * @see #size
- */
- public void setSize(Double size) {
- this.size = size;
- }
-
- /**
- * @return the species
- * @see #species
- */
- public CellDesignerSpecies<?> getSpecies() {
- return species;
- }
-
- /**
- * @param species
- * the species to set
- * @see #species
- */
- public void setSpecies(CellDesignerSpecies<?> species) {
- this.species = species;
- }
-
- /**
- * Creates model representation of {@link ModificationResidue}.
- *
- * @return {@link ModificationResidue} representing this object in a model
- */
- public ModificationResidue createModificationResidueAlias() {
- ModificationResidue result = new ModificationResidue();
-
- result.setIdModificationResidue(this.getIdModificationResidue());
- result.setName(this.getName());
- result.setAngle(this.getAngle());
- result.setSize(this.getSize());
- result.setSide(this.getSide());
- result.setState(this.getState());
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import java.io.Serializable;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
+
+/**
+ * This class represent modification residue in a Species.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerModificationResidue implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerModificationResidue.class.getName());
+
+ /**
+ * Identifier of the modification. Must be unique in single map model.
+ */
+ private String idModificationResidue = "";
+
+ /**
+ * Name of the modification.
+ */
+ private String name = "";
+
+ private Boolean active = null;
+
+ private ModificationType modificationType;
+
+ /**
+ * Position on the species in graphic representation.
+ */
+ private Double pos;
+
+ /**
+ * Some strange parameter in CellDesigner. No idea what is it for.
+ */
+ private String side = "";
+
+ /**
+ * State in which this modification is.
+ */
+ private ModificationState state = null;
+
+ /**
+ * Where this modification is located (on which side of the border).
+ */
+ private Double angle = null;
+
+ /**
+ * How big is this modification (used only for some types of the modification).
+ */
+ private Double size = null;
+
+ /**
+ * Species to which this modification belong to.
+ */
+ private CellDesignerSpecies<?> species;
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerModificationResidue() {
+ }
+
+ /**
+ * Constructor that initialize object with the data taken from the parameter.
+ *
+ * @param mr
+ * original object from which data is taken
+ */
+ public CellDesignerModificationResidue(CellDesignerModificationResidue mr) {
+ this.idModificationResidue = mr.idModificationResidue;
+ this.name = mr.name;
+ this.angle = mr.angle;
+ this.active = mr.active;
+ this.size = mr.size;
+ this.side = mr.side;
+ this.pos = mr.pos;
+ this.state = mr.state;
+ this.modificationType = mr.modificationType;
+ }
+
+ /**
+ * Constructor that creates object from model representation of modification.
+ *
+ * @param mr
+ * model representation of {@link ModificationResidue}
+ */
+ public CellDesignerModificationResidue(ModificationResidue mr) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(mr.getSpecies(), false);
+ this.idModificationResidue = mr.getIdModificationResidue();
+ this.name = mr.getName();
+ this.angle = converter.getAngleForPoint(mr.getSpecies(), mr.getPosition());
+ this.pos = converter.getCellDesignerPositionByCoordinates(mr);
+ if (mr instanceof Residue) {
+ this.modificationType = ModificationType.RESIDUE;
+ this.state = ((Residue) mr).getState();
+ } else if (mr instanceof ModificationSite) {
+ this.modificationType = ModificationType.MODIFICATION_SITE;
+ this.state = ((ModificationSite) mr).getState();
+ } else if (mr instanceof CodingRegion) {
+ this.size = converter.getCellDesignerSize(mr);
+ this.modificationType = ModificationType.CODING_REGION;
+ } else if (mr instanceof ProteinBindingDomain) {
+ this.size = converter.getCellDesignerSize(mr);
+ this.modificationType = ModificationType.PROTEIN_BINDING_DOMAIN;
+ } else if (mr instanceof RegulatoryRegion) {
+ this.size = converter.getCellDesignerSize(mr);
+ this.modificationType = ModificationType.REGULATORY_REGION;
+ } else if (mr instanceof TranscriptionSite) {
+ TranscriptionSite transcriptionSite = (TranscriptionSite) mr;
+ this.size = converter.getCellDesignerSize(mr);
+ this.active = transcriptionSite.getActive();
+ if (transcriptionSite.getDirection().equals("LEFT")) {
+ this.modificationType = ModificationType.TRANSCRIPTION_SITE_LEFT;
+ } else {
+ this.modificationType = ModificationType.TRANSCRIPTION_SITE_RIGHT;
+ }
+ } else if (mr instanceof BindingRegion) {
+ this.modificationType = ModificationType.BINDING_REGION;
+ if (Math.abs(mr.getPosition().getX() - mr.getSpecies().getX()) < Configuration.EPSILON) {
+ this.size = ((BindingRegion) mr).getHeight() / mr.getSpecies().getHeight();
+ } else if (Math
+ .abs(mr.getPosition().getX() - mr.getSpecies().getX() - mr.getSpecies().getWidth()) < Configuration.EPSILON) {
+ this.size = ((BindingRegion) mr).getHeight() / mr.getSpecies().getHeight();
+ } else {
+ this.size = ((BindingRegion) mr).getWidth() / mr.getSpecies().getWidth();
+ }
+
+ } else {
+ throw new InvalidArgumentException("Unknown modification type: " + mr.getClass());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param id
+ * identifier of the modification residue
+ */
+ public CellDesignerModificationResidue(String id) {
+ this.idModificationResidue = id;
+ }
+
+ /**
+ * Updates fields in the object with the data given in the parameter
+ * modification.
+ *
+ * @param mr
+ * modification residue from which data will be used to update
+ */
+ public void update(CellDesignerModificationResidue mr) {
+ if (mr.getName() != null && !mr.getName().equals("")) {
+ this.name = mr.name;
+ }
+ if (mr.getAngle() != null) {
+ this.angle = mr.angle;
+ }
+ if (mr.getActive() != null) {
+ this.active = mr.active;
+ }
+ if (mr.getSize() != null) {
+ this.size = mr.size;
+ }
+ if (mr.getSide() != null && !mr.getSide().equals("")) {
+ this.side = mr.side;
+ }
+ if (mr.getState() != null) {
+ this.state = mr.state;
+ }
+ if (mr.getPos() != null) {
+ this.setPos(mr.getPos());
+ }
+ if (mr.getModificationType() != null) {
+ this.setModificationType(mr.modificationType);
+ }
+ }
+
+ @Override
+ public String toString() {
+ String result = getIdModificationResidue() + "," + getName() + "," + getState() + "," + getAngle() + "," + getSize()
+ + getPos() + "," + "," + getSide() + ",";
+ return result;
+ }
+
+ /**
+ * Creates copy of the object.
+ *
+ * @return copy of the object.
+ */
+ public CellDesignerModificationResidue copy() {
+ if (this.getClass() == CellDesignerModificationResidue.class) {
+ return new CellDesignerModificationResidue(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * Sets {@link #angle} .
+ *
+ * @param text
+ * angle in text format
+ */
+ public void setAngle(String text) {
+ try {
+ if (text != null && !text.equals("")) {
+ angle = Double.parseDouble(text);
+ } else {
+ angle = null;
+ }
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid angle: " + text, e);
+ }
+
+ }
+
+ /**
+ * Sets {@link #size}.
+ *
+ * @param text
+ * size in text format.
+ */
+ public void setSize(String text) {
+ try {
+ if (text != null && !text.equals("")) {
+ size = Double.parseDouble(text);
+ } else {
+ size = null;
+ }
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid size: " + text, e);
+ }
+ }
+
+ /**
+ * @return the id
+ * @see #idModificationResidue
+ */
+ public String getIdModificationResidue() {
+ return idModificationResidue;
+ }
+
+ /**
+ * @param idModificationResidue
+ * the id to set
+ * @see #idModificationResidue
+ */
+ public void setIdModificationResidue(String idModificationResidue) {
+ this.idModificationResidue = idModificationResidue;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the side
+ * @see #side
+ */
+ public String getSide() {
+ return side;
+ }
+
+ /**
+ * @param side
+ * the side to set
+ * @see #side
+ */
+ public void setSide(String side) {
+ this.side = side;
+ }
+
+ /**
+ * @return the state
+ * @see #state
+ */
+ public ModificationState getState() {
+ return state;
+ }
+
+ /**
+ * @param state
+ * the state to set
+ * @see #state
+ */
+ public void setState(ModificationState state) {
+ this.state = state;
+ }
+
+ /**
+ * @return the angle
+ * @see #angle
+ */
+ public Double getAngle() {
+ return angle;
+ }
+
+ /**
+ * @param angle
+ * the angle to set
+ * @see #angle
+ */
+ public void setAngle(Double angle) {
+ this.angle = angle;
+ }
+
+ /**
+ * @return the size
+ * @see #size
+ */
+ public Double getSize() {
+ return size;
+ }
+
+ /**
+ * @param size
+ * the size to set
+ * @see #size
+ */
+ public void setSize(Double size) {
+ this.size = size;
+ }
+
+ /**
+ * @return the species
+ * @see #species
+ */
+ public CellDesignerSpecies<?> getSpecies() {
+ return species;
+ }
+
+ /**
+ * @param species
+ * the species to set
+ * @see #species
+ */
+ public void setSpecies(CellDesignerSpecies<?> species) {
+ this.species = species;
+ }
+
+ /**
+ * Creates model representation of {@link ModificationResidue}.
+ *
+ * @return {@link ModificationResidue} representing this object in a model
+ */
+ public ModificationResidue createModificationResidue(Element element) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, false);
+
+ if (modificationType == null) {
+ throw new InvalidArgumentException("No type information for modification: " + idModificationResidue);
+ } else if (modificationType.equals(ModificationType.RESIDUE)) {
+ return createResidue(element, converter);
+ } else if (modificationType.equals(ModificationType.BINDING_REGION)) {
+ return createBindingRegion(element, converter);
+ } else if (modificationType.equals(ModificationType.MODIFICATION_SITE)) {
+ return createModificationSite(element, converter);
+ } else if (modificationType.equals(ModificationType.CODING_REGION)) {
+ return createCodingRegion(element, converter);
+ } else if (modificationType.equals(ModificationType.PROTEIN_BINDING_DOMAIN)) {
+ return createProteinBindingDomain(element, converter);
+ } else if (modificationType.equals(ModificationType.REGULATORY_REGION)) {
+ return createRegulatoryRegion(element, converter);
+ } else if (modificationType.equals(ModificationType.TRANSCRIPTION_SITE_LEFT)
+ || modificationType.equals(ModificationType.TRANSCRIPTION_SITE_RIGHT)) {
+ return createTranscriptionSite(element, converter);
+ } else {
+ throw new InvalidArgumentException("Unknown modification type: " + modificationType);
+ }
+
+ }
+
+ private ProteinBindingDomain createProteinBindingDomain(Element element, CellDesignerAliasConverter converter) {
+ ProteinBindingDomain result = new ProteinBindingDomain();
+ result.setWidth(converter.getWidthBySize(element, size));
+ result.setIdModificationResidue(idModificationResidue);
+ result.setName(name);
+ result.setPosition(converter.getCoordinatesByPosition(element, pos, result.getWidth()));
+ return result;
+ }
+
+ private BindingRegion createBindingRegion(Element element, CellDesignerAliasConverter converter) {
+ BindingRegion result = new BindingRegion();
+ result.setIdModificationResidue(idModificationResidue);
+ result.setName(name);
+ result.setPosition(converter.getResidueCoordinates(element, angle));
+ if (Math.abs(result.getPosition().getX() - element.getX()) < Configuration.EPSILON) {
+ result.setHeight(element.getHeight() * size);
+ } else if (Math.abs(result.getPosition().getX() - element.getX() - element.getWidth()) < Configuration.EPSILON) {
+ result.setHeight(element.getHeight() * size);
+ } else {
+ result.setWidth(element.getWidth() * size);
+ }
+ return result;
+ }
+
+ private CodingRegion createCodingRegion(Element element, CellDesignerAliasConverter converter) {
+ CodingRegion result = new CodingRegion();
+ result.setWidth(converter.getWidthBySize(element, size));
+ result.setIdModificationResidue(idModificationResidue);
+ result.setName(name);
+ if (pos == null) {
+ pos = angle;
+ }
+ result.setPosition(converter.getCoordinatesByPosition(element, pos, result.getWidth()));
+ return result;
+ }
+
+ private RegulatoryRegion createRegulatoryRegion(Element element, CellDesignerAliasConverter converter) {
+ RegulatoryRegion result = new RegulatoryRegion();
+ result.setWidth(converter.getWidthBySize(element, size));
+ result.setIdModificationResidue(idModificationResidue);
+ result.setName(name);
+ result.setPosition(converter.getCoordinatesByPosition(element, angle, result.getWidth()));
+ return result;
+ }
+
+ private TranscriptionSite createTranscriptionSite(Element element, CellDesignerAliasConverter converter) {
+ TranscriptionSite result = new TranscriptionSite();
+ result.setWidth(converter.getWidthBySize(element, size));
+ result.setIdModificationResidue(idModificationResidue);
+ result.setName(name);
+ result.setActive(active);
+ result.setPosition(converter.getCoordinatesByPosition(element, angle, result.getWidth()));
+ if (modificationType.equals(ModificationType.TRANSCRIPTION_SITE_LEFT)) {
+ result.setDirection("LEFT");
+ } else {
+ result.setDirection("RIGHT");
+ }
+ return result;
+ }
+
+ private ModificationSite createModificationSite(Element element, CellDesignerAliasConverter converter) {
+ ModificationSite result = new ModificationSite();
+ result.setState(this.getState());
+ result.setIdModificationResidue(this.getIdModificationResidue());
+ result.setName(this.getName());
+ if (angle == null) {
+ angle = pos;
+ }
+ if (angle == null) {
+ logger.warn("Angle is not defined using 0 as default");
+ angle = 0.0;
+ }
+ result.setPosition(converter.getCoordinatesByPosition(element, angle));
+ return result;
+ }
+
+ private Residue createResidue(Element element, CellDesignerAliasConverter converter) {
+ Residue result = new Residue();
+ result.setState(this.getState());
+ result.setIdModificationResidue(this.getIdModificationResidue());
+ result.setName(this.getName());
+ if (angle == null) {
+ logger.warn("Angle is not defined using 0 as default");
+ angle = 0.0;
+ }
+ result.setPosition(converter.getResidueCoordinates(element, angle));
+ return result;
+ }
+
+ public ModificationType getModificationType() {
+ return modificationType;
+ }
+
+ public void setModificationType(ModificationType modificationType) {
+ this.modificationType = modificationType;
+ }
+
+ /**
+ * Sets position from the string.
+ *
+ * @param text
+ * position to parse and set
+ * @see #pos
+ */
+ public void setPos(String text) {
+ try {
+ pos = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid pos: " + text, e);
+ }
+ }
+
+ /**
+ * @return the pos
+ * @see #pos
+ */
+ public Double getPos() {
+ return pos;
+ }
+
+ /**
+ * @param pos
+ * the pos to set
+ * @see #pos
+ */
+ public void setPos(Double pos) {
+ this.pos = pos;
+ }
+
+ public Boolean getActive() {
+ return active;
+ }
+
+ public void setActive(Boolean active) {
+ this.active = active;
+ }
+
+ public void setActive(String text) {
+ if (text == null) {
+ this.active = null;
+ } else {
+ this.active = "true".equalsIgnoreCase(text);
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java
deleted file mode 100644
index bbb44414758cd125082930ee1f9f62f290b94edd..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java
+++ /dev/null
@@ -1,301 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import java.io.Serializable;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-
-/**
- * This structure contains information about rna region (rna fragment of
- * interest) for a specific
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna
- * Rna}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerRnaRegion implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default {@link #size} of the region.
- */
- private static final double DEFAULT_SIZE = 0.1;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerRnaRegion.class.getName());
-
- /**
- * Identifier of the region. Unique in the
- * {@link lcsb.mapviewer.model.map.model.Model}.
- */
- private String idRnaRegion = "";
-
- /**
- * Type of the region in the rna. There are three possible values:
- * <ul>
- * <li>Coding region,</li>
- * <li>Protein binding domain,</li>
- * <li>Modification site.</li>
- * </ul>
- */
- private String type = "";
-
- /**
- * Defines a state of the region (for instance ubiquitinated etc).
- *
- * @see ModificationState
- */
- private ModificationState state = null;
-
- /**
- * Name of the region.
- */
- private String name = "";
-
- /**
- * Size of the region in the graphic representation.
- */
- private double size = DEFAULT_SIZE;
-
- /**
- * Position on the species in graphic representation.
- */
- private Double pos;
-
- /**
- * Defines a species where the region belongs to.
- */
- private CellDesignerRna species;
-
- /**
- * Default constructor.
- */
- public CellDesignerRnaRegion() {
-
- }
-
- /**
- * Creates object with the data taken from paramter region.
- *
- * @param mr
- * original {@link CellDesignerRnaRegion}
- */
- public CellDesignerRnaRegion(CellDesignerRnaRegion mr) {
- this.idRnaRegion = mr.idRnaRegion;
- this.size = mr.size;
- setPos(mr.getPos());
- this.type = mr.type;
- this.state = mr.state;
- this.name = mr.name;
- }
-
- /**
- * Sets {@link #size}.
- *
- * @param text
- * new size value in string format
- */
- public void setSize(String text) {
- try {
- size = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
-
- }
-
- /**
- * Sets {@link #pos}.
- *
- * @param text
- * new {@link #pos} value in string format
- */
- public void setPos(String text) {
- try {
- setPos(Double.parseDouble(text));
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid pos: " + text, e);
- }
-
- }
-
- /**
- * Updates fields in the object with the data given in the parameter rna
- * region.
- *
- * @param mr
- * {@link CellDesignerRnaRegion} from which data will be used to
- * update
- */
- public void update(CellDesignerRnaRegion mr) {
- if (this.idRnaRegion != null && !this.idRnaRegion.equals("") && !this.idRnaRegion.equals(mr.getIdRnaRegion())) {
- throw new InvalidArgumentException("Cannot update from mr with different id");
- }
- this.size = mr.getSize();
- if (mr.getState() != null) {
- this.state = mr.getState();
- }
- if (mr.getName() != null) {
- this.name = mr.getName();
- }
- if (mr.getPos() != null) {
- this.setPos(mr.getPos());
- }
-
- }
-
- @Override
- public String toString() {
- String result = "" + getIdRnaRegion() + "," + getType() + "," + getPos() + "," + getSize() + "," + getState() + ",";
- return result;
-
- }
-
- /**
- * @return the id
- * @see #id
- */
- public String getIdRnaRegion() {
- return idRnaRegion;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setIdRnaRegion(String id) {
- this.idRnaRegion = id;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
- /**
- * @return the state
- * @see #state
- */
- public ModificationState getState() {
- return state;
- }
-
- /**
- * @param state
- * the state to set
- * @see #state
- */
- public void setState(ModificationState state) {
- this.state = state;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the size
- * @see #size
- */
- public double getSize() {
- return size;
- }
-
- /**
- * @param size
- * the size to set
- * @see #size
- */
- public void setSize(double size) {
- this.size = size;
- }
-
- /**
- * @return the pos
- * @see #pos
- */
- public Double getPos() {
- return pos;
- }
-
- /**
- * @param pos
- * the pos to set
- * @see #pos
- */
- public void setPos(Double pos) {
- this.pos = pos;
- }
-
- /**
- * @return the species
- * @see #species
- */
- public CellDesignerRna getSpecies() {
- return species;
- }
-
- /**
- * @param species
- * the species to set
- * @see #species
- */
- public void setSpecies(CellDesignerRna species) {
- this.species = species;
- }
-
- /**
- * Creates model representation of {@link RnaRegion}.
- *
- * @return {@link RnaRegion} representing this object in a model
- */
- public RnaRegion createRnaRegionAlias() {
- RnaRegion result = new RnaRegion();
- result.setIdRnaRegion(this.idRnaRegion);
- result.setSize(this.size);
- result.setPos(this.getPos());
- result.setType(this.getType());
- result.setState(this.state);
- result.setName(this.name);
- return result;
- }
-
-}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java
new file mode 100644
index 0000000000000000000000000000000000000000..ca6bad57fea0d469996ef35f783add2a83a098ac
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ModificationType.java
@@ -0,0 +1,33 @@
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public enum ModificationType {
+ BINDING_REGION(null), //
+ CODING_REGION("CodingRegion"), //
+ PROTEIN_BINDING_DOMAIN("proteinBindingDomain"), //
+ RESIDUE(null), //
+ REGULATORY_REGION("RegulatoryRegion"), //
+ TRANSCRIPTION_SITE_RIGHT("transcriptionStartingSiteR"), //
+ TRANSCRIPTION_SITE_LEFT("transcriptionStartingSiteL"), //
+ MODIFICATION_SITE("Modification Site");//
+
+ private String cellDesignerName;
+
+ ModificationType(String cellDesignerName) {
+ this.cellDesignerName = cellDesignerName;
+ }
+
+ public String getCellDesignerName() {
+ return cellDesignerName;
+ }
+
+ public static ModificationType getByCellDesignerName(String name) {
+ for (ModificationType type : ModificationType.values()) {
+ if (type.getCellDesignerName() != null && type.getCellDesignerName().equals(name)) {
+ return type;
+ }
+ }
+ throw new InvalidArgumentException("Unknown CellDesigner name: " + name);
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
index c6a42cda6e92d8b5083242f18163c373e5d0374f..2e9562224a93b787b2e21c676b552c2e88503108 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
@@ -1,167 +1,170 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-
-/**
- * Structure for storing the state of the Species in CellDesigner format.
- *
- * @author Piotr Gawron
- *
- */
-public class SpeciesState {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(SpeciesState.class.getName());
-
- /**
- * How many dimers are in the species.
- */
- private int homodimer = 1;
-
- /**
- * String state description.
- */
- private String structuralState = null;
-
- /**
- * List of species modification.
- */
- private List<CellDesignerModificationResidue> modifications = new ArrayList<CellDesignerModificationResidue>();
-
- /**
- * Adds modification to the state.
- *
- * @param modificationResidue
- * modification to add
- */
- public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
- for (CellDesignerModificationResidue modification : modifications) {
- if (modification.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
- modification.update(modificationResidue);
- return;
- }
- }
- modifications.add(modificationResidue);
- }
-
- /**
- * Default constructor.
- */
- public SpeciesState() {
- }
-
- /**
- * Creates species state description from species element.
- *
- * @param species
- * object for which description is created
- */
- public SpeciesState(Species species) {
- if (species instanceof Protein) {
- Protein protein = (Protein) species;
- setStructuralState(protein.getStructuralState());
- for (ModificationResidue mr : protein.getModificationResidues()) {
- addModificationResidue(new CellDesignerModificationResidue(mr));
- }
-
- } else if (species instanceof Complex) {
- Complex complex = (Complex) species;
- setStructuralState(complex.getStructuralState());
- } else if (species instanceof Rna) {
- Rna rna = (Rna) species;
- for (RnaRegion region : rna.getRegions()) {
- CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
- mr.setIdModificationResidue(region.getIdRnaRegion());
- mr.setSize(region.getSize());
- mr.setState(region.getState());
- addModificationResidue(mr);
- }
- } else if (species instanceof Gene) {
- Gene gene = (Gene) species;
- for (ModificationResidue mr : gene.getModificationResidues()) {
- addModificationResidue(new CellDesignerModificationResidue(mr));
- }
- }
- setHomodimer(species.getHomodimer());
- }
-
- /**
- *
- * @param homodimer
- * new {@link #homodimer} value to set (in string format)
- */
- public void setHomodimer(String homodimer) {
- try {
- this.homodimer = Integer.parseInt(homodimer);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid homodir value: " + homodimer);
- }
- }
-
- /**
- * @return the homodimer
- * @see #homodimer
- */
- public int getHomodimer() {
- return homodimer;
- }
-
- /**
- * @param homodimer
- * the homodimer to set
- * @see #homodimer
- */
- public void setHomodimer(int homodimer) {
- this.homodimer = homodimer;
- }
-
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState
- * the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- this.structuralState = structuralState;
- }
-
- /**
- * @return the modifications
- * @see #modifications
- */
- public List<CellDesignerModificationResidue> getModifications() {
- return modifications;
- }
-
- /**
- * @param modifications
- * the modifications to set
- * @see #modifications
- */
- public void setModifications(List<CellDesignerModificationResidue> modifications) {
- this.modifications = modifications;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Structure for storing the state of the Species in CellDesigner format.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SpeciesState {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(SpeciesState.class.getName());
+
+ /**
+ * How many dimers are in the species.
+ */
+ private int homodimer = 1;
+
+ /**
+ * String state description.
+ */
+ private String structuralState = null;
+
+ /**
+ * List of species modification.
+ */
+ private List<CellDesignerModificationResidue> modifications = new ArrayList<>();
+
+ /**
+ * Adds modification to the state.
+ *
+ * @param modificationResidue
+ * modification to add
+ */
+ public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
+ for (CellDesignerModificationResidue modification : modifications) {
+ if (modification.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
+ modification.update(modificationResidue);
+ return;
+ }
+ }
+ modifications.add(modificationResidue);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public SpeciesState() {
+ }
+
+ /**
+ * Creates species state description from species element.
+ *
+ * @param species
+ * object for which description is created
+ */
+ public SpeciesState(Species species) {
+ if (species instanceof Protein) {
+ Protein protein = (Protein) species;
+ setStructuralState(protein.getStructuralState());
+ for (ModificationResidue mr : protein.getModificationResidues()) {
+ addModificationResidue(new CellDesignerModificationResidue(mr));
+ }
+
+ } else if (species instanceof Complex) {
+ Complex complex = (Complex) species;
+ setStructuralState(complex.getStructuralState());
+ } else if (species instanceof Rna) {
+ Rna rna = (Rna) species;
+ for (ModificationResidue region : rna.getRegions()) {
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue(region);
+ addModificationResidue(mr);
+ }
+ } else if (species instanceof AntisenseRna) {
+ AntisenseRna rna = (AntisenseRna) species;
+ for (ModificationResidue region : rna.getRegions()) {
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue(region);
+ addModificationResidue(mr);
+ }
+ } else if (species instanceof Gene) {
+ Gene gene = (Gene) species;
+ for (ModificationResidue mr : gene.getModificationResidues()) {
+ addModificationResidue(new CellDesignerModificationResidue(mr));
+ }
+ }
+ setHomodimer(species.getHomodimer());
+ }
+
+ /**
+ *
+ * @param homodimer
+ * new {@link #homodimer} value to set (in string format)
+ */
+ public void setHomodimer(String homodimer) {
+ try {
+ this.homodimer = Integer.parseInt(homodimer);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid homodir value: " + homodimer);
+ }
+ }
+
+ /**
+ * @return the homodimer
+ * @see #homodimer
+ */
+ public int getHomodimer() {
+ return homodimer;
+ }
+
+ /**
+ * @param homodimer
+ * the homodimer to set
+ * @see #homodimer
+ */
+ public void setHomodimer(int homodimer) {
+ this.homodimer = homodimer;
+ }
+
+ /**
+ * @return the structuralState
+ * @see #structuralState
+ */
+ public String getStructuralState() {
+ return structuralState;
+ }
+
+ /**
+ * @param structuralState
+ * the structuralState to set
+ * @see #structuralState
+ */
+ public void setStructuralState(String structuralState) {
+ this.structuralState = structuralState;
+ }
+
+ /**
+ * @return the modifications
+ * @see #modifications
+ */
+ public List<CellDesignerModificationResidue> getModifications() {
+ return modifications;
+ }
+
+ /**
+ * @param modifications
+ * the modifications to set
+ * @see #modifications
+ */
+ public void setModifications(List<CellDesignerModificationResidue> modifications) {
+ this.modifications = modifications;
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
index d6dc3214fc927f4b37110b664eca7564438c4f8e..16b51dec9d76cb8896541fbfeea1492724f58d9b 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
@@ -34,6 +34,7 @@ import lcsb.mapviewer.converter.model.celldesigner.unit.UnitXmlParserTest;
InvalidGroupExceptionTest.class, //
LayerXmlParserTest.class, //
NestedComplexParsingTests.class, //
+ ModificationTest.class, //
ParameterXmlParserTest.class, //
ReconDataInCellDesignerXmlParserTest.class, //
UnitXmlParserTest.class,//
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 6f97c0fbcdefd8a56ad20e1efcaa555006056e4d..a6f4b663a9292549d996eab2e7e4f1f33aef0abc 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -26,6 +26,7 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -120,8 +121,8 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
parser.createModel(new ConverterParams().filename("testFiles/invalid/sample10.xml"));
fail("Exceptin expected");
- } catch (InvalidInputDataExecption e) {
- assertTrue(e.getMessage().contains("Unknown element of model/listOfReactions"));
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("No type information for modification"));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -998,5 +999,4 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
throw e;
}
}
-
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
index d673a7a4e33416b980e8b7bb6f3554f81f22b69d..4df1c5bfb34dd918ef1e21c1aedd417bc53f5b61 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
@@ -33,8 +33,10 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class ComplexParserTests extends CellDesignerTestFunctions {
@@ -99,7 +101,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
try {
Model model = getModelForFile("testFiles/elements_with_kinetic_data.xml");
model.setName(null);
-
+
String xml = new CellDesignerXmlParser().toXml(model);
ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
Model model2 = new CellDesignerXmlParser()
@@ -118,7 +120,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
try {
Model model = getModelForFile("testFiles/reactions/kinetics.xml");
model.setName(null);
-
+
String xml = new CellDesignerXmlParser().toXml(model);
ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
Model model2 = new CellDesignerXmlParser()
@@ -222,12 +224,14 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
try {
model = getModelForFile("testFiles/problematic/acetyled_protein.xml");
- Set<ModificationState> residues = new HashSet<ModificationState>();
+ Set<ModificationState> residues = new HashSet<>();
for (Element element : model.getElements()) {
if (element instanceof Species) {
- Protein p = (Protein) element;
- for (ModificationResidue mr : p.getModificationResidues()) {
- residues.add(mr.getState());
+ Protein protein = (Protein) element;
+ for (ModificationResidue mr : protein.getModificationResidues()) {
+ if (mr instanceof AbstractSiteModification) {
+ residues.add(((AbstractSiteModification) mr).getState());
+ }
}
}
}
@@ -235,8 +239,9 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
// of residues
assertEquals(2, residues.size());
- assertEquals(ModificationState.ACETYLATED,
- ((Protein) model.getElementByElementId("sa2")).getModificationResidues().get(0).getState());
+ AbstractSiteModification modification = (AbstractSiteModification) ((Protein) model.getElementByElementId("sa2"))
+ .getModificationResidues().get(0);
+ assertEquals(ModificationState.ACETYLATED, modification.getState());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -278,8 +283,8 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
model = getModelForFile("testFiles/problematic/problematic_acetylation.xml");
Protein p1 = (Protein) model.getElementByElementId("sa73");
Protein p2 = (Protein) model.getElementByElementId("sa27");
- assertEquals(ModificationState.ACETYLATED, p1.getModificationResidues().get(0).getState());
- assertFalse(ModificationState.ACETYLATED.equals(p2.getModificationResidues().get(0).getState()));
+ assertEquals(ModificationState.ACETYLATED, ((Residue) p1.getModificationResidues().get(0)).getState());
+ assertFalse(ModificationState.ACETYLATED.equals(((Residue) p2.getModificationResidues().get(0)).getState()));
} catch (Exception e) {
e.printStackTrace();
@@ -417,60 +422,4 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
}
}
- @Test
- public void testRnaWithRegion() throws Exception {
- try {
- Model model = getModelForFile("testFiles/rnaWithRegion.xml");
- for (Element species : model.getNotComplexSpeciesList()) {
- Rna rna = (Rna) species;
- assertEquals(1, rna.getRegions().size());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProtinWithModifications() throws Exception {
- try {
- Model model = getModelForFile("testFiles/proteinWithEverPossibleModification.xml");
- Protein protein = (Protein) model.getElementByElementId("sa1");
- assertEquals(14, protein.getModificationResidues().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAntisenseRnaWithRegion() throws Exception {
- try {
- Model model = getModelForFile("testFiles/antisenseRnaWithRegion.xml");
- for (Species species : model.getNotComplexSpeciesList()) {
- AntisenseRna rna = (AntisenseRna) species;
- assertEquals(1, rna.getRegions().size());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPhosporylatedProteinToXml() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/phosphorylated_protein.xml");
- model.setName(null);
- CellDesignerXmlParser p = new CellDesignerXmlParser();
- String xml = p.toXml(model);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = p.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
- assertEquals(0, comparator.compare(model, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..bacc86fe1bd0cb526203cd376f465c01c1198e43
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java
@@ -0,0 +1,264 @@
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
+
+public class ModificationTest extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(ModificationTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testBindingRegion() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/modifications/protein_with_binding_region.xml");
+ Protein protein = model.getElementByElementId("sa1");
+ assertEquals(1, protein.getModificationResidues().size());
+ ModificationResidue residue = protein.getModificationResidues().get(0);
+
+ assertTrue(residue instanceof BindingRegion);
+ BindingRegion bindingRegion = (BindingRegion) residue;
+ assertEquals(bindingRegion.getPosition().getX(), protein.getX(), Configuration.EPSILON);
+ assertTrue(bindingRegion.getWidth() < bindingRegion.getHeight());
+
+ testXmlSerialization(model);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private void testXmlSerialization(Model model)
+ throws InconsistentModelException, UnsupportedEncodingException, InvalidInputDataExecption {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model);
+ InputStream is = new ByteArrayInputStream(xml.getBytes("UTF-8"));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ model.setName(null);
+ ModelComparator comparator = new ModelComparator();
+ assertEquals(0, comparator.compare(model, model2));
+ }
+
+ @Test
+ public void testRegulatoryRegion() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/modifications/gene_with_regulatory_region.xml");
+ Gene gene = model.getElementByElementId("sa1");
+ assertEquals(1, gene.getModificationResidues().size());
+
+ ModificationResidue residue = gene.getModificationResidues().get(0);
+ assertTrue(residue instanceof RegulatoryRegion);
+ RegulatoryRegion bindingRegion = (RegulatoryRegion) residue;
+ assertEquals(bindingRegion.getPosition().getY(), gene.getY(), Configuration.EPSILON);
+ assertTrue(bindingRegion.getWidth() > bindingRegion.getHeight());
+
+ testXmlSerialization(model);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGeneCodingRegion() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/modifications/gene_with_coding_region.xml");
+ Gene gene = model.getElementByElementId("sa1");
+ assertEquals(1, gene.getModificationResidues().size());
+
+ ModificationResidue residue = gene.getModificationResidues().get(0);
+ assertTrue(residue instanceof CodingRegion);
+ CodingRegion bindingRegion = (CodingRegion) residue;
+ assertEquals(bindingRegion.getPosition().getY(), gene.getY(), Configuration.EPSILON);
+ assertTrue(bindingRegion.getWidth() > bindingRegion.getHeight());
+
+ testXmlSerialization(model);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGeneModificationSite() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/modifications/gene_with_modification_site.xml");
+ Gene gene = model.getElementByElementId("sa1");
+ assertEquals(1, gene.getModificationResidues().size());
+
+ ModificationResidue residue = gene.getModificationResidues().get(0);
+ assertTrue(residue instanceof ModificationSite);
+ ModificationSite bindingRegion = (ModificationSite) residue;
+ assertEquals(bindingRegion.getPosition().getY(), gene.getY(), Configuration.EPSILON);
+
+ testXmlSerialization(model);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRegulatoryTranscriptionSiteRight() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/modifications/gene_with_transcription_site_right.xml");
+ Gene gene = model.getElementByElementId("sa1");
+ assertEquals(1, gene.getModificationResidues().size());
+ ModificationResidue residue = gene.getModificationResidues().get(0);
+
+ assertTrue(residue instanceof TranscriptionSite);
+ TranscriptionSite transcriptionSite = (TranscriptionSite) residue;
+ assertEquals(transcriptionSite.getPosition().getY(), gene.getY(), Configuration.EPSILON);
+ assertEquals("RIGHT", transcriptionSite.getDirection());
+ assertTrue(transcriptionSite.getActive());
+
+ testXmlSerialization(model);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRegulatoryTranscriptionSiteLeft() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/modifications/gene_with_transcription_site_left.xml");
+ Gene gene = model.getElementByElementId("sa1");
+ assertEquals(1, gene.getModificationResidues().size());
+ ModificationResidue residue = gene.getModificationResidues().get(0);
+
+ assertTrue(residue instanceof TranscriptionSite);
+ TranscriptionSite transcriptionSite = (TranscriptionSite) residue;
+ assertEquals(transcriptionSite.getPosition().getY(), gene.getY(), Configuration.EPSILON);
+ assertEquals("LEFT", transcriptionSite.getDirection());
+ assertFalse(transcriptionSite.getActive());
+
+ testXmlSerialization(model);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProtinWithResidues() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/modifications/protein_with_residues.xml");
+ Protein protein = (Protein) model.getElementByElementId("sa1");
+ assertEquals(14, protein.getModificationResidues().size());
+
+ ModificationResidue residue = protein.getModificationResidues().get(0);
+
+ assertTrue(residue instanceof Residue);
+
+ testXmlSerialization(model);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRnaWithRegion() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/modifications/rna_with_region.xml");
+ Rna rna = model.getElementByElementId("sa1");
+ assertEquals(1, rna.getRegions().size());
+ assertTrue(rna.getRegions().get(0) instanceof CodingRegion);
+
+ rna = model.getElementByElementId("sa2");
+ assertEquals(1, rna.getRegions().size());
+ assertTrue(rna.getRegions().get(0) instanceof ProteinBindingDomain);
+
+ rna = model.getElementByElementId("sa3");
+ assertEquals(1, rna.getRegions().size());
+ assertTrue(rna.getRegions().get(0) instanceof ModificationSite);
+
+ testXmlSerialization(model);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAntisenseRnaWithRegion() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/modifications/antisense_rna_with_region.xml");
+ AntisenseRna rna = model.getElementByElementId("sa1");
+ assertEquals(1, rna.getRegions().size());
+ assertTrue(rna.getRegions().get(0) instanceof CodingRegion);
+
+ rna = model.getElementByElementId("sa2");
+ assertEquals(1, rna.getRegions().size());
+ assertTrue(rna.getRegions().get(0) instanceof ProteinBindingDomain);
+
+ rna = model.getElementByElementId("sa3");
+ assertEquals(1, rna.getRegions().size());
+ assertTrue(rna.getRegions().get(0) instanceof ModificationSite);
+
+ rna = model.getElementByElementId("sa4");
+ assertEquals(1, rna.getRegions().size());
+ assertTrue(rna.getRegions().get(0) instanceof ModificationSite);
+ ModificationSite modificationSite = (ModificationSite) rna.getRegions().get(0);
+ assertEquals(ModificationState.PHOSPHORYLATED, modificationSite.getState());
+
+ testXmlSerialization(model);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPhosporylatedProteinToXml() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/phosphorylated_protein.xml");
+
+ testXmlSerialization(model);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java
index 43901d78ddb32c72e15623045db96d523c8a8d63..a9e13b63447e44f04ffc5c13934f0814b9aa00ca 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java
@@ -11,6 +11,7 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
@@ -22,60 +23,62 @@ import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
public class AbstractCellDesignerAliasConverterTest {
+ Logger logger = Logger.getLogger(AbstractCellDesignerAliasConverterTest.class);
- AbstractCellDesignerAliasConverter<Species> converter = new AbstractCellDesignerAliasConverter<Species>(false) {
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- return null;
- }
- @Override
- protected PathIterator getBoundPathIterator(Species alias) {
- return null;
- }
- };
+ AbstractCellDesignerAliasConverter<Species> converter = new AbstractCellDesignerAliasConverter<Species>(false) {
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ return null;
+ }
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @Override
+ protected PathIterator getBoundPathIterator(Species alias) {
+ return null;
+ }
+ };
- @Before
- public void setUp() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @Test
- public void testGetAnchorPointCoordinatesForInvalidImplementation() {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
- try {
- Protein alias = new GenericProtein("id");
- alias.setWidth(1);
- alias.setHeight(1);
- converter.getAnchorPointCoordinates(alias, 0);
- assertEquals(1, appender.getWarnings().size());
- } finally {
- Logger.getRootLogger().removeAppender(appender);
- }
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testGetters() {
- CellDesignerEllipseTransformation ellipseTransformation = new CellDesignerEllipseTransformation();
- LineTransformation lineTransformation = new LineTransformation();
- CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
- CellDesignerRectangleTransformation rectangleTransformation = new CellDesignerRectangleTransformation();
- converter.setEllipseTransformation(ellipseTransformation);
- converter.setLineTransformation(lineTransformation);
- converter.setPolygonTransformation(polygonTransformation);
- converter.setRectangleTransformation(rectangleTransformation);
+ @Test
+ public void testGetAnchorPointCoordinatesForInvalidImplementation() {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+ try {
+ Protein alias = new GenericProtein("id");
+ alias.setWidth(1);
+ alias.setHeight(1);
+ converter.getAnchorPointCoordinates(alias, 0);
+ assertEquals(1, appender.getWarnings().size());
+ } finally {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+ }
- assertEquals(ellipseTransformation, converter.getEllipseTransformation());
- assertEquals(lineTransformation, converter.getLineTransformation());
- assertEquals(polygonTransformation, converter.getPolygonTransformation());
- assertEquals(rectangleTransformation, converter.getRectangleTransformation());
- }
+ @Test
+ public void testGetters() {
+ CellDesignerEllipseTransformation ellipseTransformation = new CellDesignerEllipseTransformation();
+ LineTransformation lineTransformation = new LineTransformation();
+ CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
+ CellDesignerRectangleTransformation rectangleTransformation = new CellDesignerRectangleTransformation();
+ converter.setEllipseTransformation(ellipseTransformation);
+ converter.setLineTransformation(lineTransformation);
+ converter.setPolygonTransformation(polygonTransformation);
+ converter.setRectangleTransformation(rectangleTransformation);
+
+ assertEquals(ellipseTransformation, converter.getEllipseTransformation());
+ assertEquals(lineTransformation, converter.getLineTransformation());
+ assertEquals(polygonTransformation, converter.getPolygonTransformation());
+ assertEquals(rectangleTransformation, converter.getRectangleTransformation());
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java
index 270eafe9ce34158d15cf0e33013fd53237b18c1f..0ffe3ee44b73d7443d00770a5f8fa12c0e085de8 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java
@@ -1,75 +1,74 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertNotNull;
-
-import java.awt.geom.PathIterator;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class GeneCellDesignerAliasConverterTest {
-
- GeneCellDesignerAliasConverter converter = new GeneCellDesignerAliasConverter(false);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetInvalidAliasPointCoordinates() {
- Species alias = new Gene("id");
- alias.setX(1);
- alias.setY(12);
- alias.setWidth(10);
- alias.setHeight(10);
- assertNotNull(converter.getPointCoordinates(alias, null));
- }
-
- @Test
- public void testGetPath() {
- Model model = new ModelFullIndexed(null);
- Species alias = new Gene("id");
- alias.setX(1);
- alias.setY(12);
- alias.setWidth(10);
- alias.setHeight(10);
-
- alias.setModel(model);
- PathIterator path = converter.getBoundPathIterator(alias);
-
- assertNotNull(path);
- }
-
- @Test
- public void testGetPath2() {
- GeneCellDesignerAliasConverter converter = new GeneCellDesignerAliasConverter(true);
-
- Model model = new ModelFullIndexed(null);
- Species alias = new Gene("id");
- alias.setX(1);
- alias.setY(12);
- alias.setWidth(10);
- alias.setHeight(10);
-
- alias.setModel(model);
- PathIterator path = converter.getBoundPathIterator(alias);
-
- assertNotNull(path);
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.geom.PathIterator;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Gene;
+
+public class GeneCellDesignerAliasConverterTest {
+
+ GeneCellDesignerAliasConverter converter = new GeneCellDesignerAliasConverter(false);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetInvalidAliasPointCoordinates() {
+ Gene alias = new Gene("id");
+ alias.setX(1);
+ alias.setY(12);
+ alias.setWidth(10);
+ alias.setHeight(10);
+ assertNotNull(converter.getPointCoordinates(alias, null));
+ }
+
+ @Test
+ public void testGetPath() {
+ Model model = new ModelFullIndexed(null);
+ Gene alias = new Gene("id");
+ alias.setX(1);
+ alias.setY(12);
+ alias.setWidth(10);
+ alias.setHeight(10);
+
+ alias.setModel(model);
+ PathIterator path = converter.getBoundPathIterator(alias);
+
+ assertNotNull(path);
+ }
+
+ @Test
+ public void testGetPath2() {
+ GeneCellDesignerAliasConverter converter = new GeneCellDesignerAliasConverter(true);
+
+ Model model = new ModelFullIndexed(null);
+ Gene alias = new Gene("id");
+ alias.setX(1);
+ alias.setY(12);
+ alias.setWidth(10);
+ alias.setHeight(10);
+
+ alias.setModel(model);
+ PathIterator path = converter.getBoundPathIterator(alias);
+
+ assertNotNull(path);
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java
index a7f210b2f4ac4d5e1ad02aebf1a6c4a2c41f634b..c7cbcccba4e4ead4f6ee2bfcf59278362f525d02 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java
@@ -1,57 +1,56 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class IonCellDesignerAliasConverterTest {
-
- IonCellDesignerAliasConverter converter = new IonCellDesignerAliasConverter(false);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetAnchorPointCoordinatesForInvalidAlias() {
- Species alias = new Ion("id");
- alias.setWidth(-1);
- Point2D point = converter.getAnchorPointCoordinates(alias, 0);
- assertNotNull(point);
- }
-
- @Test
- public void testGetAnchorPointCoordinatesForInvalidAlias2() {
- Species alias = new Ion("id");
- Point2D point = converter.getAnchorPointCoordinates(alias, 0);
- assertNotNull(point);
- }
-
- @Test
- public void testNotImplementedMethod() {
- try {
- converter.getBoundPathIterator(null);
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("This class doesn't have bound"));
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Ion;
+
+public class IonCellDesignerAliasConverterTest {
+
+ IonCellDesignerAliasConverter converter = new IonCellDesignerAliasConverter(false);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetAnchorPointCoordinatesForInvalidAlias() {
+ Ion alias = new Ion("id");
+ alias.setWidth(-1);
+ Point2D point = converter.getAnchorPointCoordinates(alias, 0);
+ assertNotNull(point);
+ }
+
+ @Test
+ public void testGetAnchorPointCoordinatesForInvalidAlias2() {
+ Ion alias = new Ion("id");
+ Point2D point = converter.getAnchorPointCoordinates(alias, 0);
+ assertNotNull(point);
+ }
+
+ @Test
+ public void testNotImplementedMethod() {
+ try {
+ converter.getBoundPathIterator(null);
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("This class doesn't have bound"));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
index 4e8055b91cfd6533fa7fdc3b95c1e77e27d00725..e16751241a1f39ac4481125f94b0308193b257a3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
@@ -1,50 +1,96 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertEquals;
-
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class ProteinConverterTest extends CellDesignerTestFunctions {
- static Logger logger = Logger.getLogger(ProteinConverterTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetAnchorForAlias() throws Exception {
- try {
-
- GenericProtein alias = new GenericProtein("id");
- alias.setWidth(200);
- alias.setHeight(300);
- alias.setX(100.0);
- alias.setY(50.0);
-
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(alias, false);
-
- for (CellDesignerAnchor anchor : CellDesignerAnchor.values()) {
- Point2D point = converter.getPointCoordinates(alias, anchor);
- CellDesignerAnchor newAnchor = converter.getAnchorForCoordinates(alias, point);
- assertEquals(anchor, newAnchor);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+
+public class ProteinConverterTest extends CellDesignerTestFunctions {
+ static Logger logger = Logger.getLogger(ProteinConverterTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetAnchorForAlias() throws Exception {
+ try {
+
+ GenericProtein alias = new GenericProtein("id");
+ alias.setWidth(200);
+ alias.setHeight(300);
+ alias.setX(100.0);
+ alias.setY(50.0);
+
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(alias, false);
+
+ for (CellDesignerAnchor anchor : CellDesignerAnchor.values()) {
+ Point2D point = converter.getPointCoordinates(alias, anchor);
+ CellDesignerAnchor newAnchor = converter.getAnchorForCoordinates(alias, point);
+ assertEquals(anchor, newAnchor);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAngleConversion() {
+ Protein protein = new GenericProtein("id");
+ protein.setWidth(10);
+ protein.setHeight(60);
+ protein.setX(200);
+ protein.setY(500);
+
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(protein, false);
+
+ for (double angle = 0.0; angle < Math.PI * 2; angle += 0.1) {
+ Point2D point = converter.getResidueCoordinates(protein, angle);
+ double angle2 = converter.getAngleForPoint(protein, point);
+ assertEquals(angle, angle2, Configuration.EPSILON);
+ }
+ }
+
+ @Test
+ public void testGetResidueCoords() throws Exception {
+ try {
+ GenericProtein protein = new GenericProtein("id");
+ protein.setX(135);
+ protein.setY(194.0);
+ protein.setWidth(130);
+ protein.setHeight(67);
+
+ CellDesignerAliasConverter conv = new CellDesignerAliasConverter(protein, false);
+ assertEquals(135.0, conv.getResidueCoordinates(protein, 3.141592653589793).getX(), 2);
+ assertEquals(265., conv.getResidueCoordinates(protein, 0.0).getX(), 2);
+ assertEquals(135.0, conv.getResidueCoordinates(protein, 2.41).getX(), 2);
+ assertEquals(194.0, conv.getResidueCoordinates(protein, 1.98).getY(), 2);
+ assertEquals(194.0, conv.getResidueCoordinates(protein, 1.59).getY(), 2);
+ assertEquals(265.0, conv.getResidueCoordinates(protein, 6.28).getX(), 2);
+ assertEquals(261.0, conv.getResidueCoordinates(protein, 4.13).getY(), 2);
+ assertEquals(261.0, conv.getResidueCoordinates(protein, 4.86).getY(), 2);
+ assertEquals(265.0, conv.getResidueCoordinates(protein, 5.69).getX(), 2);
+ assertEquals(194.0, conv.getResidueCoordinates(protein, 0.99).getY(), 2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java
index efb1d2ed7e887d4dd40d462736d28da992b8e056..25479733a03204fbd77d8c713a8a4f742d4a02d5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java
@@ -1,99 +1,98 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class SimpleMoleculeCellDesignerAliasConverterTest {
-
- SimpleMoleculeCellDesignerAliasConverter converter = new SimpleMoleculeCellDesignerAliasConverter(false);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testPathIterator() {
- try {
- converter.getBoundPathIterator(null);
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- }
- }
-
- @Test
- public void testGetSbgnPointCoordinates() {
- SimpleMoleculeCellDesignerAliasConverter converter = new SimpleMoleculeCellDesignerAliasConverter(true);
-
- Model model = new ModelFullIndexed(null);
- Species alias = new SimpleMolecule("id");
- alias.setX(4);
- alias.setY(5);
- alias.setWidth(6);
- alias.setHeight(7);
- alias.setModel(model);
-
- Point2D point = converter.getPointCoordinates(alias, CellDesignerAnchor.E);
- assertNotNull(point);
-
- }
-
- @Test
- public void testGetSbgnAnchorPointCoordinates() {
- SimpleMoleculeCellDesignerAliasConverter converter = new SimpleMoleculeCellDesignerAliasConverter(true);
-
- Model model = new ModelFullIndexed(null);
- Species alias = new SimpleMolecule("id");
- alias.setX(4);
- alias.setY(5);
- alias.setWidth(6);
- alias.setHeight(7);
- alias.setModel(model);
-
- Point2D point = converter.getAnchorPointCoordinates(alias, 2);
- assertNotNull(point);
-
- }
-
- @Test
- public void testGetAnchorPointCoordinatesForEmptyAlias() {
- SimpleMoleculeCellDesignerAliasConverter converter = new SimpleMoleculeCellDesignerAliasConverter(true);
-
- Model model = new ModelFullIndexed(null);
- Species alias = new SimpleMolecule("id");
- alias.setX(4);
- alias.setY(5);
- alias.setWidth(0);
- alias.setHeight(0);
- alias.setModel(model);
-
- Point2D point = converter.getAnchorPointCoordinates(alias, 2);
- assertEquals(0.0, point.distance(new Point2D.Double(4, 5)), Configuration.EPSILON);
-
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+
+public class SimpleMoleculeCellDesignerAliasConverterTest {
+
+ SimpleMoleculeCellDesignerAliasConverter converter = new SimpleMoleculeCellDesignerAliasConverter(false);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testPathIterator() {
+ try {
+ converter.getBoundPathIterator(null);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ }
+ }
+
+ @Test
+ public void testGetSbgnPointCoordinates() {
+ SimpleMoleculeCellDesignerAliasConverter converter = new SimpleMoleculeCellDesignerAliasConverter(true);
+
+ Model model = new ModelFullIndexed(null);
+ SimpleMolecule alias = new SimpleMolecule("id");
+ alias.setX(4);
+ alias.setY(5);
+ alias.setWidth(6);
+ alias.setHeight(7);
+ alias.setModel(model);
+
+ Point2D point = converter.getPointCoordinates(alias, CellDesignerAnchor.E);
+ assertNotNull(point);
+
+ }
+
+ @Test
+ public void testGetSbgnAnchorPointCoordinates() {
+ SimpleMoleculeCellDesignerAliasConverter converter = new SimpleMoleculeCellDesignerAliasConverter(true);
+
+ Model model = new ModelFullIndexed(null);
+ SimpleMolecule alias = new SimpleMolecule("id");
+ alias.setX(4);
+ alias.setY(5);
+ alias.setWidth(6);
+ alias.setHeight(7);
+ alias.setModel(model);
+
+ Point2D point = converter.getAnchorPointCoordinates(alias, 2);
+ assertNotNull(point);
+
+ }
+
+ @Test
+ public void testGetAnchorPointCoordinatesForEmptyAlias() {
+ SimpleMoleculeCellDesignerAliasConverter converter = new SimpleMoleculeCellDesignerAliasConverter(true);
+
+ Model model = new ModelFullIndexed(null);
+ SimpleMolecule alias = new SimpleMolecule("id");
+ alias.setX(4);
+ alias.setY(5);
+ alias.setWidth(0);
+ alias.setHeight(0);
+ alias.setModel(model);
+
+ Point2D point = converter.getAnchorPointCoordinates(alias, 2);
+ assertEquals(0.0, point.distance(new Point2D.Double(4, 5)), Configuration.EPSILON);
+
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java
index 3479f9ce228f0cbade97c71b91a0dbc5ed6bcc32..030765507000c2ce88f5e9e3ef8ebde8eebc8886 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java
@@ -1,50 +1,49 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class UnknownCellDesignerAliasConverterTest {
- UnknownCellDesignerAliasConverter converter = new UnknownCellDesignerAliasConverter(false);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetBoundPathIterator() {
- try {
- converter.getBoundPathIterator(null);
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("This class doesn't provide boundPath"));
- }
- }
-
- @Test
- public void testGetAnchorPointCoordinates() {
- Species alias = new GenericProtein("id");
- alias.setWidth(0);
- alias.setHeight(0);
- Point2D point = converter.getAnchorPointCoordinates(alias, 0);
- assertNotNull(point);
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Unknown;
+
+public class UnknownCellDesignerAliasConverterTest {
+ UnknownCellDesignerAliasConverter converter = new UnknownCellDesignerAliasConverter(false);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetBoundPathIterator() {
+ try {
+ converter.getBoundPathIterator(null);
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("This class doesn't provide boundPath"));
+ }
+ }
+
+ @Test
+ public void testGetAnchorPointCoordinates() {
+ Unknown unknown = new Unknown("id");
+ unknown.setWidth(0);
+ unknown.setHeight(0);
+ Point2D point = converter.getAnchorPointCoordinates(unknown, 0);
+ assertNotNull(point);
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java
index 9e5b0c45d076b0244c63c04c43a969dd0a6bc8dc..0bad270ff1b9f3502e87f12e58130ef484ffab93 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java
@@ -22,138 +22,137 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
public class AntisenseRnaXmlParserTest extends CellDesignerTestFunctions {
- protected Logger logger = Logger.getLogger(AntisenseRnaXmlParserTest.class.getName());
-
- AntisenseRnaXmlParser antisenseRnaParser;
- String testAntisenseRnaFile = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
- + System.getProperty("file.separator") + "antisense_rna.xml";
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- antisenseRnaParser = new AntisenseRnaXmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlSpecies() throws Exception {
- try {
- String xmlString = readFile(testAntisenseRnaFile);
- Pair<String, CellDesignerAntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
- CellDesignerAntisenseRna antisenseRna = result.getRight();
- assertEquals("arn1", result.getLeft());
- assertEquals("s1", antisenseRna.getName());
- assertTrue(antisenseRna.getNotes().contains("some notes"));
- assertEquals(1, antisenseRna.getRegions().size());
- CellDesignerAntisenseRnaRegion region = antisenseRna.getRegions().get(0);
- assertEquals("tr1", region.getIdAntisenseRnaRegion());
- assertEquals("zzz", region.getName());
- assertEquals(0.3, region.getSize(), 1e-6);
- assertEquals(0.29999999999999993, region.getPos(), 1e-6);
- assertEquals(AntisenseRnaRegionType.CODING_REGION, region.getType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/antisense_rna.xml");
- antisenseRnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfRegions"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/antisense_rna2.xml");
- antisenseRnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:antisenseRna"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies3() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/antisense_rna3.xml");
- antisenseRnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown antisense rna region type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies4() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/antisense_rna4.xml");
- antisenseRnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:region"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- String xmlString = readFile(testAntisenseRnaFile);
- Pair<String, CellDesignerAntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
- CellDesignerAntisenseRna antisenseRna = result.getRight();
-
- String transformedXml = antisenseRnaParser.toXml(antisenseRna.createModelElement());
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("celldesigner:AntisenseRNA", root.item(0).getNodeName());
-
- Pair<String, CellDesignerAntisenseRna> result2 = antisenseRnaParser.parseXmlElement(xmlString);
- CellDesignerAntisenseRna antisenseRna2 = result2.getRight();
- assertEquals(result.getLeft(), result2.getLeft());
- assertEquals(antisenseRna.getName(), antisenseRna2.getName());
- assertEquals(antisenseRna.getNotes().trim(), antisenseRna2.getNotes().trim());
-
- assertEquals(1, antisenseRna2.getRegions().size());
- CellDesignerAntisenseRnaRegion region = antisenseRna.getRegions().get(0);
- CellDesignerAntisenseRnaRegion region2 = antisenseRna2.getRegions().get(0);
- assertEquals(region.getIdAntisenseRnaRegion(), region2.getIdAntisenseRnaRegion());
- assertEquals(region.getName(), region2.getName());
- assertEquals(region.getSize(), region2.getSize(), 1e-6);
- assertEquals(region.getPos(), region2.getPos(), 1e-6);
- assertEquals(region.getType(), region2.getType());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ protected Logger logger = Logger.getLogger(AntisenseRnaXmlParserTest.class.getName());
+
+ AntisenseRnaXmlParser antisenseRnaParser;
+ String testAntisenseRnaFile = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
+ + System.getProperty("file.separator") + "antisense_rna.xml";
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ antisenseRnaParser = new AntisenseRnaXmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlSpecies() throws Exception {
+ try {
+ String xmlString = readFile(testAntisenseRnaFile);
+ Pair<String, CellDesignerAntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna antisenseRna = result.getRight();
+ assertEquals("arn1", result.getLeft());
+ assertEquals("s1", antisenseRna.getName());
+ assertTrue(antisenseRna.getNotes().contains("some notes"));
+ assertEquals(1, antisenseRna.getRegions().size());
+ CellDesignerModificationResidue region = antisenseRna.getRegions().get(0);
+ assertEquals("tr1", region.getIdModificationResidue());
+ assertEquals("zzz", region.getName());
+ assertEquals(0.3, region.getSize(), 1e-6);
+ assertEquals(0.29999999999999993, region.getPos(), 1e-6);
+ assertEquals(ModificationType.CODING_REGION, region.getModificationType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/antisense_rna.xml");
+ antisenseRnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfRegions"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/antisense_rna2.xml");
+ antisenseRnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:antisenseRna"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies3() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/antisense_rna3.xml");
+ antisenseRnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies4() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/antisense_rna4.xml");
+ antisenseRnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:region"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ String xmlString = readFile(testAntisenseRnaFile);
+ Pair<String, CellDesignerAntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna antisenseRna = result.getRight();
+
+ String transformedXml = antisenseRnaParser.toXml(antisenseRna.createModelElement());
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("celldesigner:AntisenseRNA", root.item(0).getNodeName());
+
+ Pair<String, CellDesignerAntisenseRna> result2 = antisenseRnaParser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna antisenseRna2 = result2.getRight();
+ assertEquals(result.getLeft(), result2.getLeft());
+ assertEquals(antisenseRna.getName(), antisenseRna2.getName());
+ assertEquals(antisenseRna.getNotes().trim(), antisenseRna2.getNotes().trim());
+
+ assertEquals(1, antisenseRna2.getRegions().size());
+ CellDesignerModificationResidue region = antisenseRna.getRegions().get(0);
+ CellDesignerModificationResidue region2 = antisenseRna2.getRegions().get(0);
+ assertEquals(region.getIdModificationResidue(), region2.getIdModificationResidue());
+ assertEquals(region.getName(), region2.getName());
+ assertEquals(region.getSize(), region2.getSize(), 1e-6);
+ assertEquals(region.getPos(), region2.getPos(), 1e-6);
+ assertEquals(region.getModificationType(), region2.getModificationType());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
index 6a669466785baead3685bb12a3aa3f6c5890f2c9..c4c864b485e6fd2b397d287c2db5d960f4cad2a9 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
@@ -1,162 +1,171 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.StringReader;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Document;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-public class GeneXmlParserTest extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(GeneXmlParserTest.class.getName());
-
- GeneXmlParser geneParser;
- String testGeneFile = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
- + System.getProperty("file.separator") + "gene.xml";
-
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- geneParser = new GeneXmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlSpecies() {
- try {
- String xmlString = readFile(testGeneFile);
- Pair<String, CellDesignerGene> result = geneParser.parseXmlElement(xmlString);
- CellDesignerGene gene = result.getRight();
- assertEquals("gn3", result.getLeft());
- assertEquals("BCL6", gene.getName());
- assertTrue(gene.getNotes().contains("B-cell CLL/lymphoma 6"));
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unexpected exception occured");
- }
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- String xmlString = readFile(testGeneFile);
- Pair<String, CellDesignerGene> result = geneParser.parseXmlElement(xmlString);
- CellDesignerGene gene = result.getRight();
- String transformedXml = geneParser.toXml(gene.createModelElement());
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("celldesigner:gene", root.item(0).getNodeName());
-
- Pair<String, CellDesignerGene> result2 = geneParser.parseXmlElement(geneParser.toXml(gene.createModelElement()));
- CellDesignerGene gene2 = result2.getRight();
- assertEquals(gene.getName(), gene2.getName());
- assertTrue(gene2.getNotes().trim().contains(gene.getNotes().trim()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParsePhosphorylatedGene() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/phosphorylated_gene.xml");
- Gene gene = (Gene) model.getElementByElementId("sa1");
- assertEquals(1, gene.getModificationResidues().size());
- ModificationResidue residue = gene.getModificationResidues().get(0);
- assertEquals(ModificationState.PHOSPHORYLATED, residue.getState());
- assertEquals("some name", residue.getName());
-
- // check xml transformation
- String xml = geneParser.toXml(gene);
- assertNotNull(xml);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidGeneInput() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_gene_1.xml");
- geneParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidGeneInput2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_gene_2.xml");
- geneParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidModificationResidue() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_modification_residue.xml");
- geneParser.getModificationResidue(getNodeFromXmlString(xmlString));
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModificationResidueToXml() throws Exception {
- try {
- ModificationResidue mr = new ModificationResidue();
- mr.setIdModificationResidue("i");
- mr.setName("a");
- mr.setSide("2");
- mr.setAngle(3.0);
- String xmlString = geneParser.toXml(mr);
- assertNotNull(xmlString);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.io.StringReader;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
+
+public class GeneXmlParserTest extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(GeneXmlParserTest.class.getName());
+
+ GeneXmlParser geneParser;
+ String testGeneFile = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
+ + System.getProperty("file.separator") + "gene.xml";
+
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ geneParser = new GeneXmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlSpecies() {
+ try {
+ String xmlString = readFile(testGeneFile);
+ Pair<String, CellDesignerGene> result = geneParser.parseXmlElement(xmlString);
+ CellDesignerGene gene = result.getRight();
+ assertEquals("gn3", result.getLeft());
+ assertEquals("BCL6", gene.getName());
+ assertTrue(gene.getNotes().contains("B-cell CLL/lymphoma 6"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unexpected exception occured");
+ }
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ String xmlString = readFile(testGeneFile);
+ Pair<String, CellDesignerGene> result = geneParser.parseXmlElement(xmlString);
+ CellDesignerGene gene = result.getRight();
+ String transformedXml = geneParser.toXml(gene.createModelElement());
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("celldesigner:gene", root.item(0).getNodeName());
+
+ Pair<String, CellDesignerGene> result2 = geneParser.parseXmlElement(geneParser.toXml(gene.createModelElement()));
+ CellDesignerGene gene2 = result2.getRight();
+ assertEquals(gene.getName(), gene2.getName());
+ assertTrue(gene2.getNotes().trim().contains(gene.getNotes().trim()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParsePhosphorylatedGene() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/phosphorylated_gene.xml");
+ Gene gene = (Gene) model.getElementByElementId("sa1");
+ assertEquals(1, gene.getModificationResidues().size());
+ ModificationSite residue = (ModificationSite) gene.getModificationResidues().get(0);
+ assertEquals(ModificationState.PHOSPHORYLATED, residue.getState());
+ assertEquals("some name", residue.getName());
+
+ // check xml transformation
+ String xml = geneParser.toXml(gene);
+ assertNotNull(xml);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidGeneInput() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_gene_1.xml");
+ geneParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidGeneInput2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_gene_2.xml");
+ geneParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidModificationResidue() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_modification_residue.xml");
+ geneParser.getModificationResidue(getNodeFromXmlString(xmlString));
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModificationResidueToXml() throws Exception {
+ try {
+ Gene protein = new Gene("id");
+ protein.setX(10);
+ protein.setY(10);
+ protein.setWidth(10);
+ protein.setHeight(10);
+ ModificationSite mr = new ModificationSite();
+ mr.setIdModificationResidue("i");
+ mr.setName("a");
+ mr.setPosition(new Point2D.Double(3.0, 2.0));
+ mr.setSpecies(protein);
+ String xmlString = geneParser.toXml(mr);
+ assertNotNull(xmlString);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java
index fbca38d03ad44990cf3d380f77a92a5356eb7135..9c5ca3758170dd3a8f2e9e9fa08aca3ed459d826 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java
@@ -1,173 +1,183 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.StringReader;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.w3c.dom.Document;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-
-public class ProteinXmlParserTest extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(ProteinXmlParserTest.class.getName());
-
- ProteinXmlParser proteinParser;
- String testProteinFile = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
- + System.getProperty("file.separator") + "protein.xml";
-
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- proteinParser = new ProteinXmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlSpecies() throws Exception {
- try {
- String xmlString = readFile(testProteinFile);
- Pair<String, CellDesignerProtein<?>> result = proteinParser.parseXmlElement(xmlString);
- CellDesignerProtein<?> protein = result.getRight();
- assertEquals("pr23", result.getLeft());
- assertEquals("SDHA", protein.getName());
- assertTrue(protein instanceof CellDesignerGenericProtein);
- assertEquals(1, protein.getModificationResidues().size());
- assertEquals("rs1", protein.getModificationResidues().get(0).getIdModificationResidue());
- assertEquals("S176 bla bla", protein.getModificationResidues().get(0).getName());
- assertEquals("Difference to big", 3.141592653589793, protein.getModificationResidues().get(0).getAngle(), 1e-6);
- assertEquals("none", protein.getModificationResidues().get(0).getSide());
- assertTrue(protein.getNotes().contains("UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- String xmlString = readFile(testProteinFile);
-
- Pair<String, CellDesignerProtein<?>> result = proteinParser.parseXmlElement(xmlString);
- CellDesignerProtein<?> protein = result.getRight();
- String transformedXml = proteinParser.toXml(protein.createModelElement("id"));
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("celldesigner:protein", root.item(0).getNodeName());
-
- Pair<String, CellDesignerProtein<?>> result2 = proteinParser.parseXmlElement(proteinParser.toXml(protein.createModelElement("id")));
- CellDesignerProtein<?> protein2 = result2.getRight();
- assertEquals(protein.getName(), protein2.getName());
- assertEquals(protein.getClass(), protein2.getClass());
- assertEquals(protein.getModificationResidues().size(), protein2.getModificationResidues().size());
- assertEquals(protein.getModificationResidues().get(0).getIdModificationResidue(), protein2.getModificationResidues().get(0).getIdModificationResidue());
- assertEquals(protein.getModificationResidues().get(0).getName(), protein2.getModificationResidues().get(0).getName());
- assertEquals("Difference to big", protein.getModificationResidues().get(0).getAngle(), protein2.getModificationResidues().get(0).getAngle(), 1e-6);
- assertEquals(protein.getModificationResidues().get(0).getSide(), protein2.getModificationResidues().get(0).getSide());
-
- // proteins won't have notes because it makes the xml messy (everything
- // will be in species notes)
- // assertEquals(protein.getNotes().trim(), protein2.getNotes().trim());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXml() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/protein.xml");
- proteinParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Protein node in Sbml model is of unknown type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXml2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/protein2.xml");
- proteinParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfModificationResidues"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXml3() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/protein3.xml");
- proteinParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:protein"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXml4() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/protein4.xml");
- proteinParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:modificationResidue"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidProteinToXml() throws Exception {
- try {
- proteinParser.toXml(Mockito.mock(Protein.class));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid protein class type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.StringReader;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+
+public class ProteinXmlParserTest extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(ProteinXmlParserTest.class.getName());
+
+ ProteinXmlParser proteinParser;
+ String testProteinFile = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
+ + System.getProperty("file.separator") + "protein.xml";
+
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ proteinParser = new ProteinXmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlSpecies() throws Exception {
+ try {
+ String xmlString = readFile(testProteinFile);
+ Pair<String, CellDesignerProtein<?>> result = proteinParser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> protein = result.getRight();
+ assertEquals("pr23", result.getLeft());
+ assertEquals("SDHA", protein.getName());
+ assertTrue(protein instanceof CellDesignerGenericProtein);
+ assertEquals(1, protein.getModificationResidues().size());
+ assertEquals("rs1", protein.getModificationResidues().get(0).getIdModificationResidue());
+ assertEquals("S176 bla bla", protein.getModificationResidues().get(0).getName());
+ assertEquals("Difference to big", 3.141592653589793, protein.getModificationResidues().get(0).getAngle(), 1e-6);
+ assertEquals("none", protein.getModificationResidues().get(0).getSide());
+ assertTrue(protein.getNotes().contains("UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ String xmlString = readFile(testProteinFile);
+
+ Pair<String, CellDesignerProtein<?>> result = proteinParser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> protein = result.getRight();
+ String transformedXml = proteinParser.toXml(protein.createModelElement("id"));
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("celldesigner:protein", root.item(0).getNodeName());
+
+ elements = new CellDesignerElementCollection();
+ proteinParser = new ProteinXmlParser(elements);
+ Protein proteinWithLayout = protein.createModelElement("id");
+ proteinWithLayout.setWidth(10);
+ proteinWithLayout.setHeight(10);
+ protein.updateModelElementAfterLayoutAdded(proteinWithLayout);
+ Pair<String, CellDesignerProtein<?>> result2 = proteinParser
+ .parseXmlElement(proteinParser.toXml(proteinWithLayout));
+
+ CellDesignerProtein<?> protein2 = result2.getRight();
+ assertEquals(protein.getName(), protein2.getName());
+ assertEquals(protein.getClass(), protein2.getClass());
+ assertEquals(protein.getModificationResidues().size(), protein2.getModificationResidues().size());
+ assertEquals(protein.getModificationResidues().get(0).getIdModificationResidue(),
+ protein2.getModificationResidues().get(0).getIdModificationResidue());
+ assertEquals(protein.getModificationResidues().get(0).getName(),
+ protein2.getModificationResidues().get(0).getName());
+ assertEquals("Difference to big", protein.getModificationResidues().get(0).getAngle(),
+ protein2.getModificationResidues().get(0).getAngle(), 1e-6);
+
+ // proteins won't have notes because it makes the xml messy (everything
+ // will be in species notes)
+ // assertEquals(protein.getNotes().trim(), protein2.getNotes().trim());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXml() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/protein.xml");
+ proteinParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Protein node in Sbml model is of unknown type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXml2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/protein2.xml");
+ proteinParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfModificationResidues"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXml3() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/protein3.xml");
+ proteinParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:protein"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXml4() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/protein4.xml");
+ proteinParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:modificationResidue"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidProteinToXml() throws Exception {
+ try {
+ proteinParser.toXml(Mockito.mock(Protein.class));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid protein class type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParserTest.java
index 9e743299ad6ad5cdc65bba0bade4b0c171962ee9..dfc6456045a088430a8951941a1a20850ac05500 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParserTest.java
@@ -1,146 +1,146 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.StringReader;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Document;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
-
-public class RnaXmlParserTest extends CellDesignerTestFunctions {
- protected Logger logger = Logger.getLogger(RnaXmlParserTest.class.getName());
-
- RnaXmlParser rnaParser;
- String testRnaFile = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
- + System.getProperty("file.separator") + "rna.xml";
- String testRnaFile2 = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
- + System.getProperty("file.separator") + "rna_with_region.xml";
-
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- rnaParser = new RnaXmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlSpecies() throws Exception {
- try {
- String xmlString = readFile(testRnaFile);
- Pair<String, CellDesignerRna> result = rnaParser.parseXmlElement(xmlString);
- CellDesignerRna rna = result.getRight();
- assertEquals("rn36", result.getLeft());
- assertEquals("BCL6", rna.getName());
- assertTrue(rna.getNotes().contains("B-cell CLL/lymphoma "));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesWithRegion() throws Exception {
- try {
- String xmlString = readFile(testRnaFile2);
- Pair<String, CellDesignerRna> result = rnaParser.parseXmlElement(xmlString);
- CellDesignerRna rna = result.getRight();
- assertNotNull(rna);
- assertNotNull(rna.getRegions());
- assertEquals(1, rna.getRegions().size());
- assertEquals("tr1", rna.getRegions().get(0).getIdRnaRegion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- String xmlString = readFile(testRnaFile);
- Pair<String, CellDesignerRna> result = rnaParser.parseXmlElement(xmlString);
- CellDesignerRna rna = result.getRight();
-
- String transformedXml = rnaParser.toXml(rna.createModelElement("id"));
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("celldesigner:RNA", root.item(0).getNodeName());
-
- Pair<String, CellDesignerRna> result2 = rnaParser.parseXmlElement(rnaParser.toXml(rna.createModelElement("id")));
- CellDesignerRna rna2 = result2.getRight();
- assertEquals(rna.getName(), rna2.getName());
- assertTrue(rna2.getNotes().trim().contains(rna.getNotes().trim()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/rna.xml");
- rnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfRegions"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/rna2.xml");
- rnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:rna"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies3() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/rna3.xml");
- rnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:region"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.StringReader;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+
+public class RnaXmlParserTest extends CellDesignerTestFunctions {
+ protected Logger logger = Logger.getLogger(RnaXmlParserTest.class.getName());
+
+ RnaXmlParser rnaParser;
+ String testRnaFile = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
+ + System.getProperty("file.separator") + "rna.xml";
+ String testRnaFile2 = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
+ + System.getProperty("file.separator") + "rna_with_region.xml";
+
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ rnaParser = new RnaXmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlSpecies() throws Exception {
+ try {
+ String xmlString = readFile(testRnaFile);
+ Pair<String, CellDesignerRna> result = rnaParser.parseXmlElement(xmlString);
+ CellDesignerRna rna = result.getRight();
+ assertEquals("rn36", result.getLeft());
+ assertEquals("BCL6", rna.getName());
+ assertTrue(rna.getNotes().contains("B-cell CLL/lymphoma "));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesWithRegion() throws Exception {
+ try {
+ String xmlString = readFile(testRnaFile2);
+ Pair<String, CellDesignerRna> result = rnaParser.parseXmlElement(xmlString);
+ CellDesignerRna rna = result.getRight();
+ assertNotNull(rna);
+ assertNotNull(rna.getRegions());
+ assertEquals(1, rna.getRegions().size());
+ assertEquals("tr1", rna.getRegions().get(0).getIdModificationResidue());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ String xmlString = readFile(testRnaFile);
+ Pair<String, CellDesignerRna> result = rnaParser.parseXmlElement(xmlString);
+ CellDesignerRna rna = result.getRight();
+
+ String transformedXml = rnaParser.toXml(rna.createModelElement("id"));
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("celldesigner:RNA", root.item(0).getNodeName());
+
+ Pair<String, CellDesignerRna> result2 = rnaParser.parseXmlElement(rnaParser.toXml(rna.createModelElement("id")));
+ CellDesignerRna rna2 = result2.getRight();
+ assertEquals(rna.getName(), rna2.getName());
+ assertTrue(rna2.getNotes().trim().contains(rna.getNotes().trim()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/rna.xml");
+ rnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfRegions"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/rna2.xml");
+ rnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:rna"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies3() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/rna3.xml");
+ rnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:region"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
index 3d7c15ee19bf6537aca5cd461a8cc592adbb934b..786cd6cd4062b9ea122a2f0a67f8195fe51d5269 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
@@ -40,9 +40,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerRnaRegion;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
import lcsb.mapviewer.model.map.species.Gene;
@@ -1142,36 +1140,4 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
}
}
- @Test
- public void testCreateRnaRegion() throws Exception {
- try {
- CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
- mr.setSize(1.0);
- mr.setAngle(1.0);
-
- CellDesignerRnaRegion region = parser.createRnaRegion(mr);
- assertNotNull(region.getPos());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateAntisenseRnaRegion() throws Exception {
- try {
- CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
- mr.setSize(1.0);
- mr.setAngle(1.0);
-
- CellDesignerAntisenseRnaRegion region = parser.createAntisenseRnaRegion(mr);
- assertNotNull(region.getPos());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java
index 15e84c09a0fe585775018cb555f53a1619092c6c..6afe5cf8ea271e6816f6824ebb77240eeac0db31 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java
@@ -8,7 +8,6 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.fields.AllFieldsTes
@RunWith(Suite.class)
@SuiteClasses({ AllFieldsTests.class, //
- AntisenseRnaRegionTest.class, //
AntisenseRnaTest.class, //
CellDesignerChemicalTest.class, //
CompartmentTest.class, //
@@ -26,7 +25,6 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.fields.AllFieldsTes
PhenotypeTest.class, //
ProteinTest.class, //
ReceptorProteinTest.class, //
- RnaRegionTest.class, //
RnaTest.class, //
SimpleMoleculeTest.class, //
SpeciesStateTest.class, //
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
deleted file mode 100644
index dc475ce8fdb30d22c30d4c618050393ffbafdd6a..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
+++ /dev/null
@@ -1,175 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-public class AntisenseRnaRegionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerAntisenseRnaRegion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerAntisenseRnaRegion antisenseRna = new CellDesignerAntisenseRnaRegion();
- CellDesignerAntisenseRnaRegion antisenseRna2 = new CellDesignerAntisenseRnaRegion(antisenseRna);
- assertNotNull(antisenseRna2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- CellDesignerAntisenseRnaRegion antisenseRna = new CellDesignerAntisenseRnaRegion();
- antisenseRna.setState(ModificationState.EMPTY);
- antisenseRna.setName("as");
- antisenseRna.setPos(3.0);
- CellDesignerAntisenseRnaRegion antisenseRna2 = new CellDesignerAntisenseRnaRegion();
- antisenseRna2.update(antisenseRna);
- assertEquals(antisenseRna.getState(), antisenseRna2.getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidUpdate() {
- try {
- CellDesignerAntisenseRnaRegion antisenseRna = new CellDesignerAntisenseRnaRegion();
- CellDesignerAntisenseRnaRegion antisenseRna2 = new CellDesignerAntisenseRnaRegion();
- antisenseRna.setIdAntisenseRnaRegion("@1");
- antisenseRna2.setIdAntisenseRnaRegion("@");
- antisenseRna2.update(antisenseRna);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- CellDesignerAntisenseRnaRegion region = new CellDesignerAntisenseRnaRegion(new CellDesignerAntisenseRnaRegion());
- int id = 91;
- CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
- double pos = 4.6;
- double size = 5.3;
- AntisenseRnaRegionType type = AntisenseRnaRegionType.CODING_REGION;
- String name = "nam";
- String idAntisenseRnaRegion = "iddd";
-
- region.setId(id);
- region.setSpecies(species);
- region.setPos(pos);
- region.setSize(size);
- region.setType(type);
- region.setName(name);
- region.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
- region.setState(ModificationState.ACETYLATED);
-
- assertEquals(id, region.getId());
- assertEquals(species, region.getSpecies());
- assertEquals(pos, region.getPos(), Configuration.EPSILON);
- assertEquals(size, region.getSize(), Configuration.EPSILON);
- assertEquals(type, region.getType());
- assertEquals(name, region.getName());
- assertEquals(idAntisenseRnaRegion, region.getIdAntisenseRnaRegion());
-
- assertEquals(ModificationState.ACETYLATED, region.getState());
-
- try {
- region.setSize("text");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
-
- try {
- region.setPos("text");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
-
- region.setSize("1.0");
- region.setPos("1.0");
- assertEquals(1.0, region.getPos(), Configuration.EPSILON);
- assertEquals(1.0, region.getSize(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToString() {
- try {
- assertNotNull(new CellDesignerAntisenseRnaRegion().toString());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerAntisenseRnaRegion degraded = new CellDesignerAntisenseRnaRegion().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new CellDesignerAntisenseRnaRegion() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java
index 98b0de4f63163d0347a47dc5acf0cdbd0e0e1bed..c9cd5cd3f3216ecfe0df7bb2958903555990951e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java
@@ -1,159 +1,159 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-public class AntisenseRnaTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerAntisenseRna());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerAntisenseRna original = new CellDesignerAntisenseRna();
- original.addRegion(new CellDesignerAntisenseRnaRegion());
- CellDesignerAntisenseRna aRna = new CellDesignerAntisenseRna(original);
- assertNotNull(aRna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddRnaRegion() {
- try {
- CellDesignerAntisenseRna original = new CellDesignerAntisenseRna();
- CellDesignerAntisenseRnaRegion region = new CellDesignerAntisenseRnaRegion();
- region.setIdAntisenseRnaRegion("id1");
- original.addRegion(region);
-
- CellDesignerAntisenseRnaRegion region2 = new CellDesignerAntisenseRnaRegion();
- region2.setIdAntisenseRnaRegion("id1");
- region2.setName("nam");
- original.addRegion(region2);
-
- assertEquals(1, original.getRegions().size());
-
- assertEquals("nam", original.getRegions().get(0).getName());
-
- CellDesignerAntisenseRnaRegion region3 = new CellDesignerAntisenseRnaRegion();
- region3.setIdAntisenseRnaRegion("id2");
- region3.setName("nam");
- original.addRegion(region3);
-
- assertEquals(2, original.getRegions().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- CellDesignerAntisenseRna original = new CellDesignerAntisenseRna();
- CellDesignerAntisenseRnaRegion region2 = new CellDesignerAntisenseRnaRegion();
- region2.setIdAntisenseRnaRegion("id1");
- region2.setName("nam");
- original.addRegion(region2);
- CellDesignerAntisenseRnaRegion region3 = new CellDesignerAntisenseRnaRegion();
- region3.setIdAntisenseRnaRegion("id2");
- region3.setName("nam");
- original.addRegion(region3);
-
- CellDesignerAntisenseRna copy = new CellDesignerAntisenseRna(original);
- copy.addRegion(new CellDesignerAntisenseRnaRegion());
- copy.getRegions().get(0).setState(ModificationState.ACETYLATED);
-
- original.update(copy);
-
- boolean acetylatedFound = false;
- for (CellDesignerAntisenseRnaRegion region : copy.getRegions()) {
- if (ModificationState.ACETYLATED.equals(region.getState())) {
- acetylatedFound = true;
- }
- }
- assertTrue(acetylatedFound);
- assertEquals(3, copy.getRegions().size());
-
- original.update(new CellDesignerGenericProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- CellDesignerAntisenseRna aRna = new CellDesignerAntisenseRna(new CellDesignerSpecies<AntisenseRna>());
-
- List<CellDesignerAntisenseRnaRegion> regions = new ArrayList<>();
-
- aRna.setRegions(regions);
-
- assertEquals(regions, aRna.getRegions());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerAntisenseRna aRna = new CellDesignerAntisenseRna().copy();
- assertNotNull(aRna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerAntisenseRna antisenseRna = Mockito.spy(CellDesignerAntisenseRna.class);
- antisenseRna.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+public class AntisenseRnaTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerAntisenseRna());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerAntisenseRna original = new CellDesignerAntisenseRna();
+ original.addRegion(new CellDesignerModificationResidue());
+ CellDesignerAntisenseRna aRna = new CellDesignerAntisenseRna(original);
+ assertNotNull(aRna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddRnaRegion() {
+ try {
+ CellDesignerAntisenseRna original = new CellDesignerAntisenseRna();
+ CellDesignerModificationResidue region = new CellDesignerModificationResidue();
+ region.setIdModificationResidue("id1");
+ original.addRegion(region);
+
+ CellDesignerModificationResidue region2 = new CellDesignerModificationResidue();
+ region2.setIdModificationResidue("id1");
+ region2.setName("nam");
+ original.addRegion(region2);
+
+ assertEquals(1, original.getRegions().size());
+
+ assertEquals("nam", original.getRegions().get(0).getName());
+
+ CellDesignerModificationResidue region3 = new CellDesignerModificationResidue();
+ region3.setIdModificationResidue("id2");
+ region3.setName("nam");
+ original.addRegion(region3);
+
+ assertEquals(2, original.getRegions().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ CellDesignerAntisenseRna original = new CellDesignerAntisenseRna();
+ CellDesignerModificationResidue region2 = new CellDesignerModificationResidue();
+ region2.setIdModificationResidue("id1");
+ region2.setName("nam");
+ original.addRegion(region2);
+ CellDesignerModificationResidue region3 = new CellDesignerModificationResidue();
+ region3.setIdModificationResidue("id2");
+ region3.setName("nam");
+ original.addRegion(region3);
+
+ CellDesignerAntisenseRna copy = new CellDesignerAntisenseRna(original);
+ copy.addRegion(new CellDesignerModificationResidue());
+ copy.getRegions().get(0).setState(ModificationState.ACETYLATED);
+
+ original.update(copy);
+
+ boolean acetylatedFound = false;
+ for (CellDesignerModificationResidue region : copy.getRegions()) {
+ if (ModificationState.ACETYLATED.equals(region.getState())) {
+ acetylatedFound = true;
+ }
+ }
+ assertTrue(acetylatedFound);
+ assertEquals(3, copy.getRegions().size());
+
+ original.update(new CellDesignerGenericProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ CellDesignerAntisenseRna aRna = new CellDesignerAntisenseRna(new CellDesignerSpecies<AntisenseRna>());
+
+ List<CellDesignerModificationResidue> regions = new ArrayList<>();
+
+ aRna.setRegions(regions);
+
+ assertEquals(regions, aRna.getRegions());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerAntisenseRna aRna = new CellDesignerAntisenseRna().copy();
+ assertNotNull(aRna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerAntisenseRna antisenseRna = Mockito.spy(CellDesignerAntisenseRna.class);
+ antisenseRna.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
index d3ab45debf52ddc34a8c4a15b061cb51d6c91f83..766eeb156ebd85cf1b1c9eca3e0f3bd553a61428 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
@@ -1,128 +1,127 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.model.map.species.Gene;
-
-public class GeneTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerGene());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerGene original = new CellDesignerGene();
- original.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerGene gene = new CellDesignerGene(original);
- assertNotNull(gene);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
- CellDesignerGene gene = new CellDesignerGene(new CellDesignerSpecies<Gene>());
- gene.setModificationResidues(modificationResidues);
- assertEquals(modificationResidues, gene.getModificationResidues());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerGene degraded = new CellDesignerGene().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerGene gene = Mockito.spy(CellDesignerGene.class);
- gene.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- CellDesignerGene gene = new CellDesignerGene();
- CellDesignerGene gene2 = new CellDesignerGene();
- List<CellDesignerModificationResidue> residues = new ArrayList<>();
- residues.add(new CellDesignerModificationResidue());
-
- gene2.setModificationResidues(residues);
-
- gene.update(gene2);
- assertEquals(1, gene.getModificationResidues().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddModificationResidue() {
- try {
- CellDesignerGene gene = new CellDesignerGene();
- CellDesignerModificationResidue mr = new CellDesignerModificationResidue("id1");
- CellDesignerModificationResidue mr2 = new CellDesignerModificationResidue("id1");
- CellDesignerModificationResidue mr3 = new CellDesignerModificationResidue("id2");
-
- gene.addModificationResidue(mr);
- assertEquals(1, gene.getModificationResidues().size());
- gene.addModificationResidue(mr2);
- assertEquals(1, gene.getModificationResidues().size());
- gene.addModificationResidue(mr3);
- assertEquals(2, gene.getModificationResidues().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+
+public class GeneTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerGene());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerGene original = new CellDesignerGene();
+ original.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerGene gene = new CellDesignerGene(original);
+ assertNotNull(gene);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
+ CellDesignerGene gene = new CellDesignerGene(new CellDesignerSpecies<>());
+ gene.setModificationResidues(modificationResidues);
+ assertEquals(modificationResidues, gene.getModificationResidues());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerGene degraded = new CellDesignerGene().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerGene gene = Mockito.spy(CellDesignerGene.class);
+ gene.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ CellDesignerGene gene = new CellDesignerGene();
+ CellDesignerGene gene2 = new CellDesignerGene();
+ List<CellDesignerModificationResidue> residues = new ArrayList<>();
+ residues.add(new CellDesignerModificationResidue());
+
+ gene2.setModificationResidues(residues);
+
+ gene.update(gene2);
+ assertEquals(1, gene.getModificationResidues().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddModificationResidue() {
+ try {
+ CellDesignerGene gene = new CellDesignerGene();
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue("id1");
+ CellDesignerModificationResidue mr2 = new CellDesignerModificationResidue("id1");
+ CellDesignerModificationResidue mr3 = new CellDesignerModificationResidue("id2");
+
+ gene.addModificationResidue(mr);
+ assertEquals(1, gene.getModificationResidues().size());
+ gene.addModificationResidue(mr2);
+ assertEquals(1, gene.getModificationResidues().size());
+ gene.addModificationResidue(mr3);
+ assertEquals(2, gene.getModificationResidues().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
index a42eadbe87a04de39d955a0de6320bc74489389d..ac1641c2acc9101eb05eeee34f6f5d72afe3c926 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-
-public class IonTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerIon());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerIon degraded = new CellDesignerIon(new CellDesignerSpecies<IonChannelProtein>());
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerIon degraded = new CellDesignerIon().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerIon ion = Mockito.spy(CellDesignerIon.class);
- ion.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+
+public class IonTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerIon());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerIon degraded = new CellDesignerIon(new CellDesignerSpecies<IonChannelProtein>());
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerIon degraded = new CellDesignerIon().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerIon ion = Mockito.spy(CellDesignerIon.class);
+ ion.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
deleted file mode 100644
index 0ab0de88d9e272ff9f38d460d082d727e370e8d1..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
+++ /dev/null
@@ -1,131 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerRnaRegion;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-public class RnaRegionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerRnaRegion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- CellDesignerRnaRegion region = new CellDesignerRnaRegion(new CellDesignerRnaRegion());
- assertNotNull(region);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetSize() {
- try {
- CellDesignerRnaRegion region = new CellDesignerRnaRegion();
- try {
- region.setSize("as");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- region.setSize("0.0");
- assertEquals(0.0, region.getSize(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetPos() {
- try {
- CellDesignerRnaRegion region = new CellDesignerRnaRegion();
- try {
- region.setPos("as");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- region.setPos("1.0");
- assertEquals(1.0, region.getPos(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- CellDesignerRnaRegion region = new CellDesignerRnaRegion();
- CellDesignerRnaRegion region2 = new CellDesignerRnaRegion();
- region2.setState(ModificationState.ACETYLATED);
- region2.setName("asd");
- region2.setPos(2.2);
- region.update(region2);
- assertEquals(region2.getName(), region.getName());
- assertEquals(region2.getPos(), region.getPos());
- assertEquals(region2.getState(), region.getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate2() {
- try {
- CellDesignerRnaRegion region = new CellDesignerRnaRegion();
- region.setIdRnaRegion("1");
- CellDesignerRnaRegion region2 = new CellDesignerRnaRegion();
- region2.setIdRnaRegion("2");
- region.update(region2);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- CellDesignerRnaRegion region = new CellDesignerRnaRegion();
- double size = 2.5;
- CellDesignerRna species = new CellDesignerRna();
- region.setSize(size);
- region.setSpecies(species);
- assertEquals(size, region.getSize(), Configuration.EPSILON);
- assertEquals(species, region.getSpecies());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java
index 6cd1da2342857438181a8a639ffc677142238285..a4ae5659f7d94ffc28087b406297b6b225c7588f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java
@@ -1,161 +1,156 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerRnaRegion;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-public class RnaTest {
- Logger logger = Logger.getLogger(RnaTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerRna());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerRna rna = new CellDesignerRna(new CellDesignerSpecies<Rna>());
- assertNotNull(rna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- CellDesignerRna rna = new CellDesignerRna(new CellDesignerSpecies<Rna>());
- List<CellDesignerRnaRegion> regions = new ArrayList<>();
-
- rna.setRegions(regions);
-
- assertEquals(regions, rna.getRegions());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerRna rna = new CellDesignerRna().copy();
- assertNotNull(rna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerRna rna = Mockito.spy(CellDesignerRna.class);
- rna.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddRnaRegion() {
- try {
- CellDesignerRna original = new CellDesignerRna();
- CellDesignerRnaRegion region = new CellDesignerRnaRegion();
- region.setIdRnaRegion("id1");
- original.addRegion(region);
-
- CellDesignerRnaRegion region2 = new CellDesignerRnaRegion();
- region2.setIdRnaRegion("id1");
- region2.setName("nam");
- original.addRegion(region2);
-
- assertEquals(1, original.getRegions().size());
-
- assertEquals("nam", original.getRegions().get(0).getName());
-
- CellDesignerRnaRegion region3 = new CellDesignerRnaRegion();
- region3.setIdRnaRegion("id2");
- region3.setName("nam");
- original.addRegion(region3);
-
- assertEquals(2, original.getRegions().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- CellDesignerRna original = new CellDesignerRna();
- CellDesignerRnaRegion region2 = new CellDesignerRnaRegion();
- region2.setIdRnaRegion("id1");
- region2.setName("nam");
- original.addRegion(region2);
- CellDesignerRnaRegion region3 = new CellDesignerRnaRegion();
- region3.setIdRnaRegion("id2");
- region3.setName("nam");
- original.addRegion(region3);
-
- CellDesignerRna copy = new CellDesignerRna(original);
- copy.addRegion(new CellDesignerRnaRegion());
- copy.getRegions().get(0).setState(ModificationState.ACETYLATED);
-
- logger.debug(copy.getRegions().size());
-
- original.update(copy);
-
- boolean acetylatedFound = false;
- for (CellDesignerRnaRegion region : copy.getRegions()) {
- if (ModificationState.ACETYLATED.equals(region.getState())) {
- acetylatedFound = true;
- }
- }
- assertTrue(acetylatedFound);
- assertEquals(3, original.getRegions().size());
- assertEquals(3, copy.getRegions().size());
-
- original.update(new CellDesignerGenericProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+public class RnaTest {
+ Logger logger = Logger.getLogger(RnaTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerRna());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerRna rna = new CellDesignerRna(new CellDesignerSpecies<Rna>());
+ assertNotNull(rna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ CellDesignerRna rna = new CellDesignerRna(new CellDesignerSpecies<Rna>());
+ List<CellDesignerModificationResidue> regions = new ArrayList<>();
+
+ rna.setRegions(regions);
+
+ assertEquals(regions, rna.getRegions());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerRna rna = new CellDesignerRna().copy();
+ assertNotNull(rna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerRna rna = Mockito.spy(CellDesignerRna.class);
+ rna.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddRnaRegion() {
+ try {
+ CellDesignerRna original = new CellDesignerRna();
+ CellDesignerModificationResidue region = new CellDesignerModificationResidue("id1");
+ original.addRegion(region);
+
+ CellDesignerModificationResidue region2 = new CellDesignerModificationResidue("id1");
+ region2.setName("nam");
+ original.addRegion(region2);
+
+ assertEquals(1, original.getRegions().size());
+
+ assertEquals("nam", original.getRegions().get(0).getName());
+
+ CellDesignerModificationResidue region3 = new CellDesignerModificationResidue("id2");
+ region3.setName("nam");
+ original.addRegion(region3);
+
+ assertEquals(2, original.getRegions().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ CellDesignerRna original = new CellDesignerRna();
+ CellDesignerModificationResidue region2 = new CellDesignerModificationResidue("id1");
+ region2.setName("nam");
+ original.addRegion(region2);
+ CellDesignerModificationResidue region3 = new CellDesignerModificationResidue("id2");
+ region3.setName("nam");
+ original.addRegion(region3);
+
+ CellDesignerRna copy = new CellDesignerRna(original);
+ copy.addRegion(new CellDesignerModificationResidue());
+ copy.getRegions().get(0).setState(ModificationState.ACETYLATED);
+
+ logger.debug(copy.getRegions().size());
+
+ original.update(copy);
+
+ boolean acetylatedFound = false;
+ for (CellDesignerModificationResidue region : copy.getRegions()) {
+ if (ModificationState.ACETYLATED.equals(region.getState())) {
+ acetylatedFound = true;
+ }
+ }
+ assertTrue(acetylatedFound);
+ assertEquals(3, original.getRegions().size());
+ assertEquals(3, copy.getRegions().size());
+
+ original.update(new CellDesignerGenericProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
index b8814cdb37b451fa5d4708772d7588f460dbc8f5..5e24aa5ddb18578a19104fcb598e0a3daee9e618 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
@@ -1,78 +1,87 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-
-public class SpeciesStateTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- List<CellDesignerModificationResidue> modifications = new ArrayList<>();
- SpeciesState state = new SpeciesState();
- state.setModifications(modifications);
- assertEquals(modifications, state.getModifications());
- }
-
- @Test
- public void testSetHomodimer() {
- try {
- SpeciesState state = new SpeciesState();
-
- state.setHomodimer("inv");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- }
-
- @Test
- public void testConstructorFromRna() {
- Rna rna = new Rna("1");
- rna.addRegion(new RnaRegion());
- SpeciesState state = new SpeciesState(rna);
- assertEquals(1, state.getModifications().size());
- }
-
- @Test
- public void testConstructorFromGene() {
- Gene gene = new Gene("2");
- gene.addModificationResidue(new ModificationResidue());
- SpeciesState state = new SpeciesState(gene);
- assertEquals(1, state.getModifications().size());
- }
-
- @Test
- public void testAddModifResidue() {
- SpeciesState state = new SpeciesState();
- state.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
- mr.setName("a");
- state.addModificationResidue(mr);
- assertEquals(1, state.getModifications().size());
- assertEquals("a", state.getModifications().get(0).getName());
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+
+public class SpeciesStateTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ List<CellDesignerModificationResidue> modifications = new ArrayList<>();
+ SpeciesState state = new SpeciesState();
+ state.setModifications(modifications);
+ assertEquals(modifications, state.getModifications());
+ }
+
+ @Test
+ public void testSetHomodimer() {
+ try {
+ SpeciesState state = new SpeciesState();
+
+ state.setHomodimer("inv");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ }
+
+ @Test
+ public void testConstructorFromRna() {
+ Rna rna = new Rna("1");
+ rna.setWidth(60);
+ rna.setHeight(10);
+ CodingRegion mr = new CodingRegion();
+ mr.setPosition(new Point2D.Double(10, 40));
+ rna.addRegion(mr);
+ SpeciesState state = new SpeciesState(rna);
+ assertEquals(1, state.getModifications().size());
+ }
+
+ @Test
+ public void testConstructorFromGene() {
+ Gene gene = new Gene("2");
+ gene.setWidth(60);
+ gene.setHeight(10);
+ ModificationSite mr = new ModificationSite();
+ mr.setPosition(new Point2D.Double(10, 40));
+ gene.addModificationResidue(mr);
+ SpeciesState state = new SpeciesState(gene);
+ assertEquals(1, state.getModifications().size());
+ }
+
+ @Test
+ public void testAddModifResidue() {
+ SpeciesState state = new SpeciesState();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
+ mr.setName("a");
+ state.addModificationResidue(mr);
+ assertEquals(1, state.getModifications().size());
+ assertEquals("a", state.getModifications().get(0).getName());
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java
index 7c08337d3f4a9fa2410a8c28b97781d81464519c..54887f8d0dc9c053aa0a906bd572ccdfe1e5e21b 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java
@@ -6,7 +6,6 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ CellDesignerModificationResidueTest.class, //
- CellDesignerRnaRegionTest.class,//
})
public class AllFieldsTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegionTest.java
deleted file mode 100644
index f7e08b5a6855f3be58f1abe85af4107084b2b8b0..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegionTest.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CellDesignerRnaRegionTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testToString() {
- CellDesignerRnaRegion region = new CellDesignerRnaRegion();
- assertNotNull(region.toString());
- }
-
-}
diff --git a/converter-CellDesigner/testFiles/gene_modifications.xml b/converter-CellDesigner/testFiles/gene_modifications.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0d9d681ce5a94a3c6f30f2943a448ecb2c70f6ee
--- /dev/null
+++ b/converter-CellDesigner/testFiles/gene_modifications.xml
@@ -0,0 +1,94 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="192.0" y="114.5" w="189.0" h="42.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="189.0" height="42.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="s2" type="GENE">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="p1" size="0.0" pos="0.3" type="Modification Site" active="false"/>
+<celldesigner:region id="tr2" name="p2" size="0.1" pos="0.41000000000000003" type="CodingRegion" active="false"/>
+<celldesigner:region id="tr3" name="p3" size="0.1" pos="0.57" type="RegulatoryRegion" active="false"/>
+<celldesigner:region id="tr4" name="p4" size="0.1" pos="0.75" type="transcriptionStartingSiteL" active="true"/>
+<celldesigner:region id="tr5" name="p5" size="0.14" pos="0.8599999999999999" type="transcriptionStartingSiteR" active="false"/>
+</celldesigner:listOfRegions>
+</celldesigner:gene>
+</celldesigner:listOfGenes>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/antisenseRnaWithRegion.xml b/converter-CellDesigner/testFiles/modifications/antisense_rna_with_region.xml
similarity index 79%
rename from converter-CellDesigner/testFiles/antisenseRnaWithRegion.xml
rename to converter-CellDesigner/testFiles/modifications/antisense_rna_with_region.xml
index 91a7ef532f90c06d73ccca1838f9b614c6da0d32..1fe9f35b3629c6a645b4dd8149d238891b8f3c8a 100644
--- a/converter-CellDesigner/testFiles/antisenseRnaWithRegion.xml
+++ b/converter-CellDesigner/testFiles/modifications/antisense_rna_with_region.xml
@@ -22,7 +22,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
+<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
@@ -41,12 +41,12 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
+<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa3" species="s3">
+<celldesigner:speciesAlias id="sa3" species="s4">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="192.0" y="247.5" w="90.0" h="25.0"/>
<celldesigner:font size="12"/>
@@ -60,7 +60,26 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa4" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="300.0" y="207.0" w="90.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="90.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffff6666" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
@@ -151,6 +170,22 @@
<celldesigner:speciesIdentity>
<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
<celldesigner:antisensernaReference>arn3</celldesigner:antisensernaReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="tr1" state="phosphorylated"/>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s4" id="s4" name="s3" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn3</celldesigner:antisensernaReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
diff --git a/converter-CellDesigner/testFiles/modifications/gene_with_coding_region.xml b/converter-CellDesigner/testFiles/modifications/gene_with_coding_region.xml
new file mode 100644
index 0000000000000000000000000000000000000000..74823057f625a7b537811c6239ac483311ec5714
--- /dev/null
+++ b/converter-CellDesigner/testFiles/modifications/gene_with_coding_region.xml
@@ -0,0 +1,90 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="291.0" y="217.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="s1" type="GENE">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="xx" size="0.48" pos="0.14" type="CodingRegion" active="false"/>
+</celldesigner:listOfRegions>
+</celldesigner:gene>
+</celldesigner:listOfGenes>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/modifications/gene_with_modification_site.xml b/converter-CellDesigner/testFiles/modifications/gene_with_modification_site.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0069db65c5f247483fad3d090444318d115ce480
--- /dev/null
+++ b/converter-CellDesigner/testFiles/modifications/gene_with_modification_site.xml
@@ -0,0 +1,95 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="173.0" y="245.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="s1" type="GENE">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="site" size="0.0" pos="0.62" type="Modification Site" active="false"/>
+</celldesigner:listOfRegions>
+</celldesigner:gene>
+</celldesigner:listOfGenes>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="tr1" state="phosphorylated"/>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/modifications/gene_with_regulatory_region.xml b/converter-CellDesigner/testFiles/modifications/gene_with_regulatory_region.xml
new file mode 100644
index 0000000000000000000000000000000000000000..aeaa0225240167c2c647aa552635d4060e1cd788
--- /dev/null
+++ b/converter-CellDesigner/testFiles/modifications/gene_with_regulatory_region.xml
@@ -0,0 +1,90 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="224.0" y="259.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="s1" type="GENE">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="xx" size="0.78" pos="0.0" type="RegulatoryRegion" active="false"/>
+</celldesigner:listOfRegions>
+</celldesigner:gene>
+</celldesigner:listOfGenes>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/modifications/gene_with_transcription_site_left.xml b/converter-CellDesigner/testFiles/modifications/gene_with_transcription_site_left.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b22c0d9ebf37d9eaf023083ad4aba9b9efc59b1c
--- /dev/null
+++ b/converter-CellDesigner/testFiles/modifications/gene_with_transcription_site_left.xml
@@ -0,0 +1,90 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="197.0" y="177.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="s1" type="GENE">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" size="0.38" pos="0.2" type="transcriptionStartingSiteL" active="false"/>
+</celldesigner:listOfRegions>
+</celldesigner:gene>
+</celldesigner:listOfGenes>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/modifications/gene_with_transcription_site_right.xml b/converter-CellDesigner/testFiles/modifications/gene_with_transcription_site_right.xml
new file mode 100644
index 0000000000000000000000000000000000000000..06a066d1c4ec627a2b0b1967efdf3dc750a48b67
--- /dev/null
+++ b/converter-CellDesigner/testFiles/modifications/gene_with_transcription_site_right.xml
@@ -0,0 +1,90 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="278.0" y="218.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="s1" type="GENE">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="qwe" size="0.1" pos="0.25" type="transcriptionStartingSiteR" active="true"/>
+</celldesigner:listOfRegions>
+</celldesigner:gene>
+</celldesigner:listOfGenes>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/modifications/protein_with_binding_region.xml b/converter-CellDesigner/testFiles/modifications/protein_with_binding_region.xml
new file mode 100644
index 0000000000000000000000000000000000000000..87ded130833443025cdefd580dda92c5bc18237b
--- /dev/null
+++ b/converter-CellDesigner/testFiles/modifications/protein_with_binding_region.xml
@@ -0,0 +1,90 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="238.0" y="123.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC">
+<celldesigner:listOfBindingRegions>
+<celldesigner:bindingRegion angle="3.141592653589793" id="rs1" name="test" size="0.42"/>
+</celldesigner:listOfBindingRegions>
+</celldesigner:protein>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/proteinWithEverPossibleModification.xml b/converter-CellDesigner/testFiles/modifications/protein_with_residues.xml
similarity index 100%
rename from converter-CellDesigner/testFiles/proteinWithEverPossibleModification.xml
rename to converter-CellDesigner/testFiles/modifications/protein_with_residues.xml
diff --git a/converter-CellDesigner/testFiles/rnaWithRegion.xml b/converter-CellDesigner/testFiles/modifications/rna_with_region.xml
similarity index 100%
rename from converter-CellDesigner/testFiles/rnaWithRegion.xml
rename to converter-CellDesigner/testFiles/modifications/rna_with_region.xml
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index c6d7b706742e0c5560469a846910d2ecf5059124..39b313a2589585494b053bd25fd6f23cf36cb1b6 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -1,1028 +1,1019 @@
-package lcsb.mapviewer.converter.model.sbgnml;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.stream.Collectors;
-
-import org.apache.commons.lang3.RandomStringUtils;
-import org.apache.log4j.Logger;
-import org.sbgn.ArcClazz;
-import org.sbgn.GlyphClazz;
-import org.sbgn.Language;
-import org.sbgn.bindings.Arc;
-import org.sbgn.bindings.Arc.End;
-import org.sbgn.bindings.Arc.Next;
-import org.sbgn.bindings.Arc.Start;
-import org.sbgn.bindings.Bbox;
-import org.sbgn.bindings.Glyph;
-import org.sbgn.bindings.Label;
-import org.sbgn.bindings.Map;
-import org.sbgn.bindings.Port;
-import org.sbgn.bindings.Sbgn;
-
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.modifier.Inhibition;
-import lcsb.mapviewer.model.map.modifier.Modulation;
-import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
-import lcsb.mapviewer.model.map.modifier.Trigger;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.AssociationOperator;
-import lcsb.mapviewer.model.map.reaction.DissociationOperator;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.OrOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.SplitOperator;
-import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
-import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
-import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-import lcsb.mapviewer.model.map.species.Unknown;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * Class used to export SBGN-ML files from the model.
- *
- * @author Michał Kuźma
- *
- */
-public class SbgnmlXmlExporter {
-
- /**
- * Helps in providing human readable identifiers of elements for logging.
- */
- private ElementUtils eu = new ElementUtils();
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(SbgnmlXmlExporter.class.getName());
-
- /**
- * Counter of the arcs parsed so far, used in generating arc's id.
- */
- private int arcCounter;
-
- /**
- * Set of all the operators parsed so far, used in generating operator's id.
- */
- private Set<NodeOperator> parsedOperators;
-
- /**
- * Map of operator IDs used when parsing arcs targeting an operator.
- */
- private java.util.Map<NodeOperator, String> operatorIds;
-
- /**
- * Map of all glyphs and ports generated so far with id as key.
- */
- private java.util.Map<String, Object> sourceTargetMap;
-
- /**
- * Side margin for units of information.
- */
- private static final double UNIT_OF_INFORMATION_MARGIN = 10.0;
-
- /**
- * Height of generated units of information.
- */
- private static final double UNIT_OF_INFORMATION_HEIGHT = 12.0;
-
- /**
- * Height and width of generated operators.
- */
- private static final double OPERATOR_SIZE = 40.0;
-
- /**
- * Distance between operator circle and port point.
- */
- private static final double OPERATOR_PORT_DISTANCE = 20.0;
-
- /**
- * Distance between process glyph and port point.
- */
- private static final double PROCESS_PORT_DISTANCE = 10.0;
-
- /**
- * Length of random alphabetic string added in the begining of ID, if it is a
- * number. SBGN-ML doesn't accept numbers as ID.
- */
- private static final int ID_RANDOM_STRING_LENGTH = 5;
-
- /**
- * Transforms model into SBGN-ML xml.
- *
- * @param model
- * model that should be transformed
- * @return SBGM-ML xml string for the model
- */
- public Sbgn toSbgnml(Model model) {
- // Reset global variables
- arcCounter = 0;
- parsedOperators = new HashSet<>();
- operatorIds = new HashMap<>();
- sourceTargetMap = new HashMap<>();
-
- Map map = new Map();
- map.setLanguage(Language.PD.getName());
- Sbgn sbgnData = new Sbgn();
-
- List<Species> aliases = model.getSpeciesList();
-
- for (Species a : aliases) {
- if (a.getComplex() == null) {
- Glyph newGlyph = aliasToGlyph(a);
- map.getGlyph().add(newGlyph);
- }
- }
-
- for (Reaction reaction : model.getReactions()) {
- try {
- map.getGlyph().add(getProcessGlyphFromReaction(reaction));
- } catch (InvalidArgumentException ex) {
- // Reduced notation
- try {
- map.getArc().add(getArcFromReducedReaction(reaction));
- } catch (InvalidArgumentException e) {
- logger.warn(
- "Invalid arc type." + " Reduced notation reaction found of type that is not compliant with SBGN-ML format." + " Reaction: "
- + reaction.getIdReaction());
- }
- continue;
- }
- map.getArc().addAll(getArcsFromReaction(reaction, map.getGlyph()));
- }
-
- sbgnData.setMap(map);
-
- return sbgnData;
- }
-
- /**
- * Creates new glyph element with all parameters from given alias.
- *
- * @param alias
- * alias with all parameters for the glyph
- * @return newly created glyph
- */
- private Glyph aliasToGlyph(Element alias) {
- Glyph newGlyph = new Glyph();
- boolean idIsANumber = true;
- try {
- Integer.parseInt(alias.getElementId().substring(0, 1));
- } catch (NumberFormatException e) {
- idIsANumber = false;
- }
- if (idIsANumber) {
- newGlyph.setId(RandomStringUtils.randomAlphabetic(ID_RANDOM_STRING_LENGTH).concat(alias.getElementId()));
- } else {
- newGlyph.setId(alias.getElementId());
- }
- newGlyph.setClazz(getGlyphClazzFromElement(alias).getClazz());
- newGlyph.setLabel(getGlyphLabelFromAlias(alias));
-
- Bbox bbox = new Bbox();
- bbox.setX(alias.getX().floatValue());
- bbox.setY(alias.getY().floatValue());
- bbox.setW(alias.getWidth().floatValue());
- bbox.setH(alias.getHeight().floatValue());
- newGlyph.setBbox(bbox);
-
- if (GlyphClazz.fromClazz(newGlyph.getClazz()).equals(GlyphClazz.MACROMOLECULE)
- || GlyphClazz.fromClazz(newGlyph.getClazz()).equals(GlyphClazz.MACROMOLECULE_MULTIMER)) {
- Protein protein = (Protein) alias;
- for (ModificationResidue mr : protein.getModificationResidues()) {
- Glyph stateVariableGlyph = parseStateVariable(mr, newGlyph);
- stateVariableGlyph.setId(newGlyph.getId().concat("-").concat(stateVariableGlyph.getId()));
- newGlyph.getGlyph().add(stateVariableGlyph);
- }
- }
-
- Glyph unitOfInformationGlyph = getUnitOfInformationGlyph(alias);
- if (unitOfInformationGlyph != null) {
- newGlyph.getGlyph().add(unitOfInformationGlyph);
- }
-
- if (alias instanceof Complex) {
- Complex complexAlias = (Complex) alias;
- for (Species a : complexAlias.getElements()) {
- Glyph childGlyph = aliasToGlyph(a);
- newGlyph.getGlyph().add(childGlyph);
- }
- }
-
- sourceTargetMap.put(newGlyph.getId(), newGlyph);
- return newGlyph;
- }
-
- /**
- * Creates new glyph element with all parameters from given operator.
- *
- * @param operator
- * operator with all parameters for the glyph
- * @return newly created glyph
- */
- private Glyph operatorToGlyph(NodeOperator operator) {
- Glyph newGlyph = new Glyph();
- newGlyph.setId("operator".concat(Integer.toString(parsedOperators.size())));
- parsedOperators.add(operator);
- operatorIds.put(operator, newGlyph.getId());
- if (operator instanceof AndOperator) {
- newGlyph.setClazz(GlyphClazz.AND.getClazz());
- } else if (operator instanceof OrOperator) {
- newGlyph.setClazz(GlyphClazz.OR.getClazz());
- }
-
- Bbox bbox = new Bbox();
- bbox.setX((float) (operator.getLine().getPoints().get(0).getX() - OPERATOR_SIZE / 2));
- bbox.setY((float) (operator.getLine().getPoints().get(0).getY() - OPERATOR_SIZE / 2));
- bbox.setW((float) OPERATOR_SIZE);
- bbox.setH((float) OPERATOR_SIZE);
- newGlyph.setBbox(bbox);
-
- Port port2 = new Port();
- port2.setId(newGlyph.getId().concat(".2"));
- Point2D centerPoint = operator.getLine().getPoints().get(0);
- Point2D nextPoint = operator.getLine().getPoints().get(1);
- double dx = nextPoint.getX() - centerPoint.getX();
- double dy = nextPoint.getY() - centerPoint.getY();
- double portToCenterDistance = OPERATOR_SIZE / 2 + OPERATOR_PORT_DISTANCE;
-
- double dx2, dy2;
- if (dx != 0) {
- dx2 = Math.sqrt(Math.pow(portToCenterDistance, 2) / (1 + Math.pow(dy / dx, 2)));
- dy2 = dx2 * dy / dx;
- } else {
- dx2 = 0;
- if (dy > 0) {
- dy2 = portToCenterDistance;
- } else {
- dy2 = -portToCenterDistance;
- }
- }
-
- port2.setX((float) (centerPoint.getX() + dx2));
- port2.setY((float) (centerPoint.getY() + dy2));
- sourceTargetMap.put(port2.getId(), port2);
- newGlyph.getPort().add(port2);
-
- Port port1 = new Port();
- port1.setId(newGlyph.getId().concat(".1"));
- Point2D portPoint1 = new Point2D.Double(2 * centerPoint.getX() - port2.getX(), 2 * centerPoint.getY() - port2.getY());
- port1.setX((float) portPoint1.getX());
- port1.setY((float) portPoint1.getY());
- sourceTargetMap.put(port1.getId(), port1);
- newGlyph.getPort().add(port1);
-
- sourceTargetMap.put(newGlyph.getId(), newGlyph);
-
- return newGlyph;
- }
-
- /**
- * Returns GlyphClazz adequate for given element, based on it's class.
- *
- * @param element
- * element to extract GlyphCLazz from
- * @return GlyphClazz adequate for given alias
- */
- private GlyphClazz getGlyphClazzFromElement(Element element) {
- if (element instanceof Protein) {
- Protein protein = (Protein) element;
- if (protein.getHomodimer() == 1) {
- return GlyphClazz.MACROMOLECULE;
- } else {
- return GlyphClazz.MACROMOLECULE_MULTIMER;
- }
- }
-
- if (element instanceof SimpleMolecule) {
- SimpleMolecule simpleMolecule = (SimpleMolecule) element;
- if (simpleMolecule.getHomodimer() == 1) {
- return GlyphClazz.SIMPLE_CHEMICAL;
- } else {
- return GlyphClazz.SIMPLE_CHEMICAL_MULTIMER;
- }
- }
-
- if (element instanceof Ion) {
- Ion ion = (Ion) element;
- if (ion.getHomodimer() == 1) {
- return GlyphClazz.SIMPLE_CHEMICAL;
- } else {
- return GlyphClazz.SIMPLE_CHEMICAL_MULTIMER;
- }
- }
-
- if (element instanceof Gene) {
- Gene gene = (Gene) element;
- if (gene.getHomodimer() == 1) {
- return GlyphClazz.NUCLEIC_ACID_FEATURE;
- } else {
- return GlyphClazz.NUCLEIC_ACID_FEATURE_MULTIMER;
- }
- }
-
- if (element instanceof Rna) {
- Rna rna = (Rna) element;
- if (rna.getHomodimer() == 1) {
- return GlyphClazz.NUCLEIC_ACID_FEATURE;
- } else {
- return GlyphClazz.NUCLEIC_ACID_FEATURE_MULTIMER;
- }
- }
-
- if (element instanceof AntisenseRna) {
- AntisenseRna rna = (AntisenseRna) element;
- if (rna.getHomodimer() == 1) {
- return GlyphClazz.NUCLEIC_ACID_FEATURE;
- } else {
- return GlyphClazz.NUCLEIC_ACID_FEATURE_MULTIMER;
- }
- }
-
- if (element instanceof Complex) {
- Complex complexSpecies = (Complex) element;
- if (complexSpecies.getHomodimer() == 1) {
- return GlyphClazz.COMPLEX;
- } else {
- return GlyphClazz.COMPLEX_MULTIMER;
- }
- }
-
- if (element instanceof Degraded) {
- return GlyphClazz.SOURCE_AND_SINK;
- }
-
- if (element instanceof Phenotype) {
- return GlyphClazz.PHENOTYPE;
- }
-
- if (element instanceof Compartment) {
- return GlyphClazz.COMPARTMENT;
- }
- if (element instanceof Unknown) {
- return GlyphClazz.UNSPECIFIED_ENTITY;
- }
-
- logger.warn(eu.getElementTag(element) + "Element type is not supported by SBGN-ML format. Unspecified Entity type assigned.");
- return GlyphClazz.UNSPECIFIED_ENTITY;
- }
-
- /**
- * Returns label for a glyph with name extracted from given element.
- *
- * @param element
- * element with the name
- * @return label for a glyph
- */
- private Label getGlyphLabelFromAlias(Element element) {
- Label label = new Label();
- label.setText(element.getName());
- return label;
- }
-
- /**
- * Returns state variable glyph parsed from {@link ModificationResidue}.
- *
- * @param mr
- * {@link ModificationResidue} to be parsed
- * @param parentGlyph
- * parent glyph for the state variable
- * @return state variable glyph
- */
- private Glyph parseStateVariable(ModificationResidue mr, Glyph parentGlyph) {
- Glyph glyph = new Glyph();
- glyph.setId(mr.getIdModificationResidue());
- glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
-
- if (mr.getState() != null) {
- Glyph.State state = new Glyph.State();
- state.setValue(mr.getState().getAbbreviation());
- state.setVariable(mr.getName());
- glyph.setState(state);
- }
-
- Bbox bbox = new Bbox();
-
- final float filledWidth = 70.0f;
- final float filledHeight = 28.0f;
- final float emptyWidth = 20.0f;
- final float emptyHeight = 22.0f;
- if (glyph.getState() != null) {
- bbox.setH(filledHeight);
- bbox.setW(filledWidth);
- } else {
- bbox.setH(emptyHeight);
- bbox.setW(emptyWidth);
- }
-
- float angle = mr.getAngle().floatValue();
- angle /= Math.PI;
-
- final float rightBorderLimit = 0.25f;
- final float topBorderLimit = 0.75f;
- final float leftBorderLimit = 1.25f;
- float svCenterX, svCenterY;
- if (angle < rightBorderLimit) {
- svCenterX = parentGlyph.getBbox().getW();
- svCenterY = parentGlyph.getBbox().getH() / 2 - (angle * 2 * parentGlyph.getBbox().getH());
- } else if (angle < topBorderLimit) {
- svCenterX = parentGlyph.getBbox().getW() * (1.0f - 2 * (angle - rightBorderLimit));
- svCenterY = 0;
- } else if (angle < leftBorderLimit) {
- svCenterX = 0;
- svCenterY = parentGlyph.getBbox().getH() * 2 * (angle - topBorderLimit);
- } else {
- svCenterX = parentGlyph.getBbox().getW() * 2 * (angle - leftBorderLimit);
- svCenterY = parentGlyph.getBbox().getH();
- }
-
- bbox.setX(svCenterX - bbox.getW() / 2.0f + parentGlyph.getBbox().getX());
- bbox.setY(svCenterY - bbox.getH() / 2.0f + parentGlyph.getBbox().getY());
-
- glyph.setBbox(bbox);
-
- return glyph;
- }
-
- /**
- * Returns glyph with unit of information extracted from the alias or null if
- * no unit of information was found.
- *
- * @param alias
- * input alias
- * @return glyph with unit of information extracted from the alias or null if
- * no unit of information was found
- */
- private Glyph getUnitOfInformationGlyph(Element alias) {
- Glyph uoiGlyph = null;
-
- String uoiText = "";
- if (alias instanceof Species) {
- Species species = (Species) alias;
- int homodir = species.getHomodimer();
- if (homodir > 1) {
- uoiText = "N:".concat(Integer.toString(homodir));
- }
- }
-
- if (alias instanceof TruncatedProtein) {
- if (!uoiText.equals("")) {
- uoiText = uoiText.concat("; ");
- }
- uoiText = uoiText.concat("ct:truncatedProtein");
- }
-
- if (alias instanceof Species) {
- Species speciesAlias = (Species) alias;
- if ((speciesAlias.getStateLabel() != null) && (speciesAlias.getStatePrefix() != null)) {
- if (!uoiText.equals("")) {
- uoiText = uoiText.concat("; ");
- }
- if (!speciesAlias.getStatePrefix().equals("free input")) {
- uoiText = uoiText.concat(speciesAlias.getStatePrefix()).concat(":");
- }
- uoiText = uoiText.concat(speciesAlias.getStateLabel());
- }
- }
-
- if (!uoiText.contains("ct:")) {
- if (alias instanceof Rna) {
- if (!uoiText.equals("")) {
- uoiText = uoiText.concat("; ");
- }
- uoiText = uoiText.concat("ct:RNA");
- }
- if (alias instanceof AntisenseRna) {
- if (!uoiText.equals("")) {
- uoiText = uoiText.concat("; ");
- }
- uoiText = uoiText.concat("ct:antisenseRNA");
- }
- if (alias instanceof Gene) {
- if (!uoiText.equals("")) {
- uoiText = uoiText.concat("; ");
- }
- uoiText = uoiText.concat("ct:gene");
- }
- }
-
- if (!uoiText.equals("")) {
- uoiGlyph = new Glyph();
- uoiGlyph.setClazz(GlyphClazz.UNIT_OF_INFORMATION.getClazz());
- uoiGlyph.setId(alias.getElementId().concat("uoi"));
-
- Label label = new Label();
- label.setText(uoiText);
- uoiGlyph.setLabel(label);
-
- Bbox bbox = new Bbox();
- bbox.setX((float) (alias.getX() + UNIT_OF_INFORMATION_MARGIN));
- bbox.setY((float) (alias.getY() - UNIT_OF_INFORMATION_HEIGHT / 2));
- bbox.setH((float) UNIT_OF_INFORMATION_HEIGHT);
- bbox.setW((float) (alias.getWidth() - 2 * UNIT_OF_INFORMATION_MARGIN));
- uoiGlyph.setBbox(bbox);
- }
-
- return uoiGlyph;
- }
-
- /**
- * Returns process glyph created based on reaction's center point.
- *
- * @param reaction
- * reaction to be parsed
- * @return process glyph for given reaction
- */
- private Glyph getProcessGlyphFromReaction(Reaction reaction) {
- Glyph processGlyph = new Glyph();
- processGlyph.setId(reaction.getIdReaction());
- processGlyph.setClazz(getGlyphClazzFromReaction(reaction).getClazz());
- Bbox bbox = new Bbox();
-
- Line2D line = reaction.getCenterLine();
- Point2D startPoint = line.getP1();
- Point2D endPoint = line.getP2();
-
- double pointX = (startPoint.getX() + endPoint.getX()) / 2;
- double pointY = (startPoint.getY() + endPoint.getY()) / 2;
- Point2D pointNW = new Point2D.Double(pointX - ReactionConverter.RECT_SIZE / 2, pointY - ReactionConverter.RECT_SIZE / 2);
- bbox.setX((float) pointNW.getX());
- bbox.setY((float) pointNW.getY());
- bbox.setH((float) ReactionConverter.RECT_SIZE);
- bbox.setW((float) ReactionConverter.RECT_SIZE);
-
- processGlyph.setBbox(bbox);
-
- Port reactantPort = new Port();
- reactantPort.setId(reaction.getIdReaction().concat(".1"));
- sourceTargetMap.put(reactantPort.getId(), reactantPort);
-
- Port productPort = new Port();
- productPort.setId(reaction.getIdReaction().concat(".2"));
- sourceTargetMap.put(productPort.getId(), productPort);
-
- // Set glyph orientation and ports' coordinates.
- double reactantDxAverage = 0.0;
- double reactantDyAverage = 0.0;
- double productDxAverage = 0.0;
- double productDyAverage = 0.0;
-
- for (Reactant r : reaction.getReactants()) {
- Point2D reactantPoint;
- List<Point2D> reactantArcPoints = r.getLine().getPoints();
- if (reaction instanceof HeterodimerAssociationReaction) {
- reactantPoint = reactantArcPoints.get(reactantArcPoints.size() - 1);
- } else {
- reactantPoint = reactantArcPoints.get(reactantArcPoints.size() - 2);
- }
- reactantDxAverage += reactantPoint.getX() - pointX;
- reactantDyAverage += reactantPoint.getY() - pointY;
- }
- reactantDxAverage /= reaction.getReactants().size();
- reactantDyAverage /= reaction.getReactants().size();
-
- for (Product p : reaction.getProducts()) {
- List<Point2D> productArcPoints = p.getLine().getPoints();
- Point2D productPoint;
- if (reaction instanceof DissociationReaction) {
- productPoint = productArcPoints.get(0);
- } else {
- productPoint = productArcPoints.get(1);
- }
- productDxAverage += productPoint.getX() - pointX;
- productDyAverage += productPoint.getY() - pointY;
- }
- productDxAverage /= reaction.getProducts().size();
- productDyAverage /= reaction.getProducts().size();
-
- boolean horizontalOrientation;
- if ((reactantDxAverage * productDxAverage < 0) && (reactantDyAverage * productDyAverage < 0)) {
- horizontalOrientation = (Math.abs(productDxAverage - reactantDxAverage) > Math.abs(productDyAverage - reactantDyAverage));
- } else {
- horizontalOrientation = (reactantDxAverage * productDxAverage < 0);
- }
- if (horizontalOrientation) {
- processGlyph.setOrientation("horizontal");
- reactantPort.setY((float) pointY);
- productPort.setY((float) pointY);
- if (reactantDxAverage < 0) {
- reactantPort.setX((float) (pointX - PROCESS_PORT_DISTANCE));
- productPort.setX((float) (pointX + PROCESS_PORT_DISTANCE));
- } else {
- reactantPort.setX((float) (pointX + PROCESS_PORT_DISTANCE));
- productPort.setX((float) (pointX - PROCESS_PORT_DISTANCE));
- }
- } else {
- reactantPort.setX((float) pointX);
- productPort.setX((float) pointX);
- if (reactantDyAverage < 0) {
- reactantPort.setY((float) (pointY - PROCESS_PORT_DISTANCE));
- productPort.setY((float) (pointY + PROCESS_PORT_DISTANCE));
- } else {
- reactantPort.setY((float) (pointY + PROCESS_PORT_DISTANCE));
- productPort.setY((float) (pointY - PROCESS_PORT_DISTANCE));
- }
- processGlyph.setOrientation("vertical");
- }
-
- processGlyph.getPort().add(reactantPort);
- processGlyph.getPort().add(productPort);
-
- sourceTargetMap.put(processGlyph.getId(), processGlyph);
-
- return processGlyph;
- }
-
- /**
- * Returns {@link GlyphClazz} appropriate to given reaction.
- *
- * @param reaction
- * {@link Reaction} to extract {@link GlyphClazz} from
- * @return {@link GlyphClazz} appropriate to given reaction
- */
- private GlyphClazz getGlyphClazzFromReaction(Reaction reaction) {
- if (reaction instanceof StateTransitionReaction) {
- return GlyphClazz.PROCESS;
- }
- if (reaction instanceof HeterodimerAssociationReaction) {
- return GlyphClazz.ASSOCIATION;
- }
- if (reaction instanceof DissociationReaction) {
- return GlyphClazz.DISSOCIATION;
- }
- if (reaction instanceof KnownTransitionOmittedReaction) {
- return GlyphClazz.OMITTED_PROCESS;
- }
- if (reaction instanceof UnknownTransitionReaction) {
- return GlyphClazz.UNCERTAIN_PROCESS;
- }
- throw new InvalidArgumentException();
- }
-
- /**
- * Returns arc extracted from given reduced notation reaction.
- *
- * @param reaction
- * reduced notation reaction
- * @return arc extracted from given reduced notation reaction
- */
- private Arc getArcFromReducedReaction(Reaction reaction) {
- if ((reaction.getReactants().size() != 1) || (reaction.getProducts().size() != 1)) {
- throw new InvalidArgumentException();
- }
- Arc arc = new Arc();
- arc.setId(reaction.getIdReaction());
-
- if (reaction instanceof NegativeInfluenceReaction) {
- arc.setClazz(ArcClazz.INHIBITION.getClazz());
- } else if (reaction instanceof ReducedModulationReaction) {
- arc.setClazz(ArcClazz.MODULATION.getClazz());
- } else if (reaction instanceof ReducedTriggerReaction) {
- arc.setClazz(ArcClazz.NECESSARY_STIMULATION.getClazz());
- } else if (reaction instanceof ReducedPhysicalStimulationReaction) {
- arc.setClazz(ArcClazz.STIMULATION.getClazz());
- } else {
- throw new InvalidArgumentException();
- }
-
- if (reaction.getProducts().get(0).getElement() instanceof Phenotype) {
- logger.warn("Found Phenotype being a reactant in process. That is discouraged");
- }
-
- arc.setSource(sourceTargetMap.get(reaction.getReactants().get(0).getElement().getElementId()));
- arc.setTarget(sourceTargetMap.get(reaction.getProducts().get(0).getElement().getElementId()));
-
- List<Point2D> pointList = reaction.getReactants().get(0).getLine().getPoints();
- pointList.addAll(reaction.getProducts().get(0).getLine().getPoints());
-
- removeRedundantPoints(pointList);
-
- Start start = new Start();
- start.setX((float) pointList.get(0).getX());
- start.setY((float) pointList.get(0).getY());
- arc.setStart(start);
-
- End end = new End();
- end.setX((float) pointList.get(pointList.size() - 1).getX());
- end.setY((float) pointList.get(pointList.size() - 1).getY());
- arc.setEnd(end);
-
- for (int i = 1; i < pointList.size() - 1; i++) {
- Point2D nextPoint = pointList.get(i);
- Next next = new Next();
- next.setX((float) nextPoint.getX());
- next.setY((float) nextPoint.getY());
- arc.getNext().add(next);
- }
-
- return arc;
- }
-
- /**
- * Removes redundant points from the list.
- *
- * @param pointList
- * list of points to be fixed
- */
- private void removeRedundantPoints(List<Point2D> pointList) {
- boolean allDone = false;
- while (!allDone) {
- allDone = true;
- for (int i = 1; i < pointList.size() - 1; i++) {
- double dx1 = pointList.get(i).getX() - pointList.get(i - 1).getX();
- double dy1 = pointList.get(i).getY() - pointList.get(i - 1).getY();
- double dx2 = pointList.get(i + 1).getX() - pointList.get(i).getX();
- double dy2 = pointList.get(i + 1).getY() - pointList.get(i).getY();
-
- DoubleComparator doubleComparator = new DoubleComparator();
- if (((doubleComparator.compare(dy1 / dx1, dy2 / dx2) == 0)
- || (pointList.get(i - 1).getY() == pointList.get(i).getY()) && (pointList.get(i).getY() == pointList.get(i + 1).getY()))
- && between(pointList.get(i).getX(), pointList.get(i - 1).getX(), pointList.get(i + 1).getX())) {
- pointList.remove(i);
- allDone = false;
- }
- }
- }
- }
-
- /**
- * Checks if argument x is between s1 and s2.
- *
- * @param x
- * number to checked if it is in the middle
- * @param s1
- * one side argument
- * @param s2
- * second side argument
- * @return true if x is between s1 and s2
- */
- private boolean between(double x, double s1, double s2) {
- if ((x >= s1) && (x <= s2)) {
- return true;
- }
- if ((x <= s1) && (x >= s2)) {
- return true;
- }
- return false;
- }
-
- /**
- * Returns set of all arcs used in the reaction.
- *
- * @param reaction
- * the reaction to extract arcs from
- * @param glyphList
- * list of all glyphs in the map; used only for parsing operators
- * @return set of all arcs used in the reaction
- */
- private List<Arc> getArcsFromReaction(Reaction reaction, List<Glyph> glyphList) {
- List<Arc> arcList = new ArrayList<>();
-
- // Parse all nodes except NodeOperators
- for (AbstractNode node : reaction.getNodes().stream().filter(n -> !(n instanceof NodeOperator)).collect(Collectors.toList())) {
- try {
- arcList.add(getArcFromNode(node, glyphList));
- } catch (InvalidArgumentException ex) {
- logger.warn("Node skipped in export process, since it is not compliant with SBGN-ML format: " + node.getClass().getName());
- continue;
- }
- }
-
- // Now parse NodeOperators
- for (AbstractNode node : reaction.getOperators().stream().filter(o -> {
- if (o.getInputs().stream().filter(i -> i instanceof Reactant).count() > 0) {
- return false;
- }
- if (o instanceof SplitOperator || o instanceof AssociationOperator || o instanceof DissociationOperator) {
- return false;
- }
- return true;
- }).collect(Collectors.toList())) {
- try {
- arcList.add(getArcFromNode(node, glyphList));
- } catch (InvalidArgumentException ex) {
- logger.warn("Node skipped in export process, since it is not compliant with SBGN-ML format: " + node.getClass().getName());
- continue;
- }
- }
-
- return arcList;
-
- }
-
- /**
- * Returns arc for given node.
- *
- * @param node
- * node to parse arc from
- * @param glyphList
- * list of all glyphs in the map; used only for parsing operators
- * @return SBGN-ML arc for given node
- */
- private Arc getArcFromNode(AbstractNode node, List<Glyph> glyphList) {
- Arc arc = new Arc();
- arc.setId("arc".concat(Integer.toString(arcCounter)));
- arcCounter += 1;
-
- boolean logicArc = false;
- if (node instanceof Modifier) {
- for (NodeOperator operator : node.getReaction().getOperators()) {
- if (operator.getInputs().contains(node)) {
- logicArc = true;
- }
- }
- }
- if (logicArc) {
- arc.setClazz(ArcClazz.LOGIC_ARC.getClazz());
- } else {
- arc.setClazz(getArcClazzFromNode(node));
- }
-
- if (node instanceof Reactant) {
- arc.setSource(sourceTargetMap.get(((Reactant) node).getElement().getElementId()));
- arc.setTarget(sourceTargetMap.get(node.getReaction().getIdReaction().concat(".1")));
- } else if (node instanceof Product) {
- arc.setSource(sourceTargetMap.get(node.getReaction().getIdReaction().concat(".2")));
- arc.setTarget(sourceTargetMap.get(((Product) node).getElement().getElementId()));
- } else if (node instanceof Modifier) {
- arc.setSource(sourceTargetMap.get(((Modifier) node).getElement().getElementId()));
- if (!node.getLine().getEndAtd().getArrowType().equals(ArrowType.NONE)) {
- arc.setTarget(sourceTargetMap.get(node.getReaction().getIdReaction()));
- } else {
- for (NodeOperator operator : node.getReaction().getOperators()) {
- if (operator.getInputs().contains(node)) {
- if (!parsedOperators.contains(operator)) {
- Glyph newOperator = operatorToGlyph(operator);
- glyphList.add(newOperator);
- }
- arc.setTarget(sourceTargetMap.get(operatorIds.get(operator).concat(".1")));
- }
- }
- }
- } else if (node instanceof NodeOperator) {
- if ((node instanceof DissociationOperator) || (node instanceof AssociationOperator)) {
- throw new InvalidArgumentException();
- }
- arc.setSource(sourceTargetMap.get(operatorIds.get(node).concat(".2")));
- if (!node.getLine().getEndAtd().getArrowType().equals(ArrowType.NONE)) {
- arc.setTarget(sourceTargetMap.get(node.getReaction().getIdReaction()));
- } else {
- for (NodeOperator operator : node.getReaction().getOperators()) {
- if (operator.getInputs().contains(node)) {
- if (!parsedOperators.contains(operator)) {
- Glyph newOperator = operatorToGlyph(operator);
- glyphList.add(newOperator);
- }
- arc.setTarget(sourceTargetMap.get(operatorIds.get(operator).concat(".1")));
- }
- }
- }
- }
-
- List<Point2D> arcPoints = node.getLine().getPoints();
- Start start = new Start();
- if ((node instanceof Product) || (node instanceof NodeOperator)) {
- Port sourcePort = (Port) arc.getSource();
- start.setX(sourcePort.getX());
- start.setY(sourcePort.getY());
- } else {
- start.setX((float) arcPoints.get(0).getX());
- start.setY((float) arcPoints.get(0).getY());
- }
- arc.setStart(start);
-
- End end = new End();
- if ((node instanceof Reactant) || ((node instanceof Modifier) && (arc.getTarget() instanceof Port))) {
- Port targetPort = (Port) arc.getTarget();
- end.setX(targetPort.getX());
- end.setY(targetPort.getY());
- } else {
- Point2D lastPoint = arcPoints.get(arcPoints.size() - 1);
- end.setX((float) lastPoint.getX());
- end.setY((float) lastPoint.getY());
- }
- arc.setEnd(end);
-
- if ((node instanceof Product) && (node.getReaction() instanceof DissociationReaction)) {
- Point2D nextPoint = arcPoints.get(0);
- Next next = new Next();
- next.setX((float) nextPoint.getX());
- next.setY((float) nextPoint.getY());
- arc.getNext().add(next);
- }
-
- DoubleComparator doubleComparator = new DoubleComparator();
- for (int i = 1; i < arcPoints.size() - 1; i++) {
- Point2D nextPoint = arcPoints.get(i);
- if ((doubleComparator.compare(nextPoint.getX(), new Double(start.getX())) == 0)
- && (doubleComparator.compare(nextPoint.getY(), new Double(start.getY())) == 0)) {
- arc.getNext().clear();
- continue;
- }
- if ((doubleComparator.compare(nextPoint.getX(), new Double(end.getX())) == 0)
- && (doubleComparator.compare(nextPoint.getY(), new Double(end.getY())) == 0)) {
- break;
- }
- Next next = new Next();
- next.setX((float) nextPoint.getX());
- next.setY((float) nextPoint.getY());
- arc.getNext().add(next);
- }
-
- if ((node instanceof Reactant) && (node.getReaction() instanceof HeterodimerAssociationReaction)) {
- Point2D nextPoint = arcPoints.get(arcPoints.size() - 1);
- Next next = new Next();
- next.setX((float) nextPoint.getX());
- next.setY((float) nextPoint.getY());
- arc.getNext().add(next);
- }
-
- return arc;
- }
-
- /**
- * Returns {@link ArcClazz} for given node.
- *
- * @param node
- * Node to extract {@link ArcClazz} from
- * @return {@link ArcClazz} for given node
- */
- private String getArcClazzFromNode(AbstractNode node) {
- if (node instanceof Reactant) {
- return ArcClazz.CONSUMPTION.getClazz();
- }
- if (node instanceof Product) {
- return ArcClazz.PRODUCTION.getClazz();
- }
- if (node instanceof Catalysis) {
- return ArcClazz.CATALYSIS.getClazz();
- }
- if (node instanceof Inhibition) {
- return ArcClazz.INHIBITION.getClazz();
- }
- if (node instanceof Modulation) {
- return ArcClazz.MODULATION.getClazz();
- }
- if (node instanceof Trigger) {
- return ArcClazz.NECESSARY_STIMULATION.getClazz();
- }
- if (node instanceof PhysicalStimulation) {
- return ArcClazz.STIMULATION.getClazz();
- }
- if (node instanceof NodeOperator) {
- ArrowType arrowType = node.getLine().getEndAtd().getArrowType();
- switch (arrowType) {
- case BLANK:
- return ArcClazz.STIMULATION.getClazz();
- case BLANK_CROSSBAR:
- return ArcClazz.NECESSARY_STIMULATION.getClazz();
- case CIRCLE:
- return ArcClazz.CATALYSIS.getClazz();
- case CROSSBAR:
- return ArcClazz.INHIBITION.getClazz();
- case DIAMOND:
- return ArcClazz.MODULATION.getClazz();
- case NONE:
- return ArcClazz.LOGIC_ARC.getClazz();
- default:
- throw new InvalidArgumentException();
-
- }
- }
- throw new InvalidArgumentException();
- }
-}
+package lcsb.mapviewer.converter.model.sbgnml;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import org.apache.commons.lang3.RandomStringUtils;
+import org.apache.log4j.Logger;
+import org.sbgn.ArcClazz;
+import org.sbgn.GlyphClazz;
+import org.sbgn.Language;
+import org.sbgn.bindings.Arc;
+import org.sbgn.bindings.Arc.End;
+import org.sbgn.bindings.Arc.Next;
+import org.sbgn.bindings.Arc.Start;
+import org.sbgn.bindings.Bbox;
+import org.sbgn.bindings.Glyph;
+import org.sbgn.bindings.Label;
+import org.sbgn.bindings.Map;
+import org.sbgn.bindings.Port;
+import org.sbgn.bindings.Sbgn;
+
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
+import lcsb.mapviewer.model.map.modifier.Trigger;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.AssociationOperator;
+import lcsb.mapviewer.model.map.reaction.DissociationOperator;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.OrOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
+import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * Class used to export SBGN-ML files from the model.
+ *
+ * @author Michał Kuźma
+ *
+ */
+public class SbgnmlXmlExporter {
+
+ /**
+ * Helps in providing human readable identifiers of elements for logging.
+ */
+ private ElementUtils eu = new ElementUtils();
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(SbgnmlXmlExporter.class.getName());
+
+ /**
+ * Counter of the arcs parsed so far, used in generating arc's id.
+ */
+ private int arcCounter;
+
+ /**
+ * Set of all the operators parsed so far, used in generating operator's id.
+ */
+ private Set<NodeOperator> parsedOperators;
+
+ /**
+ * Map of operator IDs used when parsing arcs targeting an operator.
+ */
+ private java.util.Map<NodeOperator, String> operatorIds;
+
+ /**
+ * Map of all glyphs and ports generated so far with id as key.
+ */
+ private java.util.Map<String, Object> sourceTargetMap;
+
+ /**
+ * Side margin for units of information.
+ */
+ private static final double UNIT_OF_INFORMATION_MARGIN = 10.0;
+
+ /**
+ * Height of generated units of information.
+ */
+ private static final double UNIT_OF_INFORMATION_HEIGHT = 12.0;
+
+ /**
+ * Height and width of generated operators.
+ */
+ private static final double OPERATOR_SIZE = 40.0;
+
+ /**
+ * Distance between operator circle and port point.
+ */
+ private static final double OPERATOR_PORT_DISTANCE = 20.0;
+
+ /**
+ * Distance between process glyph and port point.
+ */
+ private static final double PROCESS_PORT_DISTANCE = 10.0;
+
+ /**
+ * Length of random alphabetic string added in the begining of ID, if it is a
+ * number. SBGN-ML doesn't accept numbers as ID.
+ */
+ private static final int ID_RANDOM_STRING_LENGTH = 5;
+
+ /**
+ * Transforms model into SBGN-ML xml.
+ *
+ * @param model
+ * model that should be transformed
+ * @return SBGM-ML xml string for the model
+ */
+ public Sbgn toSbgnml(Model model) {
+ // Reset global variables
+ arcCounter = 0;
+ parsedOperators = new HashSet<>();
+ operatorIds = new HashMap<>();
+ sourceTargetMap = new HashMap<>();
+
+ Map map = new Map();
+ map.setLanguage(Language.PD.getName());
+ Sbgn sbgnData = new Sbgn();
+
+ List<Species> aliases = model.getSpeciesList();
+
+ for (Species a : aliases) {
+ if (a.getComplex() == null) {
+ Glyph newGlyph = aliasToGlyph(a);
+ map.getGlyph().add(newGlyph);
+ }
+ }
+
+ for (Reaction reaction : model.getReactions()) {
+ try {
+ map.getGlyph().add(getProcessGlyphFromReaction(reaction));
+ } catch (InvalidArgumentException ex) {
+ // Reduced notation
+ try {
+ map.getArc().add(getArcFromReducedReaction(reaction));
+ } catch (InvalidArgumentException e) {
+ logger.warn("Invalid arc type."
+ + " Reduced notation reaction found of type that is not compliant with SBGN-ML format." + " Reaction: "
+ + reaction.getIdReaction());
+ }
+ continue;
+ }
+ map.getArc().addAll(getArcsFromReaction(reaction, map.getGlyph()));
+ }
+
+ sbgnData.setMap(map);
+
+ return sbgnData;
+ }
+
+ /**
+ * Creates new glyph element with all parameters from given alias.
+ *
+ * @param alias
+ * alias with all parameters for the glyph
+ * @return newly created glyph
+ */
+ private Glyph aliasToGlyph(Element alias) {
+ Glyph newGlyph = new Glyph();
+ boolean idIsANumber = true;
+ try {
+ Integer.parseInt(alias.getElementId().substring(0, 1));
+ } catch (NumberFormatException e) {
+ idIsANumber = false;
+ }
+ if (idIsANumber) {
+ newGlyph.setId(RandomStringUtils.randomAlphabetic(ID_RANDOM_STRING_LENGTH).concat(alias.getElementId()));
+ } else {
+ newGlyph.setId(alias.getElementId());
+ }
+ newGlyph.setClazz(getGlyphClazzFromElement(alias).getClazz());
+ newGlyph.setLabel(getGlyphLabelFromAlias(alias));
+
+ Bbox bbox = new Bbox();
+ bbox.setX(alias.getX().floatValue());
+ bbox.setY(alias.getY().floatValue());
+ bbox.setW(alias.getWidth().floatValue());
+ bbox.setH(alias.getHeight().floatValue());
+ newGlyph.setBbox(bbox);
+
+ if (GlyphClazz.fromClazz(newGlyph.getClazz()).equals(GlyphClazz.MACROMOLECULE)
+ || GlyphClazz.fromClazz(newGlyph.getClazz()).equals(GlyphClazz.MACROMOLECULE_MULTIMER)) {
+ Protein protein = (Protein) alias;
+ for (ModificationResidue mr : protein.getModificationResidues()) {
+ Glyph stateVariableGlyph = parseStateVariable(mr, newGlyph);
+ stateVariableGlyph.setId(newGlyph.getId().concat("-").concat(stateVariableGlyph.getId()));
+ newGlyph.getGlyph().add(stateVariableGlyph);
+ }
+ }
+
+ Glyph unitOfInformationGlyph = getUnitOfInformationGlyph(alias);
+ if (unitOfInformationGlyph != null) {
+ newGlyph.getGlyph().add(unitOfInformationGlyph);
+ }
+
+ if (alias instanceof Complex) {
+ Complex complexAlias = (Complex) alias;
+ for (Species a : complexAlias.getElements()) {
+ Glyph childGlyph = aliasToGlyph(a);
+ newGlyph.getGlyph().add(childGlyph);
+ }
+ }
+
+ sourceTargetMap.put(newGlyph.getId(), newGlyph);
+ return newGlyph;
+ }
+
+ /**
+ * Creates new glyph element with all parameters from given operator.
+ *
+ * @param operator
+ * operator with all parameters for the glyph
+ * @return newly created glyph
+ */
+ private Glyph operatorToGlyph(NodeOperator operator) {
+ Glyph newGlyph = new Glyph();
+ newGlyph.setId("operator".concat(Integer.toString(parsedOperators.size())));
+ parsedOperators.add(operator);
+ operatorIds.put(operator, newGlyph.getId());
+ if (operator instanceof AndOperator) {
+ newGlyph.setClazz(GlyphClazz.AND.getClazz());
+ } else if (operator instanceof OrOperator) {
+ newGlyph.setClazz(GlyphClazz.OR.getClazz());
+ }
+
+ Bbox bbox = new Bbox();
+ bbox.setX((float) (operator.getLine().getPoints().get(0).getX() - OPERATOR_SIZE / 2));
+ bbox.setY((float) (operator.getLine().getPoints().get(0).getY() - OPERATOR_SIZE / 2));
+ bbox.setW((float) OPERATOR_SIZE);
+ bbox.setH((float) OPERATOR_SIZE);
+ newGlyph.setBbox(bbox);
+
+ Port port2 = new Port();
+ port2.setId(newGlyph.getId().concat(".2"));
+ Point2D centerPoint = operator.getLine().getPoints().get(0);
+ Point2D nextPoint = operator.getLine().getPoints().get(1);
+ double dx = nextPoint.getX() - centerPoint.getX();
+ double dy = nextPoint.getY() - centerPoint.getY();
+ double portToCenterDistance = OPERATOR_SIZE / 2 + OPERATOR_PORT_DISTANCE;
+
+ double dx2, dy2;
+ if (dx != 0) {
+ dx2 = Math.sqrt(Math.pow(portToCenterDistance, 2) / (1 + Math.pow(dy / dx, 2)));
+ dy2 = dx2 * dy / dx;
+ } else {
+ dx2 = 0;
+ if (dy > 0) {
+ dy2 = portToCenterDistance;
+ } else {
+ dy2 = -portToCenterDistance;
+ }
+ }
+
+ port2.setX((float) (centerPoint.getX() + dx2));
+ port2.setY((float) (centerPoint.getY() + dy2));
+ sourceTargetMap.put(port2.getId(), port2);
+ newGlyph.getPort().add(port2);
+
+ Port port1 = new Port();
+ port1.setId(newGlyph.getId().concat(".1"));
+ Point2D portPoint1 = new Point2D.Double(2 * centerPoint.getX() - port2.getX(),
+ 2 * centerPoint.getY() - port2.getY());
+ port1.setX((float) portPoint1.getX());
+ port1.setY((float) portPoint1.getY());
+ sourceTargetMap.put(port1.getId(), port1);
+ newGlyph.getPort().add(port1);
+
+ sourceTargetMap.put(newGlyph.getId(), newGlyph);
+
+ return newGlyph;
+ }
+
+ /**
+ * Returns GlyphClazz adequate for given element, based on it's class.
+ *
+ * @param element
+ * element to extract GlyphCLazz from
+ * @return GlyphClazz adequate for given alias
+ */
+ private GlyphClazz getGlyphClazzFromElement(Element element) {
+ if (element instanceof Protein) {
+ Protein protein = (Protein) element;
+ if (protein.getHomodimer() == 1) {
+ return GlyphClazz.MACROMOLECULE;
+ } else {
+ return GlyphClazz.MACROMOLECULE_MULTIMER;
+ }
+ }
+
+ if (element instanceof SimpleMolecule) {
+ SimpleMolecule simpleMolecule = (SimpleMolecule) element;
+ if (simpleMolecule.getHomodimer() == 1) {
+ return GlyphClazz.SIMPLE_CHEMICAL;
+ } else {
+ return GlyphClazz.SIMPLE_CHEMICAL_MULTIMER;
+ }
+ }
+
+ if (element instanceof Ion) {
+ Ion ion = (Ion) element;
+ if (ion.getHomodimer() == 1) {
+ return GlyphClazz.SIMPLE_CHEMICAL;
+ } else {
+ return GlyphClazz.SIMPLE_CHEMICAL_MULTIMER;
+ }
+ }
+
+ if (element instanceof Gene) {
+ Gene gene = (Gene) element;
+ if (gene.getHomodimer() == 1) {
+ return GlyphClazz.NUCLEIC_ACID_FEATURE;
+ } else {
+ return GlyphClazz.NUCLEIC_ACID_FEATURE_MULTIMER;
+ }
+ }
+
+ if (element instanceof Rna) {
+ Rna rna = (Rna) element;
+ if (rna.getHomodimer() == 1) {
+ return GlyphClazz.NUCLEIC_ACID_FEATURE;
+ } else {
+ return GlyphClazz.NUCLEIC_ACID_FEATURE_MULTIMER;
+ }
+ }
+
+ if (element instanceof AntisenseRna) {
+ AntisenseRna rna = (AntisenseRna) element;
+ if (rna.getHomodimer() == 1) {
+ return GlyphClazz.NUCLEIC_ACID_FEATURE;
+ } else {
+ return GlyphClazz.NUCLEIC_ACID_FEATURE_MULTIMER;
+ }
+ }
+
+ if (element instanceof Complex) {
+ Complex complexSpecies = (Complex) element;
+ if (complexSpecies.getHomodimer() == 1) {
+ return GlyphClazz.COMPLEX;
+ } else {
+ return GlyphClazz.COMPLEX_MULTIMER;
+ }
+ }
+
+ if (element instanceof Degraded) {
+ return GlyphClazz.SOURCE_AND_SINK;
+ }
+
+ if (element instanceof Phenotype) {
+ return GlyphClazz.PHENOTYPE;
+ }
+
+ if (element instanceof Compartment) {
+ return GlyphClazz.COMPARTMENT;
+ }
+ if (element instanceof Unknown) {
+ return GlyphClazz.UNSPECIFIED_ENTITY;
+ }
+
+ logger.warn(eu.getElementTag(element)
+ + "Element type is not supported by SBGN-ML format. Unspecified Entity type assigned.");
+ return GlyphClazz.UNSPECIFIED_ENTITY;
+ }
+
+ /**
+ * Returns label for a glyph with name extracted from given element.
+ *
+ * @param element
+ * element with the name
+ * @return label for a glyph
+ */
+ private Label getGlyphLabelFromAlias(Element element) {
+ Label label = new Label();
+ label.setText(element.getName());
+ return label;
+ }
+
+ /**
+ * Returns state variable glyph parsed from {@link ModificationResidue}.
+ *
+ * @param mr
+ * {@link ModificationResidue} to be parsed
+ * @param parentGlyph
+ * parent glyph for the state variable
+ * @return state variable glyph
+ */
+ private Glyph parseStateVariable(ModificationResidue mr, Glyph parentGlyph) {
+ Glyph glyph = new Glyph();
+ glyph.setId(mr.getIdModificationResidue());
+ glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
+
+ if (mr instanceof AbstractSiteModification) {
+ AbstractSiteModification modification = (AbstractSiteModification) mr;
+ if (modification.getState() != null) {
+ Glyph.State state = new Glyph.State();
+ state.setValue(modification.getState().getAbbreviation());
+ state.setVariable(mr.getName());
+ glyph.setState(state);
+ }
+ }
+
+ Bbox bbox = new Bbox();
+
+ final float filledWidth = 70.0f;
+ final float filledHeight = 28.0f;
+ final float emptyWidth = 20.0f;
+ final float emptyHeight = 22.0f;
+ if (glyph.getState() != null) {
+ bbox.setH(filledHeight);
+ bbox.setW(filledWidth);
+ } else {
+ bbox.setH(emptyHeight);
+ bbox.setW(emptyWidth);
+ }
+
+ bbox.setX((float) mr.getPosition().getX());
+ bbox.setY((float) mr.getPosition().getY());
+
+ glyph.setBbox(bbox);
+
+ return glyph;
+ }
+
+ /**
+ * Returns glyph with unit of information extracted from the alias or null if no
+ * unit of information was found.
+ *
+ * @param alias
+ * input alias
+ * @return glyph with unit of information extracted from the alias or null if no
+ * unit of information was found
+ */
+ private Glyph getUnitOfInformationGlyph(Element alias) {
+ Glyph uoiGlyph = null;
+
+ String uoiText = "";
+ if (alias instanceof Species) {
+ Species species = (Species) alias;
+ int homodir = species.getHomodimer();
+ if (homodir > 1) {
+ uoiText = "N:".concat(Integer.toString(homodir));
+ }
+ }
+
+ if (alias instanceof TruncatedProtein) {
+ if (!uoiText.equals("")) {
+ uoiText = uoiText.concat("; ");
+ }
+ uoiText = uoiText.concat("ct:truncatedProtein");
+ }
+
+ if (alias instanceof Species) {
+ Species speciesAlias = (Species) alias;
+ if ((speciesAlias.getStateLabel() != null) && (speciesAlias.getStatePrefix() != null)) {
+ if (!uoiText.equals("")) {
+ uoiText = uoiText.concat("; ");
+ }
+ if (!speciesAlias.getStatePrefix().equals("free input")) {
+ uoiText = uoiText.concat(speciesAlias.getStatePrefix()).concat(":");
+ }
+ uoiText = uoiText.concat(speciesAlias.getStateLabel());
+ }
+ }
+
+ if (!uoiText.contains("ct:")) {
+ if (alias instanceof Rna) {
+ if (!uoiText.equals("")) {
+ uoiText = uoiText.concat("; ");
+ }
+ uoiText = uoiText.concat("ct:RNA");
+ }
+ if (alias instanceof AntisenseRna) {
+ if (!uoiText.equals("")) {
+ uoiText = uoiText.concat("; ");
+ }
+ uoiText = uoiText.concat("ct:antisenseRNA");
+ }
+ if (alias instanceof Gene) {
+ if (!uoiText.equals("")) {
+ uoiText = uoiText.concat("; ");
+ }
+ uoiText = uoiText.concat("ct:gene");
+ }
+ }
+
+ if (!uoiText.equals("")) {
+ uoiGlyph = new Glyph();
+ uoiGlyph.setClazz(GlyphClazz.UNIT_OF_INFORMATION.getClazz());
+ uoiGlyph.setId(alias.getElementId().concat("uoi"));
+
+ Label label = new Label();
+ label.setText(uoiText);
+ uoiGlyph.setLabel(label);
+
+ Bbox bbox = new Bbox();
+ bbox.setX((float) (alias.getX() + UNIT_OF_INFORMATION_MARGIN));
+ bbox.setY((float) (alias.getY() - UNIT_OF_INFORMATION_HEIGHT / 2));
+ bbox.setH((float) UNIT_OF_INFORMATION_HEIGHT);
+ bbox.setW((float) (alias.getWidth() - 2 * UNIT_OF_INFORMATION_MARGIN));
+ uoiGlyph.setBbox(bbox);
+ }
+
+ return uoiGlyph;
+ }
+
+ /**
+ * Returns process glyph created based on reaction's center point.
+ *
+ * @param reaction
+ * reaction to be parsed
+ * @return process glyph for given reaction
+ */
+ private Glyph getProcessGlyphFromReaction(Reaction reaction) {
+ Glyph processGlyph = new Glyph();
+ processGlyph.setId(reaction.getIdReaction());
+ processGlyph.setClazz(getGlyphClazzFromReaction(reaction).getClazz());
+ Bbox bbox = new Bbox();
+
+ Line2D line = reaction.getCenterLine();
+ Point2D startPoint = line.getP1();
+ Point2D endPoint = line.getP2();
+
+ double pointX = (startPoint.getX() + endPoint.getX()) / 2;
+ double pointY = (startPoint.getY() + endPoint.getY()) / 2;
+ Point2D pointNW = new Point2D.Double(pointX - ReactionConverter.RECT_SIZE / 2,
+ pointY - ReactionConverter.RECT_SIZE / 2);
+ bbox.setX((float) pointNW.getX());
+ bbox.setY((float) pointNW.getY());
+ bbox.setH((float) ReactionConverter.RECT_SIZE);
+ bbox.setW((float) ReactionConverter.RECT_SIZE);
+
+ processGlyph.setBbox(bbox);
+
+ Port reactantPort = new Port();
+ reactantPort.setId(reaction.getIdReaction().concat(".1"));
+ sourceTargetMap.put(reactantPort.getId(), reactantPort);
+
+ Port productPort = new Port();
+ productPort.setId(reaction.getIdReaction().concat(".2"));
+ sourceTargetMap.put(productPort.getId(), productPort);
+
+ // Set glyph orientation and ports' coordinates.
+ double reactantDxAverage = 0.0;
+ double reactantDyAverage = 0.0;
+ double productDxAverage = 0.0;
+ double productDyAverage = 0.0;
+
+ for (Reactant r : reaction.getReactants()) {
+ Point2D reactantPoint;
+ List<Point2D> reactantArcPoints = r.getLine().getPoints();
+ if (reaction instanceof HeterodimerAssociationReaction) {
+ reactantPoint = reactantArcPoints.get(reactantArcPoints.size() - 1);
+ } else {
+ reactantPoint = reactantArcPoints.get(reactantArcPoints.size() - 2);
+ }
+ reactantDxAverage += reactantPoint.getX() - pointX;
+ reactantDyAverage += reactantPoint.getY() - pointY;
+ }
+ reactantDxAverage /= reaction.getReactants().size();
+ reactantDyAverage /= reaction.getReactants().size();
+
+ for (Product p : reaction.getProducts()) {
+ List<Point2D> productArcPoints = p.getLine().getPoints();
+ Point2D productPoint;
+ if (reaction instanceof DissociationReaction) {
+ productPoint = productArcPoints.get(0);
+ } else {
+ productPoint = productArcPoints.get(1);
+ }
+ productDxAverage += productPoint.getX() - pointX;
+ productDyAverage += productPoint.getY() - pointY;
+ }
+ productDxAverage /= reaction.getProducts().size();
+ productDyAverage /= reaction.getProducts().size();
+
+ boolean horizontalOrientation;
+ if ((reactantDxAverage * productDxAverage < 0) && (reactantDyAverage * productDyAverage < 0)) {
+ horizontalOrientation = (Math.abs(productDxAverage - reactantDxAverage) > Math
+ .abs(productDyAverage - reactantDyAverage));
+ } else {
+ horizontalOrientation = (reactantDxAverage * productDxAverage < 0);
+ }
+ if (horizontalOrientation) {
+ processGlyph.setOrientation("horizontal");
+ reactantPort.setY((float) pointY);
+ productPort.setY((float) pointY);
+ if (reactantDxAverage < 0) {
+ reactantPort.setX((float) (pointX - PROCESS_PORT_DISTANCE));
+ productPort.setX((float) (pointX + PROCESS_PORT_DISTANCE));
+ } else {
+ reactantPort.setX((float) (pointX + PROCESS_PORT_DISTANCE));
+ productPort.setX((float) (pointX - PROCESS_PORT_DISTANCE));
+ }
+ } else {
+ reactantPort.setX((float) pointX);
+ productPort.setX((float) pointX);
+ if (reactantDyAverage < 0) {
+ reactantPort.setY((float) (pointY - PROCESS_PORT_DISTANCE));
+ productPort.setY((float) (pointY + PROCESS_PORT_DISTANCE));
+ } else {
+ reactantPort.setY((float) (pointY + PROCESS_PORT_DISTANCE));
+ productPort.setY((float) (pointY - PROCESS_PORT_DISTANCE));
+ }
+ processGlyph.setOrientation("vertical");
+ }
+
+ processGlyph.getPort().add(reactantPort);
+ processGlyph.getPort().add(productPort);
+
+ sourceTargetMap.put(processGlyph.getId(), processGlyph);
+
+ return processGlyph;
+ }
+
+ /**
+ * Returns {@link GlyphClazz} appropriate to given reaction.
+ *
+ * @param reaction
+ * {@link Reaction} to extract {@link GlyphClazz} from
+ * @return {@link GlyphClazz} appropriate to given reaction
+ */
+ private GlyphClazz getGlyphClazzFromReaction(Reaction reaction) {
+ if (reaction instanceof StateTransitionReaction) {
+ return GlyphClazz.PROCESS;
+ }
+ if (reaction instanceof HeterodimerAssociationReaction) {
+ return GlyphClazz.ASSOCIATION;
+ }
+ if (reaction instanceof DissociationReaction) {
+ return GlyphClazz.DISSOCIATION;
+ }
+ if (reaction instanceof KnownTransitionOmittedReaction) {
+ return GlyphClazz.OMITTED_PROCESS;
+ }
+ if (reaction instanceof UnknownTransitionReaction) {
+ return GlyphClazz.UNCERTAIN_PROCESS;
+ }
+ throw new InvalidArgumentException();
+ }
+
+ /**
+ * Returns arc extracted from given reduced notation reaction.
+ *
+ * @param reaction
+ * reduced notation reaction
+ * @return arc extracted from given reduced notation reaction
+ */
+ private Arc getArcFromReducedReaction(Reaction reaction) {
+ if ((reaction.getReactants().size() != 1) || (reaction.getProducts().size() != 1)) {
+ throw new InvalidArgumentException();
+ }
+ Arc arc = new Arc();
+ arc.setId(reaction.getIdReaction());
+
+ if (reaction instanceof NegativeInfluenceReaction) {
+ arc.setClazz(ArcClazz.INHIBITION.getClazz());
+ } else if (reaction instanceof ReducedModulationReaction) {
+ arc.setClazz(ArcClazz.MODULATION.getClazz());
+ } else if (reaction instanceof ReducedTriggerReaction) {
+ arc.setClazz(ArcClazz.NECESSARY_STIMULATION.getClazz());
+ } else if (reaction instanceof ReducedPhysicalStimulationReaction) {
+ arc.setClazz(ArcClazz.STIMULATION.getClazz());
+ } else {
+ throw new InvalidArgumentException();
+ }
+
+ if (reaction.getProducts().get(0).getElement() instanceof Phenotype) {
+ logger.warn("Found Phenotype being a reactant in process. That is discouraged");
+ }
+
+ arc.setSource(sourceTargetMap.get(reaction.getReactants().get(0).getElement().getElementId()));
+ arc.setTarget(sourceTargetMap.get(reaction.getProducts().get(0).getElement().getElementId()));
+
+ List<Point2D> pointList = reaction.getReactants().get(0).getLine().getPoints();
+ pointList.addAll(reaction.getProducts().get(0).getLine().getPoints());
+
+ removeRedundantPoints(pointList);
+
+ Start start = new Start();
+ start.setX((float) pointList.get(0).getX());
+ start.setY((float) pointList.get(0).getY());
+ arc.setStart(start);
+
+ End end = new End();
+ end.setX((float) pointList.get(pointList.size() - 1).getX());
+ end.setY((float) pointList.get(pointList.size() - 1).getY());
+ arc.setEnd(end);
+
+ for (int i = 1; i < pointList.size() - 1; i++) {
+ Point2D nextPoint = pointList.get(i);
+ Next next = new Next();
+ next.setX((float) nextPoint.getX());
+ next.setY((float) nextPoint.getY());
+ arc.getNext().add(next);
+ }
+
+ return arc;
+ }
+
+ /**
+ * Removes redundant points from the list.
+ *
+ * @param pointList
+ * list of points to be fixed
+ */
+ private void removeRedundantPoints(List<Point2D> pointList) {
+ boolean allDone = false;
+ while (!allDone) {
+ allDone = true;
+ for (int i = 1; i < pointList.size() - 1; i++) {
+ double dx1 = pointList.get(i).getX() - pointList.get(i - 1).getX();
+ double dy1 = pointList.get(i).getY() - pointList.get(i - 1).getY();
+ double dx2 = pointList.get(i + 1).getX() - pointList.get(i).getX();
+ double dy2 = pointList.get(i + 1).getY() - pointList.get(i).getY();
+
+ DoubleComparator doubleComparator = new DoubleComparator();
+ if (((doubleComparator.compare(dy1 / dx1, dy2 / dx2) == 0)
+ || (pointList.get(i - 1).getY() == pointList.get(i).getY())
+ && (pointList.get(i).getY() == pointList.get(i + 1).getY()))
+ && between(pointList.get(i).getX(), pointList.get(i - 1).getX(), pointList.get(i + 1).getX())) {
+ pointList.remove(i);
+ allDone = false;
+ }
+ }
+ }
+ }
+
+ /**
+ * Checks if argument x is between s1 and s2.
+ *
+ * @param x
+ * number to checked if it is in the middle
+ * @param s1
+ * one side argument
+ * @param s2
+ * second side argument
+ * @return true if x is between s1 and s2
+ */
+ private boolean between(double x, double s1, double s2) {
+ if ((x >= s1) && (x <= s2)) {
+ return true;
+ }
+ if ((x <= s1) && (x >= s2)) {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Returns set of all arcs used in the reaction.
+ *
+ * @param reaction
+ * the reaction to extract arcs from
+ * @param glyphList
+ * list of all glyphs in the map; used only for parsing operators
+ * @return set of all arcs used in the reaction
+ */
+ private List<Arc> getArcsFromReaction(Reaction reaction, List<Glyph> glyphList) {
+ List<Arc> arcList = new ArrayList<>();
+
+ // Parse all nodes except NodeOperators
+ for (AbstractNode node : reaction.getNodes().stream().filter(n -> !(n instanceof NodeOperator))
+ .collect(Collectors.toList())) {
+ try {
+ arcList.add(getArcFromNode(node, glyphList));
+ } catch (InvalidArgumentException ex) {
+ logger.warn("Node skipped in export process, since it is not compliant with SBGN-ML format: "
+ + node.getClass().getName());
+ continue;
+ }
+ }
+
+ // Now parse NodeOperators
+ for (AbstractNode node : reaction.getOperators().stream().filter(o -> {
+ if (o.getInputs().stream().filter(i -> i instanceof Reactant).count() > 0) {
+ return false;
+ }
+ if (o instanceof SplitOperator || o instanceof AssociationOperator || o instanceof DissociationOperator) {
+ return false;
+ }
+ return true;
+ }).collect(Collectors.toList())) {
+ try {
+ arcList.add(getArcFromNode(node, glyphList));
+ } catch (InvalidArgumentException ex) {
+ logger.warn("Node skipped in export process, since it is not compliant with SBGN-ML format: "
+ + node.getClass().getName());
+ continue;
+ }
+ }
+
+ return arcList;
+
+ }
+
+ /**
+ * Returns arc for given node.
+ *
+ * @param node
+ * node to parse arc from
+ * @param glyphList
+ * list of all glyphs in the map; used only for parsing operators
+ * @return SBGN-ML arc for given node
+ */
+ private Arc getArcFromNode(AbstractNode node, List<Glyph> glyphList) {
+ Arc arc = new Arc();
+ arc.setId("arc".concat(Integer.toString(arcCounter)));
+ arcCounter += 1;
+
+ boolean logicArc = false;
+ if (node instanceof Modifier) {
+ for (NodeOperator operator : node.getReaction().getOperators()) {
+ if (operator.getInputs().contains(node)) {
+ logicArc = true;
+ }
+ }
+ }
+ if (logicArc) {
+ arc.setClazz(ArcClazz.LOGIC_ARC.getClazz());
+ } else {
+ arc.setClazz(getArcClazzFromNode(node));
+ }
+
+ if (node instanceof Reactant) {
+ arc.setSource(sourceTargetMap.get(((Reactant) node).getElement().getElementId()));
+ arc.setTarget(sourceTargetMap.get(node.getReaction().getIdReaction().concat(".1")));
+ } else if (node instanceof Product) {
+ arc.setSource(sourceTargetMap.get(node.getReaction().getIdReaction().concat(".2")));
+ arc.setTarget(sourceTargetMap.get(((Product) node).getElement().getElementId()));
+ } else if (node instanceof Modifier) {
+ arc.setSource(sourceTargetMap.get(((Modifier) node).getElement().getElementId()));
+ if (!node.getLine().getEndAtd().getArrowType().equals(ArrowType.NONE)) {
+ arc.setTarget(sourceTargetMap.get(node.getReaction().getIdReaction()));
+ } else {
+ for (NodeOperator operator : node.getReaction().getOperators()) {
+ if (operator.getInputs().contains(node)) {
+ if (!parsedOperators.contains(operator)) {
+ Glyph newOperator = operatorToGlyph(operator);
+ glyphList.add(newOperator);
+ }
+ arc.setTarget(sourceTargetMap.get(operatorIds.get(operator).concat(".1")));
+ }
+ }
+ }
+ } else if (node instanceof NodeOperator) {
+ if ((node instanceof DissociationOperator) || (node instanceof AssociationOperator)) {
+ throw new InvalidArgumentException();
+ }
+ arc.setSource(sourceTargetMap.get(operatorIds.get(node).concat(".2")));
+ if (!node.getLine().getEndAtd().getArrowType().equals(ArrowType.NONE)) {
+ arc.setTarget(sourceTargetMap.get(node.getReaction().getIdReaction()));
+ } else {
+ for (NodeOperator operator : node.getReaction().getOperators()) {
+ if (operator.getInputs().contains(node)) {
+ if (!parsedOperators.contains(operator)) {
+ Glyph newOperator = operatorToGlyph(operator);
+ glyphList.add(newOperator);
+ }
+ arc.setTarget(sourceTargetMap.get(operatorIds.get(operator).concat(".1")));
+ }
+ }
+ }
+ }
+
+ List<Point2D> arcPoints = node.getLine().getPoints();
+ Start start = new Start();
+ if ((node instanceof Product) || (node instanceof NodeOperator)) {
+ Port sourcePort = (Port) arc.getSource();
+ start.setX(sourcePort.getX());
+ start.setY(sourcePort.getY());
+ } else {
+ start.setX((float) arcPoints.get(0).getX());
+ start.setY((float) arcPoints.get(0).getY());
+ }
+ arc.setStart(start);
+
+ End end = new End();
+ if ((node instanceof Reactant) || ((node instanceof Modifier) && (arc.getTarget() instanceof Port))) {
+ Port targetPort = (Port) arc.getTarget();
+ end.setX(targetPort.getX());
+ end.setY(targetPort.getY());
+ } else {
+ Point2D lastPoint = arcPoints.get(arcPoints.size() - 1);
+ end.setX((float) lastPoint.getX());
+ end.setY((float) lastPoint.getY());
+ }
+ arc.setEnd(end);
+
+ if ((node instanceof Product) && (node.getReaction() instanceof DissociationReaction)) {
+ Point2D nextPoint = arcPoints.get(0);
+ Next next = new Next();
+ next.setX((float) nextPoint.getX());
+ next.setY((float) nextPoint.getY());
+ arc.getNext().add(next);
+ }
+
+ DoubleComparator doubleComparator = new DoubleComparator();
+ for (int i = 1; i < arcPoints.size() - 1; i++) {
+ Point2D nextPoint = arcPoints.get(i);
+ if ((doubleComparator.compare(nextPoint.getX(), new Double(start.getX())) == 0)
+ && (doubleComparator.compare(nextPoint.getY(), new Double(start.getY())) == 0)) {
+ arc.getNext().clear();
+ continue;
+ }
+ if ((doubleComparator.compare(nextPoint.getX(), new Double(end.getX())) == 0)
+ && (doubleComparator.compare(nextPoint.getY(), new Double(end.getY())) == 0)) {
+ break;
+ }
+ Next next = new Next();
+ next.setX((float) nextPoint.getX());
+ next.setY((float) nextPoint.getY());
+ arc.getNext().add(next);
+ }
+
+ if ((node instanceof Reactant) && (node.getReaction() instanceof HeterodimerAssociationReaction)) {
+ Point2D nextPoint = arcPoints.get(arcPoints.size() - 1);
+ Next next = new Next();
+ next.setX((float) nextPoint.getX());
+ next.setY((float) nextPoint.getY());
+ arc.getNext().add(next);
+ }
+
+ return arc;
+ }
+
+ /**
+ * Returns {@link ArcClazz} for given node.
+ *
+ * @param node
+ * Node to extract {@link ArcClazz} from
+ * @return {@link ArcClazz} for given node
+ */
+ private String getArcClazzFromNode(AbstractNode node) {
+ if (node instanceof Reactant) {
+ return ArcClazz.CONSUMPTION.getClazz();
+ }
+ if (node instanceof Product) {
+ return ArcClazz.PRODUCTION.getClazz();
+ }
+ if (node instanceof Catalysis) {
+ return ArcClazz.CATALYSIS.getClazz();
+ }
+ if (node instanceof Inhibition) {
+ return ArcClazz.INHIBITION.getClazz();
+ }
+ if (node instanceof Modulation) {
+ return ArcClazz.MODULATION.getClazz();
+ }
+ if (node instanceof Trigger) {
+ return ArcClazz.NECESSARY_STIMULATION.getClazz();
+ }
+ if (node instanceof PhysicalStimulation) {
+ return ArcClazz.STIMULATION.getClazz();
+ }
+ if (node instanceof NodeOperator) {
+ ArrowType arrowType = node.getLine().getEndAtd().getArrowType();
+ switch (arrowType) {
+ case BLANK:
+ return ArcClazz.STIMULATION.getClazz();
+ case BLANK_CROSSBAR:
+ return ArcClazz.NECESSARY_STIMULATION.getClazz();
+ case CIRCLE:
+ return ArcClazz.CATALYSIS.getClazz();
+ case CROSSBAR:
+ return ArcClazz.INHIBITION.getClazz();
+ case DIAMOND:
+ return ArcClazz.MODULATION.getClazz();
+ case NONE:
+ return ArcClazz.LOGIC_ARC.getClazz();
+ default:
+ throw new InvalidArgumentException();
+
+ }
+ }
+ throw new InvalidArgumentException();
+ }
+}
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index 3733c04f545ddf0b3ee7bfc46508dcc1750c2634..c38a6e2e9482a7509ab690f8e0306f6303f6a03c 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -1,1535 +1,1550 @@
-package lcsb.mapviewer.converter.model.sbgnml;
-
-import java.awt.Color;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.sbgn.ArcClazz;
-import org.sbgn.GlyphClazz;
-import org.sbgn.SbgnUtil;
-import org.sbgn.bindings.Arc;
-import org.sbgn.bindings.Arc.End;
-import org.sbgn.bindings.Arc.Next;
-import org.sbgn.bindings.Arc.Start;
-import org.sbgn.bindings.Bbox;
-import org.sbgn.bindings.Glyph;
-import org.sbgn.bindings.Map;
-import org.sbgn.bindings.Port;
-import org.sbgn.bindings.Sbgn;
-
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
-import lcsb.mapviewer.converter.model.sbgnml.structures.Process;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.modifier.Inhibition;
-import lcsb.mapviewer.model.map.modifier.Modulation;
-import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
-import lcsb.mapviewer.model.map.modifier.Trigger;
-import lcsb.mapviewer.model.map.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.OrOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.SplitOperator;
-import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
-import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
-import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.Unknown;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-/**
- * This class is a parser for SBGN-ML files.
- *
- * @author Michał Kuźma
- *
- */
-public class SbgnmlXmlParser {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(SbgnmlXmlParser.class.getName());
-
- /**
- * List of all processes to be parsed.
- */
- private List<Process> processes = new ArrayList<Process>();
-
- /**
- * List of all logic operator glyphs parsed so far.
- */
- private List<Glyph> logicOperators = new ArrayList<Glyph>();
-
- /**
- * List of all logic arcs parsed so far.
- */
- private List<Arc> logicArcs = new ArrayList<Arc>();
-
- /**
- * Default margin for container name.
- */
- private static final double CONTAINER_NAME_MARGIN = 5.0;
-
- /**
- * Part of height of the line used to cross degraded circle that goes behind
- * this circle.
- */
- private static final int CROSS_LINE_EXTENDED_LENGTH = 7;
-
- /**
- * Default color for parsed compartments.
- */
- private static final Color COMPARTMENT_COLOR = new Color(0.5f, 0.5f, 1.0f);
-
- /**
- * Method used to create a model from SBGN-ML file.
- *
- * @param params
- * parameters needed for parsing file and creating a model
- * @return valid model parsed from the file
- * @throws InvalidInputDataExecption
- * thrown when input file is invalid
- */
- public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
-
- Model model = new ModelFullIndexed(null);
- model.setIdModel(params.getFilename());
-
- // Input file
- File inputSbgnmlFile = inputStreamToFile(params.getInputStream());
-
- Sbgn sbgnData;
- // Check if input file has valid SBGN-ML data
- try {
- if (!SbgnUtil.isValid(inputSbgnmlFile)) {
- throw new InvalidInputDataExecption("Given input is not a valid SBGN-ML file.");
- }
-
- // Read data from file
- sbgnData = SbgnUtil.readFromFile(inputSbgnmlFile);
- } catch (InvalidInputDataExecption ex) {
- throw ex;
- } catch (Exception ex) {
- throw new InvalidInputDataExecption("Unable to read given file.", ex);
- }
-
- // Extract map with all the glyphs and arcs
- Map map = sbgnData.getMap();
-
- adjustSizeOfElements(map);
-
- setModelSize(map, model);
-
- // Iterate over every glyph
- for (Glyph g : map.getGlyph()) {
- parseGlyph(g, model);
- }
-
- // Iterate over every arc in the map
- for (Arc a : map.getArc()) {
- parseArc(a, model);
- }
-
- // Parse all processes created before
- for (Process p : processes) {
- try {
- parseProcess(p, model);
- } catch (Exception e) {
- logger.warn("Unable to parse the process: " + p.getCentralPoint().getId());
- }
- }
-
- return model;
- }
-
- /**
- * Writes input stream into a File.
- *
- * @param inputStream
- * Input stream to be written to File
- * @return File handle
- */
- private File inputStreamToFile(InputStream inputStream) {
- File tempFile = null;
- try {
- tempFile = File.createTempFile("stream2file", ".tmp");
- tempFile.deleteOnExit();
- try (FileOutputStream out = new FileOutputStream(tempFile)) {
- IOUtils.copy(inputStream, out);
- }
- } catch (Exception ex) {
- logger.debug("Unable to create temporary file.");
- return null;
- }
- return tempFile;
- }
-
- /**
- * Method used to adjust the size of elements that have their size represented
- * different in the SBGN-ML file. Adjusted elements: Source and Sink /
- * Degraded elements, Multimers.
- *
- * @param map
- * Map parsed from SBGN-ML file
- */
- private void adjustSizeOfElements(Map map) {
- for (Glyph g : map.getGlyph()) {
- GlyphClazz glyphClazz = GlyphClazz.fromClazz(g.getClazz());
- switch (glyphClazz) {
- case SOURCE_AND_SINK:
- g.getBbox().setH(g.getBbox().getH() + 2 * CROSS_LINE_EXTENDED_LENGTH);
- g.getBbox().setW(g.getBbox().getW() + 2 * CROSS_LINE_EXTENDED_LENGTH);
- g.getBbox().setX(g.getBbox().getX() - CROSS_LINE_EXTENDED_LENGTH);
- g.getBbox().setY(g.getBbox().getY() - CROSS_LINE_EXTENDED_LENGTH);
- break;
- case COMPLEX_MULTIMER:
- case MACROMOLECULE_MULTIMER:
- case NUCLEIC_ACID_FEATURE_MULTIMER:
- case SIMPLE_CHEMICAL_MULTIMER:
- int cardinality;
- try {
- cardinality = getMultimerCardinality(g);
- } catch (Exception ex) {
- cardinality = 2;
- logger.warn(ex.getMessage() + " Set the default value of 2.");
- }
- g.getBbox().setW(g.getBbox().getW() + (cardinality - 1) * SpeciesConverter.HOMODIMER_OFFSET);
- g.getBbox().setH(g.getBbox().getH() + (cardinality - 1) * SpeciesConverter.HOMODIMER_OFFSET);
- break;
- default:
- break;
- }
- }
- }
-
- /**
- * Method used to compute height and width of the model.
- *
- * @param map
- * Map parsed from SBGN-ML file
- * @param model
- * Model to be updated
- */
- private void setModelSize(Map map, Model model) {
- double minX = Double.MAX_VALUE;
- double minY = Double.MAX_VALUE;
- double maxX = 0;
- double maxY = 0;
-
- // Iterate over every glyph
- for (Glyph g : map.getGlyph()) {
- if (GlyphClazz.fromClazz(g.getClazz()).equals(GlyphClazz.ANNOTATION) || GlyphClazz.fromClazz(g.getClazz()).equals(GlyphClazz.TAG)) {
- continue;
- }
- Bbox bbox = g.getBbox();
- if (bbox != null) {
- if (bbox.getX() < minX) {
- minX = bbox.getX();
- }
- if (bbox.getY() < minY) {
- minY = bbox.getY();
- }
- if (bbox.getX() + bbox.getW() > maxX) {
- maxX = bbox.getX() + bbox.getW();
- }
- if (bbox.getY() + bbox.getH() > maxY) {
- maxY = bbox.getY() + bbox.getH();
- }
- }
- }
-
- // Iterate over every arc
- for (Arc a : map.getArc()) {
- // Since submaps are not yet supported, the arcs connecting them or
- // tags cannot be used when computing width and height of the model.
- boolean connectsTagOrSubmap = false;
- if (a.getSource() instanceof Glyph) {
- Glyph sourceGlyph = (Glyph) a.getSource();
- if (GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.TAG) || GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.SUBMAP)) {
- connectsTagOrSubmap = true;
- }
- }
- if (a.getTarget() instanceof Glyph) {
- Glyph targetGlyph = (Glyph) a.getTarget();
- if (GlyphClazz.fromClazz(targetGlyph.getClazz()).equals(GlyphClazz.TAG) || GlyphClazz.fromClazz(targetGlyph.getClazz()).equals(GlyphClazz.SUBMAP)) {
- connectsTagOrSubmap = true;
- }
- }
- // If the arc is not connecting a submap or a tag, check it's points
- if (!connectsTagOrSubmap) {
- Start aStart = a.getStart();
- if (aStart.getX() < minX) {
- minX = aStart.getX();
- }
- if (aStart.getX() > maxX) {
- maxX = aStart.getX();
- }
- if (aStart.getY() < minY) {
- minY = aStart.getY();
- }
- if (aStart.getY() > maxY) {
- maxY = aStart.getY();
- }
- End aEnd = a.getEnd();
- if (aEnd.getX() < minX) {
- minX = aEnd.getX();
- }
- if (aEnd.getX() > maxX) {
- maxX = aEnd.getX();
- }
- if (aEnd.getY() < minY) {
- minY = aEnd.getY();
- }
- if (aEnd.getY() > maxY) {
- maxY = aEnd.getY();
- }
- for (Next aNext : a.getNext()) {
- if (aNext.getX() < minX) {
- minX = aNext.getX();
- }
- if (aNext.getX() > maxX) {
- maxX = aNext.getX();
- }
- if (aNext.getY() < minY) {
- minY = aNext.getY();
- }
- if (aNext.getY() > maxY) {
- maxY = aNext.getY();
- }
- }
- }
- }
-
- model.setWidth(maxX + minX);
- model.setHeight(maxY + minY);
- }
-
- /**
- * Method used to parse a single glyph.
- *
- * @param g
- * glyph to be parsed
- * @param model
- * model to be updated
- * @throws Exception
- */
- private void parseGlyph(Glyph g, Model model) {
- Species newSpecies = null;
- switch (GlyphClazz.fromClazz(g.getClazz())) {
- case AND:
- case NOT:
- case OR:
- logicOperators.add(g);
- break;
- case COMPARTMENT:
- parseCompartment(g, model);
- break;
- case COMPLEX:
- parseComplex(g, null, true, model);
- break;
- case COMPLEX_MULTIMER:
- parseComplex(g, null, false, model);
- break;
- case MACROMOLECULE:
- newSpecies = new GenericProtein(g.getId());
- parseSpecies(g, newSpecies, true, model);
- break;
- case MACROMOLECULE_MULTIMER:
- newSpecies = new GenericProtein(g.getId());
- parseSpecies(g, newSpecies, false, model);
- break;
- case NUCLEIC_ACID_FEATURE:
- if (isRNA(g)) {
- newSpecies = new Rna(g.getId());
- } else {
- newSpecies = new Gene(g.getId());
- }
- parseSpecies(g, newSpecies, true, model);
- break;
- case NUCLEIC_ACID_FEATURE_MULTIMER:
- if (isRNA(g)) {
- newSpecies = new Rna(g.getId());
- } else {
- newSpecies = new Gene(g.getId());
- }
- parseSpecies(g, newSpecies, false, model);
- break;
- case PERTURBING_AGENT:
- newSpecies = new Phenotype(g.getId());
- parseSpecies(g, newSpecies, true, model);
- break;
- case PHENOTYPE:
- newSpecies = new Phenotype(g.getId());
- parseSpecies(g, newSpecies, true, model);
- break;
- case ASSOCIATION:
- case DISSOCIATION:
- case OMITTED_PROCESS:
- case PROCESS:
- case UNCERTAIN_PROCESS:
- processes.add(new Process(g));
- break;
- case SIMPLE_CHEMICAL:
- newSpecies = new SimpleMolecule(g.getId());
- parseSpecies(g, newSpecies, true, model);
- break;
- case SIMPLE_CHEMICAL_MULTIMER:
- newSpecies = new SimpleMolecule(g.getId());
- parseSpecies(g, newSpecies, false, model);
- break;
- case SOURCE_AND_SINK:
- newSpecies = new Degraded(g.getId());
- parseSpecies(g, newSpecies, true, model);
- break;
- case TAG:
- case SUBMAP:
- logger.warn("Submaps are not supported. Glyph: " + g.getId() + " has not been parsed.");
- case UNSPECIFIED_ENTITY:
- newSpecies = new Unknown(g.getId());
- parseSpecies(g, newSpecies, true, model);
- break;
- default:
- logger.warn("The glyph " + g.getId() + " of class " + g.getClazz() + " has not been parsed, since it is invalid for SBGN PD map.");
- break;
- }
- }
-
- /**
- * Method used to parse a single arc.
- *
- * @param a
- * arc to be parsed
- * @param model
- * model to be updated
- */
- private void parseArc(Arc a, Model model) {
- switch (ArcClazz.fromClazz(a.getClazz())) {
- case CONSUMPTION:
- Port arcTargetPort = (Port) a.getTarget();
- for (Process p : processes) {
- if (p.getCentralPoint().getPort().contains(arcTargetPort)) {
- p.addReagentArc(a);
- break;
- }
- }
- break;
- case PRODUCTION:
- Port arcSourcePort = (Port) a.getSource();
- for (Process p : processes) {
- if (p.getCentralPoint().getPort().contains(arcSourcePort)) {
- p.addProductArc(a);
- break;
- }
- }
- break;
- case EQUIVALENCE_ARC:
- logger.warn("Submaps are not supported. Equivalence arc: " + a.getId() + " has not been parsed.");
- break;
- case LOGIC_ARC:
- logicArcs.add(a);
- break;
- case CATALYSIS:
- case INHIBITION:
- case MODULATION:
- case NECESSARY_STIMULATION:
- case STIMULATION:
- Glyph targetGlyph = (Glyph) a.getTarget();
- if (GlyphClazz.fromClazz(targetGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)) {
- if (!(a.getSource() instanceof Glyph)) {
- logger.warn("Invalid phenotype arc: " + a.getId());
- break;
- }
- try {
- parsePhenotypeArc(a, model);
- } catch (Exception ex) {
- logger.warn(ex.getMessage());
- }
- break;
- }
- if (a.getSource() instanceof Glyph) {
- Glyph sourceGlyph = (Glyph) a.getSource();
- if (GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)
- && (model.getElementByElementId(targetGlyph.getId()) instanceof Species)) {
- try {
- parsePhenotypeArc(a, model);
- } catch (InvalidArgumentException ex) {
- logger.warn("The arc " + a.getId() + " of class " + a.getClazz() + " is not a valid reduced notation arc.");
- }
- break;
- }
- }
- for (Process p : processes) {
- if (p.getCentralPoint().getId().equals(targetGlyph.getId())) {
- p.addInfluenceArc(a);
- break;
- }
- }
- break;
- default:
- logger.warn("The arc " + a.getId() + " of class " + a.getClazz() + " has not been parsed, since it is invalid for SBGN PD map.");
- }
- }
-
- /**
- * Method used to parse arc going to or from a phenotype.
- *
- * @param a
- * arc to be parsed
- * @param model
- * model to be updated
- */
- private void parsePhenotypeArc(Arc a, Model model) {
- Reaction reaction;
-
- switch (ArcClazz.fromClazz(a.getClazz())) {
-
- case INHIBITION:
- reaction = new NegativeInfluenceReaction();
- break;
- case MODULATION:
- reaction = new ReducedModulationReaction();
- break;
- case NECESSARY_STIMULATION:
- reaction = new ReducedTriggerReaction();
- break;
- case STIMULATION:
- reaction = new ReducedPhysicalStimulationReaction();
- break;
- default:
- throw new InvalidArgumentException();
- }
-
- reaction.setIdReaction(a.getId());
- reaction.setModel(model);
-
- Reactant reactant = new Reactant();
- reactant.setReaction(reaction);
- Glyph source = (Glyph) a.getSource();
- reactant.setElement(model.getElementByElementId(source.getId()));
- List<Point2D> reactantPointList = new ArrayList<>();
- reactantPointList.add(new Point2D.Double(a.getStart().getX(), a.getStart().getY()));
- reactantPointList.add(new Point2D.Double(a.getStart().getX(), a.getStart().getY()));
- PolylineData reactantLine = new PolylineData(reactantPointList);
- ArrowTypeData atd = new ArrowTypeData();
- atd.setArrowType(ArrowType.NONE);
- atd.setArrowLineType(LineType.SOLID);
- reactantLine.setEndAtd(atd);
- reactant.setLine(reactantLine);
- reaction.addReactant(reactant);
-
- Product product = new Product();
- product.setReaction(reaction);
- Glyph target = (Glyph) a.getTarget();
- product.setElement(model.getElementByElementId(target.getId()));
- List<Point2D> productPointList = getLinePoints(a);
- PolylineData productLine = parseLine(a, productPointList);
- product.setLine(productLine);
- reaction.addProduct(product);
-
- model.addReaction(reaction);
- }
-
- /**
- * Method used to parse a single species.
- *
- * @param g
- * SBGN-ML glyph representing the species
- * @param newSpecies
- * species to be parsed
- * @param isHomodimer
- * true if parsed species is not multimer
- * @param model
- * model to be updated
- */
- private void parseSpecies(Glyph g, Species newSpecies, boolean isHomodimer, Model model) {
- newSpecies.setModel(model);
- // If Glyph has label with a name, set it as Species name. If not, set
- // Id as name.
- if (g.getLabel() != null) {
- newSpecies.setName(g.getLabel().getText());
- } else {
- newSpecies.setName(g.getId());
- }
- // Add species to parent complex if there is one
- if (newSpecies.getComplex() != null) {
- newSpecies.getComplex().addSpecies(newSpecies);
- }
- // If the species is a multimer, set it's cardinality.
- if (!isHomodimer) {
- try {
- newSpecies.setHomodimer(getMultimerCardinality(g));
- } catch (Exception ex) {
- newSpecies.setHomodimer(2);
- logger.warn(ex.getMessage() + " Set the default value of 2.");
- }
- }
-
- List<Glyph> children = g.getGlyph();
- for (Glyph child : children) {
- if (GlyphClazz.fromClazz(child.getClazz()).equals(GlyphClazz.STATE_VARIABLE)) {
- if (child.getState() == null || child.getState().getVariable() != null) {
- try {
- parseStateVariable(child, g, newSpecies);
- } catch (Exception ex) {
- logger.warn(ex.getMessage());
- }
- } else {
- String structuralState = child.getState().getValue();
- if (newSpecies instanceof Protein) {
- Protein protein = (Protein) newSpecies;
- protein.setStructuralState(structuralState);
- } else if (newSpecies instanceof Complex) {
- Complex complex = (Complex) newSpecies;
- complex.setStructuralState(structuralState);
- }
- }
- }
- }
-
- parseSpecies(g, newSpecies, model);
- }
-
- /**
- * Method used to create a new alias from SBGN-ML glyph.
- *
- * @param glyph
- * SBGN-ML glyph representing the alias
- * @param species
- * species of the alias
- * @param model
- * model to be updated
- */
- private void parseSpecies(Glyph glyph, Species species, Model model) {
- species.setHeight(new Double(glyph.getBbox().getH()));
- species.setWidth(new Double(glyph.getBbox().getW()));
- species.setX(new Double(glyph.getBbox().getX()));
- species.setY(new Double(glyph.getBbox().getY()));
-
- Compartment parentCompartment = null;
- if (glyph.getCompartmentRef() != null) {
- Glyph compartmentGlyph = (Glyph) glyph.getCompartmentRef();
- parentCompartment = model.getElementByElementId(compartmentGlyph.getId());
- } else if (species.getComplex() == null) {
- parentCompartment = findParentCompartment(species, model);
- }
- if (parentCompartment != null) {
- species.setCompartment(parentCompartment);
- parentCompartment.addElement(species);
- }
-
- // Parse units of information
- for (Glyph child : glyph.getGlyph()) {
- if (GlyphClazz.fromClazz(child.getClazz()).equals(GlyphClazz.UNIT_OF_INFORMATION)) {
- parseUnitOfInformation(child, species);
- }
- }
-
- model.addElement(species);
- }
-
- /**
- * Finds a compartment where element should be located (base on the
- * coordinates).
- *
- * @param child
- * {@link Element} for which we want to find compartment
- * @param model
- * {@link Model} where we look for a compartment
- * @return parent {@link Compartment}
- */
- private Compartment findParentCompartment(Element child, Model model) {
- Compartment nullParent = new Compartment("null");
- nullParent.setWidth(Double.MAX_VALUE);
- nullParent.setHeight(Double.MAX_VALUE);
- nullParent.setX(0.0);
- nullParent.setY(0.0);
- Compartment parent = nullParent;
- for (Compartment potentialParent : model.getCompartments()) {
- if (potentialParent.contains(child)) {
- if (parent.getSize() > potentialParent.getSize()) {
- parent = potentialParent;
- }
- }
- }
- if (parent != nullParent) {
- return parent;
- } else {
- return null;
- }
- }
-
- /**
- * Method used to retrieve multimer cardinality from a multimer glyph.
- *
- * @param g
- * multimer glyph
- * @return multimer cardinality
- * @throws Exception
- * Exception is thrown if no proper unit of information with
- * cardinality was found
- */
- private int getMultimerCardinality(Glyph g) throws Exception {
- int multimerCardinality = 0;
- // Check all the children nodes looking for unit of information with
- // cardinality
- List<Glyph> children = g.getGlyph();
- for (Glyph child : children) {
- if (GlyphClazz.fromClazz(child.getClazz()) == GlyphClazz.UNIT_OF_INFORMATION) {
- String[] splitLabel = child.getLabel().getText().split(":");
- multimerCardinality = Integer.parseInt(splitLabel[1]);
- }
- }
- // If no unit of information was found, or the cardinality is invalid,
- // raise exception
- if (multimerCardinality <= 0) {
- throw new Exception("No proper unit of information with multimer cardinality was found." + " Glyph: " + g.getId());
- }
-
- return multimerCardinality;
- }
-
- /**
- * Method used to decide if Nucleic-acid feature should be translated to RNA.
- *
- * @param g
- * Nucleic-acid feature glyph
- * @return true if input is RNA
- */
- private boolean isRNA(Glyph g) {
- boolean rna = false;
- // Check all the children nodes looking for unit of information
- List<Glyph> children = g.getGlyph();
- for (Glyph child : children) {
- if (GlyphClazz.fromClazz(child.getClazz()) == GlyphClazz.UNIT_OF_INFORMATION) {
- if (child.getLabel().getText().toLowerCase().contains("rna")) {
- rna = true;
- }
- }
- }
-
- return rna;
- }
-
- /**
- * Method used to parse state variable.
- *
- * @param unitOfInformationGlyph
- * unit of information glyph from sbgn-ml file
- * @param speciesGlyph
- * glyph that the unit of information considers
- * @param newSpecies
- * species that the unit of information considers
- * @throws Exception
- * Exception is thrown if state variable is parsed for species other
- * than Protein
- */
- private void parseStateVariable(Glyph unitOfInformationGlyph, Glyph speciesGlyph, Species newSpecies) throws Exception {
- if (!(newSpecies instanceof Protein)) {
- throw new Exception("Only macromolecule elements can have state variables.");
- }
- Protein protein = (Protein) newSpecies;
- ModificationResidue mr = new ModificationResidue();
-
- mr.setSpecies(protein);
- mr.setIdModificationResidue(unitOfInformationGlyph.getId());
- if (unitOfInformationGlyph.getState() != null) {
- // If State variable consists of value and variable
- mr.setName(unitOfInformationGlyph.getState().getVariable());
- for (ModificationState ms : ModificationState.values()) {
- if (ms.getAbbreviation().equals(unitOfInformationGlyph.getState().getValue())) {
- mr.setState(ms);
- }
- }
- }
-
- // Compute the angle from coordinates and dimensions
- Double stateVarX = new Double(unitOfInformationGlyph.getBbox().getX() + unitOfInformationGlyph.getBbox().getW() / 2 - speciesGlyph.getBbox().getX());
- Double stateVarY = new Double(unitOfInformationGlyph.getBbox().getY() + unitOfInformationGlyph.getBbox().getH() / 2 - speciesGlyph.getBbox().getY());
-
- // Angle difference between endpoints of glyph's edge (divided by Pi)
- final double edgeAngle = 0.5;
-
- // Starting angle (top-right corner)
- final double startingAngle = 0.25;
-
- // Angle of the state variable
- Double angle = startingAngle;
-
- double leftSideDif = Math.abs(stateVarX);
- double rightSideDif = Math.abs(speciesGlyph.getBbox().getW() - stateVarX);
- double topSideDif = Math.abs(stateVarY);
- double bottomSideDif = Math.abs(speciesGlyph.getBbox().getH() - stateVarY);
- double minDif = Math.min(Math.min(leftSideDif, rightSideDif), Math.min(topSideDif, bottomSideDif));
-
- if (minDif == leftSideDif) {
- // State variable is located on glyph's left edge
- angle += edgeAngle + (stateVarY / speciesGlyph.getBbox().getH()) * edgeAngle;
- } else if (minDif == rightSideDif) {
- // State variable is located on glyph's right edge
- angle -= (stateVarY / speciesGlyph.getBbox().getH()) * edgeAngle;
- } else if (minDif == topSideDif) {
- // State variable is located on glyph's top edge
- angle += edgeAngle - (stateVarX / speciesGlyph.getBbox().getW()) * edgeAngle;
- } else if (minDif == bottomSideDif) {
- // State variable is located on glyph's bottom edge
- angle += 2 * edgeAngle + (stateVarX / speciesGlyph.getBbox().getW()) * edgeAngle;
- }
-
- mr.setAngle(angle * Math.PI);
-
- protein.addModificationResidue(mr);
- }
-
- /**
- * Method used for parsing units of information.
- *
- * @param unitOfInformationGlyph
- * unit of information glyph from sbgn-ml file
- * @param alias
- * alias that the unit of information concerns
- */
- private void parseUnitOfInformation(Glyph unitOfInformationGlyph, Species alias) {
- String unitOfInformationText = unitOfInformationGlyph.getLabel().getText();
- if (unitOfInformationText.contains(":") && !unitOfInformationText.startsWith("N:")) {
- String unitOfInformationPrefix = unitOfInformationText.substring(0, unitOfInformationText.indexOf(':'));
- String unitOfInformationSuffix = unitOfInformationText.substring(unitOfInformationText.indexOf(':') + 1);
- alias.setStatePrefix(unitOfInformationPrefix);
- alias.setStateLabel(unitOfInformationSuffix);
- } else if (!unitOfInformationText.startsWith("N:")) {
- alias.setStateLabel(unitOfInformationText);
- alias.setStatePrefix("free input");
- }
- }
-
- /**
- * Method used for parsing complex species.
- *
- * @param complexGlyph
- * complex species glyph from sbgn-ml file
- * @param parentComplexSpecies
- * parent complex species
- * @param isHomodimer
- * set if the complex is a homodimer
- * @param model
- * model to update with the parsed complex species
- */
- private void parseComplex(Glyph complexGlyph, Complex parentComplexSpecies, boolean isHomodimer, Model model) {
- Complex complexSpecies = new Complex(complexGlyph.getId());
- if (parentComplexSpecies != null) {
- complexSpecies.setComplex(parentComplexSpecies);
- }
- parseSpecies(complexGlyph, complexSpecies, isHomodimer, model);
-
- Complex complexAlias = model.getElementByElementId(complexGlyph.getId());
- for (Glyph child : complexGlyph.getGlyph()) {
- Species newSpecies;
- switch (GlyphClazz.fromClazz(child.getClazz())) {
- case UNSPECIFIED_ENTITY:
- newSpecies = new Unknown(child.getId());
- newSpecies.setComplex(complexSpecies);
- parseSpecies(child, newSpecies, true, model);
- break;
- case SIMPLE_CHEMICAL:
- newSpecies = new SimpleMolecule(child.getId());
- newSpecies.setComplex(complexSpecies);
- parseSpecies(child, newSpecies, true, model);
- break;
- case MACROMOLECULE:
- newSpecies = new GenericProtein(child.getId());
- newSpecies.setComplex(complexSpecies);
- parseSpecies(child, newSpecies, true, model);
- break;
- case NUCLEIC_ACID_FEATURE:
- newSpecies = new Gene(child.getId());
- newSpecies.setComplex(complexSpecies);
- parseSpecies(child, newSpecies, true, model);
- break;
- case SIMPLE_CHEMICAL_MULTIMER:
- newSpecies = new SimpleMolecule(child.getId());
- newSpecies.setComplex(complexSpecies);
- parseSpecies(child, newSpecies, false, model);
- break;
- case MACROMOLECULE_MULTIMER:
- newSpecies = new GenericProtein(child.getId());
- newSpecies.setComplex(complexSpecies);
- parseSpecies(child, newSpecies, false, model);
- break;
- case NUCLEIC_ACID_FEATURE_MULTIMER:
- newSpecies = new Gene(child.getId());
- newSpecies.setComplex(complexSpecies);
- parseSpecies(child, newSpecies, false, model);
- break;
- case COMPLEX:
- parseComplex(child, complexSpecies, true, model);
- break;
- case COMPLEX_MULTIMER:
- parseComplex(child, complexSpecies, false, model);
- break;
- default:
- break;
- }
- Species newAlias = model.getElementByElementId(child.getId());
- if (newAlias != null) {
- newAlias.setComplex(complexAlias);
- complexAlias.addSpecies((Species) newAlias);
- }
- }
- }
-
- /**
- * Method used to compute end point for modifier line.
- *
- * @param a
- * SBGN-ML modifier arc
- * @param reaction
- * reaction to which the arc points
- * @return end point for modifier line
- */
- private Point2D getModifierEndPoint(Arc a, Reaction reaction) {
- ModifierTypeUtils utils = new ModifierTypeUtils();
- Point2D result;
-
- Line2D centerLine = reaction.getCenterLine();
- double dx = centerLine.getX2() - centerLine.getX1();
- double dy = centerLine.getY2() - centerLine.getY1();
- double centerLineAngle = Math.atan2(dy, dx);
-
- Point2D centerPoint = new Point2D.Double(centerLine.getX1() + dx / 2, centerLine.getY1() + dy / 2);
-
- // Retrieve second last point from the arc
- Point2D secondLast;
- if (a.getNext().isEmpty()) {
- secondLast = new Point2D.Double(a.getStart().getX(), a.getStart().getY());
- } else {
- Next temp = a.getNext().get(a.getNext().size() - 1);
- secondLast = new Point2D.Double(temp.getX(), temp.getY());
- }
-
- double dx2 = secondLast.getX() - centerPoint.getX();
- double dy2 = secondLast.getY() - centerPoint.getY();
- double modifierAngle = Math.atan2(dy2, dx2);
-
- double finalAngle = modifierAngle - centerLineAngle;
- while (finalAngle < -Math.PI) {
- finalAngle += 2 * Math.PI;
- }
- while (finalAngle > Math.PI) {
- finalAngle -= 2 * Math.PI;
- }
- String lineConnectionType = null;
-
- // CHECKSTYLE:OFF
- if (finalAngle < -Math.PI / 3 * 2) {
- lineConnectionType = "0,4";
- } else if (finalAngle < -Math.PI / 3) {
- lineConnectionType = "0,2";
- } else if (finalAngle < 0) {
- lineConnectionType = "0,5";
- } else if (finalAngle < Math.PI / 3) {
- lineConnectionType = "0,7";
- } else if (finalAngle < Math.PI / 3 * 2) {
- lineConnectionType = "0,3";
- } else {
- lineConnectionType = "0,6";
- }
- // CHECKSTYLE:ON
-
- result = utils.getAnchorPointOnReactionRect(reaction, lineConnectionType);
-
- return result;
- }
-
- /**
- * Method used to parse line points from SBGN-ML arc.
- *
- * @param a
- * SBGN-ML arc
- * @return list of line points
- */
- private List<Point2D> getLinePoints(Arc a) {
- List<Point2D> pointList = new ArrayList<>();
- Point2D startPoint = new Point2D.Double(a.getStart().getX(), a.getStart().getY());
- Point2D endPoint = new Point2D.Double(a.getEnd().getX(), a.getEnd().getY());
- pointList.add(startPoint);
- for (Next nextPoint : a.getNext()) {
- pointList.add(new Point2D.Double(nextPoint.getX(), nextPoint.getY()));
- }
- pointList.add(endPoint);
- return pointList;
- }
-
- /**
- * Method used for parsing lines from sbgn-ml arcs.
- *
- * @param a
- * SBGN-ML arc
- * @param pointList
- * list of points for the line
- * @return line parsed from SBGN-ML arc
- */
- private PolylineData parseLine(Arc a, List<Point2D> pointList) {
- PolylineData line = new PolylineData(pointList);
- ArrowTypeData atd = new ArrowTypeData();
-
- switch (ArcClazz.fromClazz(a.getClazz())) {
- case CATALYSIS:
- atd = ModifierType.CATALYSIS.getAtd();
- break;
- case CONSUMPTION:
- atd.setArrowType(ArrowType.NONE);
- break;
- case INHIBITION:
- atd = ModifierType.INHIBITION.getAtd();
- break;
- case MODULATION:
- atd = ModifierType.MODULATION_STRING.getAtd();
- break;
- case NECESSARY_STIMULATION:
- atd = ModifierType.TRIGGER_STRING.getAtd();
- break;
- case PRODUCTION:
- atd.setArrowType(ArrowType.FULL);
- break;
- case STIMULATION:
- atd = ModifierType.PHYSICAL_STIMULATION.getAtd();
- break;
- case LOGIC_ARC:
- atd.setArrowType(ArrowType.NONE);
- break;
- default:
- throw new InvalidArgumentException("Wrong arc class.");
- }
- atd.setArrowLineType(LineType.SOLID);
- line.setEndAtd(atd.copy());
- return line;
- }
-
- /**
- * Returns {@link AndOperator} for the reaction's reagents port.
- *
- * @param p
- * process of the reaction
- * @return operator for the reaction port
- */
- private AndOperator getReactionPortAndOperator(Process p) {
- AndOperator andOperator = new AndOperator();
- Glyph centralPoint = p.getCentralPoint();
- Double centralPointX = new Double(centralPoint.getBbox().getX() + centralPoint.getBbox().getW() / 2);
- Double centralPointY = new Double(centralPoint.getBbox().getY() + centralPoint.getBbox().getH() / 2);
- Point2D centerOfReactionPoint = new Point2D.Double(centralPointX, centralPointY);
- Point2D portPoint;
- if (p.getReagentArcs().size() > 1) {
- portPoint = new Point2D.Double(p.getReagentArcs().get(0).getEnd().getX(), p.getReagentArcs().get(0).getEnd().getY());
- } else {
- portPoint = new Point2D.Double(p.getRevReagentArcs().get(0).getStart().getX(), p.getRevReagentArcs().get(0).getStart().getY());
- }
- PolylineData line = new PolylineData(portPoint, centerOfReactionPoint);
- ArrowTypeData atd = new ArrowTypeData();
- atd.setArrowType(ArrowType.NONE);
- atd.setArrowLineType(LineType.SOLID);
- line.setEndAtd(atd);
- andOperator.setLine(line);
- return andOperator;
- }
-
- /**
- * Returns {@link SplitOperator} for the reaction's products port.
- *
- * @param p
- * process of the reaction
- * @return operator for the reaction port
- */
- private SplitOperator getReactionPortSplitOperator(Process p) {
- SplitOperator splitOperator = new SplitOperator();
- Glyph centralPoint = p.getCentralPoint();
- Double centralPointX = new Double(centralPoint.getBbox().getX() + centralPoint.getBbox().getW() / 2);
- Double centralPointY = new Double(centralPoint.getBbox().getY() + centralPoint.getBbox().getH() / 2);
- Point2D centerOfReactionPoint = new Point2D.Double(centralPointX, centralPointY);
- Point2D portPoint;
- if (!p.isReversible()) {
- portPoint = new Point2D.Double(p.getProductArcs().get(0).getStart().getX(), p.getProductArcs().get(0).getStart().getY());
- } else {
- portPoint = new Point2D.Double(p.getRevProductArcs().get(0).getStart().getX(), p.getRevProductArcs().get(0).getStart().getY());
- }
- PolylineData line = new PolylineData(centerOfReactionPoint, portPoint);
- ArrowTypeData atd = new ArrowTypeData();
- atd.setArrowType(ArrowType.NONE);
- atd.setArrowLineType(LineType.SOLID);
- line.setEndAtd(atd);
- splitOperator.setLine(line);
- return splitOperator;
- }
-
- /**
- * Returns instance of {@link Modifier} based on given {@link ArcClazz}.
- *
- * @param ac
- * {@link ArcClazz} defining the result
- * @return {@link Modifier} of class adequate to given ac
- * @throws Exception
- * thrown when no adequate Modifier has been found
- */
- private Modifier getModifierFromArcClazz(ArcClazz ac) throws Exception {
- switch (ac) {
- case CATALYSIS:
- return new Catalysis();
- case INHIBITION:
- return new Inhibition();
- case MODULATION:
- return new Modulation();
- case NECESSARY_STIMULATION:
- return new Trigger();
- case STIMULATION:
- return new PhysicalStimulation();
- default:
- logger.warn("Modifier arc of invalid class.");
- throw new Exception("Wrong arc class.");
- }
- }
-
- /**
- * Returns center point for given process.
- *
- * @param p
- * completely parsed process to compute center point from
- * @return center point for given process
- */
- private Point2D getCenterPointFromProcess(Process p) {
- Double centralPointX = new Double(p.getCentralPoint().getBbox().getX() + p.getCentralPoint().getBbox().getW() / 2);
- Double centralPointY = new Double(p.getCentralPoint().getBbox().getY() + p.getCentralPoint().getBbox().getH() / 2);
- Point2D centerOfReactionPoint = new Point2D.Double(centralPointX, centralPointY);
- return centerOfReactionPoint;
- }
-
- /**
- * Returns proper Reaction object based on given glyph clazz.
- *
- * @param glyphClazz
- * clazz of the process glyph
- * @return Reaction object based on given glyph clazz
- */
- private Reaction getReactionFromProcessGlyphClazz(String glyphClazz) {
- switch (GlyphClazz.fromClazz(glyphClazz)) {
- case ASSOCIATION:
- case DISSOCIATION:
- case PROCESS:
- return new StateTransitionReaction();
- case OMITTED_PROCESS:
- return new KnownTransitionOmittedReaction();
- case UNCERTAIN_PROCESS:
- return new UnknownTransitionReaction();
- default:
- throw new InvalidArgumentException();
-
- }
- }
-
- /**
- * Method used for parsing processes into reactions.
- *
- * @param p
- * process to be parsed
- * @param model
- * model to be updated with the parsed reaction
- * @throws Exception
- * thrown when the process was invalid
- */
- private void parseProcess(Process p, Model model) throws Exception {
- if (p.getProductArcs().isEmpty()) {
- throw new Exception(p.getCentralPoint().getId() + ": The process must have at least one outgoing arc.");
- }
- p.setProductsPort((Port) p.getProductArcs().get(0).getSource());
- for (Arc productArc : p.getProductArcs()) {
- if (!((Port) productArc.getSource()).equals(p.getProductsPort())) {
- p.setReversible(true);
- p.setReagentsPort((Port) productArc.getSource());
- }
- }
- if (p.getReagentsPort() == null && !p.getReagentArcs().isEmpty()) {
- p.setReagentsPort((Port) p.getReagentArcs().get(0).getTarget());
- }
-
- if ((p.getReagentArcs().isEmpty() && !p.isReversible()) || (p.getRevReagentArcs().isEmpty() && p.isReversible())) {
- throw new Exception(p.getCentralPoint().getId() + ": The process must have at least one incoming arc.");
- }
-
- Reaction reaction;
- if (p.getCentralPoint() == null) {
- throw new Exception("Process has no central point.");
- }
- reaction = getReactionFromProcessGlyphClazz(p.getCentralPoint().getClazz());
- reaction.setIdReaction(p.getCentralPoint().getId());
- reaction.setModel(model);
-
- reaction.setReversible(p.isReversible());
-
- // If there are multiple inputs, add "AND" operator
- AndOperator andOperator = null;
- if (p.getReagentArcs().size() > 1 || p.getRevReagentArcs().size() > 1) {
- andOperator = getReactionPortAndOperator(p);
- andOperator.setReaction(reaction);
- reaction.addNode(andOperator);
- }
-
- // If there are multiple outputs, add Split operator
- SplitOperator splitOperator = null;
- if ((p.getProductArcs().size() > 1 && !p.isReversible()) || (p.isReversible() && p.getRevProductArcs().size() > 1)) {
- splitOperator = getReactionPortSplitOperator(p);
- splitOperator.setReaction(reaction);
- reaction.addNode(splitOperator);
- }
-
- for (Arc a : p.getReagentArcs()) {
- Reactant reactant = new Reactant();
- reactant.setReaction(reaction);
- Glyph source = (Glyph) a.getSource();
- reactant.setElement(model.getElementByElementId(source.getId()));
- List<Point2D> pointList = getLinePoints(a);
- if (p.getReagentArcs().size() == 1) {
- pointList.add(getCenterPointFromProcess(p));
- } else {
- pointList.add(pointList.get(pointList.size() - 1));
- }
- PolylineData line = parseLine(a, pointList);
- reactant.setLine(line);
- if (andOperator != null) {
- andOperator.addInput(reactant);
- }
-
- reaction.addReactant(reactant);
- }
-
- for (Arc a : p.getProductArcs()) {
- if (((Port) a.getSource()).equals(p.getProductsPort())) {
- Product product = new Product();
- product.setReaction(reaction);
- Glyph target = (Glyph) a.getTarget();
- product.setElement(model.getElementByElementId(target.getId()));
- List<Point2D> pointList = getLinePoints(a);
- if (p.getRevProductArcs().size() >= 1) {
- pointList.add(0, getCenterPointFromProcess(p));
- } else {
- pointList.add(0, pointList.get(0));
- }
- PolylineData line = parseLine(a, pointList);
- product.setLine(line);
- if (splitOperator != null) {
- splitOperator.addOutput(product);
- }
-
- reaction.addProduct(product);
- } else {
- Reactant reactant = new Reactant();
- reactant.setReaction(reaction);
- Glyph source = (Glyph) a.getTarget();
- reactant.setElement(model.getElementByElementId(source.getId()));
- List<Point2D> pointList = getLinePoints(a);
- if (p.getRevReagentArcs().size() <= 1) {
- pointList.add(0, getCenterPointFromProcess(p));
- } else {
- pointList.add(0, pointList.get(0));
- }
- PolylineData line = parseLine(a, pointList);
- line = line.reverse();
- reactant.setLine(line);
- if (andOperator != null) {
- andOperator.addInput(reactant);
- }
-
- reaction.addReactant(reactant);
- }
- }
- for (Arc a : p.getModifierArcs()) {
- Modifier modifier = null;
- try {
- modifier = getModifierFromArcClazz(ArcClazz.fromClazz(a.getClazz()));
- } catch (Exception ex) {
- logger.warn("Unable to add modifier");
- continue;
- }
- if (a.getSource() instanceof Glyph) {
- Glyph sourceGlyph = (Glyph) a.getSource();
- Species modifierAlias = (Species) model.getElementByElementId(sourceGlyph.getId());
- modifier.setElement(modifierAlias);
- List<Point2D> pointList = getLinePoints(a);
- pointList.remove(pointList.size() - 1);
- pointList.add(getModifierEndPoint(a, reaction));
- PolylineData line = parseLine(a, pointList);
- modifier.setLine(line);
-
- reaction.addModifier(modifier);
- } else if (a.getSource() instanceof Port) {
- // Logic operator
- try {
- parseLogicOperator(a, reaction, ArcClazz.fromClazz(a.getClazz()), null, model);
- } catch (Exception ex) {
- logger.warn(ex.getMessage());
- }
- }
-
- }
-
- model.addReaction(reaction);
- }
-
- /**
- * Returns {@link ArrowTypeData} based on given {@link ArcClazz}.
- *
- * @param ac
- * input arc class
- * @return ArrowTypeData based on input arrow class
- * @throws Exception
- * thrown when invalid arc class was given on input
- */
- private ArrowTypeData getAtdFromArcClazz(ArcClazz ac) throws Exception {
- ArrowTypeData atd = new ArrowTypeData();
- switch (ac) {
- case CATALYSIS:
- atd = ModifierType.CATALYSIS.getAtd();
- break;
- case CONSUMPTION:
- atd.setArrowType(ArrowType.NONE);
- break;
- case INHIBITION:
- atd = ModifierType.INHIBITION.getAtd();
- break;
- case MODULATION:
- atd = ModifierType.MODULATION_STRING.getAtd();
- break;
- case NECESSARY_STIMULATION:
- atd = ModifierType.TRIGGER_STRING.getAtd();
- break;
- case PRODUCTION:
- atd.setArrowType(ArrowType.FULL);
- break;
- case STIMULATION:
- atd = ModifierType.PHYSICAL_STIMULATION.getAtd();
- break;
- case LOGIC_ARC:
- atd.setArrowType(ArrowType.NONE);
- break;
- default:
- throw new Exception("Wrong arc class.");
- }
- return atd.copy();
- }
-
- /**
- * Method used for parsing logic operators.
- *
- * @param arc
- * arc with a starting point in the logic operator
- * @param reaction
- * reaction that the logic operator is a part of
- * @param modifierClass
- * determines type of source species
- * @param targetOperator
- * target logic operator
- * @param model
- * model of the map
- * @throws Exception
- * thrown when parsed logic operator is invalid
- */
- private void parseLogicOperator(Arc arc, Reaction reaction, ArcClazz modifierClass, NodeOperator targetOperator, Model model) throws Exception {
- Port operatorPort = (Port) arc.getSource();
- Glyph logicOperator = null;
- for (Glyph lo : logicOperators) {
- if (lo.getPort().contains(operatorPort)) {
- logicOperator = lo;
- }
- }
- if (logicOperator == null) {
- throw new Exception("Missing logic operator for logic arc: " + arc.getId());
- }
-
- // LogicOperator is valid for CellDesigner only if it has exactly 2
- // inputs of Species
- final Glyph tempLogicOperator = logicOperator;
- boolean isCellDesignerValidLogicOperator = logicArcs
- .stream().filter(a -> tempLogicOperator.getPort().contains(a.getTarget()) && !(a.getSource() instanceof Port)).count() == 2;
- if (!isCellDesignerValidLogicOperator) {
- throw new Exception("Parsed operator is not valid for CellDesigner: " + logicOperator.getId());
- }
-
- NodeOperator operator;
- switch (GlyphClazz.fromClazz(logicOperator.getClazz())) {
- case AND:
- operator = new AndOperator();
- break;
- case OR:
- operator = new OrOperator();
- break;
- case NOT:
- logger.warn("NOT gates are not implemented in the platform. Glyph: " + logicOperator.getId() + " has not been parsed.");
- return;
- default:
- throw new Exception("Wrong logic operator class.");
- }
-
- // Parse line from arc and operator glyph
- Point2D operatorCenterPoint = new Point2D.Double(
- logicOperator.getBbox().getX() + logicOperator.getBbox().getW() / 2, logicOperator.getBbox().getY() + logicOperator.getBbox().getH() / 2);
-
- List<Point2D> linePoints = getLinePoints(arc);
- new ArrayList<Point2D>();
-
- if (targetOperator == null) {
- linePoints.remove(linePoints.size() - 1);
- linePoints.add(getModifierEndPoint(arc, reaction));
- }
-
- // Check if operator port is in the line from center point of the
- // operator. If so, remove that redundant point.
- double dx, dy;
- dx = linePoints.get(0).getX() - operatorCenterPoint.getX();
- dy = linePoints.get(0).getY() - operatorCenterPoint.getY();
- double dx2, dy2;
- if (arc.getNext().isEmpty()) {
- dx2 = linePoints.get(linePoints.size() - 1).getX() - linePoints.get(0).getX();
- dy2 = linePoints.get(linePoints.size() - 1).getY() - linePoints.get(0).getY();
- } else {
- dx2 = arc.getNext().get(0).getX() - linePoints.get(0).getX();
- dy2 = arc.getNext().get(0).getY() - linePoints.get(0).getY();
- }
- DoubleComparator doubleComparator = new DoubleComparator();
- if (doubleComparator.compare(dy / dx, dy2 / dx2) == 0) {
- linePoints.remove(0);
- }
- linePoints.add(0, operatorCenterPoint);
-
- PolylineData line = new PolylineData(linePoints);
- ArrowTypeData atd = getAtdFromArcClazz(ArcClazz.fromClazz(arc.getClazz()));
-
- atd.setArrowLineType(LineType.SOLID);
- line.setEndAtd(atd);
-
- operator.setLine(line);
- operator.setReaction(reaction);
-
- if (targetOperator != null) {
- operator.addOutput(targetOperator);
- targetOperator.addInput(operator);
- }
-
- for (Arc logicArc : logicArcs) {
- if (logicOperator.getPort().contains(logicArc.getTarget())) {
- if (logicArc.getSource() instanceof Port) {
- // The arc has source in logic operator
- logger.warn("Logic operators trees are not compatible with CellDesigner. Therefore they are not supported.");
- continue;
- // parseLogicOperator(logicArc, reaction, modifierClass,
- // operator, model);
- } else {
- Modifier modifier;
-
- switch (modifierClass) {
- case CATALYSIS:
- modifier = new Catalysis();
- break;
- case INHIBITION:
- modifier = new Inhibition();
- break;
- case MODULATION:
- modifier = new Modulation();
- break;
- case NECESSARY_STIMULATION:
- modifier = new Trigger();
- break;
- case STIMULATION:
- modifier = new PhysicalStimulation();
- break;
- default:
- throw new Exception("Wrong arc class.");
- }
-
- Glyph sourceGlyph = (Glyph) logicArc.getSource();
- Species modifierAlias = (Species) model.getElementByElementId(sourceGlyph.getId());
- modifier.setElement(modifierAlias);
- List<Point2D> pointList = getLinePoints(logicArc);
- pointList.add(operatorCenterPoint);
- PolylineData newLine = parseLine(logicArc, pointList);
- modifier.setLine(newLine);
-
- operator.addInput(modifier);
-
- reaction.addModifier(modifier);
- }
- }
- }
- reaction.addNode(operator);
- }
-
- /**
- * Method used for parsing compartments.
- *
- * @param glyph
- * compartment glyph from sbgn-ml file
- * @param model
- * model to be updated with the parsed compartment
- */
- private void parseCompartment(Glyph glyph, Model model) {
-
- Compartment compartment = new SquareCompartment(glyph.getId());
- if (glyph.getLabel() != null) {
- compartment.setName(glyph.getLabel().getText());
- }
- compartment.setModel(model);
- compartment.setHeight(new Double(glyph.getBbox().getH()));
- compartment.setWidth(new Double(glyph.getBbox().getW()));
- compartment.setX(new Double(glyph.getBbox().getX()));
- compartment.setY(new Double(glyph.getBbox().getY()));
- compartment.setThickness(1.0);
- compartment.setColor(COMPARTMENT_COLOR);
-
- if (glyph.getLabel() != null && glyph.getLabel().getBbox() != null) {
- compartment.setNamePoint(glyph.getLabel().getBbox().getX(), glyph.getLabel().getBbox().getY());
- } else {
- compartment.setNamePoint(
- compartment.getX() + compartment.getThickness() + CONTAINER_NAME_MARGIN, compartment.getY() + compartment.getThickness() + CONTAINER_NAME_MARGIN);
- }
- Compartment parent = findParentCompartment(compartment, model);
- if (parent != null) {
- compartment.setCompartment(parent);
- parent.addElement(compartment);
- }
-
- model.addElement(compartment);
- }
-}
+package lcsb.mapviewer.converter.model.sbgnml;
+
+import java.awt.Color;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+import org.sbgn.ArcClazz;
+import org.sbgn.GlyphClazz;
+import org.sbgn.SbgnUtil;
+import org.sbgn.bindings.Arc;
+import org.sbgn.bindings.Arc.End;
+import org.sbgn.bindings.Arc.Next;
+import org.sbgn.bindings.Arc.Start;
+import org.sbgn.bindings.Bbox;
+import org.sbgn.bindings.Glyph;
+import org.sbgn.bindings.Map;
+import org.sbgn.bindings.Port;
+import org.sbgn.bindings.Sbgn;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
+import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
+import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
+import lcsb.mapviewer.converter.model.sbgnml.structures.Process;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.ArrowTypeData;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
+import lcsb.mapviewer.model.map.modifier.Trigger;
+import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.OrOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
+import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
+
+/**
+ * This class is a parser for SBGN-ML files.
+ *
+ * @author Michał Kuźma
+ *
+ */
+public class SbgnmlXmlParser {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(SbgnmlXmlParser.class.getName());
+
+ /**
+ * List of all processes to be parsed.
+ */
+ private List<Process> processes = new ArrayList<Process>();
+
+ /**
+ * List of all logic operator glyphs parsed so far.
+ */
+ private List<Glyph> logicOperators = new ArrayList<Glyph>();
+
+ /**
+ * List of all logic arcs parsed so far.
+ */
+ private List<Arc> logicArcs = new ArrayList<Arc>();
+
+ /**
+ * Default margin for container name.
+ */
+ private static final double CONTAINER_NAME_MARGIN = 5.0;
+
+ /**
+ * Part of height of the line used to cross degraded circle that goes behind
+ * this circle.
+ */
+ private static final int CROSS_LINE_EXTENDED_LENGTH = 7;
+
+ /**
+ * Default color for parsed compartments.
+ */
+ private static final Color COMPARTMENT_COLOR = new Color(0.5f, 0.5f, 1.0f);
+
+ /**
+ * Method used to create a model from SBGN-ML file.
+ *
+ * @param params
+ * parameters needed for parsing file and creating a model
+ * @return valid model parsed from the file
+ * @throws InvalidInputDataExecption
+ * thrown when input file is invalid
+ */
+ public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
+
+ Model model = new ModelFullIndexed(null);
+ model.setIdModel(params.getFilename());
+
+ // Input file
+ File inputSbgnmlFile = inputStreamToFile(params.getInputStream());
+
+ Sbgn sbgnData;
+ // Check if input file has valid SBGN-ML data
+ try {
+ if (!SbgnUtil.isValid(inputSbgnmlFile)) {
+ throw new InvalidInputDataExecption("Given input is not a valid SBGN-ML file.");
+ }
+
+ // Read data from file
+ sbgnData = SbgnUtil.readFromFile(inputSbgnmlFile);
+ } catch (InvalidInputDataExecption ex) {
+ throw ex;
+ } catch (Exception ex) {
+ throw new InvalidInputDataExecption("Unable to read given file.", ex);
+ }
+
+ // Extract map with all the glyphs and arcs
+ Map map = sbgnData.getMap();
+
+ adjustSizeOfElements(map);
+
+ setModelSize(map, model);
+
+ // Iterate over every glyph
+ for (Glyph g : map.getGlyph()) {
+ parseGlyph(g, model);
+ }
+
+ // Iterate over every arc in the map
+ for (Arc a : map.getArc()) {
+ parseArc(a, model);
+ }
+
+ // Parse all processes created before
+ for (Process p : processes) {
+ try {
+ parseProcess(p, model);
+ } catch (Exception e) {
+ logger.warn("Unable to parse the process: " + p.getCentralPoint().getId());
+ }
+ }
+
+ return model;
+ }
+
+ /**
+ * Writes input stream into a File.
+ *
+ * @param inputStream
+ * Input stream to be written to File
+ * @return File handle
+ */
+ private File inputStreamToFile(InputStream inputStream) {
+ File tempFile = null;
+ try {
+ tempFile = File.createTempFile("stream2file", ".tmp");
+ tempFile.deleteOnExit();
+ try (FileOutputStream out = new FileOutputStream(tempFile)) {
+ IOUtils.copy(inputStream, out);
+ }
+ } catch (Exception ex) {
+ logger.debug("Unable to create temporary file.");
+ return null;
+ }
+ return tempFile;
+ }
+
+ /**
+ * Method used to adjust the size of elements that have their size represented
+ * different in the SBGN-ML file. Adjusted elements: Source and Sink / Degraded
+ * elements, Multimers.
+ *
+ * @param map
+ * Map parsed from SBGN-ML file
+ */
+ private void adjustSizeOfElements(Map map) {
+ for (Glyph g : map.getGlyph()) {
+ GlyphClazz glyphClazz = GlyphClazz.fromClazz(g.getClazz());
+ switch (glyphClazz) {
+ case SOURCE_AND_SINK:
+ g.getBbox().setH(g.getBbox().getH() + 2 * CROSS_LINE_EXTENDED_LENGTH);
+ g.getBbox().setW(g.getBbox().getW() + 2 * CROSS_LINE_EXTENDED_LENGTH);
+ g.getBbox().setX(g.getBbox().getX() - CROSS_LINE_EXTENDED_LENGTH);
+ g.getBbox().setY(g.getBbox().getY() - CROSS_LINE_EXTENDED_LENGTH);
+ break;
+ case COMPLEX_MULTIMER:
+ case MACROMOLECULE_MULTIMER:
+ case NUCLEIC_ACID_FEATURE_MULTIMER:
+ case SIMPLE_CHEMICAL_MULTIMER:
+ int cardinality;
+ try {
+ cardinality = getMultimerCardinality(g);
+ } catch (Exception ex) {
+ cardinality = 2;
+ logger.warn(ex.getMessage() + " Set the default value of 2.");
+ }
+ g.getBbox().setW(g.getBbox().getW() + (cardinality - 1) * SpeciesConverter.HOMODIMER_OFFSET);
+ g.getBbox().setH(g.getBbox().getH() + (cardinality - 1) * SpeciesConverter.HOMODIMER_OFFSET);
+ break;
+ default:
+ break;
+ }
+ }
+ }
+
+ /**
+ * Method used to compute height and width of the model.
+ *
+ * @param map
+ * Map parsed from SBGN-ML file
+ * @param model
+ * Model to be updated
+ */
+ private void setModelSize(Map map, Model model) {
+ double minX = Double.MAX_VALUE;
+ double minY = Double.MAX_VALUE;
+ double maxX = 0;
+ double maxY = 0;
+
+ // Iterate over every glyph
+ for (Glyph g : map.getGlyph()) {
+ if (GlyphClazz.fromClazz(g.getClazz()).equals(GlyphClazz.ANNOTATION)
+ || GlyphClazz.fromClazz(g.getClazz()).equals(GlyphClazz.TAG)) {
+ continue;
+ }
+ Bbox bbox = g.getBbox();
+ if (bbox != null) {
+ if (bbox.getX() < minX) {
+ minX = bbox.getX();
+ }
+ if (bbox.getY() < minY) {
+ minY = bbox.getY();
+ }
+ if (bbox.getX() + bbox.getW() > maxX) {
+ maxX = bbox.getX() + bbox.getW();
+ }
+ if (bbox.getY() + bbox.getH() > maxY) {
+ maxY = bbox.getY() + bbox.getH();
+ }
+ }
+ }
+
+ // Iterate over every arc
+ for (Arc a : map.getArc()) {
+ // Since submaps are not yet supported, the arcs connecting them or
+ // tags cannot be used when computing width and height of the model.
+ boolean connectsTagOrSubmap = false;
+ if (a.getSource() instanceof Glyph) {
+ Glyph sourceGlyph = (Glyph) a.getSource();
+ if (GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.TAG)
+ || GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.SUBMAP)) {
+ connectsTagOrSubmap = true;
+ }
+ }
+ if (a.getTarget() instanceof Glyph) {
+ Glyph targetGlyph = (Glyph) a.getTarget();
+ if (GlyphClazz.fromClazz(targetGlyph.getClazz()).equals(GlyphClazz.TAG)
+ || GlyphClazz.fromClazz(targetGlyph.getClazz()).equals(GlyphClazz.SUBMAP)) {
+ connectsTagOrSubmap = true;
+ }
+ }
+ // If the arc is not connecting a submap or a tag, check it's points
+ if (!connectsTagOrSubmap) {
+ Start aStart = a.getStart();
+ if (aStart.getX() < minX) {
+ minX = aStart.getX();
+ }
+ if (aStart.getX() > maxX) {
+ maxX = aStart.getX();
+ }
+ if (aStart.getY() < minY) {
+ minY = aStart.getY();
+ }
+ if (aStart.getY() > maxY) {
+ maxY = aStart.getY();
+ }
+ End aEnd = a.getEnd();
+ if (aEnd.getX() < minX) {
+ minX = aEnd.getX();
+ }
+ if (aEnd.getX() > maxX) {
+ maxX = aEnd.getX();
+ }
+ if (aEnd.getY() < minY) {
+ minY = aEnd.getY();
+ }
+ if (aEnd.getY() > maxY) {
+ maxY = aEnd.getY();
+ }
+ for (Next aNext : a.getNext()) {
+ if (aNext.getX() < minX) {
+ minX = aNext.getX();
+ }
+ if (aNext.getX() > maxX) {
+ maxX = aNext.getX();
+ }
+ if (aNext.getY() < minY) {
+ minY = aNext.getY();
+ }
+ if (aNext.getY() > maxY) {
+ maxY = aNext.getY();
+ }
+ }
+ }
+ }
+
+ model.setWidth(maxX + minX);
+ model.setHeight(maxY + minY);
+ }
+
+ /**
+ * Method used to parse a single glyph.
+ *
+ * @param g
+ * glyph to be parsed
+ * @param model
+ * model to be updated
+ * @throws Exception
+ */
+ private void parseGlyph(Glyph g, Model model) {
+ Species newSpecies = null;
+ switch (GlyphClazz.fromClazz(g.getClazz())) {
+ case AND:
+ case NOT:
+ case OR:
+ logicOperators.add(g);
+ break;
+ case COMPARTMENT:
+ parseCompartment(g, model);
+ break;
+ case COMPLEX:
+ parseComplex(g, null, true, model);
+ break;
+ case COMPLEX_MULTIMER:
+ parseComplex(g, null, false, model);
+ break;
+ case MACROMOLECULE:
+ newSpecies = new GenericProtein(g.getId());
+ parseSpecies(g, newSpecies, true, model);
+ break;
+ case MACROMOLECULE_MULTIMER:
+ newSpecies = new GenericProtein(g.getId());
+ parseSpecies(g, newSpecies, false, model);
+ break;
+ case NUCLEIC_ACID_FEATURE:
+ if (isRNA(g)) {
+ newSpecies = new Rna(g.getId());
+ } else {
+ newSpecies = new Gene(g.getId());
+ }
+ parseSpecies(g, newSpecies, true, model);
+ break;
+ case NUCLEIC_ACID_FEATURE_MULTIMER:
+ if (isRNA(g)) {
+ newSpecies = new Rna(g.getId());
+ } else {
+ newSpecies = new Gene(g.getId());
+ }
+ parseSpecies(g, newSpecies, false, model);
+ break;
+ case PERTURBING_AGENT:
+ newSpecies = new Phenotype(g.getId());
+ parseSpecies(g, newSpecies, true, model);
+ break;
+ case PHENOTYPE:
+ newSpecies = new Phenotype(g.getId());
+ parseSpecies(g, newSpecies, true, model);
+ break;
+ case ASSOCIATION:
+ case DISSOCIATION:
+ case OMITTED_PROCESS:
+ case PROCESS:
+ case UNCERTAIN_PROCESS:
+ processes.add(new Process(g));
+ break;
+ case SIMPLE_CHEMICAL:
+ newSpecies = new SimpleMolecule(g.getId());
+ parseSpecies(g, newSpecies, true, model);
+ break;
+ case SIMPLE_CHEMICAL_MULTIMER:
+ newSpecies = new SimpleMolecule(g.getId());
+ parseSpecies(g, newSpecies, false, model);
+ break;
+ case SOURCE_AND_SINK:
+ newSpecies = new Degraded(g.getId());
+ parseSpecies(g, newSpecies, true, model);
+ break;
+ case TAG:
+ case SUBMAP:
+ logger.warn("Submaps are not supported. Glyph: " + g.getId() + " has not been parsed.");
+ case UNSPECIFIED_ENTITY:
+ newSpecies = new Unknown(g.getId());
+ parseSpecies(g, newSpecies, true, model);
+ break;
+ default:
+ logger.warn("The glyph " + g.getId() + " of class " + g.getClazz()
+ + " has not been parsed, since it is invalid for SBGN PD map.");
+ break;
+ }
+ }
+
+ /**
+ * Method used to parse a single arc.
+ *
+ * @param a
+ * arc to be parsed
+ * @param model
+ * model to be updated
+ */
+ private void parseArc(Arc a, Model model) {
+ switch (ArcClazz.fromClazz(a.getClazz())) {
+ case CONSUMPTION:
+ Port arcTargetPort = (Port) a.getTarget();
+ for (Process p : processes) {
+ if (p.getCentralPoint().getPort().contains(arcTargetPort)) {
+ p.addReagentArc(a);
+ break;
+ }
+ }
+ break;
+ case PRODUCTION:
+ Port arcSourcePort = (Port) a.getSource();
+ for (Process p : processes) {
+ if (p.getCentralPoint().getPort().contains(arcSourcePort)) {
+ p.addProductArc(a);
+ break;
+ }
+ }
+ break;
+ case EQUIVALENCE_ARC:
+ logger.warn("Submaps are not supported. Equivalence arc: " + a.getId() + " has not been parsed.");
+ break;
+ case LOGIC_ARC:
+ logicArcs.add(a);
+ break;
+ case CATALYSIS:
+ case INHIBITION:
+ case MODULATION:
+ case NECESSARY_STIMULATION:
+ case STIMULATION:
+ Glyph targetGlyph = (Glyph) a.getTarget();
+ if (GlyphClazz.fromClazz(targetGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)) {
+ if (!(a.getSource() instanceof Glyph)) {
+ logger.warn("Invalid phenotype arc: " + a.getId());
+ break;
+ }
+ try {
+ parsePhenotypeArc(a, model);
+ } catch (Exception ex) {
+ logger.warn(ex.getMessage());
+ }
+ break;
+ }
+ if (a.getSource() instanceof Glyph) {
+ Glyph sourceGlyph = (Glyph) a.getSource();
+ if (GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)
+ && (model.getElementByElementId(targetGlyph.getId()) instanceof Species)) {
+ try {
+ parsePhenotypeArc(a, model);
+ } catch (InvalidArgumentException ex) {
+ logger.warn("The arc " + a.getId() + " of class " + a.getClazz() + " is not a valid reduced notation arc.");
+ }
+ break;
+ }
+ }
+ for (Process p : processes) {
+ if (p.getCentralPoint().getId().equals(targetGlyph.getId())) {
+ p.addInfluenceArc(a);
+ break;
+ }
+ }
+ break;
+ default:
+ logger.warn("The arc " + a.getId() + " of class " + a.getClazz()
+ + " has not been parsed, since it is invalid for SBGN PD map.");
+ }
+ }
+
+ /**
+ * Method used to parse arc going to or from a phenotype.
+ *
+ * @param a
+ * arc to be parsed
+ * @param model
+ * model to be updated
+ */
+ private void parsePhenotypeArc(Arc a, Model model) {
+ Reaction reaction;
+
+ switch (ArcClazz.fromClazz(a.getClazz())) {
+
+ case INHIBITION:
+ reaction = new NegativeInfluenceReaction();
+ break;
+ case MODULATION:
+ reaction = new ReducedModulationReaction();
+ break;
+ case NECESSARY_STIMULATION:
+ reaction = new ReducedTriggerReaction();
+ break;
+ case STIMULATION:
+ reaction = new ReducedPhysicalStimulationReaction();
+ break;
+ default:
+ throw new InvalidArgumentException();
+ }
+
+ reaction.setIdReaction(a.getId());
+ reaction.setModel(model);
+
+ Reactant reactant = new Reactant();
+ reactant.setReaction(reaction);
+ Glyph source = (Glyph) a.getSource();
+ reactant.setElement(model.getElementByElementId(source.getId()));
+ List<Point2D> reactantPointList = new ArrayList<>();
+ reactantPointList.add(new Point2D.Double(a.getStart().getX(), a.getStart().getY()));
+ reactantPointList.add(new Point2D.Double(a.getStart().getX(), a.getStart().getY()));
+ PolylineData reactantLine = new PolylineData(reactantPointList);
+ ArrowTypeData atd = new ArrowTypeData();
+ atd.setArrowType(ArrowType.NONE);
+ atd.setArrowLineType(LineType.SOLID);
+ reactantLine.setEndAtd(atd);
+ reactant.setLine(reactantLine);
+ reaction.addReactant(reactant);
+
+ Product product = new Product();
+ product.setReaction(reaction);
+ Glyph target = (Glyph) a.getTarget();
+ product.setElement(model.getElementByElementId(target.getId()));
+ List<Point2D> productPointList = getLinePoints(a);
+ PolylineData productLine = parseLine(a, productPointList);
+ product.setLine(productLine);
+ reaction.addProduct(product);
+
+ model.addReaction(reaction);
+ }
+
+ /**
+ * Method used to parse a single species.
+ *
+ * @param g
+ * SBGN-ML glyph representing the species
+ * @param newSpecies
+ * species to be parsed
+ * @param isHomodimer
+ * true if parsed species is not multimer
+ * @param model
+ * model to be updated
+ */
+ private void parseSpecies(Glyph g, Species newSpecies, boolean isHomodimer, Model model) {
+ newSpecies.setModel(model);
+ // If Glyph has label with a name, set it as Species name. If not, set
+ // Id as name.
+ if (g.getLabel() != null) {
+ newSpecies.setName(g.getLabel().getText());
+ } else {
+ newSpecies.setName(g.getId());
+ }
+ // Add species to parent complex if there is one
+ if (newSpecies.getComplex() != null) {
+ newSpecies.getComplex().addSpecies(newSpecies);
+ }
+ // If the species is a multimer, set it's cardinality.
+ if (!isHomodimer) {
+ try {
+ newSpecies.setHomodimer(getMultimerCardinality(g));
+ } catch (Exception ex) {
+ newSpecies.setHomodimer(2);
+ logger.warn(ex.getMessage() + " Set the default value of 2.");
+ }
+ }
+
+ List<Glyph> children = g.getGlyph();
+ for (Glyph child : children) {
+ if (GlyphClazz.fromClazz(child.getClazz()).equals(GlyphClazz.STATE_VARIABLE)) {
+ if (child.getState() == null || child.getState().getVariable() != null) {
+ try {
+ parseStateVariable(child, g, newSpecies);
+ } catch (Exception ex) {
+ logger.warn(ex.getMessage());
+ }
+ } else {
+ String structuralState = child.getState().getValue();
+ if (newSpecies instanceof Protein) {
+ Protein protein = (Protein) newSpecies;
+ protein.setStructuralState(structuralState);
+ } else if (newSpecies instanceof Complex) {
+ Complex complex = (Complex) newSpecies;
+ complex.setStructuralState(structuralState);
+ }
+ }
+ }
+ }
+
+ parseSpecies(g, newSpecies, model);
+
+ adjustModificationCoordinates(newSpecies);
+
+ }
+
+ /**
+ * {@link ModificationResidue} in element might have slightly off coordinates
+ * (due to different symbol shapes). For that we need to align them to match our
+ * model.
+ *
+ * @param species
+ */
+ protected void adjustModificationCoordinates(Species species) {
+ if (species instanceof Protein) {
+ Protein protein = (Protein) species;
+ if (protein.getModificationResidues().size() > 0) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(species, true);
+ for (ModificationResidue mr : protein.getModificationResidues()) {
+ double angle = converter.getAngleForPoint(species, mr.getPosition());
+ mr.setPosition(converter.getResidueCoordinates(species, angle));
+ }
+ }
+
+ }
+ }
+
+ /**
+ * Method used to create a new alias from SBGN-ML glyph.
+ *
+ * @param glyph
+ * SBGN-ML glyph representing the alias
+ * @param species
+ * species of the alias
+ * @param model
+ * model to be updated
+ */
+ private void parseSpecies(Glyph glyph, Species species, Model model) {
+ species.setHeight(new Double(glyph.getBbox().getH()));
+ species.setWidth(new Double(glyph.getBbox().getW()));
+ species.setX(new Double(glyph.getBbox().getX()));
+ species.setY(new Double(glyph.getBbox().getY()));
+
+ Compartment parentCompartment = null;
+ if (glyph.getCompartmentRef() != null) {
+ Glyph compartmentGlyph = (Glyph) glyph.getCompartmentRef();
+ parentCompartment = model.getElementByElementId(compartmentGlyph.getId());
+ } else if (species.getComplex() == null) {
+ parentCompartment = findParentCompartment(species, model);
+ }
+ if (parentCompartment != null) {
+ species.setCompartment(parentCompartment);
+ parentCompartment.addElement(species);
+ }
+
+ // Parse units of information
+ for (Glyph child : glyph.getGlyph()) {
+ if (GlyphClazz.fromClazz(child.getClazz()).equals(GlyphClazz.UNIT_OF_INFORMATION)) {
+ parseUnitOfInformation(child, species);
+ }
+ }
+
+ model.addElement(species);
+ }
+
+ /**
+ * Finds a compartment where element should be located (base on the
+ * coordinates).
+ *
+ * @param child
+ * {@link Element} for which we want to find compartment
+ * @param model
+ * {@link Model} where we look for a compartment
+ * @return parent {@link Compartment}
+ */
+ private Compartment findParentCompartment(Element child, Model model) {
+ Compartment nullParent = new Compartment("null");
+ nullParent.setWidth(Double.MAX_VALUE);
+ nullParent.setHeight(Double.MAX_VALUE);
+ nullParent.setX(0.0);
+ nullParent.setY(0.0);
+ Compartment parent = nullParent;
+ for (Compartment potentialParent : model.getCompartments()) {
+ if (potentialParent.contains(child)) {
+ if (parent.getSize() > potentialParent.getSize()) {
+ parent = potentialParent;
+ }
+ }
+ }
+ if (parent != nullParent) {
+ return parent;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Method used to retrieve multimer cardinality from a multimer glyph.
+ *
+ * @param g
+ * multimer glyph
+ * @return multimer cardinality
+ * @throws Exception
+ * Exception is thrown if no proper unit of information with
+ * cardinality was found
+ */
+ private int getMultimerCardinality(Glyph g) throws Exception {
+ int multimerCardinality = 0;
+ // Check all the children nodes looking for unit of information with
+ // cardinality
+ List<Glyph> children = g.getGlyph();
+ for (Glyph child : children) {
+ if (GlyphClazz.fromClazz(child.getClazz()) == GlyphClazz.UNIT_OF_INFORMATION) {
+ String[] splitLabel = child.getLabel().getText().split(":");
+ multimerCardinality = Integer.parseInt(splitLabel[1]);
+ }
+ }
+ // If no unit of information was found, or the cardinality is invalid,
+ // raise exception
+ if (multimerCardinality <= 0) {
+ throw new Exception(
+ "No proper unit of information with multimer cardinality was found." + " Glyph: " + g.getId());
+ }
+
+ return multimerCardinality;
+ }
+
+ /**
+ * Method used to decide if Nucleic-acid feature should be translated to RNA.
+ *
+ * @param g
+ * Nucleic-acid feature glyph
+ * @return true if input is RNA
+ */
+ private boolean isRNA(Glyph g) {
+ boolean rna = false;
+ // Check all the children nodes looking for unit of information
+ List<Glyph> children = g.getGlyph();
+ for (Glyph child : children) {
+ if (GlyphClazz.fromClazz(child.getClazz()) == GlyphClazz.UNIT_OF_INFORMATION) {
+ if (child.getLabel().getText().toLowerCase().contains("rna")) {
+ rna = true;
+ }
+ }
+ }
+
+ return rna;
+ }
+
+ /**
+ * Method used to parse state variable.
+ *
+ * @param unitOfInformationGlyph
+ * unit of information glyph from sbgn-ml file
+ * @param speciesGlyph
+ * glyph that the unit of information considers
+ * @param newSpecies
+ * species that the unit of information considers
+ * @throws Exception
+ * Exception is thrown if state variable is parsed for species other
+ * than Protein
+ */
+ private void parseStateVariable(Glyph unitOfInformationGlyph, Glyph speciesGlyph, Species newSpecies)
+ throws Exception {
+ if (!(newSpecies instanceof Protein)) {
+ throw new Exception("Only macromolecule elements can have state variables.");
+ }
+ Protein protein = (Protein) newSpecies;
+ Residue mr = new Residue();
+
+ mr.setSpecies(protein);
+ mr.setIdModificationResidue(unitOfInformationGlyph.getId());
+ if (unitOfInformationGlyph.getState() != null) {
+ // If State variable consists of value and variable
+ mr.setName(unitOfInformationGlyph.getState().getVariable());
+ for (ModificationState ms : ModificationState.values()) {
+ if (ms.getAbbreviation().equals(unitOfInformationGlyph.getState().getValue())) {
+ mr.setState(ms);
+ }
+ }
+ }
+
+ // Compute the angle from coordinates and dimensions
+ double x = unitOfInformationGlyph.getBbox().getX() + unitOfInformationGlyph.getBbox().getW() / 2;
+ double y = unitOfInformationGlyph.getBbox().getY() + unitOfInformationGlyph.getBbox().getH() / 2;
+
+ mr.setPosition(new Point2D.Double(x, y));
+
+ protein.addModificationResidue(mr);
+ }
+
+ /**
+ * Method used for parsing units of information.
+ *
+ * @param unitOfInformationGlyph
+ * unit of information glyph from sbgn-ml file
+ * @param alias
+ * alias that the unit of information concerns
+ */
+ private void parseUnitOfInformation(Glyph unitOfInformationGlyph, Species alias) {
+ String unitOfInformationText = unitOfInformationGlyph.getLabel().getText();
+ if (unitOfInformationText.contains(":") && !unitOfInformationText.startsWith("N:")) {
+ String unitOfInformationPrefix = unitOfInformationText.substring(0, unitOfInformationText.indexOf(':'));
+ String unitOfInformationSuffix = unitOfInformationText.substring(unitOfInformationText.indexOf(':') + 1);
+ alias.setStatePrefix(unitOfInformationPrefix);
+ alias.setStateLabel(unitOfInformationSuffix);
+ } else if (!unitOfInformationText.startsWith("N:")) {
+ alias.setStateLabel(unitOfInformationText);
+ alias.setStatePrefix("free input");
+ }
+ }
+
+ /**
+ * Method used for parsing complex species.
+ *
+ * @param complexGlyph
+ * complex species glyph from sbgn-ml file
+ * @param parentComplexSpecies
+ * parent complex species
+ * @param isHomodimer
+ * set if the complex is a homodimer
+ * @param model
+ * model to update with the parsed complex species
+ */
+ private void parseComplex(Glyph complexGlyph, Complex parentComplexSpecies, boolean isHomodimer, Model model) {
+ Complex complexSpecies = new Complex(complexGlyph.getId());
+ if (parentComplexSpecies != null) {
+ complexSpecies.setComplex(parentComplexSpecies);
+ }
+ parseSpecies(complexGlyph, complexSpecies, isHomodimer, model);
+
+ Complex complexAlias = model.getElementByElementId(complexGlyph.getId());
+ for (Glyph child : complexGlyph.getGlyph()) {
+ Species newSpecies;
+ switch (GlyphClazz.fromClazz(child.getClazz())) {
+ case UNSPECIFIED_ENTITY:
+ newSpecies = new Unknown(child.getId());
+ newSpecies.setComplex(complexSpecies);
+ parseSpecies(child, newSpecies, true, model);
+ break;
+ case SIMPLE_CHEMICAL:
+ newSpecies = new SimpleMolecule(child.getId());
+ newSpecies.setComplex(complexSpecies);
+ parseSpecies(child, newSpecies, true, model);
+ break;
+ case MACROMOLECULE:
+ newSpecies = new GenericProtein(child.getId());
+ newSpecies.setComplex(complexSpecies);
+ parseSpecies(child, newSpecies, true, model);
+ break;
+ case NUCLEIC_ACID_FEATURE:
+ newSpecies = new Gene(child.getId());
+ newSpecies.setComplex(complexSpecies);
+ parseSpecies(child, newSpecies, true, model);
+ break;
+ case SIMPLE_CHEMICAL_MULTIMER:
+ newSpecies = new SimpleMolecule(child.getId());
+ newSpecies.setComplex(complexSpecies);
+ parseSpecies(child, newSpecies, false, model);
+ break;
+ case MACROMOLECULE_MULTIMER:
+ newSpecies = new GenericProtein(child.getId());
+ newSpecies.setComplex(complexSpecies);
+ parseSpecies(child, newSpecies, false, model);
+ break;
+ case NUCLEIC_ACID_FEATURE_MULTIMER:
+ newSpecies = new Gene(child.getId());
+ newSpecies.setComplex(complexSpecies);
+ parseSpecies(child, newSpecies, false, model);
+ break;
+ case COMPLEX:
+ parseComplex(child, complexSpecies, true, model);
+ break;
+ case COMPLEX_MULTIMER:
+ parseComplex(child, complexSpecies, false, model);
+ break;
+ default:
+ break;
+ }
+ Species newAlias = model.getElementByElementId(child.getId());
+ if (newAlias != null) {
+ newAlias.setComplex(complexAlias);
+ complexAlias.addSpecies((Species) newAlias);
+ }
+ }
+ }
+
+ /**
+ * Method used to compute end point for modifier line.
+ *
+ * @param a
+ * SBGN-ML modifier arc
+ * @param reaction
+ * reaction to which the arc points
+ * @return end point for modifier line
+ */
+ private Point2D getModifierEndPoint(Arc a, Reaction reaction) {
+ ModifierTypeUtils utils = new ModifierTypeUtils();
+ Point2D result;
+
+ Line2D centerLine = reaction.getCenterLine();
+ double dx = centerLine.getX2() - centerLine.getX1();
+ double dy = centerLine.getY2() - centerLine.getY1();
+ double centerLineAngle = Math.atan2(dy, dx);
+
+ Point2D centerPoint = new Point2D.Double(centerLine.getX1() + dx / 2, centerLine.getY1() + dy / 2);
+
+ // Retrieve second last point from the arc
+ Point2D secondLast;
+ if (a.getNext().isEmpty()) {
+ secondLast = new Point2D.Double(a.getStart().getX(), a.getStart().getY());
+ } else {
+ Next temp = a.getNext().get(a.getNext().size() - 1);
+ secondLast = new Point2D.Double(temp.getX(), temp.getY());
+ }
+
+ double dx2 = secondLast.getX() - centerPoint.getX();
+ double dy2 = secondLast.getY() - centerPoint.getY();
+ double modifierAngle = Math.atan2(dy2, dx2);
+
+ double finalAngle = modifierAngle - centerLineAngle;
+ while (finalAngle < -Math.PI) {
+ finalAngle += 2 * Math.PI;
+ }
+ while (finalAngle > Math.PI) {
+ finalAngle -= 2 * Math.PI;
+ }
+ String lineConnectionType = null;
+
+ // CHECKSTYLE:OFF
+ if (finalAngle < -Math.PI / 3 * 2) {
+ lineConnectionType = "0,4";
+ } else if (finalAngle < -Math.PI / 3) {
+ lineConnectionType = "0,2";
+ } else if (finalAngle < 0) {
+ lineConnectionType = "0,5";
+ } else if (finalAngle < Math.PI / 3) {
+ lineConnectionType = "0,7";
+ } else if (finalAngle < Math.PI / 3 * 2) {
+ lineConnectionType = "0,3";
+ } else {
+ lineConnectionType = "0,6";
+ }
+ // CHECKSTYLE:ON
+
+ result = utils.getAnchorPointOnReactionRect(reaction, lineConnectionType);
+
+ return result;
+ }
+
+ /**
+ * Method used to parse line points from SBGN-ML arc.
+ *
+ * @param a
+ * SBGN-ML arc
+ * @return list of line points
+ */
+ private List<Point2D> getLinePoints(Arc a) {
+ List<Point2D> pointList = new ArrayList<>();
+ Point2D startPoint = new Point2D.Double(a.getStart().getX(), a.getStart().getY());
+ Point2D endPoint = new Point2D.Double(a.getEnd().getX(), a.getEnd().getY());
+ pointList.add(startPoint);
+ for (Next nextPoint : a.getNext()) {
+ pointList.add(new Point2D.Double(nextPoint.getX(), nextPoint.getY()));
+ }
+ pointList.add(endPoint);
+ return pointList;
+ }
+
+ /**
+ * Method used for parsing lines from sbgn-ml arcs.
+ *
+ * @param a
+ * SBGN-ML arc
+ * @param pointList
+ * list of points for the line
+ * @return line parsed from SBGN-ML arc
+ */
+ private PolylineData parseLine(Arc a, List<Point2D> pointList) {
+ PolylineData line = new PolylineData(pointList);
+ ArrowTypeData atd = new ArrowTypeData();
+
+ switch (ArcClazz.fromClazz(a.getClazz())) {
+ case CATALYSIS:
+ atd = ModifierType.CATALYSIS.getAtd();
+ break;
+ case CONSUMPTION:
+ atd.setArrowType(ArrowType.NONE);
+ break;
+ case INHIBITION:
+ atd = ModifierType.INHIBITION.getAtd();
+ break;
+ case MODULATION:
+ atd = ModifierType.MODULATION_STRING.getAtd();
+ break;
+ case NECESSARY_STIMULATION:
+ atd = ModifierType.TRIGGER_STRING.getAtd();
+ break;
+ case PRODUCTION:
+ atd.setArrowType(ArrowType.FULL);
+ break;
+ case STIMULATION:
+ atd = ModifierType.PHYSICAL_STIMULATION.getAtd();
+ break;
+ case LOGIC_ARC:
+ atd.setArrowType(ArrowType.NONE);
+ break;
+ default:
+ throw new InvalidArgumentException("Wrong arc class.");
+ }
+ atd.setArrowLineType(LineType.SOLID);
+ line.setEndAtd(atd.copy());
+ return line;
+ }
+
+ /**
+ * Returns {@link AndOperator} for the reaction's reagents port.
+ *
+ * @param p
+ * process of the reaction
+ * @return operator for the reaction port
+ */
+ private AndOperator getReactionPortAndOperator(Process p) {
+ AndOperator andOperator = new AndOperator();
+ Glyph centralPoint = p.getCentralPoint();
+ Double centralPointX = new Double(centralPoint.getBbox().getX() + centralPoint.getBbox().getW() / 2);
+ Double centralPointY = new Double(centralPoint.getBbox().getY() + centralPoint.getBbox().getH() / 2);
+ Point2D centerOfReactionPoint = new Point2D.Double(centralPointX, centralPointY);
+ Point2D portPoint;
+ if (p.getReagentArcs().size() > 1) {
+ portPoint = new Point2D.Double(p.getReagentArcs().get(0).getEnd().getX(),
+ p.getReagentArcs().get(0).getEnd().getY());
+ } else {
+ portPoint = new Point2D.Double(p.getRevReagentArcs().get(0).getStart().getX(),
+ p.getRevReagentArcs().get(0).getStart().getY());
+ }
+ PolylineData line = new PolylineData(portPoint, centerOfReactionPoint);
+ ArrowTypeData atd = new ArrowTypeData();
+ atd.setArrowType(ArrowType.NONE);
+ atd.setArrowLineType(LineType.SOLID);
+ line.setEndAtd(atd);
+ andOperator.setLine(line);
+ return andOperator;
+ }
+
+ /**
+ * Returns {@link SplitOperator} for the reaction's products port.
+ *
+ * @param p
+ * process of the reaction
+ * @return operator for the reaction port
+ */
+ private SplitOperator getReactionPortSplitOperator(Process p) {
+ SplitOperator splitOperator = new SplitOperator();
+ Glyph centralPoint = p.getCentralPoint();
+ Double centralPointX = new Double(centralPoint.getBbox().getX() + centralPoint.getBbox().getW() / 2);
+ Double centralPointY = new Double(centralPoint.getBbox().getY() + centralPoint.getBbox().getH() / 2);
+ Point2D centerOfReactionPoint = new Point2D.Double(centralPointX, centralPointY);
+ Point2D portPoint;
+ if (!p.isReversible()) {
+ portPoint = new Point2D.Double(p.getProductArcs().get(0).getStart().getX(),
+ p.getProductArcs().get(0).getStart().getY());
+ } else {
+ portPoint = new Point2D.Double(p.getRevProductArcs().get(0).getStart().getX(),
+ p.getRevProductArcs().get(0).getStart().getY());
+ }
+ PolylineData line = new PolylineData(centerOfReactionPoint, portPoint);
+ ArrowTypeData atd = new ArrowTypeData();
+ atd.setArrowType(ArrowType.NONE);
+ atd.setArrowLineType(LineType.SOLID);
+ line.setEndAtd(atd);
+ splitOperator.setLine(line);
+ return splitOperator;
+ }
+
+ /**
+ * Returns instance of {@link Modifier} based on given {@link ArcClazz}.
+ *
+ * @param ac
+ * {@link ArcClazz} defining the result
+ * @return {@link Modifier} of class adequate to given ac
+ * @throws Exception
+ * thrown when no adequate Modifier has been found
+ */
+ private Modifier getModifierFromArcClazz(ArcClazz ac) throws Exception {
+ switch (ac) {
+ case CATALYSIS:
+ return new Catalysis();
+ case INHIBITION:
+ return new Inhibition();
+ case MODULATION:
+ return new Modulation();
+ case NECESSARY_STIMULATION:
+ return new Trigger();
+ case STIMULATION:
+ return new PhysicalStimulation();
+ default:
+ logger.warn("Modifier arc of invalid class.");
+ throw new Exception("Wrong arc class.");
+ }
+ }
+
+ /**
+ * Returns center point for given process.
+ *
+ * @param p
+ * completely parsed process to compute center point from
+ * @return center point for given process
+ */
+ private Point2D getCenterPointFromProcess(Process p) {
+ Double centralPointX = new Double(p.getCentralPoint().getBbox().getX() + p.getCentralPoint().getBbox().getW() / 2);
+ Double centralPointY = new Double(p.getCentralPoint().getBbox().getY() + p.getCentralPoint().getBbox().getH() / 2);
+ Point2D centerOfReactionPoint = new Point2D.Double(centralPointX, centralPointY);
+ return centerOfReactionPoint;
+ }
+
+ /**
+ * Returns proper Reaction object based on given glyph clazz.
+ *
+ * @param glyphClazz
+ * clazz of the process glyph
+ * @return Reaction object based on given glyph clazz
+ */
+ private Reaction getReactionFromProcessGlyphClazz(String glyphClazz) {
+ switch (GlyphClazz.fromClazz(glyphClazz)) {
+ case ASSOCIATION:
+ case DISSOCIATION:
+ case PROCESS:
+ return new StateTransitionReaction();
+ case OMITTED_PROCESS:
+ return new KnownTransitionOmittedReaction();
+ case UNCERTAIN_PROCESS:
+ return new UnknownTransitionReaction();
+ default:
+ throw new InvalidArgumentException();
+
+ }
+ }
+
+ /**
+ * Method used for parsing processes into reactions.
+ *
+ * @param p
+ * process to be parsed
+ * @param model
+ * model to be updated with the parsed reaction
+ * @throws Exception
+ * thrown when the process was invalid
+ */
+ private void parseProcess(Process p, Model model) throws Exception {
+ if (p.getProductArcs().isEmpty()) {
+ throw new Exception(p.getCentralPoint().getId() + ": The process must have at least one outgoing arc.");
+ }
+ p.setProductsPort((Port) p.getProductArcs().get(0).getSource());
+ for (Arc productArc : p.getProductArcs()) {
+ if (!((Port) productArc.getSource()).equals(p.getProductsPort())) {
+ p.setReversible(true);
+ p.setReagentsPort((Port) productArc.getSource());
+ }
+ }
+ if (p.getReagentsPort() == null && !p.getReagentArcs().isEmpty()) {
+ p.setReagentsPort((Port) p.getReagentArcs().get(0).getTarget());
+ }
+
+ if ((p.getReagentArcs().isEmpty() && !p.isReversible()) || (p.getRevReagentArcs().isEmpty() && p.isReversible())) {
+ throw new Exception(p.getCentralPoint().getId() + ": The process must have at least one incoming arc.");
+ }
+
+ Reaction reaction;
+ if (p.getCentralPoint() == null) {
+ throw new Exception("Process has no central point.");
+ }
+ reaction = getReactionFromProcessGlyphClazz(p.getCentralPoint().getClazz());
+ reaction.setIdReaction(p.getCentralPoint().getId());
+ reaction.setModel(model);
+
+ reaction.setReversible(p.isReversible());
+
+ // If there are multiple inputs, add "AND" operator
+ AndOperator andOperator = null;
+ if (p.getReagentArcs().size() > 1 || p.getRevReagentArcs().size() > 1) {
+ andOperator = getReactionPortAndOperator(p);
+ andOperator.setReaction(reaction);
+ reaction.addNode(andOperator);
+ }
+
+ // If there are multiple outputs, add Split operator
+ SplitOperator splitOperator = null;
+ if ((p.getProductArcs().size() > 1 && !p.isReversible())
+ || (p.isReversible() && p.getRevProductArcs().size() > 1)) {
+ splitOperator = getReactionPortSplitOperator(p);
+ splitOperator.setReaction(reaction);
+ reaction.addNode(splitOperator);
+ }
+
+ for (Arc a : p.getReagentArcs()) {
+ Reactant reactant = new Reactant();
+ reactant.setReaction(reaction);
+ Glyph source = (Glyph) a.getSource();
+ reactant.setElement(model.getElementByElementId(source.getId()));
+ List<Point2D> pointList = getLinePoints(a);
+ if (p.getReagentArcs().size() == 1) {
+ pointList.add(getCenterPointFromProcess(p));
+ } else {
+ pointList.add(pointList.get(pointList.size() - 1));
+ }
+ PolylineData line = parseLine(a, pointList);
+ reactant.setLine(line);
+ if (andOperator != null) {
+ andOperator.addInput(reactant);
+ }
+
+ reaction.addReactant(reactant);
+ }
+
+ for (Arc a : p.getProductArcs()) {
+ if (((Port) a.getSource()).equals(p.getProductsPort())) {
+ Product product = new Product();
+ product.setReaction(reaction);
+ Glyph target = (Glyph) a.getTarget();
+ product.setElement(model.getElementByElementId(target.getId()));
+ List<Point2D> pointList = getLinePoints(a);
+ if (p.getRevProductArcs().size() >= 1) {
+ pointList.add(0, getCenterPointFromProcess(p));
+ } else {
+ pointList.add(0, pointList.get(0));
+ }
+ PolylineData line = parseLine(a, pointList);
+ product.setLine(line);
+ if (splitOperator != null) {
+ splitOperator.addOutput(product);
+ }
+
+ reaction.addProduct(product);
+ } else {
+ Reactant reactant = new Reactant();
+ reactant.setReaction(reaction);
+ Glyph source = (Glyph) a.getTarget();
+ reactant.setElement(model.getElementByElementId(source.getId()));
+ List<Point2D> pointList = getLinePoints(a);
+ if (p.getRevReagentArcs().size() <= 1) {
+ pointList.add(0, getCenterPointFromProcess(p));
+ } else {
+ pointList.add(0, pointList.get(0));
+ }
+ PolylineData line = parseLine(a, pointList);
+ line = line.reverse();
+ reactant.setLine(line);
+ if (andOperator != null) {
+ andOperator.addInput(reactant);
+ }
+
+ reaction.addReactant(reactant);
+ }
+ }
+ for (Arc a : p.getModifierArcs()) {
+ Modifier modifier = null;
+ try {
+ modifier = getModifierFromArcClazz(ArcClazz.fromClazz(a.getClazz()));
+ } catch (Exception ex) {
+ logger.warn("Unable to add modifier");
+ continue;
+ }
+ if (a.getSource() instanceof Glyph) {
+ Glyph sourceGlyph = (Glyph) a.getSource();
+ Species modifierAlias = (Species) model.getElementByElementId(sourceGlyph.getId());
+ modifier.setElement(modifierAlias);
+ List<Point2D> pointList = getLinePoints(a);
+ pointList.remove(pointList.size() - 1);
+ pointList.add(getModifierEndPoint(a, reaction));
+ PolylineData line = parseLine(a, pointList);
+ modifier.setLine(line);
+
+ reaction.addModifier(modifier);
+ } else if (a.getSource() instanceof Port) {
+ // Logic operator
+ try {
+ parseLogicOperator(a, reaction, ArcClazz.fromClazz(a.getClazz()), null, model);
+ } catch (Exception ex) {
+ logger.warn(ex.getMessage());
+ }
+ }
+
+ }
+
+ model.addReaction(reaction);
+ }
+
+ /**
+ * Returns {@link ArrowTypeData} based on given {@link ArcClazz}.
+ *
+ * @param ac
+ * input arc class
+ * @return ArrowTypeData based on input arrow class
+ * @throws Exception
+ * thrown when invalid arc class was given on input
+ */
+ private ArrowTypeData getAtdFromArcClazz(ArcClazz ac) throws Exception {
+ ArrowTypeData atd = new ArrowTypeData();
+ switch (ac) {
+ case CATALYSIS:
+ atd = ModifierType.CATALYSIS.getAtd();
+ break;
+ case CONSUMPTION:
+ atd.setArrowType(ArrowType.NONE);
+ break;
+ case INHIBITION:
+ atd = ModifierType.INHIBITION.getAtd();
+ break;
+ case MODULATION:
+ atd = ModifierType.MODULATION_STRING.getAtd();
+ break;
+ case NECESSARY_STIMULATION:
+ atd = ModifierType.TRIGGER_STRING.getAtd();
+ break;
+ case PRODUCTION:
+ atd.setArrowType(ArrowType.FULL);
+ break;
+ case STIMULATION:
+ atd = ModifierType.PHYSICAL_STIMULATION.getAtd();
+ break;
+ case LOGIC_ARC:
+ atd.setArrowType(ArrowType.NONE);
+ break;
+ default:
+ throw new Exception("Wrong arc class.");
+ }
+ return atd.copy();
+ }
+
+ /**
+ * Method used for parsing logic operators.
+ *
+ * @param arc
+ * arc with a starting point in the logic operator
+ * @param reaction
+ * reaction that the logic operator is a part of
+ * @param modifierClass
+ * determines type of source species
+ * @param targetOperator
+ * target logic operator
+ * @param model
+ * model of the map
+ * @throws Exception
+ * thrown when parsed logic operator is invalid
+ */
+ private void parseLogicOperator(Arc arc, Reaction reaction, ArcClazz modifierClass, NodeOperator targetOperator,
+ Model model) throws Exception {
+ Port operatorPort = (Port) arc.getSource();
+ Glyph logicOperator = null;
+ for (Glyph lo : logicOperators) {
+ if (lo.getPort().contains(operatorPort)) {
+ logicOperator = lo;
+ }
+ }
+ if (logicOperator == null) {
+ throw new Exception("Missing logic operator for logic arc: " + arc.getId());
+ }
+
+ // LogicOperator is valid for CellDesigner only if it has exactly 2
+ // inputs of Species
+ final Glyph tempLogicOperator = logicOperator;
+ boolean isCellDesignerValidLogicOperator = logicArcs.stream()
+ .filter(a -> tempLogicOperator.getPort().contains(a.getTarget()) && !(a.getSource() instanceof Port))
+ .count() == 2;
+ if (!isCellDesignerValidLogicOperator) {
+ throw new Exception("Parsed operator is not valid for CellDesigner: " + logicOperator.getId());
+ }
+
+ NodeOperator operator;
+ switch (GlyphClazz.fromClazz(logicOperator.getClazz())) {
+ case AND:
+ operator = new AndOperator();
+ break;
+ case OR:
+ operator = new OrOperator();
+ break;
+ case NOT:
+ logger.warn(
+ "NOT gates are not implemented in the platform. Glyph: " + logicOperator.getId() + " has not been parsed.");
+ return;
+ default:
+ throw new Exception("Wrong logic operator class.");
+ }
+
+ // Parse line from arc and operator glyph
+ Point2D operatorCenterPoint = new Point2D.Double(
+ logicOperator.getBbox().getX() + logicOperator.getBbox().getW() / 2,
+ logicOperator.getBbox().getY() + logicOperator.getBbox().getH() / 2);
+
+ List<Point2D> linePoints = getLinePoints(arc);
+ new ArrayList<Point2D>();
+
+ if (targetOperator == null) {
+ linePoints.remove(linePoints.size() - 1);
+ linePoints.add(getModifierEndPoint(arc, reaction));
+ }
+
+ // Check if operator port is in the line from center point of the
+ // operator. If so, remove that redundant point.
+ double dx, dy;
+ dx = linePoints.get(0).getX() - operatorCenterPoint.getX();
+ dy = linePoints.get(0).getY() - operatorCenterPoint.getY();
+ double dx2, dy2;
+ if (arc.getNext().isEmpty()) {
+ dx2 = linePoints.get(linePoints.size() - 1).getX() - linePoints.get(0).getX();
+ dy2 = linePoints.get(linePoints.size() - 1).getY() - linePoints.get(0).getY();
+ } else {
+ dx2 = arc.getNext().get(0).getX() - linePoints.get(0).getX();
+ dy2 = arc.getNext().get(0).getY() - linePoints.get(0).getY();
+ }
+ DoubleComparator doubleComparator = new DoubleComparator();
+ if (doubleComparator.compare(dy / dx, dy2 / dx2) == 0) {
+ linePoints.remove(0);
+ }
+ linePoints.add(0, operatorCenterPoint);
+
+ PolylineData line = new PolylineData(linePoints);
+ ArrowTypeData atd = getAtdFromArcClazz(ArcClazz.fromClazz(arc.getClazz()));
+
+ atd.setArrowLineType(LineType.SOLID);
+ line.setEndAtd(atd);
+
+ operator.setLine(line);
+ operator.setReaction(reaction);
+
+ if (targetOperator != null) {
+ operator.addOutput(targetOperator);
+ targetOperator.addInput(operator);
+ }
+
+ for (Arc logicArc : logicArcs) {
+ if (logicOperator.getPort().contains(logicArc.getTarget())) {
+ if (logicArc.getSource() instanceof Port) {
+ // The arc has source in logic operator
+ logger.warn("Logic operators trees are not compatible with CellDesigner. Therefore they are not supported.");
+ continue;
+ // parseLogicOperator(logicArc, reaction, modifierClass,
+ // operator, model);
+ } else {
+ Modifier modifier;
+
+ switch (modifierClass) {
+ case CATALYSIS:
+ modifier = new Catalysis();
+ break;
+ case INHIBITION:
+ modifier = new Inhibition();
+ break;
+ case MODULATION:
+ modifier = new Modulation();
+ break;
+ case NECESSARY_STIMULATION:
+ modifier = new Trigger();
+ break;
+ case STIMULATION:
+ modifier = new PhysicalStimulation();
+ break;
+ default:
+ throw new Exception("Wrong arc class.");
+ }
+
+ Glyph sourceGlyph = (Glyph) logicArc.getSource();
+ Species modifierAlias = (Species) model.getElementByElementId(sourceGlyph.getId());
+ modifier.setElement(modifierAlias);
+ List<Point2D> pointList = getLinePoints(logicArc);
+ pointList.add(operatorCenterPoint);
+ PolylineData newLine = parseLine(logicArc, pointList);
+ modifier.setLine(newLine);
+
+ operator.addInput(modifier);
+
+ reaction.addModifier(modifier);
+ }
+ }
+ }
+ reaction.addNode(operator);
+ }
+
+ /**
+ * Method used for parsing compartments.
+ *
+ * @param glyph
+ * compartment glyph from sbgn-ml file
+ * @param model
+ * model to be updated with the parsed compartment
+ */
+ private void parseCompartment(Glyph glyph, Model model) {
+
+ Compartment compartment = new SquareCompartment(glyph.getId());
+ if (glyph.getLabel() != null) {
+ compartment.setName(glyph.getLabel().getText());
+ }
+ compartment.setModel(model);
+ compartment.setHeight(new Double(glyph.getBbox().getH()));
+ compartment.setWidth(new Double(glyph.getBbox().getW()));
+ compartment.setX(new Double(glyph.getBbox().getX()));
+ compartment.setY(new Double(glyph.getBbox().getY()));
+ compartment.setThickness(1.0);
+ compartment.setColor(COMPARTMENT_COLOR);
+
+ if (glyph.getLabel() != null && glyph.getLabel().getBbox() != null) {
+ compartment.setNamePoint(glyph.getLabel().getBbox().getX(), glyph.getLabel().getBbox().getY());
+ } else {
+ compartment.setNamePoint(compartment.getX() + compartment.getThickness() + CONTAINER_NAME_MARGIN,
+ compartment.getY() + compartment.getThickness() + CONTAINER_NAME_MARGIN);
+ }
+ Compartment parent = findParentCompartment(compartment, model);
+ if (parent != null) {
+ compartment.setCompartment(parent);
+ parent.addElement(compartment);
+ }
+
+ model.addElement(compartment);
+ }
+}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java
index 021f39c68f5fcf039fdcf0193f6d22a711e6dd64..255c1446232c9d447b90e23d74b373f387b9f613 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java
@@ -9,7 +9,8 @@ import org.junit.runners.Suite.SuiteClasses;
CellDesignerToSbgnTest.class, //
DbSerializationTest.class, //
SbgnmlXmlExporterTest.class, //
- SbgnmlXmlParserTest.class, //
+ SbgnmlXmlParserTest.class, //
+ SbgnmlXmlParserTest2.class, //
})
public class AllSbgnmlTests {
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
index c98a7c7b0094e0509ea67d57e6b168a4ac2b8c87..f6f2695890c17c904ca3d40bc12e4c3c5e27b112 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
@@ -1,110 +1,111 @@
-package lcsb.mapviewer.converter.model.sbgnml;
-
-import static org.junit.Assert.assertEquals;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.map.ModelDao;
-
-@Transactional(value = "txManager")
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
- "/test-applicationContext.xml",//
- "/dataSource.xml", //
-
-})
-@RunWith(SpringJUnit4ClassRunner.class)
-public class DbSerializationTest {
- @Autowired
- ModelDao modelDao;
- @Autowired
- DbUtils dbUtils;
-
- Logger logger = Logger.getLogger(DbSerializationTest.class.getName());
-
- private void makeDbSerializationTest(String filePath) throws Exception {
- SbgnmlXmlParser parser = new SbgnmlXmlParser();
-
- Model model = parser.createModel(new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(filePath)));
-
- modelDao.add(model);
- modelDao.flush();
- modelDao.commit();
- modelDao.evict(model);
- Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
-
- ModelComparator comparator = new ModelComparator();
- assertEquals(0, comparator.compare(model, model2));
- modelDao.delete(model2);
- }
-
- @Before
- public void setUp() throws Exception {
- // we use custom threads because in layoutservice there is commit method
- // called, and because of that hibernate session injected by spring
- // cannot
- // commit at the end of the test case
-
- dbUtils.createSessionForCurrentThread();
-
- }
-
- @After
- public void tearDown() throws Exception {
- // close session
- dbUtils.closeSessionForCurrentThread();
- }
-
- @Test
- public void VANTEDdiagramTest() throws Exception {
- makeDbSerializationTest("VANTEDdiagram.sbgn");
- }
-
- @Test
- public void activatedStat1AlphaTest() throws Exception {
- makeDbSerializationTest("activated_stat1alpha_induction_of_the_irf1_gene.sbgn");
- }
-
- @Test
- public void adhTest() throws Exception {
- makeDbSerializationTest("adh.sbgn");
- }
-
- @Test
- public void cloneMarkerTest() throws Exception {
- makeDbSerializationTest("clone-marker.sbgn");
- }
-
- @Test
- public void glycolysisTest() throws Exception {
- makeDbSerializationTest("glycolysis.sbgn");
- }
-
- @Test
- public void insulinLikeGrowthFactorSignalingTest() throws Exception {
- makeDbSerializationTest("insulin-like_growth_factor_signaling.sbgn");
- }
-
- @Test
- public void neuronalMuscleSignallingTest() throws Exception {
- makeDbSerializationTest("neuronal_muscle_signalling.sbgn");
- }
-
- @Test
- public void phenotypeTest() throws Exception {
- makeDbSerializationTest("phenotypeTest.sbgn");
- }
-
-}
+package lcsb.mapviewer.converter.model.sbgnml;
+
+import static org.junit.Assert.assertEquals;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.map.ModelDao;
+
+@Transactional(value = "txManager")
+@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
+ "/test-applicationContext.xml", //
+ "/dataSource.xml", //
+
+})
+@RunWith(SpringJUnit4ClassRunner.class)
+public class DbSerializationTest {
+ @Autowired
+ ModelDao modelDao;
+ @Autowired
+ DbUtils dbUtils;
+
+ Logger logger = Logger.getLogger(DbSerializationTest.class.getName());
+
+ private void makeDbSerializationTest(String filePath) throws Exception {
+ SbgnmlXmlParser parser = new SbgnmlXmlParser();
+
+ Model model = parser
+ .createModel(new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(filePath)));
+
+ modelDao.add(model);
+ modelDao.flush();
+ modelDao.commit();
+ modelDao.evict(model);
+ Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
+
+ ModelComparator comparator = new ModelComparator();
+ assertEquals(0, comparator.compare(model, model2));
+ modelDao.delete(model2);
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ // we use custom threads because in layoutservice there is commit method
+ // called, and because of that hibernate session injected by spring
+ // cannot
+ // commit at the end of the test case
+
+ dbUtils.createSessionForCurrentThread();
+
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ // close session
+ dbUtils.closeSessionForCurrentThread();
+ }
+
+ @Test
+ public void VANTEDdiagramTest() throws Exception {
+ makeDbSerializationTest("VANTEDdiagram.sbgn");
+ }
+
+ @Test
+ public void activatedStat1AlphaTest() throws Exception {
+ makeDbSerializationTest("activated_stat1alpha_induction_of_the_irf1_gene.sbgn");
+ }
+
+ @Test
+ public void adhTest() throws Exception {
+ makeDbSerializationTest("adh.sbgn");
+ }
+
+ @Test
+ public void cloneMarkerTest() throws Exception {
+ makeDbSerializationTest("clone-marker.sbgn");
+ }
+
+ @Test
+ public void glycolysisTest() throws Exception {
+ makeDbSerializationTest("glycolysis.sbgn");
+ }
+
+ @Test
+ public void insulinLikeGrowthFactorSignalingTest() throws Exception {
+ makeDbSerializationTest("insulin-like_growth_factor_signaling.sbgn");
+ }
+
+ @Test
+ public void neuronalMuscleSignallingTest() throws Exception {
+ makeDbSerializationTest("neuronal_muscle_signalling.sbgn");
+ }
+
+ @Test
+ public void phenotypeTest() throws Exception {
+ makeDbSerializationTest("phenotypeTest.sbgn");
+ }
+
+}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java
index 97da4b1aa9df9806b0d60f0c66fac046cd8c8d20..a6940ca9003e4793bd116d85ac473edd9d27907f 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java
@@ -1,125 +1,131 @@
-package lcsb.mapviewer.converter.model.sbgnml;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.PrintWriter;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
-import org.junit.runners.Parameterized.Parameters;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
-import lcsb.mapviewer.converter.graphics.PngImageGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-
-@RunWith(Parameterized.class)
-public class SbgnmlXmlParserTest {
-
- Logger logger = Logger.getLogger(SbgnmlXmlParserTest.class.getName());
-
- private Path filePath;
-
- public SbgnmlXmlParserTest(Path filePath) {
- this.filePath = filePath;
- }
-
- @Parameters(name = "{index} : {0}")
- public static Collection<Object[]> data() throws IOException {
- Collection<Object[]> data = new ArrayList<Object[]>();
- Files.walk(Paths.get("testFiles/sbgnmlParserTestFiles/sbgnmlFiles")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".sbgn") && !fPath.getFileName().toString().startsWith("ASTHMA")) {
- data.add(new Object[] { fPath });
- }
- });
- return data;
- }
-
- @Test
- public void createModelTest() throws Exception {
- try {
- String dir = Files.createTempDirectory("sbgn-temp-images-dir").toFile().getAbsolutePath();
-
- IConverter converter = new SbgnmlXmlConverter();
-
- Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
-
- // Create and display image of parsed map
- AbstractImageGenerator.Params params = new AbstractImageGenerator.Params()
- .height(model.getHeight()).width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
- NormalImageGenerator nig = new PngImageGenerator(params);
- String pngFilePath = dir + "/".concat(filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".sbgn"))).concat(".png");
- nig.saveToFile(pngFilePath);
-
- CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
- String xmlString = cellDesignerXmlParser.toXml(model);
-
- String cellDesignerFilePath = dir
- + "/".concat(filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".sbgn"))).concat(".xml");
- PrintWriter out = new PrintWriter(cellDesignerFilePath);
- out.print(xmlString);
- out.close();
-
- InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
-
- Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- AbstractImageGenerator.Params params2 = new AbstractImageGenerator.Params()
- .height(model2.getHeight()).width(model2.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model2);
- NormalImageGenerator nig2 = new PngImageGenerator(params2);
- String pngFilePath2 = dir
- + "/".concat(filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".sbgn"))).concat("_2.png");
- nig2.saveToFile(pngFilePath2);
-
- assertNotNull(model2);
- // for (Reaction r : model.getReactions()) {
- // logger.debug("Reaction: " + r.getIdReaction());
- // for (AbstractNode node: r.getNodes()){
- // logger.debug(node);
- // for (Point2D point: node.getLine().getPoints())
- // logger.debug(point);
- // }
- // logger.debug("--");
- // }
- // for (Reaction r : model2.getReactions()) {
- // logger.debug("Reaction: " + r.getIdReaction());
- // for (AbstractNode node: r.getNodes()){
- // logger.debug(node);
- // for (Point2D point: node.getLine().getPoints())
- // logger.debug(point);
- // }
- // logger.debug("--");
- // }
-
- // logger.debug(pngFilePath);
- // logger.debug(pngFilePath2);
- ModelComparator comparator = new ModelComparator(1.0);
- assertEquals(0, comparator.compare(model, model2));
- FileUtils.deleteDirectory(new File(dir));
-
- } catch (Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- throw e;
- }
- logger.debug(filePath);
- }
-
-}
+package lcsb.mapviewer.converter.model.sbgnml;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.PrintWriter;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
+import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Protein;
+
+@RunWith(Parameterized.class)
+public class SbgnmlXmlParserTest {
+
+ Logger logger = Logger.getLogger(SbgnmlXmlParserTest.class.getName());
+
+ private Path filePath;
+
+ public SbgnmlXmlParserTest(Path filePath) {
+ this.filePath = filePath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ Files.walk(Paths.get("testFiles/sbgnmlParserTestFiles/sbgnmlFiles")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".sbgn")
+ && !fPath.getFileName().toString().startsWith("ASTHMA")) {
+ data.add(new Object[] { fPath });
+ }
+ });
+ return data;
+ }
+
+ @Test
+ public void createModelTest() throws Exception {
+ try {
+ String dir = Files.createTempDirectory("sbgn-temp-images-dir").toFile().getAbsolutePath();
+
+ IConverter converter = new SbgnmlXmlConverter();
+
+ Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
+
+ // Create and display image of parsed map
+ AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
+ .width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
+ NormalImageGenerator nig = new PngImageGenerator(params);
+ String pngFilePath = dir + "/"
+ .concat(filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".sbgn")))
+ .concat(".png");
+ nig.saveToFile(pngFilePath);
+
+ CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
+ String xmlString = cellDesignerXmlParser.toXml(model);
+
+ String cellDesignerFilePath = dir + "/"
+ .concat(filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".sbgn")))
+ .concat(".xml");
+ PrintWriter out = new PrintWriter(cellDesignerFilePath);
+ out.print(xmlString);
+ out.close();
+
+ InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+ Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ AbstractImageGenerator.Params params2 = new AbstractImageGenerator.Params().height(model2.getHeight())
+ .width(model2.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model2);
+ NormalImageGenerator nig2 = new PngImageGenerator(params2);
+ String pngFilePath2 = dir + "/"
+ .concat(filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".sbgn")))
+ .concat("_2.png");
+ nig2.saveToFile(pngFilePath2);
+
+ assertNotNull(model2);
+ // for (Reaction r : model.getReactions()) {
+ // logger.debug("Reaction: " + r.getIdReaction());
+ // for (AbstractNode node: r.getNodes()){
+ // logger.debug(node);
+ // for (Point2D point: node.getLine().getPoints())
+ // logger.debug(point);
+ // }
+ // logger.debug("--");
+ // }
+ // for (Reaction r : model2.getReactions()) {
+ // logger.debug("Reaction: " + r.getIdReaction());
+ // for (AbstractNode node: r.getNodes()){
+ // logger.debug(node);
+ // for (Point2D point: node.getLine().getPoints())
+ // logger.debug(point);
+ // }
+ // logger.debug("--");
+ // }
+
+ // logger.debug(pngFilePath);
+ // logger.debug(pngFilePath2);
+ ModelComparator comparator = new ModelComparator(1.0);
+ assertEquals(0, comparator.compare(model, model2));
+ FileUtils.deleteDirectory(new File(dir));
+
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ throw e;
+ }
+// logger.debug(filePath);
+ }
+
+}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
new file mode 100644
index 0000000000000000000000000000000000000000..c4c7f7f03847f2a90a8d43b825cbc6c0cd5958c1
--- /dev/null
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
@@ -0,0 +1,36 @@
+package lcsb.mapviewer.converter.model.sbgnml;
+
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.field.Residue;
+
+public class SbgnmlXmlParserTest2 {
+
+ Logger logger = Logger.getLogger(SbgnmlXmlParserTest2.class.getName());
+
+ @Test
+ public void testAdjustModificationCoordinates() throws Exception {
+ SbgnmlXmlParser parser = new SbgnmlXmlParser();
+ GenericProtein protein = new GenericProtein("id");
+ protein.setWidth(50);
+ protein.setHeight(30);
+ protein.setX(200);
+ protein.setX(300);
+ Residue mr = new Residue();
+ Point2D position = new Point2D.Double(100, 20);
+ mr.setPosition(position);
+ protein.addModificationResidue(mr);
+ parser.adjustModificationCoordinates(protein);
+
+ assertTrue(mr.getPosition().distance(position) > Configuration.EPSILON);
+
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
index ee41d7e57230d4bf9f2d6cd51d5cce7839774117..48c0d1f37e3a45761188f4c398f79ab06bad4561 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
@@ -77,7 +77,7 @@ public class BioEntityConverterImpl extends BioEntityConverter<BioEntity> {
* exception is thrown.
*
* @param element
- * {@link Element} for which we are loooking for a converter
+ * {@link Element} for which we are looking for a converter
* @param colorExtractor
* object that helps to convert overlay values into colors
* @return converter that can be applied for the given element
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
index f8b7777cdc7a41ecf1397b49f59c5ff9c86d61e8..136e148f57d3389cf509eaa179a851f0c694a219 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
@@ -1,151 +1,89 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-/**
- * This class defines methods used for drawing {@link AntisenseRna} on the
- * {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-
-public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRnaConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public AntisenseRnaConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
- GeneralPath path = getAntisenseRnaPath(antisenseRna);
- Color c = graphics.getColor();
- graphics.setColor(antisenseRna.getColor());
- graphics.fill(path);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(antisenseRna));
- graphics.draw(path);
- graphics.setStroke(stroke);
-
- for (AntisenseRnaRegion mr : antisenseRna.getRegions()) {
- drawRegion(antisenseRna, mr, graphics, false, false);
- }
-
- drawText(antisenseRna, graphics, params);
- }
-
- /**
- * Returns {@link AntisenseRna} border as a {@link GeneralPath} object.
- *
- * @param antisenseRna
- * {@link AntisenseRna} for which we want to get border
- * @return border of the {@link AntisenseRna}
- */
- private GeneralPath getAntisenseRnaPath(final AntisenseRna antisenseRna) {
- // CHECKSTYLE:OFF
- GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
- path.moveTo(antisenseRna.getX(), antisenseRna.getY());
- path.lineTo(antisenseRna.getX() + antisenseRna.getWidth() * 3 / 4, antisenseRna.getY());
- path.lineTo(antisenseRna.getX() + antisenseRna.getWidth(), antisenseRna.getY() + antisenseRna.getHeight());
- path.lineTo(antisenseRna.getX() + antisenseRna.getWidth() / 4, antisenseRna.getY() + antisenseRna.getHeight());
- // CHECKSTYLE:ON
- path.closePath();
- return path;
- }
-
- @Override
- public PathIterator getBoundPathIterator(final AntisenseRna alias) {
- return getAntisenseRnaPath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * This method draws antisense rna region for given alias.
- *
- * @param antisenseRna
- * {@link AntisenseRna} on which region should be drawn
- * @param region
- * {@link AntisenseRnaRegion} to be drawn
- * @param graphics
- * {@link Graphics2D} where we draw region
- * @param drawEmptyRegion
- * flag determining if we shoudl draw empty regions
- * @param drawDescription
- * flag determining if we want to draw description as well
- */
- private void drawRegion(final AntisenseRna antisenseRna, final AntisenseRnaRegion region, final Graphics2D graphics, final boolean drawEmptyRegion,
- final boolean drawDescription) {
- if ((!drawEmptyRegion) && (region.getState() == null)) {
- return;
- }
- double diameter = DEFAULT_MODIFICATION_DIAMETER;
-
- double x = antisenseRna.getX();
- double y = antisenseRna.getY();
-
- double width = antisenseRna.getWidth();
-
- // CHECKSTYLE:OFF
- // we draw modifier on the upper border of antisense rna (which is only in
- // 3/4 of the width of alias)
- Point2D p = new Point2D.Double(x + width * 3.0 / 4.0 * region.getPos(), y - diameter);
- // CHECKSTYLE:ON
-
- Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
- Color c = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(ellipse);
- graphics.setColor(c);
- graphics.draw(ellipse);
- graphics.drawLine((int) p.getX(), (int) (p.getY() + diameter / 2), (int) p.getX(), (int) y);
-
- String text = region.getName();
- if (!text.equals("") && drawDescription) {
- double textWidth = graphics.getFontMetrics().stringWidth(text);
- Point2D p2 = new Point2D.Double(p.getX() - textWidth / 2, p.getY() - DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
- graphics.drawString(text, (int) p2.getX(), (int) p2.getY());
- }
- ModificationState state = region.getState();
- if (state != null) {
- String str = state.getAbbreviation();
- Font tmpFont = graphics.getFont();
- graphics.setFont(getStructuralFont());
- double textX = p.getX() - graphics.getFontMetrics().stringWidth(str) / 2;
- double textY = p.getY() + graphics.getFontMetrics().getAscent() / 2;
- graphics.drawString(str, (int) textX, (int) textY);
- graphics.setFont(tmpFont);
- }
-
- }
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Path2D;
+import java.awt.geom.PathIterator;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * This class defines methods used for drawing {@link AntisenseRna} on the
+ * {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(AntisenseRnaConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public AntisenseRnaConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
+ GeneralPath path = getAntisenseRnaPath(antisenseRna);
+ Color c = graphics.getColor();
+ graphics.setColor(antisenseRna.getColor());
+ graphics.fill(path);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(antisenseRna));
+ graphics.draw(path);
+ graphics.setStroke(stroke);
+
+ for (ModificationResidue mr : antisenseRna.getRegions()) {
+ drawModification(mr, graphics, false);
+ }
+
+ drawText(antisenseRna, graphics, params);
+ }
+
+ /**
+ * Returns {@link AntisenseRna} border as a {@link GeneralPath} object.
+ *
+ * @param antisenseRna
+ * {@link AntisenseRna} for which we want to get border
+ * @return border of the {@link AntisenseRna}
+ */
+ private GeneralPath getAntisenseRnaPath(final AntisenseRna antisenseRna) {
+ // CHECKSTYLE:OFF
+ GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
+ path.moveTo(antisenseRna.getX(), antisenseRna.getY());
+ path.lineTo(antisenseRna.getX() + antisenseRna.getWidth() * 3 / 4, antisenseRna.getY());
+ path.lineTo(antisenseRna.getX() + antisenseRna.getWidth(), antisenseRna.getY() + antisenseRna.getHeight());
+ path.lineTo(antisenseRna.getX() + antisenseRna.getWidth() / 4, antisenseRna.getY() + antisenseRna.getHeight());
+ // CHECKSTYLE:ON
+ path.closePath();
+ return path;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final AntisenseRna alias) {
+ return getAntisenseRnaPath(alias).getPathIterator(new AffineTransform());
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
index 8528b749fca21bab36324abe8e66c7d5f29cb16e..2877c47e251f6c0072e261749c6352846053c23e 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
@@ -1,145 +1,83 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.Rectangle;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-/**
- * This class defines methods used for drawing Gene SpeciesAlias on the
- * graphics2d object.
- *
- * @author Piotr Gawron
- *
- */
-public class GeneConverter extends SpeciesConverter<Gene> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(GeneConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public GeneConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final Gene gene, final Graphics2D graphics, final ConverterParams params) {
- Shape shape = getGeneShape(gene);
- Color c = graphics.getColor();
- graphics.setColor(gene.getColor());
- graphics.fill(shape);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(gene));
- graphics.draw(shape);
- graphics.setStroke(stroke);
-
- for (ModificationResidue mr : gene.getModificationResidues()) {
- drawModification(gene, mr, graphics, false, false);
- }
-
- drawText(gene, graphics, params);
- }
-
- /**
- * This method draws modification of the alias. If drawEmptyModification is
- * set to false then modification is not drawn if empty. If drawDescription is
- * set then also description (position) of the modification is drawn on the
- * canvas.
- *
- * @param gene
- * object that is 'parent' of the residue
- * @param mr
- * modification to be drawn
- * @param graphics
- * - where the modification should be drawn
- * @param drawEmptyModification
- * flag that indicates if we should draw empty modification
- * @param drawDescription
- * flag that indicates if we should draw description of the
- * modification
- */
- private void drawModification(final Gene gene, final ModificationResidue mr, final Graphics2D graphics, final boolean drawEmptyModification,
- final boolean drawDescription) {
- if ((!drawEmptyModification) && (mr.getState() == null)) {
- return;
- }
- double diameter = DEFAULT_MODIFICATION_DIAMETER;
-
- double x = gene.getX();
- double y = gene.getY();
-
- double width = gene.getWidth();
-
- Point2D p = new Point2D.Double(x + width * mr.getAngle(), y - DEFAULT_MODIFICATION_DIAMETER);
-
- Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
- Color c = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(ellipse);
- graphics.setColor(c);
- graphics.draw(ellipse);
- graphics.drawLine((int) p.getX(), (int) (p.getY() + diameter / 2), (int) p.getX(), (int) y);
-
- String text = mr.getName();
- if (!text.equals("") && drawDescription) {
- double textWidth = graphics.getFontMetrics().stringWidth(text);
- Point2D p2 = new Point2D.Double(p.getX() - textWidth / 2, p.getY() - DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
- graphics.drawString(text, (int) p2.getX(), (int) p2.getY());
- }
- ModificationState state = mr.getState();
- if (state != null) {
- String str = state.getAbbreviation();
- Font tmpFont = graphics.getFont();
- graphics.setFont(getStructuralFont());
- double textX = p.getX() - graphics.getFontMetrics().stringWidth(str) / 2;
- double textY = p.getY() + graphics.getFontMetrics().getAscent() / 2;
- graphics.drawString(str, (int) textX, (int) textY);
- graphics.setFont(tmpFont);
- }
-
- }
-
- /**
- * Shape representation of the {@link Gene}.
- *
- * @param gene
- * {@link Gene} for which we are looking for a {@link Shape}
- * @return {@link Shape} that represents {@link Gene}
- */
- private Shape getGeneShape(final Gene gene) {
- Shape shape;
- shape = new Rectangle(gene.getX().intValue(), gene.getY().intValue(), gene.getWidth().intValue(), gene.getHeight().intValue());
- return shape;
- }
-
- @Override
- public PathIterator getBoundPathIterator(final Gene gene) {
- return getGeneShape(gene).getPathIterator(new AffineTransform());
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Rectangle;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.PathIterator;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * This class defines methods used for drawing Gene SpeciesAlias on the
+ * graphics2d object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class GeneConverter extends SpeciesConverter<Gene> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(GeneConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public GeneConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final Gene gene, final Graphics2D graphics, final ConverterParams params) {
+ Shape shape = getGeneShape(gene);
+ Color c = graphics.getColor();
+ graphics.setColor(gene.getColor());
+ graphics.fill(shape);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(gene));
+ graphics.draw(shape);
+ graphics.setStroke(stroke);
+
+ for (ModificationResidue mr : gene.getModificationResidues()) {
+ drawModification(mr, graphics, false);
+ }
+
+ drawText(gene, graphics, params);
+ }
+
+ /**
+ * Shape representation of the {@link Gene}.
+ *
+ * @param gene
+ * {@link Gene} for which we are looking for a {@link Shape}
+ * @return {@link Shape} that represents {@link Gene}
+ */
+ private Shape getGeneShape(final Gene gene) {
+ Shape shape;
+ shape = new Rectangle(gene.getX().intValue(), gene.getY().intValue(), gene.getWidth().intValue(),
+ gene.getHeight().intValue());
+ return shape;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final Gene gene) {
+ return getGeneShape(gene).getPathIterator(new AffineTransform());
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
index 6b0237b7498984c0ee2b5f301a2b725a9fcb8c18..b8d1220e402c2eb9fe1d91dbf622a9e95ba363d5 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
@@ -26,99 +26,85 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class IonConverter extends SpeciesConverter<Ion> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(IonConverter.class.getName());
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(IonConverter.class.getName());
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public IonConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public IonConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
- @Override
- public void draw(Ion ion, final Graphics2D graphics, final ConverterParams params) {
- double diameter = getDiameter(ion);
- double x = getXCoord(ion, diameter);
- double y = getYCoord(ion);
- Shape shape = new Ellipse2D.Double(x, y, diameter, diameter);
- Color c = graphics.getColor();
- graphics.setColor(ion.getColor());
- graphics.fill(shape);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(ion));
- graphics.draw(shape);
- graphics.setStroke(stroke);
- drawText(ion, graphics, params);
- }
+ @Override
+ public void draw(Ion ion, final Graphics2D graphics, final ConverterParams params) {
+ double diameter = getDiameter(ion);
+ double x = getXCoord(ion, diameter);
+ double y = getYCoord(ion);
+ Shape shape = new Ellipse2D.Double(x, y, diameter, diameter);
+ Color c = graphics.getColor();
+ graphics.setColor(ion.getColor());
+ graphics.fill(shape);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(ion));
+ graphics.draw(shape);
+ graphics.setStroke(stroke);
+ drawText(ion, graphics, params);
+ }
- /**
- * Returns transformed y coordinate for the {@link Ion}.
- *
- * @param ion
- * {@link Ion} to to which we are looking for y coordinate
- * @return y coordinate of the {@link Ion}
- */
- private double getYCoord(final Ion ion) {
- double y = ion.getY();
- return y;
- }
+ /**
+ * Returns transformed y coordinate for the {@link Ion}.
+ *
+ * @param ion
+ * {@link Ion} to to which we are looking for y coordinate
+ * @return y coordinate of the {@link Ion}
+ */
+ private double getYCoord(final Ion ion) {
+ double y = ion.getY();
+ return y;
+ }
- /**
- * Returns transformed x coordinate for the {@link Ion}.
- *
- * @param ion
- * {@link Ion} to which we are looking for x coordinate
- * @param diameter
- * diameter of circle representation of ion
- * @return x coordinate of the {@link Ion}
- */
- private double getXCoord(final Ion ion, final double diameter) {
- double x = ion.getX() + (ion.getWidth() - diameter) / 2;
- return x;
- }
+ /**
+ * Returns transformed x coordinate for the {@link Ion}.
+ *
+ * @param ion
+ * {@link Ion} to which we are looking for x coordinate
+ * @param diameter
+ * diameter of circle representation of ion
+ * @return x coordinate of the {@link Ion}
+ */
+ private double getXCoord(final Ion ion, final double diameter) {
+ double x = ion.getX() + (ion.getWidth() - diameter) / 2;
+ return x;
+ }
- /**
- * Returns diameter of circle representation of an {@link Ion}.
- *
- * @param ion
- * {@link Ion} to to which we are looking for diameter.
- * @return diameter of {@link Ion} circle representation
- */
- private double getDiameter(final Ion ion) {
- double diameter = Math.min(ion.getWidth(), ion.getHeight());
- if (diameter < 0) {
- logger.warn("Something is wrong. Size cannot be negative");
- diameter = 0;
- }
+ /**
+ * Returns diameter of circle representation of an {@link Ion}.
+ *
+ * @param ion
+ * {@link Ion} to to which we are looking for diameter.
+ * @return diameter of {@link Ion} circle representation
+ */
+ private double getDiameter(final Ion ion) {
+ double diameter = Math.min(ion.getWidth(), ion.getHeight());
+ if (diameter < 0) {
+ logger.warn("Something is wrong. Size cannot be negative");
+ diameter = 0;
+ }
- return diameter;
- }
+ return diameter;
+ }
- @Override
- public PathIterator getBoundPathIterator(Ion ion) {
- throw new InvalidStateException("This class doesn't have bound");
- }
-
- @Override
- public Point2D getPointCoordinatesOnBorder(Ion ion, final double angle) {
- if (ion.getWidth() == 0 && ion.getHeight() == 0) {
- logger.warn("Looking for coordinates for the alias with 0 size");
- return ion.getCenter();
- }
- double diameter = getDiameter(ion);
- double x = getXCoord(ion, diameter);
- double y = getYCoord(ion);
- Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
- return result;
-
- }
+ @Override
+ public PathIterator getBoundPathIterator(Ion ion) {
+ throw new InvalidStateException("This class doesn't have bound");
+ }
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
index 0f97b3998052c234e8602675ece715111de38352..b160c0f10e4208e0a26b362457e43eb62407cb53 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
@@ -1,462 +1,383 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Area;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.RoundRectangle2D;
-import java.util.ArrayList;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * This class defines methods used for drawing {@link Protein} on the
- * {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class ProteinConverter extends SpeciesConverter<Protein> {
-
- /**
- * Width of the ion part in the open channel representation.
- */
- private static final int ION_CHANNEL_WIDTH = 20;
-
- /**
- * Width of the gap in the open channel representation.
- */
- private static final int OPEN_ION_CHANNEL_WIDTH = 20;
-
- /**
- * How big should be the arc in rectangle for protein representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 10;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ProteinConverter.class.getName());
-
- /**
- * Helps in providing human readable identifiers of elements for logging.
- */
- private ElementUtils eu = new ElementUtils();
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public ProteinConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- /**
- * Returns shape of {@link Protein}.
- *
- * @param protein
- * {@link Protein} for which we are looking for a border
- * @return Shape object defining given alias
- */
- private Shape getGenericShape(final Protein protein) {
- return new RoundRectangle2D.Double(
- protein.getX(), protein.getY(), protein.getWidth(), protein.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
- }
-
- @Override
- public void draw(final Protein protein, final Graphics2D graphics, final ConverterParams params) {
- // Local variable setting the SBGN visualization
- boolean sbgnFormat = params.isSbgnFormat();
-
- // Unit of information text (multimer cardinality and/or ion channel's
- // state)
- String unitOfInformationText = "";
- if (protein.getStatePrefix() != null && protein.getStateLabel() != null) {
- if (protein.getStatePrefix().equals("free input")) {
- unitOfInformationText = protein.getStateLabel();
- } else {
- unitOfInformationText = protein.getStatePrefix() + ":" + protein.getStateLabel();
- }
- }
-
- int homodir;
- if (sbgnFormat) {
- // If the SBGN display mode is set, multimer is shown as two stacked
- // glyphs
- if (protein.getHomodimer() > 1) {
- homodir = 2;
- } else {
- homodir = 1;
- }
- } else {
- homodir = protein.getHomodimer();
- }
-
- protein.setWidth(protein.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
- protein.setHeight(protein.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
-
- protein.setX(protein.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
- protein.setY(protein.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
-
- for (int homodimerId = 0; homodimerId < homodir; homodimerId++) {
- protein.setX(protein.getX() - SpeciesConverter.HOMODIMER_OFFSET);
- protein.setY(protein.getY() - SpeciesConverter.HOMODIMER_OFFSET);
-
- Shape shape = null;
- if (protein instanceof GenericProtein || sbgnFormat) {
- shape = getGenericShape(protein);
- if (protein.getActivity() && !sbgnFormat) {
- drawActivityGenericProtein(protein, graphics);
- }
- } else if (protein instanceof IonChannelProtein) {
- Area a1;
- if (!protein.getActivity()) {
- a1 = new Area(
- new RoundRectangle2D.Double(
- protein.getX(), protein.getY(), protein.getWidth() - ION_CHANNEL_WIDTH - 1, protein.getHeight(), RECTANGLE_CORNER_ARC_SIZE,
- RECTANGLE_CORNER_ARC_SIZE));
- } else {
- a1 = new Area(
- new RoundRectangle2D.Double(
- protein.getX(), protein.getY(), protein.getWidth() - ION_CHANNEL_WIDTH - OPEN_ION_CHANNEL_WIDTH - 1, protein.getHeight(),
- RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE));
- }
- Area a2 = new Area(
- new RoundRectangle2D.Double(
- protein.getX() + protein.getWidth() - ION_CHANNEL_WIDTH, protein.getY(), ION_CHANNEL_WIDTH, protein.getHeight(), RECTANGLE_CORNER_ARC_SIZE,
- RECTANGLE_CORNER_ARC_SIZE));
- a1.add(a2);
- shape = a1;
- } else if (protein instanceof TruncatedProtein) {
- shape = getTruncatedShape(protein);
- if (protein.getActivity()) {
- drawActivityTruncatedShape(protein, graphics);
- }
- } else if (protein instanceof ReceptorProtein) {
- shape = getReceptorShape(protein);
- if (protein.getActivity()) {
- drawActivityReceptorProtein(protein, graphics);
- }
- } else {
- logger.warn(eu.getElementTag(protein) + "Unknown shape for protein");
- shape = getDefaultAliasShape(protein);
- }
- Color c = graphics.getColor();
- graphics.setColor(protein.getColor());
- graphics.fill(shape);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(protein));
- graphics.draw(shape);
- graphics.setStroke(stroke);
-
- // SBGN display mode - units of information and state variables are
- // printed on the top element only
- if (!sbgnFormat || (homodimerId == homodir - 1)) {
- for (ModificationResidue mr : protein.getModificationResidues()) {
- // SBGN display mode - print empty state variables
- drawModification(protein, mr, graphics, sbgnFormat, false);
- }
- if (sbgnFormat) {
- // SBGN display mode - ion channel's state is marked as a unit of
- // information
- if (protein instanceof IonChannelProtein) {
- if (!unitOfInformationText.equals("")) {
- unitOfInformationText = unitOfInformationText.concat("; ");
- }
- if (protein.getActivity()) {
- unitOfInformationText = unitOfInformationText.concat("open");
- } else {
- unitOfInformationText = unitOfInformationText.concat("closed");
- }
- }
-
- // SBGN display mode - multimers have their cardinality printed as a
- // unit of information
- if (homodir > 1 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
- if (!unitOfInformationText.equals("")) {
- unitOfInformationText = unitOfInformationText.concat("; ");
- }
- unitOfInformationText = unitOfInformationText.concat("N:").concat(Integer.toString(protein.getHomodimer()));
- }
- }
- }
- }
-
- if (unitOfInformationText.equals("")) {
- unitOfInformationText = null;
- }
-
- String text = protein.getStructuralState();
- drawStructuralState(text, protein, graphics);
- drawUnitOfInformation(unitOfInformationText, protein, graphics);
- drawText(protein, graphics, params);
- protein.setWidth(protein.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
- protein.setHeight(protein.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
- }
-
- /**
- * Draws activity border of {@link GenericProtein}.
- *
- * @param protein
- * {@link Protein} that will be drawn
- * @param graphics
- * where we are drawing
- */
- private void drawActivityGenericProtein(final Protein protein, final Graphics2D graphics) {
- int border = ACTIVITY_BORDER_DISTANCE;
- protein.increaseBorder(border);
- Shape shape2 = getGenericShape(protein);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(LineType.DOTTED.getStroke());
- graphics.draw(shape2);
- graphics.setStroke(stroke);
- protein.increaseBorder(-border);
- }
-
- /**
- * Draws activity border of {@link ReceptorProtein}.
- *
- * @param protein
- * {@link Protein} that will be drawn
- * @param graphics
- * where we are drawing
- */
- public void drawActivityReceptorProtein(final Protein protein, final Graphics2D graphics) {
- int border = ACTIVITY_BORDER_DISTANCE;
- protein.setX(protein.getX() - border);
- protein.setY(protein.getY() - border);
- protein.setWidth(protein.getWidth() + border * 2);
- protein.setHeight(protein.getHeight() + border * 2);
- Shape shape2 = getReceptorShape(protein);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(LineType.DOTTED.getStroke());
- graphics.draw(shape2);
- graphics.setStroke(stroke);
- protein.setX(protein.getX() + border);
- protein.setY(protein.getY() + border);
- protein.setWidth(protein.getWidth() - border * 2);
- protein.setHeight(protein.getHeight() - border * 2);
- }
-
- /**
- * Draws activity border of {@link TruncatedProtein}.
- *
- * @param protein
- * {@link Protein} that will be drawn
- * @param graphics
- * where we are drawing
- */
- public void drawActivityTruncatedShape(final Protein protein, final Graphics2D graphics) {
- int border = ACTIVITY_BORDER_DISTANCE;
- protein.setX(protein.getX() - border);
- protein.setY(protein.getY() - border);
- protein.setWidth(protein.getWidth() + border * 2);
- protein.setHeight(protein.getHeight() + border * 2);
- Shape shape2 = getTruncatedShape(protein);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(LineType.DOTTED.getStroke());
- graphics.draw(shape2);
- graphics.setStroke(stroke);
- protein.setX(protein.getX() + border);
- protein.setY(protein.getY() + border);
- protein.setWidth(protein.getWidth() - border * 2);
- protein.setHeight(protein.getHeight() - border * 2);
- }
-
- /**
- * This method draws modification of the alias. If drawEmptyModification is
- * set to false then modification is not drawn if empty. If drawDescription is
- * set then also description (position) of the modification is drawn on the
- * canvas.
- *
- * @param protein
- * object that is 'parent' of the residue
- * @param mr
- * modification to be drawn
- * @param graphics
- * - where the modification should be drawn
- * @param drawEmptyModification
- * flag that indicates if we should draw empty modification
- * @param drawDescription
- * flag that indicates if we should draw description of the
- * modification
- */
- private void drawModification(final Protein protein, final ModificationResidue mr, final Graphics2D graphics, final boolean drawEmptyModification,
- final boolean drawDescription) {
- if ((!drawEmptyModification) && (mr.getState() == null)) {
- return;
- }
- double diameter = DEFAULT_MODIFICATION_DIAMETER;
- double angle = mr.getAngle();
- if (angle < 0) {
- angle += Math.PI * 2;
- }
- if (angle > Math.PI * 2) {
- angle -= Math.PI * 2;
- }
-
- Point2D p = getResidueCoordinates(protein, mr.getAngle());
- Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
- Color c = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(ellipse);
- graphics.setColor(c);
- graphics.draw(ellipse);
-
- String text = mr.getName();
- if (!text.equals("") && drawDescription) {
-
- protein.increaseBorder(-diameter / 2);
- Point2D p2 = getResidueCoordinates(protein, mr.getAngle());
- protein.increaseBorder(diameter / 2);
-
- double width = graphics.getFontMetrics().stringWidth(text);
- double height = graphics.getFontMetrics().getHeight();
- if (angle <= RIGHT_TOP_RESIDUE_MAX_ANGLE || angle > BOTTOM_RESIDUE_MAX_ANGLE) {
- p2.setLocation(p2.getX() - width, p2.getY());
- } else if (angle > RIGHT_TOP_RESIDUE_MAX_ANGLE && angle <= TOP_RESIDUE_MAX_ANGLE) {
- p2.setLocation(p2.getX() - width / 2, p2.getY() + height - 2);
- } else if (angle > TOP_RESIDUE_MAX_ANGLE && angle <= LEFT_RESIDUE_MAX_ANGLE) {
- p2.setLocation(p2.getX(), p2.getY());
- } else if (angle > LEFT_RESIDUE_MAX_ANGLE && angle <= BOTTOM_RESIDUE_MAX_ANGLE) {
- p2.setLocation(p2.getX() - width / 2, p2.getY() - 2);
- } else {
- throw new InvalidStateException();
- }
-
- graphics.drawString(text, (int) p2.getX(), (int) p2.getY());
- }
- ModificationState state = mr.getState();
- if (state != null) {
- String str = state.getAbbreviation();
- Font tmpFont = graphics.getFont();
- graphics.setFont(getStructuralFont());
- double x = p.getX() - graphics.getFontMetrics().stringWidth(str) / 2;
- double y = p.getY() + graphics.getFontMetrics().getAscent() / 2;
- graphics.drawString(str, (int) x, (int) y);
- graphics.setFont(tmpFont);
- }
-
- }
-
- /**
- * Returns shape of receptor protein.
- *
- * @param protein
- * alias for which we are looking for a border
- * @return Shape object defining given alias
- */
- protected Shape getReceptorShape(final Protein protein) {
- Shape shape;
- GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD);
- ArrayList<Point2D> points = getReceptorPoints(protein);
- path.moveTo(points.get(0).getX(), points.get(0).getY());
- for (int i = 1; i < points.size(); i++) {
- path.lineTo(points.get(i).getX(), points.get(i).getY());
- }
- path.closePath();
- shape = path;
- return shape;
- }
-
- /**
- * Returns shape of truncated protein.
- *
- * @param protein
- * alias for which we are looking for a border
- * @return Shape object defining given alias
- */
- protected Shape getTruncatedShape(final Protein protein) {
- Shape shape;
- GeneralPath path = new GeneralPath();
- // CHECKSTYLE:OFF
- path.moveTo(protein.getX() + 10, protein.getY());
- path.lineTo(protein.getX() + protein.getWidth(), protein.getY());
- path.lineTo(protein.getX() + protein.getWidth(), protein.getY() + protein.getHeight() * 3 / 5);
- path.lineTo(protein.getX() + protein.getWidth() * 4 / 5, protein.getY() + protein.getHeight() * 2 / 5);
- path.lineTo(protein.getX() + protein.getWidth() * 4 / 5, protein.getY() + protein.getHeight());
- path.lineTo(protein.getX() + 10, protein.getY() + protein.getHeight());
- path.curveTo(
- protein.getX() + 5, protein.getY() + protein.getHeight() - 2, protein.getX() + 2, protein.getY() + protein.getHeight() - 5, protein.getX(),
- protein.getY() + protein.getHeight() - 10);
- path.lineTo(protein.getX(), protein.getY() + 10);
- path.curveTo(protein.getX() + 2, protein.getY() + 5, protein.getX() + 5, protein.getY() + 2, protein.getX() + 10, protein.getY());
- // CHECKSTYLE:ON
-
- path.closePath();
- shape = path;
- return shape;
- }
-
- /**
- * Returns shape of receptor protein as a list of points.
- *
- * @param protein
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getReceptorPoints(final Protein protein) {
- double x = protein.getX();
- double y = protein.getY();
- double width = protein.getWidth();
- double height = protein.getHeight();
- ArrayList<Point2D> points = new ArrayList<Point2D>();
-
- // CHECKSTYLE:OFF
- points.add(new Point2D.Double(x, y + height * 2 / 5));
- points.add(new Point2D.Double(x, y));
- points.add(new Point2D.Double(x + width / 2, y + height / 5));
- points.add(new Point2D.Double(x + width, y));
- points.add(new Point2D.Double(x + width, y + height * 2 / 5));
- points.add(new Point2D.Double(x + width, y + height * 4 / 5));
- points.add(new Point2D.Double(x + width / 2, y + height));
- points.add(new Point2D.Double(x, y + height * 4 / 5));
- // CHECKSTYLE:ON
-
- return points;
- }
-
- @Override
- public PathIterator getBoundPathIterator(final Protein protein) {
- if (protein instanceof GenericProtein) {
- return getGenericShape(protein).getPathIterator(new AffineTransform());
- } else if (protein instanceof ReceptorProtein) {
- return getReceptorShape(protein).getPathIterator(new AffineTransform());
- } else if (protein instanceof IonChannelProtein) {
- return getGenericShape(protein).getPathIterator(new AffineTransform());
- } else if (protein instanceof TruncatedProtein) {
- return getTruncatedShape(protein).getPathIterator(new AffineTransform());
- } else {
- throw new InvalidArgumentException("Not implemented protein converter for type: " + protein.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Area;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Path2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.awt.geom.RoundRectangle2D;
+import java.util.ArrayList;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * This class defines methods used for drawing {@link Protein} on the
+ * {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ProteinConverter extends SpeciesConverter<Protein> {
+
+ /**
+ * Width of the ion part in the open channel representation.
+ */
+ private static final int ION_CHANNEL_WIDTH = 20;
+
+ /**
+ * Width of the gap in the open channel representation.
+ */
+ private static final int OPEN_ION_CHANNEL_WIDTH = 20;
+
+ /**
+ * How big should be the arc in rectangle for protein representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 10;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ProteinConverter.class.getName());
+
+ /**
+ * Helps in providing human readable identifiers of elements for logging.
+ */
+ private ElementUtils eu = new ElementUtils();
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public ProteinConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ /**
+ * Returns shape of {@link Protein}.
+ *
+ * @param protein
+ * {@link Protein} for which we are looking for a border
+ * @return Shape object defining given alias
+ */
+ private Shape getGenericShape(final Protein protein) {
+ return new RoundRectangle2D.Double(protein.getX(), protein.getY(), protein.getWidth(), protein.getHeight(),
+ RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+ }
+
+ @Override
+ public void draw(final Protein protein, final Graphics2D graphics, final ConverterParams params) {
+ // Local variable setting the SBGN visualization
+ boolean sbgnFormat = params.isSbgnFormat();
+
+ // Unit of information text (multimer cardinality and/or ion channel's
+ // state)
+ String unitOfInformationText = "";
+ if (protein.getStatePrefix() != null && protein.getStateLabel() != null) {
+ if (protein.getStatePrefix().equals("free input")) {
+ unitOfInformationText = protein.getStateLabel();
+ } else {
+ unitOfInformationText = protein.getStatePrefix() + ":" + protein.getStateLabel();
+ }
+ }
+
+ int homodir;
+ if (sbgnFormat) {
+ // If the SBGN display mode is set, multimer is shown as two stacked
+ // glyphs
+ if (protein.getHomodimer() > 1) {
+ homodir = 2;
+ } else {
+ homodir = 1;
+ }
+ } else {
+ homodir = protein.getHomodimer();
+ }
+
+ protein.setWidth(protein.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
+ protein.setHeight(protein.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
+
+ protein.setX(protein.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+ protein.setY(protein.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+
+ for (int homodimerId = 0; homodimerId < homodir; homodimerId++) {
+ protein.setX(protein.getX() - SpeciesConverter.HOMODIMER_OFFSET);
+ protein.setY(protein.getY() - SpeciesConverter.HOMODIMER_OFFSET);
+
+ Shape shape = null;
+ if (protein instanceof GenericProtein || sbgnFormat) {
+ shape = getGenericShape(protein);
+ if (protein.getActivity() && !sbgnFormat) {
+ drawActivityGenericProtein(protein, graphics);
+ }
+ } else if (protein instanceof IonChannelProtein) {
+ Area a1;
+ if (!protein.getActivity()) {
+ a1 = new Area(
+ new RoundRectangle2D.Double(protein.getX(), protein.getY(), protein.getWidth() - ION_CHANNEL_WIDTH - 1,
+ protein.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE));
+ } else {
+ a1 = new Area(new RoundRectangle2D.Double(protein.getX(), protein.getY(),
+ protein.getWidth() - ION_CHANNEL_WIDTH - OPEN_ION_CHANNEL_WIDTH - 1, protein.getHeight(),
+ RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE));
+ }
+ Area a2 = new Area(
+ new RoundRectangle2D.Double(protein.getX() + protein.getWidth() - ION_CHANNEL_WIDTH, protein.getY(),
+ ION_CHANNEL_WIDTH, protein.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE));
+ a1.add(a2);
+ shape = a1;
+ } else if (protein instanceof TruncatedProtein) {
+ shape = getTruncatedShape(protein);
+ if (protein.getActivity()) {
+ drawActivityTruncatedShape(protein, graphics);
+ }
+ } else if (protein instanceof ReceptorProtein) {
+ shape = getReceptorShape(protein);
+ if (protein.getActivity()) {
+ drawActivityReceptorProtein(protein, graphics);
+ }
+ } else {
+ logger.warn(eu.getElementTag(protein) + "Unknown shape for protein");
+ shape = getDefaultAliasShape(protein);
+ }
+ Color c = graphics.getColor();
+ graphics.setColor(protein.getColor());
+ graphics.fill(shape);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(protein));
+ graphics.draw(shape);
+ graphics.setStroke(stroke);
+
+ // SBGN display mode - units of information and state variables are
+ // printed on the top element only
+ if (!sbgnFormat || (homodimerId == homodir - 1)) {
+ for (ModificationResidue mr : protein.getModificationResidues()) {
+ // SBGN display mode - print empty state variables
+ drawModification(mr, graphics, sbgnFormat);
+ }
+ if (sbgnFormat) {
+ // SBGN display mode - ion channel's state is marked as a unit of
+ // information
+ if (protein instanceof IonChannelProtein) {
+ if (!unitOfInformationText.equals("")) {
+ unitOfInformationText = unitOfInformationText.concat("; ");
+ }
+ if (protein.getActivity()) {
+ unitOfInformationText = unitOfInformationText.concat("open");
+ } else {
+ unitOfInformationText = unitOfInformationText.concat("closed");
+ }
+ }
+
+ // SBGN display mode - multimers have their cardinality printed as a
+ // unit of information
+ if (homodir > 1 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
+ if (!unitOfInformationText.equals("")) {
+ unitOfInformationText = unitOfInformationText.concat("; ");
+ }
+ unitOfInformationText = unitOfInformationText.concat("N:").concat(Integer.toString(protein.getHomodimer()));
+ }
+ }
+ }
+ }
+
+ if (unitOfInformationText.equals("")) {
+ unitOfInformationText = null;
+ }
+
+ String text = protein.getStructuralState();
+ drawStructuralState(text, protein, graphics);
+ drawUnitOfInformation(unitOfInformationText, protein, graphics);
+ drawText(protein, graphics, params);
+ protein.setWidth(protein.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
+ protein.setHeight(protein.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
+ }
+
+ /**
+ * Draws activity border of {@link GenericProtein}.
+ *
+ * @param protein
+ * {@link Protein} that will be drawn
+ * @param graphics
+ * where we are drawing
+ */
+ private void drawActivityGenericProtein(final Protein protein, final Graphics2D graphics) {
+ int border = ACTIVITY_BORDER_DISTANCE;
+ protein.increaseBorder(border);
+ Shape shape2 = getGenericShape(protein);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(LineType.DOTTED.getStroke());
+ graphics.draw(shape2);
+ graphics.setStroke(stroke);
+ protein.increaseBorder(-border);
+ }
+
+ /**
+ * Draws activity border of {@link ReceptorProtein}.
+ *
+ * @param protein
+ * {@link Protein} that will be drawn
+ * @param graphics
+ * where we are drawing
+ */
+ public void drawActivityReceptorProtein(final Protein protein, final Graphics2D graphics) {
+ int border = ACTIVITY_BORDER_DISTANCE;
+ protein.setX(protein.getX() - border);
+ protein.setY(protein.getY() - border);
+ protein.setWidth(protein.getWidth() + border * 2);
+ protein.setHeight(protein.getHeight() + border * 2);
+ Shape shape2 = getReceptorShape(protein);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(LineType.DOTTED.getStroke());
+ graphics.draw(shape2);
+ graphics.setStroke(stroke);
+ protein.setX(protein.getX() + border);
+ protein.setY(protein.getY() + border);
+ protein.setWidth(protein.getWidth() - border * 2);
+ protein.setHeight(protein.getHeight() - border * 2);
+ }
+
+ /**
+ * Draws activity border of {@link TruncatedProtein}.
+ *
+ * @param protein
+ * {@link Protein} that will be drawn
+ * @param graphics
+ * where we are drawing
+ */
+ public void drawActivityTruncatedShape(final Protein protein, final Graphics2D graphics) {
+ int border = ACTIVITY_BORDER_DISTANCE;
+ protein.setX(protein.getX() - border);
+ protein.setY(protein.getY() - border);
+ protein.setWidth(protein.getWidth() + border * 2);
+ protein.setHeight(protein.getHeight() + border * 2);
+ Shape shape2 = getTruncatedShape(protein);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(LineType.DOTTED.getStroke());
+ graphics.draw(shape2);
+ graphics.setStroke(stroke);
+ protein.setX(protein.getX() + border);
+ protein.setY(protein.getY() + border);
+ protein.setWidth(protein.getWidth() - border * 2);
+ protein.setHeight(protein.getHeight() - border * 2);
+ }
+
+ /**
+ * Returns shape of receptor protein.
+ *
+ * @param protein
+ * alias for which we are looking for a border
+ * @return Shape object defining given alias
+ */
+ protected Shape getReceptorShape(final Protein protein) {
+ Shape shape;
+ GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD);
+ ArrayList<Point2D> points = getReceptorPoints(protein);
+ path.moveTo(points.get(0).getX(), points.get(0).getY());
+ for (int i = 1; i < points.size(); i++) {
+ path.lineTo(points.get(i).getX(), points.get(i).getY());
+ }
+ path.closePath();
+ shape = path;
+ return shape;
+ }
+
+ /**
+ * Returns shape of truncated protein.
+ *
+ * @param protein
+ * alias for which we are looking for a border
+ * @return Shape object defining given alias
+ */
+ protected Shape getTruncatedShape(final Protein protein) {
+ Shape shape;
+ GeneralPath path = new GeneralPath();
+ // CHECKSTYLE:OFF
+ path.moveTo(protein.getX() + 10, protein.getY());
+ path.lineTo(protein.getX() + protein.getWidth(), protein.getY());
+ path.lineTo(protein.getX() + protein.getWidth(), protein.getY() + protein.getHeight() * 3 / 5);
+ path.lineTo(protein.getX() + protein.getWidth() * 4 / 5, protein.getY() + protein.getHeight() * 2 / 5);
+ path.lineTo(protein.getX() + protein.getWidth() * 4 / 5, protein.getY() + protein.getHeight());
+ path.lineTo(protein.getX() + 10, protein.getY() + protein.getHeight());
+ path.curveTo(protein.getX() + 5, protein.getY() + protein.getHeight() - 2, protein.getX() + 2,
+ protein.getY() + protein.getHeight() - 5, protein.getX(), protein.getY() + protein.getHeight() - 10);
+ path.lineTo(protein.getX(), protein.getY() + 10);
+ path.curveTo(protein.getX() + 2, protein.getY() + 5, protein.getX() + 5, protein.getY() + 2, protein.getX() + 10,
+ protein.getY());
+ // CHECKSTYLE:ON
+
+ path.closePath();
+ shape = path;
+ return shape;
+ }
+
+ /**
+ * Returns shape of receptor protein as a list of points.
+ *
+ * @param protein
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getReceptorPoints(final Protein protein) {
+ double x = protein.getX();
+ double y = protein.getY();
+ double width = protein.getWidth();
+ double height = protein.getHeight();
+ ArrayList<Point2D> points = new ArrayList<Point2D>();
+
+ // CHECKSTYLE:OFF
+ points.add(new Point2D.Double(x, y + height * 2 / 5));
+ points.add(new Point2D.Double(x, y));
+ points.add(new Point2D.Double(x + width / 2, y + height / 5));
+ points.add(new Point2D.Double(x + width, y));
+ points.add(new Point2D.Double(x + width, y + height * 2 / 5));
+ points.add(new Point2D.Double(x + width, y + height * 4 / 5));
+ points.add(new Point2D.Double(x + width / 2, y + height));
+ points.add(new Point2D.Double(x, y + height * 4 / 5));
+ // CHECKSTYLE:ON
+
+ return points;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final Protein protein) {
+ if (protein instanceof GenericProtein) {
+ return getGenericShape(protein).getPathIterator(new AffineTransform());
+ } else if (protein instanceof ReceptorProtein) {
+ return getReceptorShape(protein).getPathIterator(new AffineTransform());
+ } else if (protein instanceof IonChannelProtein) {
+ return getGenericShape(protein).getPathIterator(new AffineTransform());
+ } else if (protein instanceof TruncatedProtein) {
+ return getTruncatedShape(protein).getPathIterator(new AffineTransform());
+ } else {
+ throw new InvalidArgumentException("Not implemented protein converter for type: " + protein.getClass());
+ }
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
index bf0b0533f521cf4572b7b00fdcca619f978c9263..c66fada0f4568f32e76f2634a9a3c49c9973b01d 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
@@ -1,162 +1,95 @@
-/**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into colors
- * when drawing {@link Species}
- */
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-
-/**
- * This class defines methods used for drawing {@link Rna} on the
- * {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class RnaConverter extends SpeciesConverter<Rna> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RnaConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public RnaConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
- GeneralPath path = getRnaPath(rna);
- Color c = graphics.getColor();
- graphics.setColor(rna.getColor());
- graphics.fill(path);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(rna));
- graphics.draw(path);
- graphics.setStroke(stroke);
-
- for (RnaRegion mr : rna.getRegions()) {
- drawModification(rna, mr, graphics, false, false);
- }
-
- drawText(rna, graphics, params);
- }
-
- /**
- * Returns shape of the {@link Rna} as a {@link GeneralPath} object.
- *
- * @param rna
- * {@link Rna} for which we are looking for a border
- * @return {@link GeneralPath} object defining border of the given {@link Rna}
- */
- private GeneralPath getRnaPath(final Rna rna) {
- // CHECKSTYLE:OFF
- GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
- path.moveTo(rna.getX() + rna.getWidth() / 4, rna.getY());
- path.lineTo(rna.getX() + rna.getWidth(), rna.getY());
- path.lineTo(rna.getX() + rna.getWidth() * 3 / 4, rna.getY() + rna.getHeight());
- path.lineTo(rna.getX(), rna.getY() + rna.getHeight());
- // CHECKSTYLE:ON
- path.closePath();
- return path;
- }
-
- @Override
- public PathIterator getBoundPathIterator(final Rna rna) {
- return getRnaPath(rna).getPathIterator(new AffineTransform());
- }
-
- /**
- * This method draws modification of the alias. If drawEmptyModification is
- * set to false then modification is not drawn if empty. If drawDescription is
- * set then also description (position) of the modification is drawn on the
- * canvas.
- *
- * @param rna
- * object that is 'parent' of the residue
- * @param region
- * {@link RnaRegion modification} to be drawn
- * @param graphics
- * - where the modification should be drawn
- * @param drawEmptyModification
- * flag that indicates if we should draw empty modification
- * @param drawDescription
- * flag that indicates if we should draw description of the
- * modification
- */
- private void drawModification(final Rna rna, final RnaRegion region, final Graphics2D graphics, final boolean drawEmptyModification,
- final boolean drawDescription) {
- if ((!drawEmptyModification) && (region.getState() == null)) {
- return;
- }
- double diameter = DEFAULT_MODIFICATION_DIAMETER;
-
- double x = rna.getX();
- double y = rna.getY();
-
- double width = rna.getWidth();
-
- // CHECKSTYLE:OFF
- // we draw modifier on the upper border of rna (which is only in
- // 3/4 of the width of alias, but starts in 1/4 of the width)
- Point2D p = new Point2D.Double(x + width / 4.0 + width * 3.0 / 4.0 * region.getPos(), y - DEFAULT_MODIFICATION_DIAMETER);
- // CHECKSTYLE:ON
-
- Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
- Color c = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(ellipse);
- graphics.setColor(c);
- graphics.draw(ellipse);
- graphics.drawLine((int) p.getX(), (int) (p.getY() + diameter / 2), (int) p.getX(), (int) y);
-
- String text = region.getName();
- if (!text.equals("") && drawDescription) {
- double textWidth = graphics.getFontMetrics().stringWidth(text);
- Point2D p2 = new Point2D.Double(p.getX() - textWidth / 2, p.getY() - DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
- graphics.drawString(text, (int) p2.getX(), (int) p2.getY());
- }
- ModificationState state = region.getState();
- if (state != null) {
- String str = state.getAbbreviation();
- Font tmpFont = graphics.getFont();
- graphics.setFont(getStructuralFont());
- double textX = p.getX() - graphics.getFontMetrics().stringWidth(str) / 2;
- double textY = p.getY() + graphics.getFontMetrics().getAscent() / 2;
- graphics.drawString(str, (int) textX, (int) textY);
- graphics.setFont(tmpFont);
- }
-
- }
-
-}
+/**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Path2D;
+import java.awt.geom.PathIterator;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * This class defines methods used for drawing {@link Rna} on the
+ * {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RnaConverter extends SpeciesConverter<Rna> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(RnaConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public RnaConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
+ GeneralPath path = getRnaPath(rna);
+ Color c = graphics.getColor();
+ graphics.setColor(rna.getColor());
+ graphics.fill(path);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(rna));
+ graphics.draw(path);
+ graphics.setStroke(stroke);
+
+ for (ModificationResidue mr : rna.getRegions()) {
+ drawModification(mr, graphics, false);
+ }
+
+ drawText(rna, graphics, params);
+ }
+
+ /**
+ * Returns shape of the {@link Rna} as a {@link GeneralPath} object.
+ *
+ * @param rna
+ * {@link Rna} for which we are looking for a border
+ * @return {@link GeneralPath} object defining border of the given {@link Rna}
+ */
+ private GeneralPath getRnaPath(final Rna rna) {
+ // CHECKSTYLE:OFF
+ GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
+ path.moveTo(rna.getX() + rna.getWidth() / 4, rna.getY());
+ path.lineTo(rna.getX() + rna.getWidth(), rna.getY());
+ path.lineTo(rna.getX() + rna.getWidth() * 3 / 4, rna.getY() + rna.getHeight());
+ path.lineTo(rna.getX(), rna.getY() + rna.getHeight());
+ // CHECKSTYLE:ON
+ path.closePath();
+ return path;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final Rna rna) {
+ return getRnaPath(rna).getPathIterator(new AffineTransform());
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
index 8ce04bcc3d88e37d14e34c3f439c3cf2f9bd26c0..8a609f533ccb963ad4a8a546636cdbf909d9a5c4 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
@@ -1,126 +1,114 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class defines methods used for drawing {@link SimpleMolecule} on the
- * {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(SimpleMoleculeConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public SimpleMoleculeConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final SimpleMolecule simpleMolecule, final Graphics2D graphics, final ConverterParams params) {
- int homodir;
- if (params.isSbgnFormat()) {
- // If the SBGN display mode is set, multimer is shown as two stacked
- // glyphs
- if (simpleMolecule.getHomodimer() > 1) {
- homodir = 2;
- } else {
- homodir = 1;
- }
- } else {
- homodir = simpleMolecule.getHomodimer();
- }
-
- simpleMolecule.setWidth(simpleMolecule.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
- simpleMolecule.setHeight(simpleMolecule.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
-
- // SBGN view - simple molecules are represented as circles
- if (params.isSbgnFormat()) {
- simpleMolecule.setX(simpleMolecule.getX() + (simpleMolecule.getWidth() - simpleMolecule.getHeight()) / 2);
- simpleMolecule.setWidth(simpleMolecule.getHeight());
- }
-
- simpleMolecule.setX(simpleMolecule.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
- simpleMolecule.setY(simpleMolecule.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
-
- for (int i = 0; i < homodir; i++) {
- simpleMolecule.setX(simpleMolecule.getX() - SpeciesConverter.HOMODIMER_OFFSET);
- simpleMolecule.setY(simpleMolecule.getY() - SpeciesConverter.HOMODIMER_OFFSET);
- Shape shape = new Ellipse2D.Double(simpleMolecule.getX(), simpleMolecule.getY(), simpleMolecule.getWidth(), simpleMolecule.getHeight());
- Color c = graphics.getColor();
- graphics.setColor(simpleMolecule.getColor());
- graphics.fill(shape);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(simpleMolecule));
- graphics.draw(shape);
- graphics.setStroke(stroke);
-
- // SBGN view - multimers are displayed with a unit of information
- // containing cardinality
- if (params.isSbgnFormat() && (i == homodir - 1)) {
- String unitOfInformationText = null;
- if (simpleMolecule.getStatePrefix() != null && simpleMolecule.getStateLabel() != null) {
- unitOfInformationText = simpleMolecule.getStatePrefix() + ":" + simpleMolecule.getStateLabel();
- }
- if (homodir == 2 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
- if (unitOfInformationText != null) {
- unitOfInformationText += "; ";
- } else {
- unitOfInformationText = "";
- }
- unitOfInformationText += "N:" + simpleMolecule.getHomodimer();
- }
-
- drawUnitOfInformation(unitOfInformationText, simpleMolecule, graphics);
- }
- }
- simpleMolecule.setWidth(simpleMolecule.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
- simpleMolecule.setHeight(simpleMolecule.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
- drawText(simpleMolecule, graphics, params);
- }
-
- @Override
- public PathIterator getBoundPathIterator(final SimpleMolecule simpleMolecule) {
- throw new InvalidStateException("This class doesn't provide boundPath");
- }
-
- @Override
- public Point2D getPointCoordinatesOnBorder(final SimpleMolecule simpleMolecule, final double angle) {
- if (simpleMolecule.getWidth() == 0 && simpleMolecule.getHeight() == 0) {
- logger.warn("Looking for coordinates on border of alias of size 0");
- return simpleMolecule.getCenter();
- }
- Point2D result;
- result = getEllipseTransformation()
- .getPointOnEllipseByRadian(simpleMolecule.getX(), simpleMolecule.getY(), simpleMolecule.getWidth(), simpleMolecule.getHeight(), angle);
- return result;
-
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class defines methods used for drawing {@link SimpleMolecule} on the
+ * {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(SimpleMoleculeConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public SimpleMoleculeConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final SimpleMolecule simpleMolecule, final Graphics2D graphics, final ConverterParams params) {
+ int homodir;
+ if (params.isSbgnFormat()) {
+ // If the SBGN display mode is set, multimer is shown as two stacked
+ // glyphs
+ if (simpleMolecule.getHomodimer() > 1) {
+ homodir = 2;
+ } else {
+ homodir = 1;
+ }
+ } else {
+ homodir = simpleMolecule.getHomodimer();
+ }
+
+ simpleMolecule.setWidth(simpleMolecule.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ simpleMolecule.setHeight(simpleMolecule.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+
+ // SBGN view - simple molecules are represented as circles
+ if (params.isSbgnFormat()) {
+ simpleMolecule.setX(simpleMolecule.getX() + (simpleMolecule.getWidth() - simpleMolecule.getHeight()) / 2);
+ simpleMolecule.setWidth(simpleMolecule.getHeight());
+ }
+
+ simpleMolecule.setX(simpleMolecule.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+ simpleMolecule.setY(simpleMolecule.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+
+ for (int i = 0; i < homodir; i++) {
+ simpleMolecule.setX(simpleMolecule.getX() - SpeciesConverter.HOMODIMER_OFFSET);
+ simpleMolecule.setY(simpleMolecule.getY() - SpeciesConverter.HOMODIMER_OFFSET);
+ Shape shape = new Ellipse2D.Double(simpleMolecule.getX(), simpleMolecule.getY(), simpleMolecule.getWidth(),
+ simpleMolecule.getHeight());
+ Color c = graphics.getColor();
+ graphics.setColor(simpleMolecule.getColor());
+ graphics.fill(shape);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(simpleMolecule));
+ graphics.draw(shape);
+ graphics.setStroke(stroke);
+
+ // SBGN view - multimers are displayed with a unit of information
+ // containing cardinality
+ if (params.isSbgnFormat() && (i == homodir - 1)) {
+ String unitOfInformationText = null;
+ if (simpleMolecule.getStatePrefix() != null && simpleMolecule.getStateLabel() != null) {
+ unitOfInformationText = simpleMolecule.getStatePrefix() + ":" + simpleMolecule.getStateLabel();
+ }
+ if (homodir == 2 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
+ if (unitOfInformationText != null) {
+ unitOfInformationText += "; ";
+ } else {
+ unitOfInformationText = "";
+ }
+ unitOfInformationText += "N:" + simpleMolecule.getHomodimer();
+ }
+
+ drawUnitOfInformation(unitOfInformationText, simpleMolecule, graphics);
+ }
+ }
+ simpleMolecule.setWidth(simpleMolecule.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ simpleMolecule.setHeight(simpleMolecule.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ drawText(simpleMolecule, graphics, params);
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final SimpleMolecule simpleMolecule) {
+ throw new InvalidStateException("This class doesn't provide boundPath");
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
index 2bf368852c188ceceb829c2009a4541d6007d2df..c707b3b147c068086f3906842bd7cfe0e68b3b04 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
@@ -1,607 +1,694 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.Rectangle;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.Line2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.geometry.EllipseTransformation;
-import lcsb.mapviewer.common.geometry.LineTransformation;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class defines basics used for drawing {@link Species} (node in the graph
- * representation) on the {@link Graphics2D} object.
- *
- * @param <T>
- * type of {@link Species} class that can be drawn with this converter
- * @author Piotr Gawron
- *
- */
-public abstract class SpeciesConverter<T extends Species> extends ElementConverter<T> {
-
- /**
- * PI value.
- */
- private static final double PI = Math.PI;
-
- /**
- * Constant determining angle of the top right corner.
- */
- protected static final double RIGHT_TOP_RESIDUE_MAX_ANGLE = 0.25 * PI;
-
- /**
- * Constant determining angle of the top left corner.
- */
- protected static final double TOP_RESIDUE_MAX_ANGLE = 0.75 * PI;
-
- /**
- * Constant determining angle of the bottom left corner.
- */
- protected static final double LEFT_RESIDUE_MAX_ANGLE = 1.25 * PI;
-
- /**
- * Constant determining angle of the bottom right corner.
- */
- protected static final double BOTTOM_RESIDUE_MAX_ANGLE = 1.75 * PI;
-
- /**
- * Default font size for the modifier description.
- */
- protected static final int DEFAULT_SPECIES_MODIFIER_FONT_SIZE = 10;
-
- /**
- * Default diameter of the modification residues.
- */
- protected static final int DEFAULT_MODIFICATION_DIAMETER = 15;
-
- /**
- * How far from the original shape should the activity border be drawn.
- */
- protected static final int ACTIVITY_BORDER_DISTANCE = 5;
-
- /**
- * Default species font size.
- */
- protected static final int DEFAULT_SPECIES_FONT_SIZE = 12;
-
- /**
- * Height of the ellipse that contain structural state description.
- */
- private static final int STRUCTURAL_STATE_HEIGHT = 20;
-
- /**
- * Height of the rectangle that contains unit of information.
- */
- private static final int UNIT_OF_INFORMATION_HEIGHT = 20;
-
- /**
- * Size of the margin in the structural state description.
- */
- private static final int TEXT_MARGIN_FOR_STRUCTURAL_STATE_DESC = 40;
-
- /**
- * Size of the margin in the unit of information description.
- */
- private static final int TEXT_MARGIN_FOR_UNIT_OF_INFORMATION_DESC = 20;
-
- /**
- * Minimum width of the structural state ellipse.
- */
- private static final int MIN_STRUCTURAL_STATE_WIDTH = 60;
-
- /**
- * Minimum width of the unit of information rectangle.
- */
- private static final int MIN_UNIT_OF_INFORMATION_WIDTH = 40;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SpeciesConverter.class.getName());
-
- /**
- * Graphical helper object with line transformation functions.
- */
- private LineTransformation lineTransformation = new LineTransformation();
-
- /**
- * Graphical helper object with ellipse transformation functions.
- */
- private EllipseTransformation ellipseTransformation = new EllipseTransformation();
-
- /**
- * Default font used to draw structural state of the species.
- */
- private Font structuralFont = null;
-
- /**
- * Default font used to draw unit of information of the species.
- */
- private Font unitOfInformationFont = null;
-
- /**
- * What is the distance between homodimer aliases when homodimer>1.
- */
- public static final int HOMODIMER_OFFSET = 6;
-
- /**
- * Object that helps to convert {@link ColorSchema} values into colors.
- */
- private ColorExtractor colorExtractor;
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- protected SpeciesConverter(ColorExtractor colorExtractor) {
- structuralFont = new Font(Font.SANS_SERIF, 0, DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
- this.colorExtractor = colorExtractor;
- };
-
- /**
- * Returns coordinates on the {@link Species} border for given angle.
- *
- * @param species
- * {@link Species} on border which the point is looked for
- * @param angle
- * angle between X axis center point of {@link Species} and point
- * that we are looking for
- * @return coordinates on the {@link Species} border that correspond to the
- * angle
- */
- protected Point2D getPointCoordinatesOnBorder(final T species, final double angle) {
- Point2D result = null;
- if (species.getWidth() == 0 && species.getHeight() == 0) {
- result = species.getCenter();
- } else {
- double dist = Math.max(species.getWidth(), species.getHeight()) * 2;
- Point2D startPoint = species.getCenter();
- double x = startPoint.getX() + Math.cos(angle) * dist;
- double y = startPoint.getY() - Math.sin(angle) * dist;
- Point2D endPoint = new Point2D.Double(x, y);
- Line2D line = new Line2D.Double(startPoint, endPoint);
- result = lineTransformation.getIntersectionWithPathIterator(line, getBoundPathIterator(species));
- }
- return result;
-
- }
-
- /**
- * Returns coordinates on the {@link Species} border for given angle for
- * residues.
- *
- * @param species
- * object on border which the point is looked for
- * @param angle
- * CellDEsigner specific angle defining coordinates (;/)
- * @return coordinates on the alias border that correspond to the angle
- */
- protected Point2D getResidueCoordinates(final T species, double angle) {
- Point2D result = null;
- if (species.getWidth() == 0 && species.getHeight() == 0) {
- result = species.getCenter();
- } else {
- double x = 0;
- double y = 0;
- while (angle > 2 * PI) {
- angle -= 2 * PI;
- }
- while (angle < 0) {
- angle += 2 * PI;
- }
- if (angle < RIGHT_TOP_RESIDUE_MAX_ANGLE) {
- // CHECKSTYLE:OFF 0.5 is much readable than any other suggestion
- double ratio = 0.5 + angle / (PI / 2);
- // CHECKSTYLE:ON
- x = species.getX() + species.getWidth();
- y = species.getY() + species.getHeight() * (1 - ratio);
- } else if (angle < TOP_RESIDUE_MAX_ANGLE) {
- double ratio = (angle - RIGHT_TOP_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = species.getY();
- x = species.getX() + species.getWidth() * (1 - ratio);
- } else if (angle < LEFT_RESIDUE_MAX_ANGLE) {
- double ratio = (angle - TOP_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = species.getY() + species.getHeight() * (ratio);
- x = species.getX();
- } else if (angle < BOTTOM_RESIDUE_MAX_ANGLE) {
- double ratio = (angle - LEFT_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = species.getY() + species.getHeight();
- x = species.getX() + species.getWidth() * ratio;
- } else if (angle <= 2 * PI + Configuration.EPSILON) {
- double ratio = (angle - BOTTOM_RESIDUE_MAX_ANGLE) / (PI / 2);
- y = species.getY() + species.getHeight() * (1 - ratio);
- x = species.getX() + species.getWidth();
- } else {
- throw new InvalidStateException();
- }
- Point2D center = species.getCenter();
- double correctedAngle = -Math.atan2((y - center.getY()), (x - center.getX()));
- result = getPointCoordinatesOnBorder(species, correctedAngle);
- }
- return result;
-
- }
-
- /**
- * Returns default shape of the {@link Species}.
- *
- * @param species
- * {@link Species} for which we are looking for a border
- * @return {@link Shape} object defining given {@link Species}
- */
- protected Shape getDefaultAliasShape(final Species species) {
- Shape shape;
- shape = new Rectangle(species.getX().intValue(), species.getY().intValue(), species.getWidth().intValue(), species.getHeight().intValue());
- return shape;
- }
-
- /**
- * Returns font that should be used for drawing description of the
- * {@link Species}.
- *
- * @param species
- * {@link Species} for which we are looking for a font
- * @param params
- * specific drawing parameters (like scale)
- * @return {@link Font} that should be used for drawing {@link Species}
- * description
- */
- protected Font getFont(final Species species, ConverterParams params) {
- double fontSize = DEFAULT_SPECIES_FONT_SIZE;
- if (species.getFontSize() != null) {
- fontSize = species.getFontSize();
- }
- return new Font(Font.SANS_SERIF, 0, (int) (fontSize * params.getScale()));
- }
-
- /**
- * Returns text describing {@link Species}.
- *
- * @param species
- * object under investigation
- * @return description of the {@link Species}
- */
- protected String getText(final T species) {
- String name = species.getName();
- if (name.equals("")) {
- name = " ";
- }
-
- return name;
- }
-
- @Override
- public void drawText(final T species, final Graphics2D graphics, final ConverterParams params) {
- String text = getText(species);
- Font oldFont = graphics.getFont();
- Font font = getFont(species, params);
- graphics.setColor(Color.BLACK);
- graphics.setFont(font);
-
- Point2D point = species.getCenter();
- if (species instanceof Complex) {
- if (((Complex) species).getElements().size() > 0) {
- if (isTransparent(species, params)) {
- point.setLocation(point.getX(), species.getY() + species.getHeight() - graphics.getFontMetrics().getAscent());
- }
- }
- }
- drawText(point, text, graphics, true, true);
- graphics.setFont(oldFont);
- }
-
- /**
- * Return width of the text.
- *
- * @param text
- * width of this text will be computed
- * @param graphics
- * the width will be computed assuming using this graphics
- * @return width of the text
- */
- protected double getTextWidth(final String text, final Graphics2D graphics) {
- if (text == null) {
- return 0;
- }
- if (text.equals("")) {
- return 0;
- }
-
- double result = 0;
- String[] lines = text.split("\n");
- for (String string : lines) {
- result = Math.max(result, graphics.getFontMetrics().stringWidth(string));
- }
-
- return result;
- }
-
- /**
- * Returns text height.
- *
- * @param text
- * height of this text will be computed
- * @param graphics
- * the height will be computed assuming using this graphics
- * @return height of the text
- */
- protected double getTextHeight(final String text, final Graphics2D graphics) {
- if (text == null) {
- return 0;
- }
- if (text.equals("")) {
- return 0;
- }
-
- double result = 0;
- int lines = text.split("\n").length;
- result = graphics.getFontMetrics().getHeight() * lines;
- return result;
- }
-
- /**
- * This method draws a string on graphics using current font. The coordinates
- * of the text is given as a point. Both parameters centered described if text
- * should be automatically centered horizontally and vertically.
- *
- * @param point
- * where the text should be drawn
- * @param text
- * text to draw
- * @param graphics
- * where we want to draw the object
- * @param horizontalCentered
- * should the text be horizontally centered
- * @param verticalCentered
- * should the text be vertically centered
- */
- protected void drawText(final Point2D point, final String text, final Graphics2D graphics, final boolean horizontalCentered,
- final boolean verticalCentered) {
- double height = getTextHeight(text, graphics);
- double x = point.getX();
- double y = point.getY();
- if (verticalCentered) {
- y -= height / 2 - graphics.getFontMetrics().getAscent();
- }
- String[] lines = text.split("\n");
-
- double lineHeight = graphics.getFontMetrics().getHeight();
- for (String string : lines) {
- double currX = x;
- if (horizontalCentered) {
- currX -= getTextWidth(string, graphics) / 2;
- }
- graphics.drawString(string, (int) currX, (int) y);
- y += lineHeight;
- }
- }
-
- /**
- * Returns line style used for drawing alias border.
- *
- * @param species
- * {@link Species} to be drawn
- * @return style of the line used to draw {@link Species}
- */
- protected Stroke getBorderLine(final Species species) {
- if (!species.isHypothetical()) {
- if (species instanceof Complex) {
- return LineType.SOLID_BOLD.getStroke();
- } else {
- return LineType.SOLID.getStroke();
- }
- } else {
- if (species instanceof Complex) {
- return LineType.DASHED_BOLD.getStroke();
- } else {
- return LineType.DASHED.getStroke();
- }
- }
- }
-
- /**
- * Returns border of the {@link Species} as {@link PathIterator}.
- *
- * @param species
- * {@link Species} for which we are looking for a border
- * @return {@link PathIterator} object defining given {@link Species}
- */
- protected abstract PathIterator getBoundPathIterator(T species);
-
- /**
- * @return the lineTransformation
- */
- protected LineTransformation getLineTransformation() {
- return lineTransformation;
- }
-
- /**
- * @param lineTransformation
- * the lineTransformation to set
- */
- protected void setLineTransformation(LineTransformation lineTransformation) {
- this.lineTransformation = lineTransformation;
- }
-
- /**
- * @return the ellipseTransformation
- */
- protected EllipseTransformation getEllipseTransformation() {
- return ellipseTransformation;
- }
-
- /**
- * @param ellipseTransformation
- * the ellipseTransformation to set
- */
- protected void setEllipseTransformation(EllipseTransformation ellipseTransformation) {
- this.ellipseTransformation = ellipseTransformation;
- }
-
- /**
- * @return the structuralFont
- */
- protected Font getStructuralFont() {
- return structuralFont;
- }
-
- /**
- * @param structuralFont
- * the structuralFont to set
- */
- protected void setStructuralFont(Font structuralFont) {
- this.structuralFont = structuralFont;
- }
-
- /**
- * @return the unitOfInformationFont
- */
- protected Font getUnitOfInformationFont() {
- return unitOfInformationFont;
- }
-
- /**
- * @param unitOfInformationFont
- * the unitOfInformationFont to set
- */
- protected void setUnitOfInformationFont(Font unitOfInformationFont) {
- this.unitOfInformationFont = unitOfInformationFont;
- }
-
- /**
- * Draws structural state description of the alias (ellipse in the top part of
- * the alias).
- *
- * @param text
- * state description text
- * @param species
- * state description should be drawn on this {@link Species}
- * @param graphics
- * where the drawing should be performed
- */
- protected void drawStructuralState(String text, T species, final Graphics2D graphics) {
- if (text == null) {
- return;
- }
-
- Point2D p = getPointCoordinatesOnBorder(species, Math.PI / 2);
-
- double width = MIN_STRUCTURAL_STATE_WIDTH;
- if (!text.trim().equals("")) {
- width = Math.max(MIN_STRUCTURAL_STATE_WIDTH, graphics.getFontMetrics().stringWidth(text) + TEXT_MARGIN_FOR_STRUCTURAL_STATE_DESC);
- }
- width = Math.min(width, species.getWidth());
- double height = STRUCTURAL_STATE_HEIGHT;
-
- Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - width / 2, p.getY() - height / 2, width, height);
- Color c = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(ellipse);
- graphics.setColor(c);
- graphics.draw(ellipse);
- if (!text.trim().equals("")) {
- Font font = graphics.getFont();
- graphics.setFont(getStructuralFont());
-
- width = graphics.getFontMetrics().stringWidth(text);
- height = graphics.getFontMetrics().getAscent() - graphics.getFontMetrics().getDescent();
-
- graphics.drawString(text, (int) (p.getX() - width / 2), (int) (p.getY() + height / 2));
- graphics.setFont(font);
- }
-
- }
-
- /**
- * Draws unit of information for the {@link Species} (rectangle in the top
- * part of the alias).
- *
- * @param text
- * unit of information text
- * @param species
- * unit of information should be drawn on this {@link Species}
- * @param graphics
- * where the drawing should be performed
- */
- protected void drawUnitOfInformation(String text, T species, final Graphics2D graphics) {
- if (text == null) {
- return;
- }
-
- Point2D p = getPointCoordinatesOnBorder(species, Math.PI / 2);
-
- double width = MIN_UNIT_OF_INFORMATION_WIDTH;
- if (!text.trim().equals("")) {
- width = Math.max(MIN_UNIT_OF_INFORMATION_WIDTH, graphics.getFontMetrics().stringWidth(text) + TEXT_MARGIN_FOR_UNIT_OF_INFORMATION_DESC);
- }
- width = Math.min(width, species.getWidth());
- double height = UNIT_OF_INFORMATION_HEIGHT;
-
- Rectangle2D rectangle = new Rectangle2D.Double(p.getX() - width / 2, p.getY() - height / 2, width, height);
- Color c = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(rectangle);
- graphics.setColor(c);
- graphics.draw(rectangle);
- if (!text.trim().equals("")) {
- Font font = graphics.getFont();
- graphics.setFont(getUnitOfInformationFont());
-
- width = graphics.getFontMetrics().stringWidth(text);
- height = graphics.getFontMetrics().getAscent() - graphics.getFontMetrics().getDescent();
-
- graphics.drawString(text, (int) (p.getX() - width / 2), (int) (p.getY() + height / 2));
- graphics.setFont(font);
- }
- }
-
- @Override
- public void draw(T species, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
- draw(species, graphics, params);
-
- Color oldColor = graphics.getColor();
- int count = 0;
- double width = species.getWidth() / visualizedLayoutsColorSchemas.size();
- for (ColorSchema schema : visualizedLayoutsColorSchemas) {
- if (schema != null) {
- double startX = (double) count / (double) visualizedLayoutsColorSchemas.size();
- graphics.setColor(Color.BLACK);
-
- int x = (int) (startX * species.getWidth() + species.getX());
- graphics.drawRect(x, species.getY().intValue(), (int) width, species.getHeight().intValue());
-
- Color color = colorExtractor.getNormalizedColor(schema);
- Color bgAlphaColor = new Color(color.getRed(), color.getGreen(), color.getBlue(), LAYOUT_ALPHA);
- graphics.setColor(bgAlphaColor);
- graphics.fillRect(x, species.getY().intValue(), (int) width, species.getHeight().intValue());
- }
- count++;
- }
- graphics.setColor(oldColor);
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.Rectangle;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.geometry.EllipseTransformation;
+import lcsb.mapviewer.common.geometry.LineTransformation;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
+import lcsb.mapviewer.converter.graphics.geometry.ArrowTransformation;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AbstractRegionModification;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
+
+/**
+ * This class defines basics used for drawing {@link Species} (node in the graph
+ * representation) on the {@link Graphics2D} object.
+ *
+ * @param <T>
+ * type of {@link Species} class that can be drawn with this converter
+ * @author Piotr Gawron
+ *
+ */
+public abstract class SpeciesConverter<T extends Species> extends ElementConverter<T> {
+
+ /**
+ * Default font size for the modifier description.
+ */
+ protected static final int DEFAULT_SPECIES_MODIFIER_FONT_SIZE = 10;
+
+ /**
+ * Default diameter of the modification residues.
+ */
+ protected static final int DEFAULT_MODIFICATION_DIAMETER = 15;
+
+ /**
+ * How far from the original shape should the activity border be drawn.
+ */
+ protected static final int ACTIVITY_BORDER_DISTANCE = 5;
+
+ /**
+ * Default species font size.
+ */
+ protected static final int DEFAULT_SPECIES_FONT_SIZE = 12;
+
+ /**
+ * Height of the ellipse that contain structural state description.
+ */
+ private static final int STRUCTURAL_STATE_HEIGHT = 20;
+
+ /**
+ * Height of the rectangle that contains unit of information.
+ */
+ private static final int UNIT_OF_INFORMATION_HEIGHT = 20;
+
+ /**
+ * Size of the margin in the structural state description.
+ */
+ private static final int TEXT_MARGIN_FOR_STRUCTURAL_STATE_DESC = 40;
+
+ /**
+ * Size of the margin in the unit of information description.
+ */
+ private static final int TEXT_MARGIN_FOR_UNIT_OF_INFORMATION_DESC = 20;
+
+ /**
+ * Minimum width of the structural state ellipse.
+ */
+ private static final int MIN_STRUCTURAL_STATE_WIDTH = 60;
+
+ /**
+ * Minimum width of the unit of information rectangle.
+ */
+ private static final int MIN_UNIT_OF_INFORMATION_WIDTH = 40;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SpeciesConverter.class.getName());
+
+ /**
+ * Graphical helper object with line transformation functions.
+ */
+ private LineTransformation lineTransformation = new LineTransformation();
+ private ArrowTransformation arrowTransformation = new ArrowTransformation();
+
+ /**
+ * Graphical helper object with ellipse transformation functions.
+ */
+ private EllipseTransformation ellipseTransformation = new EllipseTransformation();
+
+ /**
+ * Default font used to draw structural state of the species.
+ */
+ private Font structuralFont = null;
+
+ /**
+ * Default font used to draw unit of information of the species.
+ */
+ private Font unitOfInformationFont = null;
+
+ /**
+ * What is the distance between homodimer aliases when homodimer>1.
+ */
+ public static final int HOMODIMER_OFFSET = 6;
+
+ /**
+ * Object that helps to convert {@link ColorSchema} values into colors.
+ */
+ private ColorExtractor colorExtractor;
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ protected SpeciesConverter(ColorExtractor colorExtractor) {
+ structuralFont = new Font(Font.SANS_SERIF, 0, DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
+ this.colorExtractor = colorExtractor;
+ };
+
+ /**
+ * Returns default shape of the {@link Species}.
+ *
+ * @param species
+ * {@link Species} for which we are looking for a border
+ * @return {@link Shape} object defining given {@link Species}
+ */
+ protected Shape getDefaultAliasShape(final Species species) {
+ Shape shape;
+ shape = new Rectangle(species.getX().intValue(), species.getY().intValue(), species.getWidth().intValue(),
+ species.getHeight().intValue());
+ return shape;
+ }
+
+ /**
+ * Returns font that should be used for drawing description of the
+ * {@link Species}.
+ *
+ * @param species
+ * {@link Species} for which we are looking for a font
+ * @param params
+ * specific drawing parameters (like scale)
+ * @return {@link Font} that should be used for drawing {@link Species}
+ * description
+ */
+ protected Font getFont(final Species species, ConverterParams params) {
+ double fontSize = DEFAULT_SPECIES_FONT_SIZE;
+ if (species.getFontSize() != null) {
+ fontSize = species.getFontSize();
+ }
+ return new Font(Font.SANS_SERIF, 0, (int) (fontSize * params.getScale()));
+ }
+
+ /**
+ * Returns text describing {@link Species}.
+ *
+ * @param species
+ * object under investigation
+ * @return description of the {@link Species}
+ */
+ protected String getText(final T species) {
+ String name = species.getName();
+ if (name.equals("")) {
+ name = " ";
+ }
+
+ return name;
+ }
+
+ @Override
+ public void drawText(final T species, final Graphics2D graphics, final ConverterParams params) {
+ String text = getText(species);
+ Font oldFont = graphics.getFont();
+ Font font = getFont(species, params);
+ graphics.setColor(Color.BLACK);
+ graphics.setFont(font);
+
+ Point2D point = species.getCenter();
+ if (species instanceof Complex) {
+ if (((Complex) species).getElements().size() > 0) {
+ if (isTransparent(species, params)) {
+ point.setLocation(point.getX(), species.getY() + species.getHeight() - graphics.getFontMetrics().getAscent());
+ }
+ }
+ }
+ drawText(point, text, graphics, true, true);
+ graphics.setFont(oldFont);
+ }
+
+ /**
+ * Return width of the text.
+ *
+ * @param text
+ * width of this text will be computed
+ * @param graphics
+ * the width will be computed assuming using this graphics
+ * @return width of the text
+ */
+ protected double getTextWidth(final String text, final Graphics2D graphics) {
+ if (text == null) {
+ return 0;
+ }
+ if (text.equals("")) {
+ return 0;
+ }
+
+ double result = 0;
+ String[] lines = text.split("\n");
+ for (String string : lines) {
+ result = Math.max(result, graphics.getFontMetrics().stringWidth(string));
+ }
+
+ return result;
+ }
+
+ /**
+ * Returns text height.
+ *
+ * @param text
+ * height of this text will be computed
+ * @param graphics
+ * the height will be computed assuming using this graphics
+ * @return height of the text
+ */
+ protected double getTextHeight(final String text, final Graphics2D graphics) {
+ if (text == null) {
+ return 0;
+ }
+ if (text.equals("")) {
+ return 0;
+ }
+
+ double result = 0;
+ int lines = text.split("\n").length;
+ result = graphics.getFontMetrics().getHeight() * lines;
+ return result;
+ }
+
+ /**
+ * This method draws a string on graphics using current font. The coordinates of
+ * the text is given as a point. Both parameters centered described if text
+ * should be automatically centered horizontally and vertically.
+ *
+ * @param point
+ * where the text should be drawn
+ * @param text
+ * text to draw
+ * @param graphics
+ * where we want to draw the object
+ * @param horizontalCentered
+ * should the text be horizontally centered
+ * @param verticalCentered
+ * should the text be vertically centered
+ */
+ protected void drawText(final Point2D point, final String text, final Graphics2D graphics,
+ final boolean horizontalCentered, final boolean verticalCentered) {
+ double height = getTextHeight(text, graphics);
+ double x = point.getX();
+ double y = point.getY();
+ if (verticalCentered) {
+ y -= height / 2 - graphics.getFontMetrics().getAscent();
+ }
+ String[] lines = text.split("\n");
+
+ double lineHeight = graphics.getFontMetrics().getHeight();
+ for (String string : lines) {
+ double currX = x;
+ if (horizontalCentered) {
+ currX -= getTextWidth(string, graphics) / 2;
+ }
+ graphics.drawString(string, (int) currX, (int) y);
+ y += lineHeight;
+ }
+ }
+
+ /**
+ * Returns line style used for drawing alias border.
+ *
+ * @param species
+ * {@link Species} to be drawn
+ * @return style of the line used to draw {@link Species}
+ */
+ protected Stroke getBorderLine(final Species species) {
+ if (!species.isHypothetical()) {
+ if (species instanceof Complex) {
+ return LineType.SOLID_BOLD.getStroke();
+ } else {
+ return LineType.SOLID.getStroke();
+ }
+ } else {
+ if (species instanceof Complex) {
+ return LineType.DASHED_BOLD.getStroke();
+ } else {
+ return LineType.DASHED.getStroke();
+ }
+ }
+ }
+
+ /**
+ * Returns border of the {@link Species} as {@link PathIterator}.
+ *
+ * @param species
+ * {@link Species} for which we are looking for a border
+ * @return {@link PathIterator} object defining given {@link Species}
+ */
+ protected abstract PathIterator getBoundPathIterator(T species);
+
+ /**
+ * @return the lineTransformation
+ */
+ protected LineTransformation getLineTransformation() {
+ return lineTransformation;
+ }
+
+ /**
+ * @param lineTransformation
+ * the lineTransformation to set
+ */
+ protected void setLineTransformation(LineTransformation lineTransformation) {
+ this.lineTransformation = lineTransformation;
+ }
+
+ /**
+ * @return the ellipseTransformation
+ */
+ protected EllipseTransformation getEllipseTransformation() {
+ return ellipseTransformation;
+ }
+
+ /**
+ * @param ellipseTransformation
+ * the ellipseTransformation to set
+ */
+ protected void setEllipseTransformation(EllipseTransformation ellipseTransformation) {
+ this.ellipseTransformation = ellipseTransformation;
+ }
+
+ /**
+ * @return the structuralFont
+ */
+ protected Font getStructuralFont() {
+ return structuralFont;
+ }
+
+ /**
+ * @param structuralFont
+ * the structuralFont to set
+ */
+ protected void setStructuralFont(Font structuralFont) {
+ this.structuralFont = structuralFont;
+ }
+
+ /**
+ * @return the unitOfInformationFont
+ */
+ protected Font getUnitOfInformationFont() {
+ return unitOfInformationFont;
+ }
+
+ /**
+ * @param unitOfInformationFont
+ * the unitOfInformationFont to set
+ */
+ protected void setUnitOfInformationFont(Font unitOfInformationFont) {
+ this.unitOfInformationFont = unitOfInformationFont;
+ }
+
+ /**
+ * Draws structural state description of the alias (ellipse in the top part of
+ * the alias).
+ *
+ * @param text
+ * state description text
+ * @param species
+ * state description should be drawn on this {@link Species}
+ * @param graphics
+ * where the drawing should be performed
+ */
+ protected void drawStructuralState(String text, T species, final Graphics2D graphics) {
+ if (text == null) {
+ return;
+ }
+
+ Point2D p = new Point2D.Double(species.getCenterX(), species.getY());
+
+ double width = MIN_STRUCTURAL_STATE_WIDTH;
+ if (!text.trim().equals("")) {
+ width = Math.max(MIN_STRUCTURAL_STATE_WIDTH,
+ graphics.getFontMetrics().stringWidth(text) + TEXT_MARGIN_FOR_STRUCTURAL_STATE_DESC);
+ }
+ width = Math.min(width, species.getWidth());
+ double height = STRUCTURAL_STATE_HEIGHT;
+
+ Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - width / 2, p.getY() - height / 2, width, height);
+ Color c = graphics.getColor();
+ graphics.setColor(Color.WHITE);
+ graphics.fill(ellipse);
+ graphics.setColor(c);
+ graphics.draw(ellipse);
+ if (!text.trim().equals("")) {
+ Font font = graphics.getFont();
+ graphics.setFont(getStructuralFont());
+
+ width = graphics.getFontMetrics().stringWidth(text);
+ height = graphics.getFontMetrics().getAscent() - graphics.getFontMetrics().getDescent();
+
+ graphics.drawString(text, (int) (p.getX() - width / 2), (int) (p.getY() + height / 2));
+ graphics.setFont(font);
+ }
+
+ }
+
+ /**
+ * Draws unit of information for the {@link Species} (rectangle in the top part
+ * of the alias).
+ *
+ * @param text
+ * unit of information text
+ * @param species
+ * unit of information should be drawn on this {@link Species}
+ * @param graphics
+ * where the drawing should be performed
+ */
+ protected void drawUnitOfInformation(String text, T species, final Graphics2D graphics) {
+ if (text == null) {
+ return;
+ }
+
+ Point2D p = new Point2D.Double(species.getCenterX(), species.getY());
+
+ double width = MIN_UNIT_OF_INFORMATION_WIDTH;
+ if (!text.trim().equals("")) {
+ width = Math.max(MIN_UNIT_OF_INFORMATION_WIDTH,
+ graphics.getFontMetrics().stringWidth(text) + TEXT_MARGIN_FOR_UNIT_OF_INFORMATION_DESC);
+ }
+ width = Math.min(width, species.getWidth());
+ double height = UNIT_OF_INFORMATION_HEIGHT;
+
+ Rectangle2D rectangle = new Rectangle2D.Double(p.getX() - width / 2, p.getY() - height / 2, width, height);
+ Color c = graphics.getColor();
+ graphics.setColor(Color.WHITE);
+ graphics.fill(rectangle);
+ graphics.setColor(c);
+ graphics.draw(rectangle);
+ if (!text.trim().equals("")) {
+ Font font = graphics.getFont();
+ graphics.setFont(getUnitOfInformationFont());
+
+ width = graphics.getFontMetrics().stringWidth(text);
+ height = graphics.getFontMetrics().getAscent() - graphics.getFontMetrics().getDescent();
+
+ graphics.drawString(text, (int) (p.getX() - width / 2), (int) (p.getY() + height / 2));
+ graphics.setFont(font);
+ }
+ }
+
+ @Override
+ public void draw(T species, Graphics2D graphics, ConverterParams params,
+ List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
+ draw(species, graphics, params);
+
+ Color oldColor = graphics.getColor();
+ int count = 0;
+ double width = species.getWidth() / visualizedLayoutsColorSchemas.size();
+ for (ColorSchema schema : visualizedLayoutsColorSchemas) {
+ if (schema != null) {
+ double startX = (double) count / (double) visualizedLayoutsColorSchemas.size();
+ graphics.setColor(Color.BLACK);
+
+ int x = (int) (startX * species.getWidth() + species.getX());
+ graphics.drawRect(x, species.getY().intValue(), (int) width, species.getHeight().intValue());
+
+ Color color = colorExtractor.getNormalizedColor(schema);
+ Color bgAlphaColor = new Color(color.getRed(), color.getGreen(), color.getBlue(), LAYOUT_ALPHA);
+ graphics.setColor(bgAlphaColor);
+ graphics.fillRect(x, species.getY().intValue(), (int) width, species.getHeight().intValue());
+ }
+ count++;
+ }
+ graphics.setColor(oldColor);
+ }
+
+ /**
+ * This method draws modification of the alias. If drawEmptyModification is set
+ * to false then modification is not drawn if empty. If drawDescription is set
+ * then also description (position) of the modification is drawn on the canvas.
+ *
+ * @param protein
+ * object that is 'parent' of the residue
+ * @param mr
+ * modification to be drawn
+ * @param graphics
+ * - where the modification should be drawn
+ * @param drawEmptyModification
+ * flag that indicates if we should draw empty modification
+ */
+ protected void drawModification(final ModificationResidue mr, final Graphics2D graphics,
+ boolean drawEmptyModification) {
+ if (mr instanceof Residue) {
+ drawResidue((Residue) mr, graphics, drawEmptyModification);
+ } else if (mr instanceof ModificationSite) {
+ drawModificationSite((ModificationSite) mr, graphics, drawEmptyModification);
+ } else if (mr instanceof BindingRegion) {
+ drawBindingRegion((BindingRegion) mr, graphics);
+ } else if (mr instanceof ProteinBindingDomain) {
+ drawProteinBindingDomain((ProteinBindingDomain) mr, graphics);
+ } else if (mr instanceof CodingRegion) {
+ drawCodingRegion((CodingRegion) mr, graphics);
+ } else if (mr instanceof RegulatoryRegion) {
+ drawRegulatoryRegion((RegulatoryRegion) mr, graphics);
+ } else if (mr instanceof TranscriptionSite) {
+ drawTranscriptionSite((TranscriptionSite) mr, graphics);
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + mr.getClass());
+ }
+ }
+
+ protected void drawResidue(final Residue residue, final Graphics2D graphics, boolean drawEmptyModification) {
+ if (!drawEmptyModification && residue.getState() == null) {
+ return;
+ }
+ double diameter = DEFAULT_MODIFICATION_DIAMETER;
+ Point2D p = residue.getPosition();
+ Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
+ Color c = graphics.getColor();
+ graphics.setColor(Color.WHITE);
+ graphics.fill(ellipse);
+ graphics.setColor(c);
+ graphics.draw(ellipse);
+
+ ModificationState state = residue.getState();
+ if (state != null) {
+ String str = state.getAbbreviation();
+ Font tmpFont = graphics.getFont();
+ graphics.setFont(getStructuralFont());
+ double x = p.getX() - graphics.getFontMetrics().stringWidth(str) / 2;
+ double y = p.getY() + graphics.getFontMetrics().getAscent() / 2;
+ graphics.drawString(str, (int) x, (int) y);
+ graphics.setFont(tmpFont);
+ }
+ }
+
+ /**
+ * This method draws {@link ModificationSite} of the {@link Species}. If
+ * drawEmptyModification is set to false then modification is not drawn if
+ * empty.
+ *
+ * @param modificationSite
+ * modification to be drawn
+ * @param graphics
+ * - where the modification should be drawn
+ * @param drawEmptyModification
+ * flag that indicates if we should draw empty modification
+ */
+ protected void drawModificationSite(final ModificationSite modificationSite, final Graphics2D graphics,
+ boolean drawEmptyModification) {
+ if (!drawEmptyModification && modificationSite.getState() == null) {
+ return;
+ }
+ double diameter = DEFAULT_MODIFICATION_DIAMETER;
+
+ double y = modificationSite.getPosition().getY();
+
+ Point2D p = new Point2D.Double(modificationSite.getPosition().getX(), y - DEFAULT_MODIFICATION_DIAMETER);
+
+ Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
+ Color c = graphics.getColor();
+ graphics.setColor(Color.WHITE);
+ graphics.fill(ellipse);
+ graphics.setColor(c);
+ graphics.draw(ellipse);
+ graphics.drawLine((int) p.getX(), (int) (p.getY() + diameter / 2), (int) p.getX(), (int) y);
+
+ ModificationState state = modificationSite.getState();
+ if (state != null) {
+ String str = state.getAbbreviation();
+ Font tmpFont = graphics.getFont();
+ graphics.setFont(getStructuralFont());
+ double textX = p.getX() - graphics.getFontMetrics().stringWidth(str) / 2;
+ double textY = p.getY() + graphics.getFontMetrics().getAscent() / 2;
+ graphics.drawString(str, (int) textX, (int) textY);
+ graphics.setFont(tmpFont);
+ }
+ }
+
+ protected void drawBindingRegion(final BindingRegion bindingRegion, final Graphics2D graphics) {
+ drawRegionModification(bindingRegion, graphics);
+ }
+
+ protected void drawProteinBindingDomain(final ProteinBindingDomain proteinBindingDomain, final Graphics2D graphics) {
+ drawRegionModification(proteinBindingDomain, graphics);
+ }
+
+ protected void drawCodingRegion(final CodingRegion codingRegion, final Graphics2D graphics) {
+ drawRegionModification(codingRegion, graphics);
+ }
+
+ private void drawRegionModification(AbstractRegionModification modification, Graphics2D graphics) {
+ Point2D rectangleCenter = modification.getPosition();
+ double width = modification.getWidth();
+ double height = modification.getHeight();
+ Rectangle2D rectangle = new Rectangle2D.Double(rectangleCenter.getX() - width / 2,
+ rectangleCenter.getY() - height / 2, width, height);
+ Color c = graphics.getColor();
+ graphics.setColor(Color.WHITE);
+ graphics.fill(rectangle);
+ graphics.setColor(c);
+ graphics.draw(rectangle);
+
+ String str = modification.getName();
+ if (str != null && !str.trim().equals("")) {
+ Font tmpFont = graphics.getFont();
+ graphics.setFont(getStructuralFont());
+ double textX = rectangleCenter.getX() - graphics.getFontMetrics().stringWidth(str) / 2;
+ double textY = rectangleCenter.getY() + graphics.getFontMetrics().getAscent() / 2;
+ graphics.drawString(str, (int) textX, (int) textY);
+ graphics.setFont(tmpFont);
+ }
+
+ }
+
+ protected void drawRegulatoryRegion(final RegulatoryRegion regulatoryRegion, final Graphics2D graphics) {
+ drawRegionModification(regulatoryRegion, graphics);
+ }
+
+ protected void drawTranscriptionSite(final TranscriptionSite transcriptionSite, final Graphics2D graphics) {
+
+ Color color = graphics.getColor();
+ if (transcriptionSite.getActive()) {
+ color = Color.RED;
+ } else {
+ color = Color.BLACK;
+ }
+ double y = transcriptionSite.getPosition().getY();
+ double x = transcriptionSite.getPosition().getX();
+ PolylineData line = new PolylineData();
+ if (transcriptionSite.getDirection().equals("RIGHT")) {
+ x += transcriptionSite.getWidth() / 2;
+ line.addPoint(new Point2D.Double(x, y));
+
+ y -= DEFAULT_MODIFICATION_DIAMETER;
+ line.addPoint(new Point2D.Double(x, y));
+
+ x -= transcriptionSite.getWidth();
+ line.addPoint(new Point2D.Double(x, y));
+ } else {
+ x -= transcriptionSite.getWidth() / 2;
+ line.addPoint(new Point2D.Double(x, y));
+
+ y -= DEFAULT_MODIFICATION_DIAMETER;
+ line.addPoint(new Point2D.Double(x, y));
+
+ x += transcriptionSite.getWidth();
+ line.addPoint(new Point2D.Double(x, y));
+ }
+ line.setColor(color);
+ line.getEndAtd().setArrowType(ArrowType.FULL);
+
+ arrowTransformation.drawLine(line, graphics);
+
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
index 8103b5141e06e83004616ac0ccd9e8941fdd2e97..a3aec15bac0cde37f378eaa13f253f5ed9fcb783 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
@@ -1,82 +1,72 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.Unknown;
-
-/**
- * This class defines methods used for drawing {@link Unknown} on the
- * {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownConverter extends SpeciesConverter<Unknown> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(UnknownConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public UnknownConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(Unknown unknown, final Graphics2D graphics, final ConverterParams params) {
- if (unknown.getActivity()) {
- int border = ACTIVITY_BORDER_DISTANCE;
- unknown.increaseBorder(border);
- Shape shape2 = new Ellipse2D.Double(unknown.getX(), unknown.getY(), unknown.getWidth(), unknown.getHeight());
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(LineType.DOTTED.getStroke());
- graphics.draw(shape2);
- graphics.setStroke(stroke);
- unknown.increaseBorder(-border);
- }
-
- Shape shape = new Ellipse2D.Double(unknown.getX(), unknown.getY(), unknown.getWidth(), unknown.getHeight());
- Color c = graphics.getColor();
- graphics.setColor(unknown.getColor());
- graphics.fill(shape);
- graphics.setColor(c);
- drawText(unknown, graphics, params);
- }
-
- @Override
- public PathIterator getBoundPathIterator(Unknown unknown) {
- throw new InvalidStateException("This class doesn't provide boundPath");
- }
-
- @Override
- public Point2D getPointCoordinatesOnBorder(Unknown unknown, final double angle) {
- if (unknown.getWidth() == 0 && unknown.getHeight() == 0) {
- logger.warn("Looking for coordinates for unknown of 0 size");
- return unknown.getCenter();
- }
- Point2D result;
- result = getEllipseTransformation().getPointOnEllipseByRadian(unknown.getX(), unknown.getY(), unknown.getWidth(), unknown.getHeight(), angle);
- return result;
- }
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
+
+/**
+ * This class defines methods used for drawing {@link Unknown} on the
+ * {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownConverter extends SpeciesConverter<Unknown> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(UnknownConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public UnknownConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(Unknown unknown, final Graphics2D graphics, final ConverterParams params) {
+ if (unknown.getActivity()) {
+ int border = ACTIVITY_BORDER_DISTANCE;
+ unknown.increaseBorder(border);
+ Shape shape2 = new Ellipse2D.Double(unknown.getX(), unknown.getY(), unknown.getWidth(), unknown.getHeight());
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(LineType.DOTTED.getStroke());
+ graphics.draw(shape2);
+ graphics.setStroke(stroke);
+ unknown.increaseBorder(-border);
+ }
+
+ Shape shape = new Ellipse2D.Double(unknown.getX(), unknown.getY(), unknown.getWidth(), unknown.getHeight());
+ Color c = graphics.getColor();
+ graphics.setColor(unknown.getColor());
+ graphics.fill(shape);
+ graphics.setColor(c);
+ drawText(unknown, graphics, params);
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Unknown unknown) {
+ throw new InvalidStateException("This class doesn't provide boundPath");
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
index 3b8f0499b32142579e6ae3bd38d58823a2b4bea4..4f67a317af0d6b5d8d8a9f5cba8062e9bd0ce1f1 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
@@ -1,188 +1,333 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.image.BufferedImage;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ProteinConverter;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class SpeciesConverterTest {
-
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetResidueCoords() throws Exception {
- try {
- GenericProtein alias = new GenericProtein("id");
- alias.setX(135);
- alias.setY(194.0);
- alias.setWidth(130);
- alias.setHeight(67);
- ProteinConverter conv = new ProteinConverter(null);
- assertEquals(135.0, conv.getResidueCoordinates(alias, 3.141592653589793).getX(), 2);
- assertEquals(265., conv.getResidueCoordinates(alias, 0.0).getX(), 2);
- assertEquals(135.0, conv.getResidueCoordinates(alias, 2.41).getX(), 2);
- assertEquals(194.0, conv.getResidueCoordinates(alias, 1.98).getY(), 2);
- assertEquals(194.0, conv.getResidueCoordinates(alias, 1.59).getY(), 2);
- assertEquals(265.0, conv.getResidueCoordinates(alias, 6.28).getX(), 2);
- assertEquals(261.0, conv.getResidueCoordinates(alias, 4.13).getY(), 2);
- assertEquals(261.0, conv.getResidueCoordinates(alias, 4.86).getY(), 2);
- assertEquals(265.0, conv.getResidueCoordinates(alias, 5.69).getX(), 2);
- assertEquals(194.0, conv.getResidueCoordinates(alias, 0.99).getY(), 2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDrawAliasWithLayouts() throws Exception {
- try {
- BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- ProteinConverter rc = new ProteinConverter(colorExtractor);
-
- GenericProtein alias = createAlias();
- rc.draw(alias, graphics, new ConverterParams());
-
- int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
-
- GenericProtein alias2 = createAlias();
-
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
-
- ColorSchema schema = new GenericColorSchema();
- schema.setColor(Color.RED);
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(schema);
-
- rc.draw(alias2, graphics, new ConverterParams(), schemas);
-
- int val2 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
-
- assertTrue(val != val2);
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawAfterDrawingReactionWithLayouts() throws Exception {
- try {
- BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- ProteinConverter rc = new ProteinConverter(colorExtractor);
-
- GenericProtein alias = createAlias();
- rc.draw(alias, graphics, new ConverterParams());
-
- int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
-
- GenericProtein alias2 = createAlias();
-
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
-
- ColorSchema schema = new GenericColorSchema();
- schema.setColor(Color.RED);
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(schema);
-
- rc.draw(alias2, graphics, new ConverterParams(), schemas);
-
- int val2 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
-
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
-
- rc.draw(alias2, graphics, new ConverterParams(), new ArrayList<>());
-
- int val3 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
-
- assertTrue(val != val2);
- assertEquals(val, val3);
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawReactionWithFewLayouts() throws Exception {
- try {
- BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- ProteinConverter rc = new ProteinConverter(colorExtractor);
-
- GenericProtein alias = createAlias();
- rc.draw(alias, graphics, new ConverterParams());
-
- int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
-
- GenericProtein alias2 = createAlias();
-
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
-
- ColorSchema schema = new GenericColorSchema();
- schema.setColor(Color.RED);
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(schema);
- schemas.add(null);
- schema = new GenericColorSchema();
- schema.setColor(Color.BLUE);
- schemas.add(schema);
-
- rc.draw(alias2, graphics, new ConverterParams(), schemas);
-
- int val2 = bi.getRGB((int) (alias.getX() + alias.getWidth() / 4), (int) alias.getCenterY());
- int val3 = bi.getRGB((int) (alias.getCenterX()), (int) alias.getCenterY());
- int val4 = bi.getRGB((int) (alias.getX() + 3 * alias.getWidth() / 4), (int) alias.getCenterY());
-
- assertTrue(val != val2);
- assertEquals(val, val3);
- assertTrue(val != val4);
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- private GenericProtein createAlias() {
- GenericProtein alias = new GenericProtein("id");
- alias.setName("NAME_OF_THE_ELEMENT");
- alias.setX(10);
- alias.setY(20);
- alias.setWidth(100);
- alias.setHeight(80);
- alias.setColor(Color.WHITE);
-
- return alias;
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyBoolean;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+
+import java.awt.Color;
+import java.awt.Desktop;
+import java.awt.Graphics2D;
+import java.awt.geom.Point2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.MapGenerator;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.GenericColorSchema;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
+
+public class SpeciesConverterTest {
+ Logger logger = Logger.getLogger(SpeciesConverterTest.class);
+
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDrawAliasWithLayouts() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ ProteinConverter rc = new ProteinConverter(colorExtractor);
+
+ GenericProtein alias = createProtein();
+ rc.draw(alias, graphics, new ConverterParams());
+
+ int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
+
+ GenericProtein alias2 = createProtein();
+
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setColor(Color.RED);
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+
+ rc.draw(alias2, graphics, new ConverterParams(), schemas);
+
+ int val2 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
+
+ assertTrue(val != val2);
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawAfterDrawingReactionWithLayouts() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ ProteinConverter rc = new ProteinConverter(colorExtractor);
+
+ GenericProtein alias = createProtein();
+ rc.draw(alias, graphics, new ConverterParams());
+
+ int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
+
+ GenericProtein alias2 = createProtein();
+
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setColor(Color.RED);
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+
+ rc.draw(alias2, graphics, new ConverterParams(), schemas);
+
+ int val2 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
+
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+
+ rc.draw(alias2, graphics, new ConverterParams(), new ArrayList<>());
+
+ int val3 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
+
+ assertTrue(val != val2);
+ assertEquals(val, val3);
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithFewLayouts() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ ProteinConverter rc = new ProteinConverter(colorExtractor);
+
+ GenericProtein alias = createProtein();
+ rc.draw(alias, graphics, new ConverterParams());
+
+ int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
+
+ GenericProtein alias2 = createProtein();
+
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setColor(Color.RED);
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+ schemas.add(null);
+ schema = new GenericColorSchema();
+ schema.setColor(Color.BLUE);
+ schemas.add(schema);
+
+ rc.draw(alias2, graphics, new ConverterParams(), schemas);
+
+ int val2 = bi.getRGB((int) (alias.getX() + alias.getWidth() / 4), (int) alias.getCenterY());
+ int val3 = bi.getRGB((int) (alias.getCenterX()), (int) alias.getCenterY());
+ int val4 = bi.getRGB((int) (alias.getX() + 3 * alias.getWidth() / 4), (int) alias.getCenterY());
+
+ assertTrue(val != val2);
+ assertEquals(val, val3);
+ assertTrue(val != val4);
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawResidue() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+
+ ModificationResidue residue = new Residue();
+ residue.setPosition(new Point2D.Double(10,10));
+
+ ProteinConverter converter = Mockito.spy(new ProteinConverter(colorExtractor));
+ converter.drawModification(residue, graphics, false);
+ verify(converter, times(1)).drawResidue(any(), any(), anyBoolean());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawBindingRegion() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+
+ Protein protein = createProtein();
+ BindingRegion bindingRegion = new BindingRegion();
+ bindingRegion.setPosition(new Point2D.Double(10,10));
+ bindingRegion.setWidth(100.0);
+ bindingRegion.setHeight(10.0);
+ protein.addModificationResidue(bindingRegion);
+
+ ProteinConverter converter = Mockito.spy(new ProteinConverter(colorExtractor));
+ converter.drawModification(bindingRegion, graphics, false);
+ verify(converter, times(1)).drawBindingRegion(any(), any());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawModificationSite() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+
+ ModificationSite modificationSite = new ModificationSite();
+ modificationSite.setPosition(new Point2D.Double(10,10));
+
+ ProteinConverter converter = Mockito.spy(new ProteinConverter(colorExtractor));
+ converter.drawModification(modificationSite, graphics, false);
+ verify(converter, times(1)).drawModificationSite(any(), any(), anyBoolean());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawProteinBindingRegion() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+
+ ProteinBindingDomain proteinBindingRegion = new ProteinBindingDomain();
+ proteinBindingRegion.setPosition(new Point2D.Double(10,10));
+ proteinBindingRegion.setWidth(100);
+ proteinBindingRegion.setHeight(20);
+
+ ProteinConverter converter = Mockito.spy(new ProteinConverter(colorExtractor));
+ converter.drawModification(proteinBindingRegion, graphics, false);
+ verify(converter, times(1)).drawProteinBindingDomain(any(), any());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawCodingRegion() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+
+ CodingRegion codingRegion = new CodingRegion();
+ codingRegion.setPosition(new Point2D.Double(10,10));
+ codingRegion.setWidth(100);
+ codingRegion.setHeight(20);
+
+ ProteinConverter converter = Mockito.spy(new ProteinConverter(colorExtractor));
+ converter.drawModification(codingRegion, graphics, false);
+ verify(converter, times(1)).drawCodingRegion(any(), any());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawRegulatoryRegion() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+
+ RegulatoryRegion regulatoryRegion = new RegulatoryRegion();
+ regulatoryRegion.setPosition(new Point2D.Double(10,10));
+ regulatoryRegion.setWidth(100);
+ regulatoryRegion.setHeight(20);
+
+ ProteinConverter converter = Mockito.spy(new ProteinConverter(colorExtractor));
+ converter.drawModification(regulatoryRegion, graphics, false);
+ verify(converter, times(1)).drawRegulatoryRegion(any(), any());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawTranscriptionSite() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+
+ TranscriptionSite transcriptionSite = new TranscriptionSite();
+ transcriptionSite.setPosition(new Point2D.Double(10,10));
+ transcriptionSite.setWidth(100);
+ transcriptionSite.setHeight(20);
+ transcriptionSite.setActive(true);
+ transcriptionSite.setDirection("LEFT");
+
+ ProteinConverter converter = Mockito.spy(new ProteinConverter(colorExtractor));
+ converter.drawModification(transcriptionSite, graphics, false);
+ verify(converter, times(1)).drawTranscriptionSite(any(), any());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private GenericProtein createProtein() {
+ GenericProtein protein = new GenericProtein("id");
+ protein.setName("NAME_OF_THE_ELEMENT");
+ protein.setX(10);
+ protein.setY(20);
+ protein.setWidth(100);
+ protein.setHeight(80);
+ protein.setColor(Color.WHITE);
+
+ return protein;
+ }
+}
diff --git a/frontend-js/package-lock.json b/frontend-js/package-lock.json
index 04da0d18baf99baf8600ce5a7c047f3f3d088759..01cbb59d840e3cdcdf0b2eb1a9390d077da6aabe 100644
--- a/frontend-js/package-lock.json
+++ b/frontend-js/package-lock.json
@@ -336,9 +336,9 @@
"integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c="
},
"base62": {
- "version": "1.2.0",
- "resolved": "https://registry.npmjs.org/base62/-/base62-1.2.0.tgz",
- "integrity": "sha1-MeflYNyEbJ9EwaUx32UU2jVHQVc="
+ "version": "1.2.8",
+ "resolved": "https://registry.npmjs.org/base62/-/base62-1.2.8.tgz",
+ "integrity": "sha512-V6YHUbjLxN1ymqNLb1DPHoU1CpfdL7d2YTIp5W3U4hhoG4hhxNmsFDs66M9EXxBiSEke5Bt5dwdfMwwZF70iLA=="
},
"base64-arraybuffer": {
"version": "0.1.5",
@@ -942,9 +942,9 @@
"detective": "4.5.0",
"glob": "5.0.15",
"graceful-fs": "4.1.11",
- "iconv-lite": "0.4.18",
+ "iconv-lite": "0.4.23",
"mkdirp": "0.5.1",
- "private": "0.1.7",
+ "private": "0.1.8",
"q": "1.5.0",
"recast": "0.11.23"
},
@@ -1576,9 +1576,9 @@
}
},
"es6-promise": {
- "version": "4.1.1",
- "resolved": "https://registry.npmjs.org/es6-promise/-/es6-promise-4.1.1.tgz",
- "integrity": "sha512-OaU1hHjgJf+b0NzsxCg7NdIYERD6Hy/PEmFLTjw+b65scuisG3Kt4QoTvJ66BBkPZ581gr0kpoVzKnxniM8nng=="
+ "version": "4.2.4",
+ "resolved": "https://registry.npmjs.org/es6-promise/-/es6-promise-4.2.4.tgz",
+ "integrity": "sha512-/NdNZVJg+uZgtm9eS3O6lrOLYmQag2DjdEXuPaHlZ6RuVqgqaVZfgYCepEIKsLqwdQArOPtC3XzRLqGGfT8KQQ=="
},
"escape-html": {
"version": "1.0.3",
@@ -1742,7 +1742,7 @@
"core-js": "1.2.7",
"loose-envify": "1.3.1",
"promise": "7.3.1",
- "ua-parser-js": "0.7.14",
+ "ua-parser-js": "0.7.18",
"whatwg-fetch": "0.9.0"
}
},
@@ -2308,9 +2308,12 @@
"dev": true
},
"iconv-lite": {
- "version": "0.4.18",
- "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.4.18.tgz",
- "integrity": "sha512-sr1ZQph3UwHTR0XftSbK85OvBbxe/abLGzEnPENCQwmHf7sck8Oyu4ob3LgBxWWxRoM+QszeUyl7jbqapu2TqA=="
+ "version": "0.4.23",
+ "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.4.23.tgz",
+ "integrity": "sha512-neyTUVFtahjf0mB3dZT77u+8O0QB89jFdnBkd5P1JgYPbPaia3gXXOVL2fq8VyU2gMMD7SaN7QukTB/pmXYvDA==",
+ "requires": {
+ "safer-buffer": "2.1.2"
+ }
},
"ieee754": {
"version": "1.1.8",
@@ -2560,7 +2563,7 @@
"resolved": "https://registry.npmjs.org/jbinary/-/jbinary-2.1.3.tgz",
"integrity": "sha1-JDLiOYmZPpcKE8uw7eQcp/xMkZk=",
"requires": {
- "es6-promise": "4.1.1",
+ "es6-promise": "4.2.4",
"jdataview": "2.5.0",
"request": "2.82.0"
}
@@ -2860,7 +2863,7 @@
"resolved": "https://registry.npmjs.org/jstransform/-/jstransform-11.0.3.tgz",
"integrity": "sha1-CaeJk+CuTU70SH9hVakfYZDLQiM=",
"requires": {
- "base62": "1.2.0",
+ "base62": "1.2.8",
"commoner": "0.10.8",
"esprima-fb": "15001.1.0-dev-harmony-fb",
"object-assign": "2.1.1",
@@ -3709,9 +3712,9 @@
"dev": true
},
"pileup": {
- "version": "0.6.8",
- "resolved": "https://registry.npmjs.org/pileup/-/pileup-0.6.8.tgz",
- "integrity": "sha1-LYhmfpRLC4I9A3tTSto1lnHBh04=",
+ "version": "0.6.9",
+ "resolved": "https://registry.npmjs.org/pileup/-/pileup-0.6.9.tgz",
+ "integrity": "sha1-y/xM24/tNzOOX0k6gJQfkE/bGko=",
"requires": {
"backbone": "1.1.2",
"d3": "3.5.17",
@@ -3765,9 +3768,9 @@
"integrity": "sha1-gV7R9uvGWSb4ZbMQwHE7yzMVzks="
},
"private": {
- "version": "0.1.7",
- "resolved": "https://registry.npmjs.org/private/-/private-0.1.7.tgz",
- "integrity": "sha1-aM5eih7woju1cMwoU3tTMqumPvE="
+ "version": "0.1.8",
+ "resolved": "https://registry.npmjs.org/private/-/private-0.1.8.tgz",
+ "integrity": "sha512-VvivMrbvd2nKkiG38qjULzlc+4Vx4wm/whI9pQD35YrARNnhxeiRktSOhSukRLFNlzg6Br/cJPet5J/u19r/mg=="
},
"process": {
"version": "0.11.10",
@@ -3970,7 +3973,7 @@
"requires": {
"ast-types": "0.9.6",
"esprima": "3.1.3",
- "private": "0.1.7",
+ "private": "0.1.8",
"source-map": "0.5.7"
},
"dependencies": {
@@ -4204,6 +4207,11 @@
"resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.1.1.tgz",
"integrity": "sha512-kKvNJn6Mm93gAczWVJg7wH+wGYWNrDHdWvpUmHyEsgCtIwwo3bqPtV4tR5tuPaUhTOo/kvhVwd8XwwOllGYkbg=="
},
+ "safer-buffer": {
+ "version": "2.1.2",
+ "resolved": "https://registry.npmjs.org/safer-buffer/-/safer-buffer-2.1.2.tgz",
+ "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
+ },
"sax": {
"version": "1.2.4",
"resolved": "https://registry.npmjs.org/sax/-/sax-1.2.4.tgz",
@@ -4889,9 +4897,9 @@
"dev": true
},
"ua-parser-js": {
- "version": "0.7.14",
- "resolved": "https://registry.npmjs.org/ua-parser-js/-/ua-parser-js-0.7.14.tgz",
- "integrity": "sha1-EQ1T+kw/MmwSEpK76skE0uAzh8o="
+ "version": "0.7.18",
+ "resolved": "https://registry.npmjs.org/ua-parser-js/-/ua-parser-js-0.7.18.tgz",
+ "integrity": "sha512-LtzwHlVHwFGTptfNSgezHp7WUlwiqb0gA9AALRbKaERfxwJoiX0A73QbTToxteIAuIaFshhgIZfqK8s7clqgnA=="
},
"uglify-js": {
"version": "2.8.29",
diff --git a/frontend-js/package.json b/frontend-js/package.json
index fcd4f0d0d2735dc543b139ec23b5e5d5723696a0..e7b7690cf6bef4f7510e9f923e9a56e95b9cd01d 100644
--- a/frontend-js/package.json
+++ b/frontend-js/package.json
@@ -50,7 +50,7 @@
"log4js": "0.6.38",
"multi-checkbox-list": "^0.2.0",
"openlayers": "^4.6.5",
- "pileup": "^0.6.8",
+ "pileup": "^0.6.9",
"request": "^2.82.0",
"spectrum-colorpicker": "^1.8.0",
"text-encoding": "^0.6.4",
diff --git a/frontend-js/src/main/css/global.css b/frontend-js/src/main/css/global.css
index 76b792e6ce97a518f4fad838bcd6dec930e59c4a..c72de9f83c7cbc4dc258674be5bef70f29f49d7c 100644
--- a/frontend-js/src/main/css/global.css
+++ b/frontend-js/src/main/css/global.css
@@ -42,25 +42,25 @@
clear: both;
}
-.mapChartNameDiv {
+.minerva-chart-name {
width: 150px;
float: left;
display: inline-block;
}
-.mapChartRowEvenDiv {
+.minerva-chart-row-even, .minerva-chart-row-odd {
+ position: relative;
white-space: nowrap;
overflow: hidden;
margin: 1px;
width: 360px;
+}
+
+.minerva-chart-row-even {
background-color: #D3D3D3;
}
-.mapChartRowOddDiv {
- white-space: nowrap;
- overflow: hidden;
- margin: 1px;
- width: 360px;
+.minerva-chart-row-odd {
background-color: #C0C0C0;
}
@@ -503,14 +503,15 @@ h1 {
font-weight: 400;
}
-.minerva-projects-tab, .minerva-users-tab, .minerva-configuration-tab {
+.minerva-projects-tab, .minerva-users-tab, .minerva-configuration-tab, .minerva-genome-tab {
margin-left: 10px;
margin-top: 10px;
}
.minerva-projects-tab .minerva-menu-row button,
.minerva-edit-project-dialog .minerva-menu-row button,
-.minerva-users-tab .minerva-menu-row button {
+.minerva-users-tab .minerva-menu-row button,
+.minerva-genome-tab .minerva-menu-row button {
margin: 5px;
}
@@ -748,7 +749,7 @@ a.adminLink:hover {
}
.popover {
- max-width: 600px;
+ max-width: 800px;
min-width: 390px;
}
diff --git a/frontend-js/src/main/js/Admin.js b/frontend-js/src/main/js/Admin.js
index 8d779cee92e6d3de479481d76aee4f4d5d7ae3c7..db99eea31a4051d60d1d9642413373c01763bafd 100644
--- a/frontend-js/src/main/js/Admin.js
+++ b/frontend-js/src/main/js/Admin.js
@@ -9,6 +9,7 @@ var GuiUtils = require('./gui/leftPanel/GuiUtils');
var ObjectWithListeners = require('./ObjectWithListeners');
var ConfigurationAdminPanel = require('./gui/admin/ConfigurationAdminPanel');
+var GenomeAdminPanel = require('./gui/admin/GenomeAdminPanel');
var MapsAdminPanel = require('./gui/admin/MapsAdminPanel');
var UsersAdminPanel = require('./gui/admin/UsersAdminPanel');
@@ -19,9 +20,8 @@ var Functions = require('./Functions');
/**
* Default constructor.
*
- * @param options
- * CustomMapOptions object representing all parameters needed for map
- * creation
+ * @param {CustomMapOptions} options
+ * object representing all parameters needed for map creation
*/
function Admin(options) {
var self = this;
@@ -55,6 +55,9 @@ Admin.prototype._createGui = function () {
}, {
name: "CONFIGURATION",
panelClass: ConfigurationAdminPanel
+ }, {
+ name: "GENOMES",
+ panelClass: GenomeAdminPanel
}];
var tabDiv = Functions.createElement({
diff --git a/frontend-js/src/main/js/Configuration.js b/frontend-js/src/main/js/Configuration.js
index 8254c7ae0b3d8934091205cd54967228bb26af87..beadc52c9e654e11957de7f8934dbacf0f27fa0c 100644
--- a/frontend-js/src/main/js/Configuration.js
+++ b/frontend-js/src/main/js/Configuration.js
@@ -120,9 +120,18 @@ Configuration.prototype.getOptions = function () {
return result;
};
+/**
+ *
+ * @param {string[]} overlayTypes
+ */
Configuration.prototype.setOverlayTypes = function (overlayTypes) {
this._overlayTypes = overlayTypes;
};
+
+/**
+ *
+ * @returns {string[]}
+ */
Configuration.prototype.getOverlayTypes = function () {
return this._overlayTypes;
};
diff --git a/frontend-js/src/main/js/Functions.js b/frontend-js/src/main/js/Functions.js
index 8463ed20aca1303186807c1b202ca9261d24b01d..b233ee58d6325cbc9a2ed659ee42cc9409f0a316 100644
--- a/frontend-js/src/main/js/Functions.js
+++ b/frontend-js/src/main/js/Functions.js
@@ -1,620 +1,675 @@
-"use strict";
-
-var Promise = require("bluebird");
-var Point = require('./map/canvas/Point');
-
-/* exported logger */
-
-var logger = require('./logger');
-
-var xss = require('xss');
-
-var Functions = {};
-
-/**
- * Bounds value between opt_min and opt_max (result will be not smaller than
- * opt_min and not bigger than opt_max).
- */
-Functions.bound = function (value, minVal, maxVal) {
- if (minVal !== null && minVal !== undefined) {
- value = Math.max(value, minVal);
- }
- if (maxVal !== null && maxVal !== undefined) {
- value = Math.min(value, maxVal);
- }
- return value;
-};
-
-Functions.degreesToRadians = function (deg) {
- return deg * (Math.PI / 180);
-};
-
-Functions.radiansToDegrees = function (rad) {
- return rad / (Math.PI / 180);
-};
-
-Functions.intToColorString = function (value) {
- /* jslint bitwise: true */
- var trimmedValue = (value & 0xFFFFFF);
- var colorStr = trimmedValue.toString(16);
- while (colorStr.length < 6) {
- colorStr = "0" + colorStr;
- }
- return '#' + colorStr;
-};
-
-
-/**
- *
- * @param {string} color
- * @param {number} opacity
- * @returns {string}
- */
-Functions.colorToRgbaString = function (color, opacity) {
- if (color[0] !== '#' || color.length !== 7) {
- throw new Error("Expected color in #RRGGBB format");
- }
- var red = parseInt(color.substr(1, 2), 16);
- var green = parseInt(color.substr(3, 2), 16);
- var blue = parseInt(color.substr(5, 2), 16);
- var alpha = opacity !== undefined ? opacity : 1.0;
- return "rgba(" + red + "," + green + "," + blue + "," + alpha + ")";
-};
-
-/**
- * Returns stack trace.
- *
- * @returns {string} stack trace
- */
-Functions.stackTrace = function () {
- var err = new Error();
- return err.stack;
-};
-
-/**
- * Returns the position of the element on html page.
- *
- * @param element
- * element for which we want to get the position (top left corner)
- *
- * @return {Point} coordinates of the element
- *
- */
-Functions.getPosition = function (element) {
- var xPosition = 0;
- var yPosition = 0;
-
- while (element) {
- xPosition += (element.offsetLeft - element.scrollLeft + element.clientLeft);
- yPosition += (element.offsetTop - element.scrollTop + element.clientTop);
- element = element.offsetParent;
- }
- return new Point(xPosition, yPosition);
-};
-
-/**
- * Checks if the point given as a first argument belongs to a polygon defined as
- * a second parameter. Both: point and polygon should use google.map.point
- * class.
- *
- * @param {Point} point
- * point which we want to check
- *
- * @param {Point[]} polygon
- * polygon where we check the point
- */
-
-Functions.pointInsidePolygon = function (point, polygon) {
- var x = point.x;
- var y = point.y;
-
- var inside = false;
- for (var i = 0, j = polygon.length - 1; i < polygon.length; j = i++) {
- var xi = polygon[i].x, yi = polygon[i].y;
- var xj = polygon[j].x, yj = polygon[j].y;
- var intersect = ((yi > y) !== (yj > y)) && (x < (xj - xi) * (y - yi) / (yj - yi) + xi);
- if (intersect) {
- inside = !inside;
- }
- }
- return inside;
-};
-
-/**
- * In a browser variable we store information about browser user is currently
- * using. Right now only IE is supported.
- */
-Functions.browser = {
- init: function () {
-
- this.name = "Unknown";
- this.version = "Unknown";
-
- if (typeof navigator !== 'undefined') {
- // Get the user agent string
- var ua = navigator.userAgent;
- this.compatibilityMode = false;
- var re;
- if (navigator.appName === 'Microsoft Internet Explorer') {
- this.name = "IE";
- re = new RegExp("MSIE ([0-9]+[\.0-9]*)");
- if (re.exec(ua) !== undefined && re.exec(ua) !== null) {
- this.version = parseFloat(RegExp.$1);
- }
- if (ua.indexOf("MSIE 7.0") > -1) {
- this.compatibilityMode = true;
- }
- } else if (navigator.appName === 'Netscape') {
- this.name = "Other";
- ua = navigator.userAgent;
- re = new RegExp("Trident/.*rv[ :]*([0-9]{1,}[\.0-9]{0,})");
- if (re.exec(ua) !== undefined && re.exec(ua) !== null) {
- this.version = parseFloat(RegExp.$1);
- }
- }
- }
- }
-};
-
-Functions.browser.init();
-
-/**
- * Returns true if parameter is integer, false otherwise.
- *
- * @param n
- * object to check
- */
-Functions.isInt = function (n) {
- return Number(n) === n && n % 1 === 0;
-};
-
-/**
- * Returns true if parameter is a DOM element, false otherwise.
- *
- * @param o
- * object to check
- */
-Functions.isDomElement = function (o) {
- if (!o) {
- return false;
- }
- return (typeof HTMLElement === "object" ? o instanceof HTMLElement : // DOM2
- o && typeof o === "object" && o !== null && o.nodeType === 1 && typeof o.nodeName === "string");
-};
-
-/**
- *
- * @returns {Promise<string>}
- */
-Functions.overlayToColor = function (elementOverlay) {
- var self = this;
- /* jslint bitwise: true */
- if (elementOverlay === null || elementOverlay === undefined) {
- return Promise.reject("elementOverlay cannot be null!");
- } else if (elementOverlay.color !== undefined && elementOverlay.color !== null) {
- return Promise.resolve(self.intToColorString(elementOverlay.color.rgb));
- } else {
- var ratio = 0;
- var promiseColors;
- if (elementOverlay.value !== undefined && elementOverlay.value !== null) {
- if (elementOverlay.value < 0) {
- ratio = -elementOverlay.value;
- promiseColors = [ServerConnector.getMinOverlayColorInt(), ServerConnector.getNeutralOverlayColorInt()];
- } else {
- ratio = elementOverlay.value;
- promiseColors = [ServerConnector.getMaxOverlayColorInt(), ServerConnector.getNeutralOverlayColorInt()];
- }
- } else {
- ratio = 1;
- promiseColors = [ServerConnector.getSimpleOverlayColorInt(), ServerConnector.getNeutralOverlayColorInt()];
- }
-
- return Promise.all(promiseColors).then(function (colors) {
- var maxColor = colors[0];
- var neutralColor = colors[1];
-
- ratio = 1 - ratio;
- var MAX_RED = 0xFF0000;
- var MAX_GREEN = 0x00FF00;
- var MAX_BLUE = 0x0000FF;
-
- var red = maxColor & MAX_RED;
- var neutralRed = neutralColor & MAX_RED;
-
- red = red + (neutralRed - red) * ratio;
- red = parseInt(red);
- red = red & MAX_RED;
-
- var green = maxColor & MAX_GREEN;
- var neutralGreen = neutralColor & MAX_GREEN;
- green = green + (neutralGreen - green) * ratio;
- green = parseInt(green);
- green = green & MAX_GREEN;
-
- var blue = maxColor & MAX_BLUE;
- var neutralBlue = neutralColor & MAX_BLUE;
- blue = blue + (neutralBlue - blue) * ratio;
- blue = parseInt(blue);
- blue = blue & MAX_BLUE;
-
- var color = red | green | blue;
- return self.intToColorString(color);
- });
- }
-};
-
-Functions.getElementByName = function (element, name) {
- if (element !== undefined) {
- if (element.getAttribute("name") === name) {
- return element;
- }
- var children = element.children;
- for (var i = 0; i < children.length; i++) {
- var child = children[i];
- var res = this.getElementByName(child, name);
- if (res !== undefined) {
- return res;
- }
- }
- }
- return undefined;
-};
-
-
-/**
- *
- * @param {HTMLElement}element
- * @param {string} name class name
- * @returns {HTMLElement|undefined}
- */
-Functions.getElementByClassName = function (element, name) {
- if (name.indexOf(".") !== 0) {
- name = "." + name;
- }
- return $(name, element)[0];
-};
-
-/**
- *
- * @param {Object} params
- * @param {string} params.type type of the {HTMLElement} to be created
- * @param {string} [params.inputType] type of the input to be created
- * @param {string} [params.className] css class of the element
- * @param {string} [params.style] css styling
- * @param {string} [params.value]
- * @param {string|HTMLElement} [params.content]
- *
- * @returns {HTMLElement}
- */
-Functions.createElement = function (params) {
- var result = document.createElement(params.type);
- if (params.id !== null && params.id !== undefined) {
- result.id = params.id;
- }
- if (params.name !== null && params.name !== undefined) {
- result.setAttribute("name", params.name);
- }
- if (params.className !== null && params.className !== undefined) {
- result.className = params.className;
- }
- if (params.inputType !== null && params.inputType !== undefined) {
- result.type = params.inputType;
- }
- if (params.content !== null && params.content !== undefined) {
- if (Functions.isDomElement(params.content)) {
- result.appendChild(params.content);
- } else if (params.xss !== false) {
- var content = xss(params.content);
- if (content !== params.content) {
- logger.warn("XSS changed content: " + params.content);
- }
- result.innerHTML = content;
- } else {
- result.innerHTML = params.content;
- }
- }
- if (params.style !== null && params.style !== undefined) {
- result.style.cssText = params.style;
- }
- if (params.onclick !== null && params.onclick !== undefined) {
- result.onclick = params.onclick;
- }
- if (params.onchange !== null && params.onchange !== undefined) {
- result.onchange = params.onchange;
- }
- if (params.href !== null && params.href !== undefined) {
- result.href = params.href;
- }
- if (params.src !== null && params.src !== undefined) {
- result.src = params.src;
- }
- if (params.value !== null && params.value !== undefined) {
- result.value = params.value;
- }
- if (params.title !== null && params.title !== undefined) {
- result.title = params.title;
- }
- if (params.index !== null && params.index !== undefined) {
- result.index = params.index;
- }
- if (params.data !== null && params.data !== undefined) {
- $(result).attr("data", params.data);
- }
- return result;
-};
-
-function sqr(x) {
- return x * x;
-}
-
-function dist2(v, w) {
- return sqr(v.x - w.x) + sqr(v.y - w.y);
-}
-
-function distToSegmentSquared(p, v, w) {
- var l2 = dist2(v, w);
-
- if (l2 === 0) {
- return dist2(p, v);
- }
-
- var t = ((p.x - v.x) * (w.x - v.x) + (p.y - v.y) * (w.y - v.y)) / l2;
-
- if (t < 0) {
- return dist2(p, v);
- }
- if (t > 1) {
- return dist2(p, w);
- }
-
- return dist2(p, new Point(v.x + t * (w.x - v.x), v.y + t * (w.y - v.y)));
-}
-
-Functions.distance = function (p1, el2) {
- if (el2 instanceof Point) {
- var p2 = el2;
- return Math.sqrt((Math.pow(p1.x - p2.x, 2)) + (Math.pow(p1.y - p2.y, 2)));
- } else {
- return Math.sqrt(distToSegmentSquared(p1, el2.start, el2.end));
- }
-};
-
-Functions.removeChildren = function (element) {
- while (element.firstChild) {
- element.removeChild(element.firstChild);
- }
-};
-
-/**
- *
- * @returns {Promise} resolved after javascript is loaded
- */
-Functions.loadScript = function (url) {
- return new Promise(function (resolve) {
- var scriptExists = false;
- var scripts = document.getElementsByTagName('script');
- for (var i = scripts.length; i--;) {
- if (scripts[i].src === url)
- scriptExists = true;
- }
- if (!scriptExists) {
- var head = document.getElementsByTagName('head')[0];
- var script = document.createElement('script');
- script.type = 'text/javascript';
- script.src = url;
- script.onload = function () {
- resolve();
- };
- head.appendChild(script);
- } else {
- resolve();
- }
- });
-};
-
-Functions.computeMD5 = function (s) {
- function L(k, d) {
- return (k << d) | (k >>> (32 - d))
- }
-
- function K(G, k) {
- var I, d, F, H, x;
- F = (G & 2147483648);
- H = (k & 2147483648);
- I = (G & 1073741824);
- d = (k & 1073741824);
- x = (G & 1073741823) + (k & 1073741823);
- if (I & d) {
- return (x ^ 2147483648 ^ F ^ H)
- }
- if (I | d) {
- if (x & 1073741824) {
- return (x ^ 3221225472 ^ F ^ H)
- } else {
- return (x ^ 1073741824 ^ F ^ H)
- }
- } else {
- return (x ^ F ^ H)
- }
- }
-
- function r(d, F, k) {
- return (d & F) | ((~d) & k)
- }
-
- function q(d, F, k) {
- return (d & k) | (F & (~k))
- }
-
- function p(d, F, k) {
- return (d ^ F ^ k)
- }
-
- function n(d, F, k) {
- return (F ^ (d | (~k)))
- }
-
- function u(G, F, aa, Z, k, H, I) {
- G = K(G, K(K(r(F, aa, Z), k), I));
- return K(L(G, H), F)
- }
-
- function f(G, F, aa, Z, k, H, I) {
- G = K(G, K(K(q(F, aa, Z), k), I));
- return K(L(G, H), F)
- }
-
- function D(G, F, aa, Z, k, H, I) {
- G = K(G, K(K(p(F, aa, Z), k), I));
- return K(L(G, H), F)
- }
-
- function t(G, F, aa, Z, k, H, I) {
- G = K(G, K(K(n(F, aa, Z), k), I));
- return K(L(G, H), F)
- }
-
- function e(G) {
- var Z;
- var F = G.length;
- var x = F + 8;
- var k = (x - (x % 64)) / 64;
- var I = (k + 1) * 16;
- var aa = Array(I - 1);
- var d = 0;
- var H = 0;
- while (H < F) {
- Z = (H - (H % 4)) / 4;
- d = (H % 4) * 8;
- aa[Z] = (aa[Z] | (G.charCodeAt(H) << d));
- H++
- }
- Z = (H - (H % 4)) / 4;
- d = (H % 4) * 8;
- aa[Z] = aa[Z] | (128 << d);
- aa[I - 2] = F << 3;
- aa[I - 1] = F >>> 29;
- return aa
- }
-
- function B(x) {
- var k = "", F = "", G, d;
- for (d = 0; d <= 3; d++) {
- G = (x >>> (d * 8)) & 255;
- F = "0" + G.toString(16);
- k = k + F.substr(F.length - 2, 2)
- }
- return k
- }
-
- function J(k) {
- k = k.replace(/rn/g, "n");
- var d = "";
- for (var F = 0; F < k.length; F++) {
- var x = k.charCodeAt(F);
- if (x < 128) {
- d += String.fromCharCode(x)
- } else {
- if ((x > 127) && (x < 2048)) {
- d += String.fromCharCode((x >> 6) | 192);
- d += String.fromCharCode((x & 63) | 128)
- } else {
- d += String.fromCharCode((x >> 12) | 224);
- d += String.fromCharCode(((x >> 6) & 63) | 128);
- d += String.fromCharCode((x & 63) | 128)
- }
- }
- }
- return d
- }
-
- var C = Array();
- var P, h, E, v, g, Y, X, W, V;
- var S = 7, Q = 12, N = 17, M = 22;
- var A = 5, z = 9, y = 14, w = 20;
- var o = 4, m = 11, l = 16, j = 23;
- var U = 6, T = 10, R = 15, O = 21;
- s = J(s);
- C = e(s);
- Y = 1732584193;
- X = 4023233417;
- W = 2562383102;
- V = 271733878;
- for (P = 0; P < C.length; P += 16) {
- h = Y;
- E = X;
- v = W;
- g = V;
- Y = u(Y, X, W, V, C[P + 0], S, 3614090360);
- V = u(V, Y, X, W, C[P + 1], Q, 3905402710);
- W = u(W, V, Y, X, C[P + 2], N, 606105819);
- X = u(X, W, V, Y, C[P + 3], M, 3250441966);
- Y = u(Y, X, W, V, C[P + 4], S, 4118548399);
- V = u(V, Y, X, W, C[P + 5], Q, 1200080426);
- W = u(W, V, Y, X, C[P + 6], N, 2821735955);
- X = u(X, W, V, Y, C[P + 7], M, 4249261313);
- Y = u(Y, X, W, V, C[P + 8], S, 1770035416);
- V = u(V, Y, X, W, C[P + 9], Q, 2336552879);
- W = u(W, V, Y, X, C[P + 10], N, 4294925233);
- X = u(X, W, V, Y, C[P + 11], M, 2304563134);
- Y = u(Y, X, W, V, C[P + 12], S, 1804603682);
- V = u(V, Y, X, W, C[P + 13], Q, 4254626195);
- W = u(W, V, Y, X, C[P + 14], N, 2792965006);
- X = u(X, W, V, Y, C[P + 15], M, 1236535329);
- Y = f(Y, X, W, V, C[P + 1], A, 4129170786);
- V = f(V, Y, X, W, C[P + 6], z, 3225465664);
- W = f(W, V, Y, X, C[P + 11], y, 643717713);
- X = f(X, W, V, Y, C[P + 0], w, 3921069994);
- Y = f(Y, X, W, V, C[P + 5], A, 3593408605);
- V = f(V, Y, X, W, C[P + 10], z, 38016083);
- W = f(W, V, Y, X, C[P + 15], y, 3634488961);
- X = f(X, W, V, Y, C[P + 4], w, 3889429448);
- Y = f(Y, X, W, V, C[P + 9], A, 568446438);
- V = f(V, Y, X, W, C[P + 14], z, 3275163606);
- W = f(W, V, Y, X, C[P + 3], y, 4107603335);
- X = f(X, W, V, Y, C[P + 8], w, 1163531501);
- Y = f(Y, X, W, V, C[P + 13], A, 2850285829);
- V = f(V, Y, X, W, C[P + 2], z, 4243563512);
- W = f(W, V, Y, X, C[P + 7], y, 1735328473);
- X = f(X, W, V, Y, C[P + 12], w, 2368359562);
- Y = D(Y, X, W, V, C[P + 5], o, 4294588738);
- V = D(V, Y, X, W, C[P + 8], m, 2272392833);
- W = D(W, V, Y, X, C[P + 11], l, 1839030562);
- X = D(X, W, V, Y, C[P + 14], j, 4259657740);
- Y = D(Y, X, W, V, C[P + 1], o, 2763975236);
- V = D(V, Y, X, W, C[P + 4], m, 1272893353);
- W = D(W, V, Y, X, C[P + 7], l, 4139469664);
- X = D(X, W, V, Y, C[P + 10], j, 3200236656);
- Y = D(Y, X, W, V, C[P + 13], o, 681279174);
- V = D(V, Y, X, W, C[P + 0], m, 3936430074);
- W = D(W, V, Y, X, C[P + 3], l, 3572445317);
- X = D(X, W, V, Y, C[P + 6], j, 76029189);
- Y = D(Y, X, W, V, C[P + 9], o, 3654602809);
- V = D(V, Y, X, W, C[P + 12], m, 3873151461);
- W = D(W, V, Y, X, C[P + 15], l, 530742520);
- X = D(X, W, V, Y, C[P + 2], j, 3299628645);
- Y = t(Y, X, W, V, C[P + 0], U, 4096336452);
- V = t(V, Y, X, W, C[P + 7], T, 1126891415);
- W = t(W, V, Y, X, C[P + 14], R, 2878612391);
- X = t(X, W, V, Y, C[P + 5], O, 4237533241);
- Y = t(Y, X, W, V, C[P + 12], U, 1700485571);
- V = t(V, Y, X, W, C[P + 3], T, 2399980690);
- W = t(W, V, Y, X, C[P + 10], R, 4293915773);
- X = t(X, W, V, Y, C[P + 1], O, 2240044497);
- Y = t(Y, X, W, V, C[P + 8], U, 1873313359);
- V = t(V, Y, X, W, C[P + 15], T, 4264355552);
- W = t(W, V, Y, X, C[P + 6], R, 2734768916);
- X = t(X, W, V, Y, C[P + 13], O, 1309151649);
- Y = t(Y, X, W, V, C[P + 4], U, 4149444226);
- V = t(V, Y, X, W, C[P + 11], T, 3174756917);
- W = t(W, V, Y, X, C[P + 2], R, 718787259);
- X = t(X, W, V, Y, C[P + 9], O, 3951481745);
- Y = K(Y, h);
- X = K(X, E);
- W = K(W, v);
- V = K(V, g)
- }
- var i = B(Y) + B(X) + B(W) + B(V);
- return i.toLowerCase()
-};
-module.exports = Functions;
+"use strict";
+
+var Promise = require("bluebird");
+var Point = require('./map/canvas/Point');
+
+var logger = require('./logger');
+
+var xss = require('xss');
+
+function Functions() {
+ /**
+ * In a browser variable we store information about browser user is currently
+ * using. Right now only IE is supported.
+ */
+ this.browser = {
+ init: function () {
+
+ this.name = "Unknown";
+ this.version = "Unknown";
+
+ if (typeof navigator !== 'undefined') {
+ // Get the user agent string
+ var ua = navigator.userAgent;
+ this.compatibilityMode = false;
+ var re;
+ if (navigator.appName === 'Microsoft Internet Explorer') {
+ this.name = "IE";
+ re = new RegExp("MSIE ([0-9]+[\.0-9]*)");
+ if (re.exec(ua) !== undefined && re.exec(ua) !== null) {
+ this.version = parseFloat(RegExp.$1);
+ }
+ if (ua.indexOf("MSIE 7.0") > -1) {
+ this.compatibilityMode = true;
+ }
+ } else if (navigator.appName === 'Netscape') {
+ this.name = "Other";
+ ua = navigator.userAgent;
+ re = new RegExp("Trident/.*rv[ :]*([0-9]{1,}[\.0-9]{0,})");
+ if (re.exec(ua) !== undefined && re.exec(ua) !== null) {
+ this.version = parseFloat(RegExp.$1);
+ }
+ }
+ }
+ }
+ };
+
+ this.browser.init();
+}
+
+/**
+ * Bounds value between opt_min and opt_max (result will be not smaller than
+ * opt_min and not bigger than opt_max).
+ */
+Functions.prototype.bound = function (value, minVal, maxVal) {
+ if (minVal !== null && minVal !== undefined) {
+ value = Math.max(value, minVal);
+ }
+ if (maxVal !== null && maxVal !== undefined) {
+ value = Math.min(value, maxVal);
+ }
+ return value;
+};
+
+Functions.prototype.degreesToRadians = function (deg) {
+ return deg * (Math.PI / 180);
+};
+
+Functions.prototype.radiansToDegrees = function (rad) {
+ return rad / (Math.PI / 180);
+};
+
+Functions.prototype.intToColorString = function (value) {
+ /* jslint bitwise: true */
+ var trimmedValue = (value & 0xFFFFFF);
+ var colorStr = trimmedValue.toString(16);
+ while (colorStr.length < 6) {
+ colorStr = "0" + colorStr;
+ }
+ return '#' + colorStr;
+};
+
+/**
+ *
+ * @param value
+ * @returns {number|undefined}
+ */
+Functions.prototype.getIntOrUndefined = function (value) {
+ if (this.isInt(value)) {
+ return value;
+ } else if (value === undefined || value === null) {
+ return undefined;
+ } else {
+ logger.warn("Invalid argument type: " + value);
+ return undefined;
+ }
+};
+
+
+/**
+ *
+ * @param {string} color
+ * @param {number} opacity
+ * @returns {string}
+ */
+Functions.prototype.colorToRgbaString = function (color, opacity) {
+ if (color[0] !== '#' || color.length !== 7) {
+ throw new Error("Expected color in #RRGGBB format, but found: " + color);
+ }
+ var red = parseInt(color.substr(1, 2), 16);
+ var green = parseInt(color.substr(3, 2), 16);
+ var blue = parseInt(color.substr(5, 2), 16);
+ var alpha = opacity !== undefined ? opacity : 1.0;
+ return "rgba(" + red + "," + green + "," + blue + "," + alpha + ")";
+};
+
+
+/**
+ *
+ * @param {LayoutAlias[]|LayoutReaction[]} overlayData
+ * @returns {Promise<Array>}
+ */
+Functions.prototype.overlaysToColorDataStructure = function (overlayData) {
+ var promises = [];
+ for (var i = 0; i < overlayData.length; i++) {
+ promises.push(this.overlayToColor(overlayData[i]));
+ }
+ return Promise.all(promises).then(function (colors) {
+ var countByColor = [], color;
+ for (var i = 0; i < colors.length; i++) {
+ color = colors[i];
+ if (countByColor[color] !== undefined) {
+ countByColor[color]++;
+ } else {
+ countByColor[color] = 1;
+ }
+ }
+ var result = [];
+ for (color in countByColor) {
+ if (countByColor.hasOwnProperty(color)) {
+ result.push({color: color, amount: countByColor[color]});
+ }
+ }
+ var compare = function (a, b) {
+ return a.color.localeCompare(b.color);
+ };
+ result.sort(compare);
+ return result;
+ });
+
+};
+
+/**
+ * Returns stack trace.
+ *
+ * @returns {string} stack trace
+ */
+Functions.prototype.stackTrace = function () {
+ var err = new Error();
+ return err.stack;
+};
+
+/**
+ * Returns the position of the element on html page.
+ *
+ * @param element
+ * element for which we want to get the position (top left corner)
+ *
+ * @return {Point} coordinates of the element
+ *
+ */
+Functions.prototype.getPosition = function (element) {
+ var xPosition = 0;
+ var yPosition = 0;
+
+ while (element) {
+ xPosition += (element.offsetLeft - element.scrollLeft + element.clientLeft);
+ yPosition += (element.offsetTop - element.scrollTop + element.clientTop);
+ element = element.offsetParent;
+ }
+ return new Point(xPosition, yPosition);
+};
+
+/**
+ * Checks if the point given as a first argument belongs to a polygon defined as
+ * a second parameter. Both: point and polygon should use google.map.point
+ * class.
+ *
+ * @param {Point} point
+ * point which we want to check
+ *
+ * @param {Point[]} polygon
+ * polygon where we check the point
+ */
+
+Functions.prototype.pointInsidePolygon = function (point, polygon) {
+ var x = point.x;
+ var y = point.y;
+
+ var inside = false;
+ for (var i = 0, j = polygon.length - 1; i < polygon.length; j = i++) {
+ var xi = polygon[i].x, yi = polygon[i].y;
+ var xj = polygon[j].x, yj = polygon[j].y;
+ var intersect = ((yi > y) !== (yj > y)) && (x < (xj - xi) * (y - yi) / (yj - yi) + xi);
+ if (intersect) {
+ inside = !inside;
+ }
+ }
+ return inside;
+};
+
+/**
+ * Returns true if parameter is integer, false otherwise.
+ *
+ * @param n
+ * object to check
+ */
+Functions.prototype.isInt = function (n) {
+ return Number(n) === n && n % 1 === 0;
+};
+
+/**
+ * Returns true if parameter is a DOM element, false otherwise.
+ *
+ * @param o
+ * object to check
+ */
+Functions.prototype.isDomElement = function (o) {
+ if (!o) {
+ return false;
+ }
+ return (typeof HTMLElement === "object" ? o instanceof HTMLElement : // DOM2
+ o && typeof o === "object" && o !== null && o.nodeType === 1 && typeof o.nodeName === "string");
+};
+
+/**
+ *
+ * @param {LayoutAlias|LayoutReaction} elementOverlay
+ *
+ * @returns {Promise<string>}
+ */
+
+Functions.prototype.overlayToColor = function (elementOverlay) {
+ var self = this;
+ if (elementOverlay === null || elementOverlay === undefined) {
+ return Promise.reject("elementOverlay cannot be null!");
+ } else if (elementOverlay.color !== undefined && elementOverlay.color !== null) {
+ return Promise.resolve(self.intToColorString(elementOverlay.color.rgb));
+ } else {
+ var ratio = 0;
+ var promiseColors;
+ if (elementOverlay.value !== undefined && elementOverlay.value !== null) {
+ if (elementOverlay.value < 0) {
+ ratio = -elementOverlay.value;
+ promiseColors = [ServerConnector.getMinOverlayColorInt(), ServerConnector.getNeutralOverlayColorInt()];
+ } else {
+ ratio = elementOverlay.value;
+ promiseColors = [ServerConnector.getMaxOverlayColorInt(), ServerConnector.getNeutralOverlayColorInt()];
+ }
+ } else {
+ ratio = 1;
+ promiseColors = [ServerConnector.getSimpleOverlayColorInt(), ServerConnector.getNeutralOverlayColorInt()];
+ }
+
+ return Promise.all(promiseColors).then(function (colors) {
+ var maxColor = colors[0];
+ var neutralColor = colors[1];
+
+ ratio = 1 - ratio;
+ var MAX_RED = 0xFF0000;
+ var MAX_GREEN = 0x00FF00;
+ var MAX_BLUE = 0x0000FF;
+
+ var red = maxColor & MAX_RED;
+ var neutralRed = neutralColor & MAX_RED;
+
+ red = red + (neutralRed - red) * ratio;
+ red = parseInt(red);
+ red = red & MAX_RED;
+
+ var green = maxColor & MAX_GREEN;
+ var neutralGreen = neutralColor & MAX_GREEN;
+ green = green + (neutralGreen - green) * ratio;
+ green = parseInt(green);
+ green = green & MAX_GREEN;
+
+ var blue = maxColor & MAX_BLUE;
+ var neutralBlue = neutralColor & MAX_BLUE;
+ blue = blue + (neutralBlue - blue) * ratio;
+ blue = parseInt(blue);
+ blue = blue & MAX_BLUE;
+
+ var color = red | green | blue;
+ return self.intToColorString(color);
+ });
+ }
+};
+
+Functions.prototype.getElementByName = function (element, name) {
+ if (element !== undefined) {
+ if (element.getAttribute("name") === name) {
+ return element;
+ }
+ var children = element.children;
+ for (var i = 0; i < children.length; i++) {
+ var child = children[i];
+ var res = this.getElementByName(child, name);
+ if (res !== undefined) {
+ return res;
+ }
+ }
+ }
+ return undefined;
+};
+
+
+/**
+ *
+ * @param {HTMLElement}element
+ * @param {string} name class name
+ * @returns {HTMLElement|undefined}
+ */
+Functions.prototype.getElementByClassName = function (element, name) {
+ if (name.indexOf(".") !== 0) {
+ name = "." + name;
+ }
+ return $(name, element)[0];
+};
+
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.type type of the {HTMLElement} to be created
+ * @param {string} [params.inputType] type of the input to be created
+ * @param {string} [params.className] css class of the element
+ * @param {string} [params.style] css styling
+ * @param {string} [params.value]
+ * @param {string|HTMLElement} [params.content]
+ *
+ * @returns {HTMLElement}
+ */
+Functions.prototype.createElement = function (params) {
+ var result = document.createElement(params.type);
+ if (params.id !== null && params.id !== undefined) {
+ result.id = params.id;
+ }
+ if (params.name !== null && params.name !== undefined) {
+ result.setAttribute("name", params.name);
+ }
+ if (params.className !== null && params.className !== undefined) {
+ result.className = params.className;
+ }
+ if (params.inputType !== null && params.inputType !== undefined) {
+ result.type = params.inputType;
+ }
+ if (params.content !== null && params.content !== undefined) {
+ if (this.isDomElement(params.content)) {
+ result.appendChild(params.content);
+ } else if (params.xss !== false) {
+ var content = xss(params.content);
+ if (content !== params.content) {
+ logger.warn("XSS changed content: " + params.content);
+ }
+ result.innerHTML = content;
+ } else {
+ result.innerHTML = params.content;
+ }
+ }
+ if (params.style !== null && params.style !== undefined) {
+ result.style.cssText = params.style;
+ }
+ if (params.onclick !== null && params.onclick !== undefined) {
+ result.onclick = params.onclick;
+ }
+ if (params.onchange !== null && params.onchange !== undefined) {
+ result.onchange = params.onchange;
+ }
+ if (params.href !== null && params.href !== undefined) {
+ result.href = params.href;
+ }
+ if (params.src !== null && params.src !== undefined) {
+ result.src = params.src;
+ }
+ if (params.value !== null && params.value !== undefined) {
+ result.value = params.value;
+ }
+ if (params.title !== null && params.title !== undefined) {
+ result.title = params.title;
+ }
+ if (params.index !== null && params.index !== undefined) {
+ result.index = params.index;
+ }
+ if (params.data !== null && params.data !== undefined) {
+ $(result).attr("data", params.data);
+ }
+ return result;
+};
+
+function sqr(x) {
+ return x * x;
+}
+
+function dist2(v, w) {
+ return sqr(v.x - w.x) + sqr(v.y - w.y);
+}
+
+function distToSegmentSquared(p, v, w) {
+ var l2 = dist2(v, w);
+
+ if (l2 === 0) {
+ return dist2(p, v);
+ }
+
+ var t = ((p.x - v.x) * (w.x - v.x) + (p.y - v.y) * (w.y - v.y)) / l2;
+
+ if (t < 0) {
+ return dist2(p, v);
+ }
+ if (t > 1) {
+ return dist2(p, w);
+ }
+
+ return dist2(p, new Point(v.x + t * (w.x - v.x), v.y + t * (w.y - v.y)));
+}
+
+Functions.prototype.distance = function (p1, el2) {
+ if (el2 instanceof Point) {
+ var p2 = el2;
+ return Math.sqrt((Math.pow(p1.x - p2.x, 2)) + (Math.pow(p1.y - p2.y, 2)));
+ } else {
+ return Math.sqrt(distToSegmentSquared(p1, el2.start, el2.end));
+ }
+};
+
+Functions.prototype.removeChildren = function (element) {
+ while (element.firstChild) {
+ element.removeChild(element.firstChild);
+ }
+};
+
+/**
+ *
+ * @returns {Promise} resolved after javascript is loaded
+ */
+Functions.prototype.loadScript = function (url) {
+ return new Promise(function (resolve) {
+ var scriptExists = false;
+ var scripts = document.getElementsByTagName('script');
+ for (var i = scripts.length; i--;) {
+ if (scripts[i].src === url)
+ scriptExists = true;
+ }
+ if (!scriptExists) {
+ var head = document.getElementsByTagName('head')[0];
+ var script = document.createElement('script');
+ script.type = 'text/javascript';
+ script.src = url;
+ script.onload = function () {
+ resolve();
+ };
+ head.appendChild(script);
+ } else {
+ resolve();
+ }
+ });
+};
+
+Functions.prototype.computeMD5 = function (s) {
+ function L(k, d) {
+ return (k << d) | (k >>> (32 - d))
+ }
+
+ function K(G, k) {
+ var I, d, F, H, x;
+ F = (G & 2147483648);
+ H = (k & 2147483648);
+ I = (G & 1073741824);
+ d = (k & 1073741824);
+ x = (G & 1073741823) + (k & 1073741823);
+ if (I & d) {
+ return (x ^ 2147483648 ^ F ^ H)
+ }
+ if (I | d) {
+ if (x & 1073741824) {
+ return (x ^ 3221225472 ^ F ^ H)
+ } else {
+ return (x ^ 1073741824 ^ F ^ H)
+ }
+ } else {
+ return (x ^ F ^ H)
+ }
+ }
+
+ function r(d, F, k) {
+ return (d & F) | ((~d) & k)
+ }
+
+ function q(d, F, k) {
+ return (d & k) | (F & (~k))
+ }
+
+ function p(d, F, k) {
+ return (d ^ F ^ k)
+ }
+
+ function n(d, F, k) {
+ return (F ^ (d | (~k)))
+ }
+
+ function u(G, F, aa, Z, k, H, I) {
+ G = K(G, K(K(r(F, aa, Z), k), I));
+ return K(L(G, H), F)
+ }
+
+ function f(G, F, aa, Z, k, H, I) {
+ G = K(G, K(K(q(F, aa, Z), k), I));
+ return K(L(G, H), F)
+ }
+
+ function D(G, F, aa, Z, k, H, I) {
+ G = K(G, K(K(p(F, aa, Z), k), I));
+ return K(L(G, H), F)
+ }
+
+ function t(G, F, aa, Z, k, H, I) {
+ G = K(G, K(K(n(F, aa, Z), k), I));
+ return K(L(G, H), F)
+ }
+
+ function e(G) {
+ var Z;
+ var F = G.length;
+ var x = F + 8;
+ var k = (x - (x % 64)) / 64;
+ var I = (k + 1) * 16;
+ var aa = Array(I - 1);
+ var d = 0;
+ var H = 0;
+ while (H < F) {
+ Z = (H - (H % 4)) / 4;
+ d = (H % 4) * 8;
+ aa[Z] = (aa[Z] | (G.charCodeAt(H) << d));
+ H++
+ }
+ Z = (H - (H % 4)) / 4;
+ d = (H % 4) * 8;
+ aa[Z] = aa[Z] | (128 << d);
+ aa[I - 2] = F << 3;
+ aa[I - 1] = F >>> 29;
+ return aa
+ }
+
+ function B(x) {
+ var k = "", F = "", G, d;
+ for (d = 0; d <= 3; d++) {
+ G = (x >>> (d * 8)) & 255;
+ F = "0" + G.toString(16);
+ k = k + F.substr(F.length - 2, 2)
+ }
+ return k
+ }
+
+ function J(k) {
+ k = k.replace(/rn/g, "n");
+ var d = "";
+ for (var F = 0; F < k.length; F++) {
+ var x = k.charCodeAt(F);
+ if (x < 128) {
+ d += String.fromCharCode(x)
+ } else {
+ if ((x > 127) && (x < 2048)) {
+ d += String.fromCharCode((x >> 6) | 192);
+ d += String.fromCharCode((x & 63) | 128)
+ } else {
+ d += String.fromCharCode((x >> 12) | 224);
+ d += String.fromCharCode(((x >> 6) & 63) | 128);
+ d += String.fromCharCode((x & 63) | 128)
+ }
+ }
+ }
+ return d
+ }
+
+ var C = Array();
+ var P, h, E, v, g, Y, X, W, V;
+ var S = 7, Q = 12, N = 17, M = 22;
+ var A = 5, z = 9, y = 14, w = 20;
+ var o = 4, m = 11, l = 16, j = 23;
+ var U = 6, T = 10, R = 15, O = 21;
+ s = J(s);
+ C = e(s);
+ Y = 1732584193;
+ X = 4023233417;
+ W = 2562383102;
+ V = 271733878;
+ for (P = 0; P < C.length; P += 16) {
+ h = Y;
+ E = X;
+ v = W;
+ g = V;
+ Y = u(Y, X, W, V, C[P + 0], S, 3614090360);
+ V = u(V, Y, X, W, C[P + 1], Q, 3905402710);
+ W = u(W, V, Y, X, C[P + 2], N, 606105819);
+ X = u(X, W, V, Y, C[P + 3], M, 3250441966);
+ Y = u(Y, X, W, V, C[P + 4], S, 4118548399);
+ V = u(V, Y, X, W, C[P + 5], Q, 1200080426);
+ W = u(W, V, Y, X, C[P + 6], N, 2821735955);
+ X = u(X, W, V, Y, C[P + 7], M, 4249261313);
+ Y = u(Y, X, W, V, C[P + 8], S, 1770035416);
+ V = u(V, Y, X, W, C[P + 9], Q, 2336552879);
+ W = u(W, V, Y, X, C[P + 10], N, 4294925233);
+ X = u(X, W, V, Y, C[P + 11], M, 2304563134);
+ Y = u(Y, X, W, V, C[P + 12], S, 1804603682);
+ V = u(V, Y, X, W, C[P + 13], Q, 4254626195);
+ W = u(W, V, Y, X, C[P + 14], N, 2792965006);
+ X = u(X, W, V, Y, C[P + 15], M, 1236535329);
+ Y = f(Y, X, W, V, C[P + 1], A, 4129170786);
+ V = f(V, Y, X, W, C[P + 6], z, 3225465664);
+ W = f(W, V, Y, X, C[P + 11], y, 643717713);
+ X = f(X, W, V, Y, C[P + 0], w, 3921069994);
+ Y = f(Y, X, W, V, C[P + 5], A, 3593408605);
+ V = f(V, Y, X, W, C[P + 10], z, 38016083);
+ W = f(W, V, Y, X, C[P + 15], y, 3634488961);
+ X = f(X, W, V, Y, C[P + 4], w, 3889429448);
+ Y = f(Y, X, W, V, C[P + 9], A, 568446438);
+ V = f(V, Y, X, W, C[P + 14], z, 3275163606);
+ W = f(W, V, Y, X, C[P + 3], y, 4107603335);
+ X = f(X, W, V, Y, C[P + 8], w, 1163531501);
+ Y = f(Y, X, W, V, C[P + 13], A, 2850285829);
+ V = f(V, Y, X, W, C[P + 2], z, 4243563512);
+ W = f(W, V, Y, X, C[P + 7], y, 1735328473);
+ X = f(X, W, V, Y, C[P + 12], w, 2368359562);
+ Y = D(Y, X, W, V, C[P + 5], o, 4294588738);
+ V = D(V, Y, X, W, C[P + 8], m, 2272392833);
+ W = D(W, V, Y, X, C[P + 11], l, 1839030562);
+ X = D(X, W, V, Y, C[P + 14], j, 4259657740);
+ Y = D(Y, X, W, V, C[P + 1], o, 2763975236);
+ V = D(V, Y, X, W, C[P + 4], m, 1272893353);
+ W = D(W, V, Y, X, C[P + 7], l, 4139469664);
+ X = D(X, W, V, Y, C[P + 10], j, 3200236656);
+ Y = D(Y, X, W, V, C[P + 13], o, 681279174);
+ V = D(V, Y, X, W, C[P + 0], m, 3936430074);
+ W = D(W, V, Y, X, C[P + 3], l, 3572445317);
+ X = D(X, W, V, Y, C[P + 6], j, 76029189);
+ Y = D(Y, X, W, V, C[P + 9], o, 3654602809);
+ V = D(V, Y, X, W, C[P + 12], m, 3873151461);
+ W = D(W, V, Y, X, C[P + 15], l, 530742520);
+ X = D(X, W, V, Y, C[P + 2], j, 3299628645);
+ Y = t(Y, X, W, V, C[P + 0], U, 4096336452);
+ V = t(V, Y, X, W, C[P + 7], T, 1126891415);
+ W = t(W, V, Y, X, C[P + 14], R, 2878612391);
+ X = t(X, W, V, Y, C[P + 5], O, 4237533241);
+ Y = t(Y, X, W, V, C[P + 12], U, 1700485571);
+ V = t(V, Y, X, W, C[P + 3], T, 2399980690);
+ W = t(W, V, Y, X, C[P + 10], R, 4293915773);
+ X = t(X, W, V, Y, C[P + 1], O, 2240044497);
+ Y = t(Y, X, W, V, C[P + 8], U, 1873313359);
+ V = t(V, Y, X, W, C[P + 15], T, 4264355552);
+ W = t(W, V, Y, X, C[P + 6], R, 2734768916);
+ X = t(X, W, V, Y, C[P + 13], O, 1309151649);
+ Y = t(Y, X, W, V, C[P + 4], U, 4149444226);
+ V = t(V, Y, X, W, C[P + 11], T, 3174756917);
+ W = t(W, V, Y, X, C[P + 2], R, 718787259);
+ X = t(X, W, V, Y, C[P + 9], O, 3951481745);
+ Y = K(Y, h);
+ X = K(X, E);
+ W = K(W, v);
+ V = K(V, g)
+ }
+ var i = B(Y) + B(X) + B(W) + B(V);
+ return i.toLowerCase()
+};
+
+var singleton = new Functions();
+
+module.exports = singleton;
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 8801a35ab120a35a26c219803fb6108e45debece..a4d4f5bb0fcce4131ef7fe74359107037b8247e7 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -124,6 +124,12 @@ ServerConnector.getNeutralOverlayColorInt = function () {
});
};
+/**
+ *
+ * @param url
+ * @param description
+ * @returns {Promise}
+ */
ServerConnector.sendGetRequest = function (url, description) {
return this.sendRequest({
url: url,
@@ -153,7 +159,7 @@ function isSessionExpiredError(error) {
/**
*
* @param params
- * @returns {PromiseLike}
+ * @returns {PromiseLike|Promise}
*/
ServerConnector.sendRequest = function (params) {
var self = this;
@@ -225,6 +231,12 @@ ServerConnector._sendRequest = function (params) {
});
};
+/**
+ *
+ * @param {string} url
+ * @param {Object} params
+ * @returns {Promise}
+ */
ServerConnector.sendPostRequest = function (url, params) {
return this.sendRequest({
method: "POST",
@@ -243,9 +255,9 @@ ServerConnector.sendDeleteRequest = function (url, json) {
/**
*
- * @param url
- * @param json
- * @returns {PromiseLike}
+ * @param {string} url
+ * @param {Object} json
+ * @returns {Promise}
*/
ServerConnector.sendPatchRequest = function (url, json) {
return this.sendRequest({
@@ -255,6 +267,10 @@ ServerConnector.sendPatchRequest = function (url, json) {
});
};
+/**
+ *
+ * @returns {string}
+ */
ServerConnector.getApiBaseUrl = function () {
return this.getServerBaseUrl() + "/api/";
};
@@ -307,6 +323,15 @@ ServerConnector.createGetParams = function (params, prefix) {
return result;
};
+/**
+ *
+ * @param {Object} paramObj
+ * @param {string} [paramObj.type]
+ * @param {string} paramObj.url
+ * @param {Object} [paramObj.params]
+ *
+ * @returns {string}
+ */
ServerConnector.getApiUrl = function (paramObj) {
var type = paramObj.type;
var params = this.createGetParams(paramObj.params);
@@ -411,12 +436,124 @@ ServerConnector.getSbmlParameterUrl = function (queryParams, filterParams) {
});
};
+/**
+ *
+ * @param {Object} queryParams
+ * @param {string} [queryParams.version]
+ * @param {string} [queryParams.organism]
+ * @param {string} [queryParams.type]
+ * @param {string} [queryParams.genomeId]
+ * @param {Object} filterParams
+ *
+ * @returns {string}
+ */
ServerConnector.getReferenceGenomeUrl = function (queryParams, filterParams) {
- var version = this.getIdOrAsterisk(queryParams.version);
+ if (queryParams.genomeId !== undefined) {
+ return this.getApiUrl({
+ type: "genomics/" + queryParams.genomeId + "/",
+ params: filterParams
+ });
+ } else {
+ var version = this.getIdOrAsterisk(queryParams.version);
+
+ return this.getApiUrl({
+ type: "genomics/taxonomies/" + queryParams.organism + "/genomeTypes/" + queryParams.type + "/versions/" + version
+ + "/",
+ params: filterParams
+ });
+ }
+};
+
+/**
+ *
+ * @param {Object} queryParams
+ * @param {string} queryParams.genomeId
+ * @param {string} queryParams.mappingId
+ * @param {Object} [filterParams]
+ *
+ * @returns {string}
+ */
+ServerConnector.getReferenceGenomeGeneMappingUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ type: "genomics/" + queryParams.genomeId + "/geneMapping/" + queryParams.mappingId + "/",
+ params: filterParams
+ });
+};
+/**
+ *
+ * @param {Object} queryParams
+ * @param {string} queryParams.genomeId
+ * @param {Object} [filterParams]
+ *
+ * @returns {string}
+ */
+ServerConnector.getReferenceGenomeGeneMappingsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
- type: "genomics/taxonomies/" + queryParams.organism + "/genomeTypes/" + queryParams.type + "/versions/" + version
- + "/",
+ type: "genomics/" + queryParams.genomeId + "/geneMapping/",
+ params: filterParams
+ });
+};
+
+/**
+ *
+ * @param {Object} queryParams
+ * @param {string} queryParams.version
+ * @param {Annotation} queryParams.organism
+ * @param {string} queryParams.type
+ * @param {Object} filterParams
+ *
+ * @returns {string}
+ */
+ServerConnector.getAvailableGenomeUrlsUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ type: "genomics/taxonomies/" + queryParams.organism.getResource() + "/genomeTypes/" + queryParams.type + "/versions/" + queryParams.version
+ + ":getAvailableRemoteUrls",
+ params: filterParams
+ });
+};
+
+/**
+ *
+ * @param {Object} queryParams
+ * @param {Annotation} queryParams.organism
+ * @param {Object} [filterParams]
+ *
+ * @returns {string}
+ */
+ServerConnector.getReferenceGenomeTypesUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ type: "genomics/taxonomies/" + queryParams.organism.getResource() + "/genomeTypes/",
+ params: filterParams
+ });
+};
+
+/**
+ *
+ * @param {Object} queryParams
+ * @param {Annotation} queryParams.organism
+ * @param {string} queryParams.type
+ * @param {Object} [filterParams]
+ *
+ * @returns {string}
+ */
+ServerConnector.getReferenceGenomeVersionsUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ type: "genomics/taxonomies/" + queryParams.organism.getResource() + "/genomeTypes/" + queryParams.type + "/versions/",
+ params: filterParams
+ });
+};
+
+/**
+ *
+ * @param {Object} [queryParams]
+ * @param {Object} [filterParams]
+ *
+ * @returns {string}
+ */
+ServerConnector.getReferenceGenomeOrganismsUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ type: "genomics/taxonomies/",
params: filterParams
});
};
@@ -718,6 +855,21 @@ ServerConnector.getUsersUrl = function (queryParams, filterParams) {
});
};
+/**
+ *
+ * @param {Object} [queryParams]
+ * @param {Object} [filterParams]
+ *
+ * @returns {string}
+ */
+ServerConnector.getReferenceGenomesUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ type: "genomics/",
+ params: filterParams
+ });
+};
+
+
ServerConnector.getUserUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url: this.getUsersUrl() + queryParams.login,
@@ -1001,6 +1153,11 @@ ServerConnector.getLoggedUser = function () {
}
};
+/**
+ *
+ * @param {string} login
+ * @returns {Promise}
+ */
ServerConnector.getUser = function (login) {
var self = this;
var queryParams = {
@@ -1027,7 +1184,7 @@ ServerConnector.getUser = function (login) {
/**
*
* @param {User} user
- * @returns {PromiseLike<any>}
+ * @returns {Promise}
*/
ServerConnector.updateUser = function (user) {
var self = this;
@@ -1040,7 +1197,8 @@ ServerConnector.updateUser = function (user) {
surname: user.getSurname(),
password: user.getPassword(),
email: user.getEmail(),
- termsOfUseConsent: user.isTermsOfUseConsent()
+ termsOfUseConsent: user.isTermsOfUseConsent(),
+ connectedToLdap: user.isConnectedToLdap()
}
};
return self.sendPatchRequest(self.getUserUrl(queryParams), filterParams).then(function () {
@@ -1048,8 +1206,13 @@ ServerConnector.updateUser = function (user) {
}).then(function (configuration) {
return self.updateUserPrivileges({user: user, privileges: user.privilegesToExport(configuration)});
});
-
};
+
+/**
+ *
+ * @param {User} user
+ * @returns {Promise}
+ */
ServerConnector.addUser = function (user) {
var self = this;
var queryParams = {
@@ -1067,18 +1230,29 @@ ServerConnector.addUser = function (user) {
}).then(function (configuration) {
return self.updateUserPrivileges({user: user, privileges: user.privilegesToExport(configuration)});
});
-
};
+/**
+ *
+ * @param {string} login
+ * @returns {Promise}
+ */
ServerConnector.removeUser = function (login) {
var self = this;
var queryParams = {
login: login
};
return self.sendDeleteRequest(self.getUserUrl(queryParams));
-
};
+/**
+ *
+ * @param {Object} params
+ * @param {User} params.user
+ * @param {Object} params.privileges
+ *
+ * @returns {Promise}
+ */
ServerConnector.updateUserPrivileges = function (params) {
var self = this;
var queryParams = {
@@ -1101,6 +1275,11 @@ ServerConnector.updateUserPrivileges = function (params) {
});
};
+/**
+ *
+ * @param {Error} error
+ * @returns {Promise}
+ */
ServerConnector.processNetworkError = function (error) {
if ((error instanceof NetworkError)) {
switch (error.statusCode) {
@@ -1116,7 +1295,14 @@ ServerConnector.processNetworkError = function (error) {
}
};
-
+/**
+ *
+ * @param {Object} params
+ * @param {User} params.user
+ * @param {UserPreferences} params.preferences
+ *
+ * @returns {Promise}
+ */
ServerConnector.updateUserPreferences = function (params) {
var self = this;
var queryParams = {
@@ -1137,6 +1323,12 @@ ServerConnector.updateUserPreferences = function (params) {
});
};
+/**
+ *
+ * @param {boolean} forceRefresh
+ *
+ * @returns {Promise}
+ */
ServerConnector.getUsers = function (forceRefresh) {
var self = this;
@@ -1160,9 +1352,35 @@ ServerConnector.getUsers = function (forceRefresh) {
return self.processNetworkError(error);
});
}
+};
+/**
+ *
+ * @returns {Promise<Array>}
+ */
+ServerConnector.getReferenceGenomes = function () {
+ var self = this;
+
+ return self.sendGetRequest(self.getReferenceGenomesUrl()).then(function (content) {
+ var result = [];
+ var parsedData = JSON.parse(content);
+ for (var i = 0; i < parsedData.length; i++) {
+ var genome = new ReferenceGenome(parsedData[i]);
+ result.push(genome)
+ }
+ return result;
+ });
};
+/**
+ *
+ * @param {Object} [params]
+ * @param {string} [params.creator] user login
+ * @param {boolean} [params.publicOverlay]
+ * @param {string} [params.projectId]
+ *
+ * @returns {Promise<Array>}
+ */
ServerConnector.getOverlays = function (params) {
var self = this;
if (params === undefined) {
@@ -1187,6 +1405,13 @@ ServerConnector.getOverlays = function (params) {
});
};
+/**
+ *
+ * @param {number} overlayId
+ * @param {string} [projectId]
+ *
+ * @returns {Promise}
+ */
ServerConnector.getOverlayElements = function (overlayId, projectId) {
var self = this;
if (overlayId === undefined) {
@@ -1244,6 +1469,11 @@ ServerConnector.getFullOverlayElement = function (params) {
});
};
+/**
+ *
+ * @param {string} [projectId]
+ * @returns {Promise}
+ */
ServerConnector.getProjectId = function (projectId) {
var self = this;
if (projectId !== undefined && projectId !== null && projectId !== "") {
@@ -1733,7 +1963,6 @@ ServerConnector.addComment = function (params) {
delete filterParams.modelId;
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- console.log(self.addCommentUrl(queryParams));
return self.sendPostRequest(self.addCommentUrl(queryParams), filterParams);
}).then(function (content) {
var response = JSON.parse(content);
@@ -1761,6 +1990,7 @@ ServerConnector.addOverlay = function (params) {
content: overlay.getContent(),
filename: overlay.getFilename(),
googleLicenseConsent: overlay.isGoogleLicenseConsent(),
+ type: overlay.getType(),
fileId: params.fileId
};
return self.getProjectId(params.projectId).then(function (result) {
@@ -1771,6 +2001,12 @@ ServerConnector.addOverlay = function (params) {
});
};
+/**
+ *
+ * @param {string} name
+ * @param {string} content
+ * @returns {Promise}
+ */
ServerConnector.addOverlayFromString = function (name, content) {
var fileName = name + ".txt";
var overlay = new DataOverlay({
@@ -1945,14 +2181,163 @@ ServerConnector.getPublications = function (params) {
});
};
+/**
+ *
+ * @param {Object} params
+ * @param {string} [params.version]
+ * @param {string} [params.organism]
+ * @param {string} [params.type]
+ * @param {string|number} [params.genomeId]
+ *
+ * @returns {Promise}
+ */
ServerConnector.getReferenceGenome = function (params) {
var self = this;
var filterParams = {};
- return self.sendGetRequest(self.getReferenceGenomeUrl(params, filterParams)).then(function (content) {
- return new ReferenceGenome(JSON.parse(content));
+ if (params.genomeId !== undefined) {
+ return self.getReferenceGenomes().then(function (referenceGenomes) {
+ for (var i = 0; i < referenceGenomes.length; i++) {
+ var genome = referenceGenomes[i];
+ if (genome.getId() === params.genomeId) {
+ return genome;
+ }
+ }
+ return null;
+ });
+ } else {
+ return self.sendGetRequest(self.getReferenceGenomeUrl(params, filterParams)).then(function (content) {
+ return new ReferenceGenome(JSON.parse(content));
+ });
+ }
+};
+
+
+/**
+ *
+ * @param {Object} params
+ * @param {string|number} params.genomeId
+ * @param {string} params.mappingName
+ * @param {string} params.mappingUrl
+ *
+ * @returns {Promise}
+ */
+ServerConnector.addGeneMapping = function (params) {
+ var self = this;
+ var data = {
+ name: params.mappingName,
+ url: params.mappingUrl
+ };
+ return self.sendPostRequest(self.getReferenceGenomeGeneMappingsUrl(params), data);
+};
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.version
+ * @param {Annotation} params.organism
+ * @param {string} params.type
+ *
+ * @returns {Promise<string[]>}
+ */
+ServerConnector.getAvailableGenomeUrls = function (params) {
+ var self = this;
+ var filterParams = {};
+ return self.sendGetRequest(self.getAvailableGenomeUrlsUrl(params, filterParams)).then(function (content) {
+ var result = [];
+ var raw = JSON.parse(content);
+ for (var i = 0; i < raw.length; i++) {
+ result.push(raw[i].url);
+ }
+ return result;
+ });
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @returns {Promise<ReferenceGenome>}
+ */
+ServerConnector.addReferenceGenome = function (genome) {
+ var self = this;
+ var data = {
+ organismId: genome.getOrganism().getResource(),
+ type: genome.getType(),
+ version: genome.getVersion(),
+ sourceUrl: genome.getSourceUrl()
+ };
+ return self.sendPostRequest(self.getReferenceGenomesUrl(), data);
+};
+
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.genomeId
+ * @param {string} params.mappingId
+ *
+ * @returns {Promise}
+ */
+ServerConnector.removeReferenceGenomeGeneMapping = function (params) {
+ var self = this;
+ return self.sendDeleteRequest(self.getReferenceGenomeGeneMappingUrl(params));
+};
+
+
+/**
+ *
+ * @param {Object} params
+ * @param {Annotation} params.organism
+ * @returns {Promise}
+ */
+ServerConnector.getReferenceGenomeTypes = function (params) {
+ var self = this;
+ var filterParams = {};
+ return self.sendGetRequest(self.getReferenceGenomeTypesUrl(params, filterParams)).then(function (content) {
+ return JSON.parse(content);
});
};
+/**
+ *
+ * @param {Object} params
+ * @param {Annotation} params.organism
+ * @param {string} params.type
+ * @returns {Promise}
+ */
+ServerConnector.getReferenceGenomeVersions = function (params) {
+ var self = this;
+ var filterParams = {};
+ return self.sendGetRequest(self.getReferenceGenomeVersionsUrl(params, filterParams)).then(function (content) {
+ return JSON.parse(content);
+ });
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+ServerConnector.getReferenceGenomeOrganisms = function () {
+ var self = this;
+ return self.sendGetRequest(self.getReferenceGenomeOrganismsUrl()).then(function (content) {
+ var array = JSON.parse(content);
+ var result = [];
+ for (var i = 0; i < array.length; i++) {
+ result.push(new Annotation(array[i]));
+ }
+ return result;
+ });
+};
+
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.genomeId
+ * @returns {Promise}
+ */
+ServerConnector.removeReferenceGenome = function (params) {
+ var self = this;
+ var filterParams = {};
+ return self.sendDeleteRequest(self.getReferenceGenomeUrl(params, filterParams));
+};
+
ServerConnector.uploadFile = function (params) {
var CHUNK_SIZE = 65535 * 8;
var self = this;
@@ -2093,6 +2478,10 @@ ServerConnector.setPluginUserParam = function (params) {
});
};
+/**
+ *
+ * @returns {Promise}
+ */
ServerConnector.getSubmapConnections = function () {
var self = this;
var queryParams = {};
diff --git a/frontend-js/src/main/js/gui/AbstractGuiElement.js b/frontend-js/src/main/js/gui/AbstractGuiElement.js
index 3ba1e7fdc6fd227ac9871e8fd87e19a625c9c160..95a72bfd8f964fe589c8d764a06b0d91fbbf89b8 100644
--- a/frontend-js/src/main/js/gui/AbstractGuiElement.js
+++ b/frontend-js/src/main/js/gui/AbstractGuiElement.js
@@ -10,7 +10,13 @@ var logger = require('../logger');
/**
*
- * @param params
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
* @constructor
*
* @extends ObjectWithListeners
@@ -21,9 +27,10 @@ function AbstractGuiElement(params) {
var self = this;
self.setElement(params.element);
+ self.setConfiguration(params.configuration);
self.setProject(params.project);
self.setMap(params.customMap);
- self.setConfiguration(params.configuration);
+ self.setServerConnector(params.serverConnector);
self._controlElements = [];
@@ -91,6 +98,11 @@ AbstractGuiElement.prototype.getProject = function () {
};
+/**
+ *
+ * @param {string} type
+ * @param {HTMLElement} element
+ */
AbstractGuiElement.prototype.setControlElement = function (type, element) {
if (type === null || type === undefined) {
throw new Error("Unknown control element type");
@@ -102,6 +114,11 @@ AbstractGuiElement.prototype.setControlElement = function (type, element) {
this._controlElements[type] = element;
};
+/**
+ *
+ * @param {string} type
+ * @returns {HTMLElement}
+ */
AbstractGuiElement.prototype.getControlElement = function (type) {
if (type === null || type === undefined) {
throw new Error("Unknown control element type");
@@ -113,11 +130,19 @@ AbstractGuiElement.prototype.getControlElement = function (type) {
return this._controlElements[type];
};
+/**
+ *
+ * @param {string} url
+ */
AbstractGuiElement.prototype.downloadFile = function (url) {
this._downloadFile = url;
window.open(url, '_blank');
};
+/**
+ *
+ * @returns {string}
+ */
AbstractGuiElement.prototype.getLastDownloadUrl = function () {
return this._downloadFile;
};
@@ -138,6 +163,26 @@ AbstractGuiElement.prototype.getConfiguration = function () {
return this._configuration;
};
+/**
+ *
+ * @param {ServerConnector} serverConnector
+ */
+AbstractGuiElement.prototype.setServerConnector = function (serverConnector) {
+ this._serverConnector = serverConnector;
+};
+
+/**
+ *
+ * @returns {ServerConnector}
+ */
+AbstractGuiElement.prototype.getServerConnector = function () {
+ if (this._serverConnector !== undefined) {
+ return this._serverConnector;
+ } else {
+ return this.getMap().getServerConnector();
+ }
+};
+
/**
*
* @param {string} [params.content]
diff --git a/frontend-js/src/main/js/gui/AddOverlayDialog.js b/frontend-js/src/main/js/gui/AddOverlayDialog.js
index d49c6a153db8f9436d021c8a4126d5cb3cbc9436..497045042e7987b2dfe9674b8806d69ad4897ec8 100644
--- a/frontend-js/src/main/js/gui/AddOverlayDialog.js
+++ b/frontend-js/src/main/js/gui/AddOverlayDialog.js
@@ -18,6 +18,19 @@ var HttpStatus = require('http-status-codes');
var Promise = require("bluebird");
var TextEncoder = require('text-encoding').TextEncoder;
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
function AddOverlayDialog(params) {
AbstractGuiElement.call(this, params);
var self = this;
@@ -28,9 +41,12 @@ function AddOverlayDialog(params) {
AddOverlayDialog.prototype = Object.create(AbstractGuiElement.prototype);
AddOverlayDialog.prototype.constructor = AddOverlayDialog;
+/**
+ *
+ */
AddOverlayDialog.prototype.createGui = function () {
var self = this;
- var guiUtils = new GuiUtils();
+ var guiUtils = new GuiUtils(self.getConfiguration());
var content = document.createElement("div");
content.style.width = "100%";
content.style.height = "100%";
@@ -52,6 +68,24 @@ AddOverlayDialog.prototype.createGui = function () {
content.appendChild(descriptionInput);
content.appendChild(guiUtils.createNewLine());
+ content.appendChild(guiUtils.createLabel("Type: "));
+ content.appendChild(guiUtils.createNewLine());
+ var types = self.getConfiguration().getOverlayTypes();
+ var typeSelect = Functions.createElement({
+ type: "select",
+ name: "overlay-type",
+ value: types[0]
+ });
+ for (var i = 0; i < types.length; i++) {
+ $(typeSelect).append($('<option>', {
+ value: types[i],
+ text: types[i]
+ }));
+ }
+
+ content.appendChild(typeSelect);
+ content.appendChild(guiUtils.createNewLine());
+
content.appendChild(guiUtils.createLabel("Upload file: "));
var fileInput = Functions.createElement({
type: "input",
@@ -100,6 +134,7 @@ AddOverlayDialog.prototype.processFile = function (file) {
var overlay = overlayParser.parse(evt.target.result);
var nameInput = $("[name='overlay-name']", self.getElement())[0];
var descriptionInput = $("[name='overlay-description']", self.getElement())[0];
+ var typeSelect = $("[name='overlay-type']", self.getElement());
if (overlay.getName() !== undefined) {
nameInput.value = overlay.getName();
} else {
@@ -116,6 +151,9 @@ AddOverlayDialog.prototype.processFile = function (file) {
if (overlay.getDescription() !== undefined) {
descriptionInput.value = overlay.getDescription();
}
+ if (overlay.getType() !== undefined) {
+ typeSelect.val(overlay.getType());
+ }
resolve(self.getFileContent());
} catch (error) {
reject(error);
@@ -155,32 +193,39 @@ AddOverlayDialog.prototype.getFileContent = function () {
}
};
+/**
+ *
+ * @returns {Promise}
+ */
AddOverlayDialog.prototype.init = function () {
return Promise.resolve();
};
+
AddOverlayDialog.prototype.addOverlay = function () {
var self = this;
var nameInput = $("[name='overlay-name']", self.getElement())[0];
var descriptionInput = $("[name='overlay-description']", self.getElement())[0];
var filename = $("[name='overlay-file']", self.getElement())[0].value;
+ var type = $("[name='overlay-type']", self.getElement()).val();
var consent = $("[name='overlay-google-consent']", self.getElement()).is(":checked");
var overlay = new DataOverlay({
name: nameInput.value,
description: descriptionInput.value,
filename: filename,
- googleLicenseConsent: consent
+ googleLicenseConsent: consent,
+ type: type
});
if (filename === undefined || filename === "") {
filename = "unknown.txt";
}
GuiConnector.showProcessing();
- return ServerConnector.uploadFile({
+ return self.getServerConnector().uploadFile({
filename: filename,
content: self.getFileContent()
}).then(function (file) {
- return ServerConnector.addOverlay({
+ return self.getServerConnector().addOverlay({
fileId: file.id,
overlay: overlay,
projectId: self.getProject().getProjectId()
diff --git a/frontend-js/src/main/js/gui/Panel.js b/frontend-js/src/main/js/gui/Panel.js
index 3a931f2420d31d7cef93b8da19600cb8ba6ddd31..75ebb3459b1ea5d8f6aa595dc1caf6b2f584d5bd 100644
--- a/frontend-js/src/main/js/gui/Panel.js
+++ b/frontend-js/src/main/js/gui/Panel.js
@@ -20,7 +20,6 @@ var xss = require('xss');
* @param {string} params.panelName
* @param {boolean} params.scrollable
* @param {string} [params.helpTip]
- * @param {ServerConnector} [params.serverConnector]
* @param params.parent
*
* @constructor
@@ -33,7 +32,6 @@ function Panel(params) {
var self = this;
self.setParent(params.parent);
- self.setServerConnector(params.serverConnector);
var configuration = params.configuration;
if (params.configuration === undefined) {
configuration = self.getMap().getConfiguration();
@@ -239,10 +237,18 @@ Panel.prototype.getParent = function () {
return this._parent;
};
+/**
+ *
+ * @param {GuiUtils} guiUtils
+ */
Panel.prototype.setGuiUtils = function (guiUtils) {
this._guiUtils = guiUtils;
};
+/**
+ *
+ * @returns {GuiUtils}
+ */
Panel.prototype.getGuiUtils = function () {
return this._guiUtils;
};
@@ -300,24 +306,4 @@ Panel.prototype.destroy = function () {
}
};
-/**
- *
- * @returns {ServerConnector}
- */
-Panel.prototype.getServerConnector = function () {
- if (this._serverConnector !== undefined) {
- return this._serverConnector;
- }
- return this.getMap().getServerConnector();
-};
-
-/**
- *
- * @param {ServerConnector} serverConnector
- */
-Panel.prototype.setServerConnector = function (serverConnector) {
- this._serverConnector = serverConnector;
-};
-
-
module.exports = Panel;
diff --git a/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js b/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js
index 58a37304c30c853f99405ebfb5f7d765595dc469..3780b8749497a11a6018655e42f606d4e09443ab 100644
--- a/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js
@@ -9,15 +9,30 @@ var GuiConnector = require('../../GuiConnector');
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
+// noinspection JSUnusedLocalSymbols
var Functions = require('../../Functions');
var Promise = require("bluebird");
+/**
+ *
+ * @param {Configuration} [params.configuration]
+ * @param {HTMLElement} params.element
+ * @param {Project} params.project
+ * @param {CustomMap} params.customMap
+ * @param {string} params.panelName
+ * @param {string} [params.helpTip]
+ * @param params.parent
+ *
+ * @constructor
+ * @extends Panel
+ */
function AbstractAdminPanel(params) {
- params.scrollable = true;
+ params["scrollable"] = true;
Panel.call(this, params);
this._createHeader(params.name);
this._initPromises = [];
+ this._eventBinds = [];
}
AbstractAdminPanel.prototype = Object.create(Panel.prototype);
@@ -30,12 +45,25 @@ AbstractAdminPanel.prototype._createHeader = function (name) {
// }));
};
+/**
+ *
+ * @returns {Promise}
+ */
AbstractAdminPanel.prototype.init = function () {
return Promise.all(this._initPromises);
};
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.event
+ * @param {jQuery} params.jQueryObject
+ * @param {string} params.preferenceName
+ * @param {Object} params.defaultValue
+ * @param {function} params.getter
+ * @param {function} params.setter
+ */
AbstractAdminPanel.prototype.bindUserGuiPreference = function (params) {
-
params.jQueryObject.on(params.event, function () {
return ServerConnector.getLoggedUser().then(function (user) {
var oldValue = user.getPreferences().getGuiPreference(params.preferenceName, params.defaultValue);
@@ -53,6 +81,18 @@ AbstractAdminPanel.prototype.bindUserGuiPreference = function (params) {
var value = user.getPreferences().getGuiPreference(params.preferenceName, params.defaultValue);
return params.setter(value);
}));
+
+ this._eventBinds.push(params);
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+AbstractAdminPanel.prototype.destroy = function () {
+ return Promise.each(this._eventBinds, function (params) {
+ params.jQueryObject.off(params.event);
+ });
};
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 0ab83e41a584db1d9547d034a2ff23d553578a4d..a436197c2afc643d766b5fcb0159975209c58744 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -160,11 +160,11 @@ AddProjectDialog.prototype.showValidatorsDialog = function () {
AddProjectDialog.prototype.createGeneralTabContent = function () {
var self = this;
- var result = new Functions.createElement({
+ var result = Functions.createElement({
type: "div"
});
- var table = new Functions.createElement({
+ var table = Functions.createElement({
type: "div",
style: "display:table; width:100%"
});
@@ -352,12 +352,12 @@ AddProjectDialog.prototype.createInputRow = function (params) {
if (params.defaultValue === undefined) {
params.defaultValue = "";
}
- var label = new Functions.createElement({
+ var label = Functions.createElement({
type: "div",
style: "display:table-cell; width:200px",
content: xss(params.labelName)
});
- var input = new Functions.createElement({
+ var input = Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='" + xss(params.inputName) + "' value='" + xss(params.defaultValue) + "' style='width:100%'/>",
@@ -409,7 +409,7 @@ AddProjectDialog.prototype.createCheckboxRow = function (params) {
};
AddProjectDialog.prototype.createRow = function (elements) {
- var result = new Functions.createElement({
+ var result = Functions.createElement({
type: "div",
style: "display:table-row"
});
@@ -420,7 +420,7 @@ AddProjectDialog.prototype.createRow = function (elements) {
if (columnNumber === 0) {
style += "width:200px;";
}
- var labelContainer = new Functions.createElement({
+ var labelContainer = Functions.createElement({
type: "div",
style: style
});
diff --git a/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
new file mode 100644
index 0000000000000000000000000000000000000000..db63e854dc8534215b76cd1b12bf8fada93cf2ce
--- /dev/null
+++ b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
@@ -0,0 +1,703 @@
+"use strict";
+
+var Promise = require("bluebird");
+
+var AbstractGuiElement = require('../AbstractGuiElement');
+var Annotation = require('../../map/data/Annotation');
+var GuiConnector = require('../../GuiConnector');
+
+var Functions = require('../../Functions');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var guiUtils = new (require('../leftPanel/GuiUtils'))();
+
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {ReferenceGenome} params.referenceGenome
+ * @param {ServerConnector} [params.serverConnector]
+
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
+function EditGenomeDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ self.setReferenceGenome(params.referenceGenome);
+
+ $(self.getElement()).css({overflow: "hidden"});
+
+ self.createGui();
+ self.registerListenerType("onSave");
+}
+
+EditGenomeDialog.prototype = Object.create(AbstractGuiElement.prototype);
+EditGenomeDialog.prototype.constructor = EditGenomeDialog;
+
+/**
+ *
+ * @param {ReferenceGenome} referenceGenome
+ */
+EditGenomeDialog.prototype.setReferenceGenome = function (referenceGenome) {
+ this._referenceGenome = referenceGenome;
+};
+
+/**
+ *
+ * @returns {ReferenceGenome}
+ */
+EditGenomeDialog.prototype.getReferenceGenome = function () {
+ return this._referenceGenome;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+EditGenomeDialog.prototype.isNew = function () {
+ return this.getReferenceGenome().getId() === undefined;
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.createGui = function () {
+ var self = this;
+ var element = self.getElement();
+
+ var tabDiv = Functions.createElement({
+ type: "div",
+ name: "tabView",
+ className: "tabbable boxed parentTabs",
+ style: "position:absolute;top:10px;bottom:40px;left:10px;right:10px"
+ });
+ element.appendChild(tabDiv);
+
+ var tabMenuDiv = Functions.createElement({
+ type: "ul",
+ className: "nav nav-tabs"
+ });
+ tabDiv.appendChild(tabMenuDiv);
+
+ var tabContentDiv = Functions.createElement({
+ type: "div",
+ className: "tab-content",
+ style: "height:100%"
+ });
+ tabDiv.appendChild(tabContentDiv);
+
+ self.createGeneralTab(tabMenuDiv, tabContentDiv);
+ self.createGeneMappingTab(tabMenuDiv, tabContentDiv);
+ $("a", tabMenuDiv).bind("click", function () {
+ //workaround for some css issues...
+ tabDiv.style.top = "40px";
+ tabDiv.style.bottom = "10px";
+ });
+
+};
+
+/**
+ *
+ * @param {HTMLElement} tabMenuDiv
+ * @param {HTMLElement} tabContentDiv
+ */
+EditGenomeDialog.prototype.createGeneralTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "DETAILS",
+ content: self.createGeneralTabContent()
+ });
+
+};
+
+/**
+ *
+ * @param {HTMLElement} tabMenuDiv
+ * @param {HTMLElement} tabContentDiv
+ */
+EditGenomeDialog.prototype.createGeneMappingTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "GENE MAPPING",
+ content: self.createGeneMappingTabContent()
+ });
+
+};
+
+var id_counter = 0;
+
+/**
+ *
+ * @param {string} tab_name
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.generateTabId = function (tab_name) {
+ var self = this;
+ var id = self.getReferenceGenome().getId();
+ if (id === undefined) {
+ id = "new_genome_" + (id_counter++);
+ }
+ return id + tab_name.replace(" ", "_") + "_TAB";
+};
+
+EditGenomeDialog.prototype.addTab = function (params) {
+ var id = this.generateTabId(params.name);
+
+ var navLi = guiUtils.createTabMenuObject({
+ id: id,
+ name: params.name,
+ navigationBar: params.tabMenuDiv
+ });
+ params.tabMenuDiv.appendChild(navLi);
+
+ var contentDiv = guiUtils.createTabContentObject({
+ id: id,
+ navigationObject: navLi,
+ navigationBar: params.tabMenuDiv
+ });
+
+ $(contentDiv).css("overflow", "auto");
+ if (params.content !== undefined) {
+ contentDiv.appendChild(params.content);
+ }
+
+ params.tabContentDiv.appendChild(contentDiv);
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
+EditGenomeDialog.prototype.createGeneralTabContent = function () {
+
+ var self = this;
+
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ var table = Functions.createElement({
+ type: "table",
+ name: "detailsTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(table);
+
+ $(table).on("change", "[name='genomeOrganismSelect']", function () {
+ return self._fillTypeSelect(self.getReferenceGenome(), self.getSelectedOrganism());
+ });
+
+ $(table).on("change", "[name='genomeTypeSelect']", function () {
+ return self._fillVersionSelect(self.getReferenceGenome(), self.getSelectedOrganism(), self.getSelectedType());
+ });
+
+ $(table).on("change", "[name='genomeVersionSelect']", function () {
+ return self._fillUrl(self.getReferenceGenome(), self.getSelectedOrganism(), self.getSelectedType(), self.getSelectedVersion());
+ });
+
+
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+ result.appendChild(menuRow);
+
+ var saveUserButton = Functions.createElement({
+ type: "button",
+ name: "saveGenome",
+ content: '<span class="ui-icon ui-icon-disk"></span> SAVE',
+ onclick: function () {
+ return self.onSaveClicked().then(function () {
+ return self.close();
+ }).catch(GuiConnector.alert);
+ },
+ xss: false
+ });
+ var cancelButton = Functions.createElement({
+ type: "button",
+ name: "cancelGenome",
+ content: '<span class="ui-icon ui-icon-cancel"></span> CANCEL',
+ onclick: function () {
+ return self.close();
+ },
+ xss: false
+ });
+ menuRow.appendChild(saveUserButton);
+ menuRow.appendChild(cancelButton);
+
+ return result;
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
+EditGenomeDialog.prototype.createGeneMappingTabContent = function () {
+
+ var self = this;
+
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ var geneMappingTable = Functions.createElement({
+ type: "table",
+ name: "geneMappingTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(geneMappingTable);
+
+ // noinspection JSUnusedGlobalSymbols
+ $(geneMappingTable).DataTable({
+ columns: [{
+ title: 'Name'
+ }, {
+ title: 'Source'
+ }, {
+ title: 'Progress'
+ }, {
+ title: 'Remove',
+ orderable: false
+ }],
+ order: [[1, "asc"]]
+ });
+
+ $(geneMappingTable).on("click", "[name='removeMapping']", function () {
+ var button = this;
+ return self.askConfirmRemoval({
+ title: "INFO",
+ content: "Do you really want to remove this gene mapping?",
+ input: false
+ }).then(function (param) {
+ if (param.status) {
+ return self.getServerConnector().removeReferenceGenomeGeneMapping({
+ mappingId: $(button).attr("data").toString(),
+ genomeId: self.getReferenceGenome().getId().toString()
+ }).then(function () {
+ return self.getServerConnector().getReferenceGenome({genomeId: self.getReferenceGenome().getId()});
+ }).then(function (referenceGenome) {
+ self.setReferenceGenome(referenceGenome);
+ return self.refresh();
+ });
+ }
+ }).catch(GuiConnector.alert);
+ });
+
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+ result.appendChild(menuRow);
+
+ var addGeneMappingButton = Functions.createElement({
+ type: "button",
+ name: "saveGenome",
+ content: '<span class="ui-icon ui-icon-disk"></span> ADD GENE MAPPING',
+ onclick: function () {
+ return self.openAddGeneMapping();
+ },
+ xss: false
+ });
+
+ menuRow.appendChild(addGeneMappingButton);
+
+ return result;
+};
+
+/**
+ *
+ * @returns {Promise|PromiseLike}
+ */
+EditGenomeDialog.prototype.onSaveClicked = function () {
+ var self = this;
+ if (!self.isNew()) {
+ return self.callListeners("onSave");
+ } else {
+ var genome = self.getReferenceGenome();
+ genome.setSourceUrl(self.getSourceUrl());
+ genome.setOrganism(self.getSelectedOrganism());
+ genome.setType(self.getSelectedType());
+ genome.setVersion(self.getSelectedVersion());
+ return self.getServerConnector().addReferenceGenome(genome).then(function () {
+ return self.callListeners("onSave");
+ });
+ }
+};
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @returns {Promise}
+ * @private
+ */
+EditGenomeDialog.prototype._fillOrganismSelect = function (genome) {
+ var self = this;
+ return self.getServerConnector().getReferenceGenomeOrganisms().then(function (organisms) {
+ var genomeOrganismSelect = $("[name=genomeOrganismSelect]", self.getElement());
+ genomeOrganismSelect.empty();
+ var selectedOrganism;
+ if (self.isNew()) {
+ selectedOrganism = organisms[0];
+ for (var i = 0; i < organisms.length; i++) {
+ if (organisms[i].getResource() === "9606") {
+ selectedOrganism = organisms[i];
+ }
+ }
+ } else {
+ selectedOrganism = genome.getOrganism();
+ }
+ $.each(organisms, function (i, organism) {
+ var disable = false;
+ if (organism.getResource() !== selectedOrganism.getResource() && !self.isNew()) {
+ disable = true;
+ }
+ genomeOrganismSelect.append($('<option>', {
+ value: organism.getResource(),
+ text: organism.getResource(),
+ disabled: disable
+ }));
+ });
+ genomeOrganismSelect.val(selectedOrganism.getResource());
+ return self._fillTypeSelect(genome, selectedOrganism);
+ });
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @param {Annotation} selectedOrganism
+ * @returns {Promise}
+ * @private
+ */
+EditGenomeDialog.prototype._fillTypeSelect = function (genome, selectedOrganism) {
+ var self = this;
+ return self.getServerConnector().getReferenceGenomeTypes({organism: selectedOrganism}).then(function (types) {
+
+ var genomeTypeSelect = $("[name=genomeTypeSelect]", self.getElement());
+ genomeTypeSelect.empty();
+
+ var selectedType;
+ if (self.isNew()) {
+ selectedType = types[0].type;
+ } else {
+ selectedType = genome.getType();
+ }
+ $.each(types, function (i, type) {
+ var disable = false;
+ if (type.type !== selectedType && !self.isNew()) {
+ disable = true;
+ }
+ genomeTypeSelect.append($('<option>', {
+ value: type.type,
+ text: type.type,
+ disabled: disable
+ }));
+ });
+ genomeTypeSelect.val(selectedType);
+ return self._fillVersionSelect(genome, selectedOrganism, selectedType);
+ })
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @param {Annotation} selectedOrganism
+ * @param {string} selectedType
+ * @returns {Promise}
+ * @private
+ */
+EditGenomeDialog.prototype._fillVersionSelect = function (genome, selectedOrganism, selectedType) {
+ var self = this;
+ return self.getServerConnector().getReferenceGenomeVersions({
+ organism: selectedOrganism,
+ type: selectedType
+ }).then(function (versions) {
+ var genomeVersionSelect = $("[name=genomeVersionSelect]", self.getElement());
+ genomeVersionSelect.empty();
+
+ var selectedVersion;
+ if (self.isNew()) {
+ selectedVersion = versions[0].version;
+ } else {
+ selectedVersion = genome.getVersion();
+ }
+ $.each(versions, function (i, version) {
+ var disable = false;
+ if (version.version !== selectedVersion && !self.isNew()) {
+ disable = true;
+ }
+ genomeVersionSelect.append($('<option>', {
+ value: version.version,
+ text: version.version,
+ disabled: disable
+ }));
+ });
+ genomeVersionSelect.val(selectedVersion);
+ return self._fillUrl(genome, selectedOrganism, selectedType, selectedVersion);
+ })
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @param {Annotation} organism
+ * @param {string} type
+ * @param {string} version
+ * @returns {Promise}
+ * @private
+ */
+EditGenomeDialog.prototype._fillUrl = function (genome, organism, type, version) {
+ var self = this;
+ var genomeSourceUrlInput = $("[name=genomeSourceUrl]", self.getElement());
+ var genomeLocalUrlInput = $("[name=genomeLocalUrl]", self.getElement());
+ var genomeProgressInput = $("[name=genomeProgress]", self.getElement());
+ genomeLocalUrlInput.prop("disabled", true);
+ genomeProgressInput.val(genome.getDownloadProgressStatus());
+ genomeProgressInput.prop("disabled", true);
+ if (!self.isNew()) {
+ genomeSourceUrlInput.val(genome.getSourceUrl());
+ genomeSourceUrlInput.prop("disabled", true);
+
+ genomeLocalUrlInput.val(genome.getLocalUrl());
+ } else {
+ genomeSourceUrlInput.prop("disabled", false);
+
+ genomeLocalUrlInput.val("");
+ return self.getServerConnector().getAvailableGenomeUrls({
+ organism: organism,
+ type: type,
+ version: version
+ }).then(function (urls) {
+ if (urls.length > 0) {
+ genomeSourceUrlInput.val(urls[0]);
+ } else {
+ genomeSourceUrlInput.val("");
+ }
+ })
+ }
+ return Promise.resolve();
+}
+;
+
+
+/**
+ *
+ * @param {ReferenceGenomeGeneMapping} geneMapping
+ * @returns {Array}
+ */
+EditGenomeDialog.prototype.geneMappingToTableRow = function (geneMapping) {
+ var row = [];
+ row[0] = geneMapping.getName();
+ row[1] = geneMapping.getSourceUrl();
+ row[2] = geneMapping.getProgress();
+ row[3] = "<button name='removeMapping' data='" + geneMapping.getId() + "'><i class='fa fa-trash-o' style='font-size:17px'></button>";
+ return row;
+};
+/**
+ *
+ * @returns {Promise}
+ */
+EditGenomeDialog.prototype.init = function () {
+ var self = this;
+
+ var detailsTable = $("[name=detailsTable]", self.getElement())[0];
+
+ // noinspection JSCheckFunctionSignatures
+ $(detailsTable).DataTable({
+ columns: [{
+ title: "Name"
+ }, {
+ title: "Value"
+ }],
+ paging: false,
+ ordering: false,
+ searching: false,
+ bInfo: false
+ });
+
+ return self.refresh();
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+EditGenomeDialog.prototype.refresh = function () {
+ var self = this;
+
+ var genome = self.getReferenceGenome();
+
+ var dataTable = $("[name=detailsTable]", self.getElement()).DataTable();
+ var data = [];
+
+ data.push(['Organism', Functions.createElement({type: "select", name: "genomeOrganismSelect"}).outerHTML]);
+ data.push(['Type', Functions.createElement({type: "select", name: "genomeTypeSelect"}).outerHTML]);
+ data.push(['Version', Functions.createElement({type: "select", name: "genomeVersionSelect"}).outerHTML]);
+ data.push(['Source url', Functions.createElement({type: "input", name: "genomeSourceUrl"}).outerHTML]);
+ data.push(['Local url', Functions.createElement({type: "input", name: "genomeLocalUrl"}).outerHTML]);
+ data.push(['Progress', Functions.createElement({type: "input", name: "genomeProgress"}).outerHTML]);
+
+ dataTable.clear().rows.add(data).draw();
+
+ dataTable = $("[name=geneMappingTable]", self.getElement()).DataTable();
+ data = [];
+ var page = dataTable.page();
+
+ for (var i = 0; i < genome.getGeneMappings().length; i++) {
+ var geneMapping = genome.getGeneMappings()[i];
+ var rowData = self.geneMappingToTableRow(geneMapping);
+ data.push(rowData);
+ }
+ //it should be simplified, but I couldn't make it work
+ dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
+
+ return self._fillOrganismSelect(genome);
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.destroy = function () {
+ var self = this;
+ var div = self.getElement();
+
+ var detailsTable = $("[name=detailsTable]", div)[0];
+ if ($.fn.DataTable.isDataTable(detailsTable)) {
+ $(detailsTable).DataTable().destroy();
+ }
+
+ var geneMappingTable = $("[name=geneMappingTable]", div)[0];
+ if ($.fn.DataTable.isDataTable(geneMappingTable)) {
+ $(geneMappingTable).DataTable().destroy();
+ }
+
+ if ($(div).hasClass("ui-dialog-content")) {
+ $(div).dialog("destroy");
+ }
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.open = function () {
+ var self = this;
+ var div = self.getElement();
+ var title;
+ if (self.isNew()) {
+ title = "Download genome";
+ } else {
+ var genome = self.getReferenceGenome();
+ title = genome.getType() + " " + genome.getOrganism().getResource() + " " + genome.getVersion();
+ }
+ if (!$(div).hasClass("ui-dialog-content")) {
+ $(div).dialog({
+ title: title,
+ width: window.innerWidth / 2,
+ height: window.innerHeight / 2
+ });
+ }
+ $(div).dialog("open");
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.close = function () {
+ var self = this;
+ $(self.getElement()).dialog("close");
+};
+
+/**
+ *
+ * @returns {Annotation}
+ */
+EditGenomeDialog.prototype.getSelectedOrganism = function () {
+ var self = this;
+ return new Annotation({
+ resource: ($("[name='genomeOrganismSelect']", self.getElement()).val()).toString(),
+ link: '',
+ id: 0,
+ type: ''
+ })
+};
+
+/**
+ *
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.getSelectedType = function () {
+ var self = this;
+ return ($("[name='genomeTypeSelect']", self.getElement()).val()).toString();
+};
+
+/**
+ *
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.getSelectedVersion = function () {
+ var self = this;
+ return ($("[name='genomeVersionSelect']", self.getElement()).val()).toString();
+};
+
+/**
+ *
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.getSourceUrl = function () {
+ var self = this;
+ return ($("[name='genomeSourceUrl']", self.getElement()).val()).toString();
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.openAddGeneMapping = function () {
+ var self = this;
+ var html = '<form style="z-index:10000"><span>Name: </span><input type="text" name="gene-mapping-name"><br>' +
+ '<span>Url: </span><input type="text" name="gene-mapping-url"><br></form>';
+ $(html).dialog({
+ modal: true,
+ title: "Add gene mapping",
+ close: function () {
+ $(this).dialog('destroy').remove();
+ },
+ buttons: {
+ 'ADD': function () {
+ var dialog = this;
+ var name = $('input[name="gene-mapping-name"]').val().toString();
+ var url = $('input[name="gene-mapping-url"]').val().toString();
+ return self.getServerConnector().addGeneMapping({
+ genomeId: self.getReferenceGenome().getId(),
+ mappingName: name,
+ mappingUrl: url
+ }).then(function () {
+ return self.getServerConnector().getReferenceGenome({genomeId: self.getReferenceGenome().getId()});
+ }).then(function (referenceGenome) {
+ self.setReferenceGenome(referenceGenome);
+ return self.refresh();
+ }).then(function () {
+ $(dialog).dialog('destroy').remove();
+ });
+ },
+ 'Cancel': function () {
+ $(this).dialog('destroy').remove();
+ }
+ }
+ });
+};
+
+module.exports = EditGenomeDialog;
diff --git a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
index dc3e4c6681148590e707f5f9075ed2aab1ce43b1..4e1127816fd5763d179ea7f7d3d66bce21ae5b04 100644
--- a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
@@ -138,22 +138,22 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
var self = this;
var project = self.getProject();
- var result = new Functions.createElement({
+ var result = Functions.createElement({
type: "div"
});
- var table = new Functions.createElement({
+ var table = Functions.createElement({
type: "div",
style: "display:table"
});
result.appendChild(table);
- var projectIdRow = new Functions.createElement({
+ var projectIdRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(projectIdRow);
- projectIdRow.appendChild(new Functions.createElement({
+ projectIdRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "ProjectId"
@@ -204,46 +204,46 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
})
}));
- var nameRow = new Functions.createElement({
+ var nameRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(nameRow);
- nameRow.appendChild(new Functions.createElement({
+ nameRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "Name"
}));
- nameRow.appendChild(new Functions.createElement({
+ nameRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='projectName' value='" + xss(project.getName()) + "'/>",
xss: false
}));
- var versionRow = new Functions.createElement({
+ var versionRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(versionRow);
- versionRow.appendChild(new Functions.createElement({
+ versionRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "Version"
}));
- versionRow.appendChild(new Functions.createElement({
+ versionRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='projectVersion' value='" + xss(project.getVersion()) + "'/>",
xss: false
}));
- var diseaseRow = new Functions.createElement({
+ var diseaseRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(diseaseRow);
- diseaseRow.appendChild(new Functions.createElement({
+ diseaseRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "Disease"
@@ -252,19 +252,19 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
if (project.getDisease() !== undefined) {
disease = xss(project.getDisease().getResource());
}
- diseaseRow.appendChild(new Functions.createElement({
+ diseaseRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='projectDisease' value='" + disease + "'/>",
xss: false
}));
- var organismRow = new Functions.createElement({
+ var organismRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(organismRow);
- organismRow.appendChild(new Functions.createElement({
+ organismRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "Organism"
@@ -273,19 +273,19 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
if (project.getOrganism() !== undefined) {
organism = xss(project.getOrganism().getResource());
}
- organismRow.appendChild(new Functions.createElement({
+ organismRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='projectOrganism' value='" + organism + "'/>",
xss: false
}));
- var emailRow = new Functions.createElement({
+ var emailRow = Functions.createElement({
type: "div",
style: "display:table-row"
});
table.appendChild(emailRow);
- emailRow.appendChild(new Functions.createElement({
+ emailRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "Notify email"
@@ -294,7 +294,7 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
if (project.getNotifyEmail() !== undefined) {
email = xss(project.getNotifyEmail());
}
- emailRow.appendChild(new Functions.createElement({
+ emailRow.appendChild(Functions.createElement({
type: "div",
style: "display:table-cell",
content: "<input name='projectNotifyEmail' value='" + email + "'/>",
@@ -962,7 +962,8 @@ EditProjectDialog.prototype.openAddOverlayDialog = function () {
self._addOverlayDialog = new AddOverlayDialog({
project: self.getProject(),
customMap: null,
- element: document.createElement("div")
+ element: document.createElement("div"),
+ configuration: self.getConfiguration()
});
self._addOverlayDialog.addListener("onAddOverlay", function () {
return self.refreshOverlays();
diff --git a/frontend-js/src/main/js/gui/admin/EditUserDialog.js b/frontend-js/src/main/js/gui/admin/EditUserDialog.js
index 6b631121bd8f81047778829264d5299aaed40cd0..3030c8cab407a8ce2f5c38275cba2f4acd858435 100644
--- a/frontend-js/src/main/js/gui/admin/EditUserDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditUserDialog.js
@@ -145,12 +145,12 @@ EditUserDialog.prototype.createGeneralTabContent = function () {
var self = this;
- var result = new Functions.createElement({
+ var result = Functions.createElement({
type: "div",
style: "margin-top:10px;"
});
- var table = new Functions.createElement({
+ var table = Functions.createElement({
type: "table",
name: "detailsTable",
className: "display",
diff --git a/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js b/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
new file mode 100644
index 0000000000000000000000000000000000000000..7abf854ec353de6035bb7ca3caf24739982c2efd
--- /dev/null
+++ b/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
@@ -0,0 +1,326 @@
+"use strict";
+
+var AbstractAdminPanel = require('./AbstractAdminPanel');
+var EditGenomeDialog = require('./EditGenomeDialog');
+
+var Functions = require('../../Functions');
+var GuiConnector = require('../../GuiConnector');
+var PrivilegeType = require('../../map/data/PrivilegeType');
+var ReferenceGenome = require('../../map/data/ReferenceGenome');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var Promise = require('bluebird');
+
+/**
+ *
+ * @param {Configuration} params.configuration
+ * @param {HTMLElement} params.element
+ *
+ * @constructor
+ */
+function GenomeAdminPanel(params) {
+ params["panelName"] = "genomes";
+ AbstractAdminPanel.call(this, params);
+
+ var self = this;
+ $(self.getElement()).addClass("minerva-genome-tab");
+
+ self._createGui();
+}
+
+GenomeAdminPanel.prototype = Object.create(AbstractAdminPanel.prototype);
+GenomeAdminPanel.prototype.constructor = GenomeAdminPanel;
+
+/**
+ *
+ * @private
+ */
+GenomeAdminPanel.prototype._createGui = function () {
+ var self = this;
+ var genomeDiv = Functions.createElement({
+ type: "div"
+ });
+ self.getElement().appendChild(genomeDiv);
+
+ genomeDiv.appendChild(self._createMenuRow());
+
+ var genomesTable = Functions.createElement({
+ type: "table",
+ name: "genomeTable",
+ className: "display",
+ style: "width:100%"
+ });
+ genomeDiv.appendChild(genomesTable);
+
+ // noinspection JSUnusedGlobalSymbols
+ $(genomesTable).DataTable({
+ columns: [{
+ title: 'Type'
+ }, {
+ title: 'Organism'
+ }, {
+ title: 'Version'
+ }, {
+ title: 'Progress'
+ }, {
+ title: 'Source'
+ }, {
+ title: 'Edit',
+ orderable: false
+ }, {
+ title: 'Remove',
+ orderable: false
+ }],
+ order: [[1, "asc"]]
+ });
+ self.bindUserGuiPreference({
+ jQueryObject: $(genomesTable),
+ event: 'length.dt',
+ preferenceName: 'admin-genome-datatable-length',
+ defaultValue: '10',
+ getter: function () {
+ return $(genomesTable).DataTable().page.len() + '';
+ },
+ setter: function (value) {
+ return $(genomesTable).DataTable().page.len(value).draw();
+ }
+ });
+
+ $(genomesTable).on("click", "[name='removeGenome']", function () {
+ var button = this;
+ return self.askConfirmRemoval({
+ title: "INFO",
+ content: "Do you really want to remove this genome?",
+ input: false
+ }).then(function (param) {
+ if (param.status) {
+ return self.getServerConnector().removeReferenceGenome({genomeId: $(button).attr("data")});
+ }
+ }).catch(GuiConnector.alert);
+ });
+
+ $(genomesTable).on("click", "[name='editGenome']", function () {
+ var button = this;
+ return self.showEditDialog(parseInt($(button).attr("data"))).catch(GuiConnector.alert);
+ });
+
+ genomeDiv.appendChild(self._createMenuRow());
+
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
+GenomeAdminPanel.prototype._createMenuRow = function () {
+ var self = this;
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+
+ var addProjectButton = Functions.createElement({
+ type: "button",
+ name: "addGenome",
+ content: '<span class="ui-icon ui-icon-circle-plus"></span> ADD GENOME',
+ onclick: function () {
+ return self.onAddClicked().catch(GuiConnector.alert);
+ },
+ xss: false
+ });
+ var refreshButton = Functions.createElement({
+ type: "button",
+ name: "refreshGenomes",
+ content: '<span class="ui-icon ui-icon-refresh"></span> REFRESH',
+ onclick: function () {
+ return self.onRefreshClicked().catch(GuiConnector.alert);
+ },
+ xss: false
+ });
+ menuRow.appendChild(addProjectButton);
+ menuRow.appendChild(refreshButton);
+ return menuRow;
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.init = function () {
+ var self = this;
+ return AbstractAdminPanel.prototype.init.call(this).then(function () {
+ return self.getServerConnector().getLoggedUser();
+ }).then(function (user) {
+ if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.MANAGE_GENOMES))) {
+ return self.onRefreshClicked();
+ } else {
+ self.disablePanel("You have no privilege to manage genomes");
+ }
+ });
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.onRefreshClicked = function () {
+ var self = this;
+ return self.getServerConnector().getReferenceGenomes().then(function (referenceGenomes) {
+ return self.setReferenceGenomes(referenceGenomes);
+ });
+};
+
+/**
+ *
+ * @param {ReferenceGenome[]} referenceGenomes
+ *
+ * @returns {Promise}
+ *
+ */
+GenomeAdminPanel.prototype.setReferenceGenomes = function (referenceGenomes) {
+ var self = this;
+
+ return self.getServerConnector().getLoggedUser().then(function (user) {
+
+ var dataTable = $("[name='genomeTable']", self.getElement()).DataTable();
+ var data = [];
+ var page = dataTable.page();
+
+ for (var i = 0; i < referenceGenomes.length; i++) {
+ var genome = referenceGenomes[i];
+ var rowData = self.genomeToTableRow(genome, user);
+ data.push(rowData);
+ }
+ //it should be simplified, but I couldn't make it work
+ dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
+ })
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @param {User} user
+ * @returns {Array}
+ */
+GenomeAdminPanel.prototype.genomeToTableRow = function (genome, user) {
+ var self = this;
+ var row = [];
+
+ row[0] = genome.getType();
+ row[1] = self.getGuiUtils().createAnnotationLink(genome.getOrganism()).outerHTML;
+ row[2] = genome.getVersion();
+ row[3] = genome.getDownloadProgressStatus();
+ row[4] = genome.getSourceUrl();
+
+ var disabled = " disabled ";
+ if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.MANAGE_GENOMES))) {
+ disabled = "";
+ }
+ row[5] = "<button name='editGenome' data='" + genome.getId() + "'" + disabled + "><i class='fa fa-edit' style='font-size:17px'></i></button>";
+ row[6] = "<button name='removeGenome' data='" + genome.getId() + "'" + disabled + "><i class='fa fa-trash-o' style='font-size:17px'></button>";
+ return row;
+};
+
+
+/**
+ *
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.destroy = function () {
+ var self = this;
+ var table = $("[name='genomeTable']", self.getElement())[0];
+ if ($.fn.DataTable.isDataTable(table)) {
+ $(table).DataTable().destroy();
+ }
+ var promises = [];
+ for (var key in self._dialogs) {
+ if (self._dialogs.hasOwnProperty(key)) {
+ promises.push(self._dialogs[key].destroy());
+ }
+ }
+ promises.push(AbstractAdminPanel.prototype.destroy.call(self));
+
+ return Promise.all(promises);
+};
+
+/**
+ *
+ * @param {ReferenceGenome} [genome]
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.getDialog = function (genome) {
+ var self = this;
+ if (self._dialogs === undefined) {
+ self._dialogs = [];
+ }
+ var id = genome.getId();
+ var dialog = self._dialogs[id];
+ if (dialog === undefined) {
+ dialog = new EditGenomeDialog({
+ element: Functions.createElement({
+ type: "div"
+ }),
+ configuration: self.getConfiguration(),
+ referenceGenome: genome,
+ customMap: null,
+ serverConnector: self.getServerConnector()
+ });
+ self._dialogs[id] = dialog;
+ if (id === undefined) {
+ dialog.addListener("onSave", function () {
+ return self.onRefreshClicked();
+ });
+ }
+ return dialog.init().then(function () {
+ return dialog;
+ });
+ } else {
+ return Promise.resolve(dialog);
+ }
+};
+
+/**
+ *
+ * @param {number} id
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.showEditDialog = function (id) {
+ var self = this;
+ GuiConnector.showProcessing();
+ return self.getServerConnector().getReferenceGenome({genomeId: id}).then(function (referenceGenome) {
+ if (referenceGenome === null) {
+ referenceGenome = new ReferenceGenome();
+ }
+ return self.getDialog(referenceGenome);
+ }).then(function (dialog) {
+ dialog.open();
+ GuiConnector.hideProcessing();
+ }).catch(function (error) {
+ GuiConnector.hideProcessing();
+ return Promise.reject(error);
+ });
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.onAddClicked = function () {
+ var self = this;
+ GuiConnector.showProcessing();
+ var referenceGenome = new ReferenceGenome();
+ return self.getDialog(referenceGenome).then(function (dialog) {
+ dialog.open();
+ GuiConnector.hideProcessing();
+ }).catch(function (error) {
+ GuiConnector.hideProcessing();
+ return Promise.reject(error);
+ });
+};
+
+
+module.exports = GenomeAdminPanel;
diff --git a/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js b/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
index 3bef291f7e7061ae3c636eeaf0018d63937e08bf..1bbc720da8c241f3792adc69edae5d5705e3f409 100644
--- a/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
@@ -6,7 +6,6 @@ var PrivilegeType = require('../../map/data/PrivilegeType');
var AbstractAdminPanel = require('./AbstractAdminPanel');
var EditUserDialog = require('./EditUserDialog');
-var SecurityError = require('../../SecurityError');
var User = require("../../map/data/User");
@@ -15,6 +14,13 @@ var GuiConnector = require('../../GuiConnector');
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
+/**
+ *
+ * @param {Object} params
+ *
+ * @constructor
+ * @extends AbstractAdminPanel
+ */
function UsersAdminPanel(params) {
var self = this;
AbstractAdminPanel.call(self, params);
@@ -25,6 +31,10 @@ function UsersAdminPanel(params) {
UsersAdminPanel.prototype = Object.create(AbstractAdminPanel.prototype);
UsersAdminPanel.prototype.constructor = UsersAdminPanel;
+/**
+ *
+ * @private
+ */
UsersAdminPanel.prototype._createGui = function () {
var self = this;
var usersDiv = Functions.createElement({
@@ -44,6 +54,11 @@ UsersAdminPanel.prototype._createGui = function () {
};
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
UsersAdminPanel.prototype._createMenuRow = function () {
var self = this;
var menuRow = Functions.createElement({
@@ -75,6 +90,11 @@ UsersAdminPanel.prototype._createMenuRow = function () {
return menuRow;
};
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
UsersAdminPanel.prototype._createUsersTableRow = function () {
var self = this;
var projectsRow = Functions.createElement({
@@ -90,7 +110,7 @@ UsersAdminPanel.prototype._createUsersTableRow = function () {
});
projectsRow.appendChild(usersTable);
- // noinspection JSUnusedGlobalSymbols
+ // noinspection JSCheckFunctionSignatures
$(usersTable).DataTable({
fnRowCallback: function (nRow, aData) {
nRow.setAttribute('id', aData[0]);
@@ -103,6 +123,8 @@ UsersAdminPanel.prototype._createUsersTableRow = function () {
title: 'Surname'
}, {
title: 'Email'
+ }, {
+ title: 'Authentication'
}, {
title: 'Edit'
}, {
@@ -136,6 +158,24 @@ UsersAdminPanel.prototype._createUsersTableRow = function () {
}).catch(GuiConnector.alert);
});
+ $(usersTable).on("click", "[name='ldap-auth']", function () {
+ var field = this;
+ var login = $(this).attr('data');
+ GuiConnector.showProcessing();
+ return self.getServerConnector().getUser(login).then(function (user) {
+ var newIsConnected = $('input:checked', field).val() === "LDAP";
+ var isConnected = user.isConnectedToLdap();
+ if (isConnected !== newIsConnected) {
+ user.setConnectedToLdap(newIsConnected);
+ return self.getServerConnector().updateUser(user);
+ }
+ }).catch(function (error) {
+ GuiConnector.alert(error);
+ }).finally(function(){
+ GuiConnector.hideProcessing();
+ });
+ });
+
$(usersTable).on("click", "[name='showEditDialog']", function () {
var button = this;
return self.showEditDialog($(button).attr("data")).then(null, GuiConnector.alert);
@@ -144,10 +184,15 @@ UsersAdminPanel.prototype._createUsersTableRow = function () {
return projectsRow;
};
+/**
+ *
+ * @param {String} login
+ * @returns {Promise}
+ */
UsersAdminPanel.prototype.showEditDialog = function (login) {
var self = this;
GuiConnector.showProcessing();
- return ServerConnector.getUser(login).then(function (user) {
+ return self.getServerConnector().getUser(login).then(function (user) {
return self.getDialog(user);
}).then(function (dialog) {
dialog.open();
@@ -158,6 +203,11 @@ UsersAdminPanel.prototype.showEditDialog = function (login) {
});
};
+/**
+ *
+ * @param {User} user
+ * @returns {Promise}
+ */
UsersAdminPanel.prototype.getDialog = function (user) {
var self = this;
if (self._dialogs === undefined) {
@@ -186,14 +236,18 @@ UsersAdminPanel.prototype.getDialog = function (user) {
}
};
+/**
+ *
+ * @returns {Promise}
+ */
UsersAdminPanel.prototype.init = function () {
var self = this;
return AbstractAdminPanel.prototype.init.call(this).then(function () {
- return ServerConnector.getLoggedUser();
+ return self.getServerConnector().getLoggedUser();
}).then(function (user) {
var privilege = self.getConfiguration().getPrivilegeType(PrivilegeType.USER_MANAGEMENT);
if (user.hasPrivilege(privilege)) {
- return ServerConnector.getUsers().then(function (users) {
+ return self.getServerConnector().getUsers().then(function (users) {
return self.setUsers(users);
});
} else {
@@ -202,6 +256,10 @@ UsersAdminPanel.prototype.init = function () {
});
};
+/**
+ *
+ * @param {User[]} users
+ */
UsersAdminPanel.prototype.setUsers = function (users) {
var self = this;
var dataTable = $($("[name='usersTable']", self.getElement())[0]).DataTable();
@@ -218,6 +276,11 @@ UsersAdminPanel.prototype.setUsers = function (users) {
};
+/**
+ *
+ * @param {User} user
+ * @param {Array} dataTableRow
+ */
UsersAdminPanel.prototype.addUpdateListener = function (user, dataTableRow) {
var self = this;
@@ -241,7 +304,12 @@ UsersAdminPanel.prototype.addUpdateListener = function (user, dataTableRow) {
user.addListener("onreload", listener);
};
-
+/**
+ *
+ * @param {User} user
+ * @param {Array} [row]
+ * @returns {Array}
+ */
UsersAdminPanel.prototype.userToTableRow = function (user, row) {
if (row === undefined) {
row = [];
@@ -251,20 +319,39 @@ UsersAdminPanel.prototype.userToTableRow = function (user, row) {
row[1] = user.getName();
row[2] = user.getSurname();
row[3] = user.getEmail();
- row[4] = "<button name='showEditDialog' data='" + user.getLogin() + "'><i class='fa fa-edit' style='font-size:17px'></i></button>";
- row[5] = "<button name='removeUser' data='" + user.getLogin() + "'><i class='fa fa-trash-o' style='font-size:17px'></i></button>";
+ var ldapFieldId = 'ldap-auth-' + user.getLogin();
+ if (user.isConnectedToLdap()) {
+ row[4] = "<fieldset name='ldap-auth' id='" + ldapFieldId + "' data='" + user.getLogin() + "'> <input type='radio' name='" + ldapFieldId + "' value='LOCAL'> LOCAL <input type='radio' name='" + ldapFieldId + "' checked value='LDAP'> LDAP </fieldset>";
+ } else {
+ if (user.isLdapAccountAvailable()) {
+ row[4] = "<fieldset name='ldap-auth' id='" + ldapFieldId + "' data='" + user.getLogin() + "'> <input type='radio' name='" + ldapFieldId + "' value='LOCAL' checked> LOCAL <input type='radio' name='" + ldapFieldId + "' value='LDAP'> LDAP </fieldset>";
+ // row[4] = "LOCAL <button name='connectLdap' data='" + user.getLogin() + "'>CONNECT LDAP</button>"
+ } else {
+ row[4] = "<fieldset name='ldap-auth' id='" + ldapFieldId + "' data='" + user.getLogin() + "'> <input type='radio' name='" + ldapFieldId + "' value='LOCAL' checked> LOCAL</fieldset>";
+ }
+ }
+
+ row[5] = "<button name='showEditDialog' data='" + user.getLogin() + "'><i class='fa fa-edit' style='font-size:17px'></i></button>";
+ row[6] = "<button name='removeUser' data='" + user.getLogin() + "'><i class='fa fa-trash-o' style='font-size:17px'></i></button>";
return row;
};
+/**
+ *
+ * @returns {Promise}
+ */
UsersAdminPanel.prototype.onRefreshClicked = function () {
var self = this;
- return ServerConnector.getUsers(true).then(function (users) {
+ return self.getServerConnector().getUsers(true).then(function (users) {
return self.setUsers(users);
});
};
+/**
+ *
+ */
UsersAdminPanel.prototype.destroy = function () {
var self = this;
var table = $("[name='usersTable']", self.getElement())[0];
@@ -277,9 +364,12 @@ UsersAdminPanel.prototype.destroy = function () {
self._dialogs[key].destroy();
}
}
-
};
+/**
+ *
+ * @returns {Promise}
+ */
UsersAdminPanel.prototype.onAddClicked = function () {
var self = this;
var user = new User({});
@@ -293,10 +383,15 @@ UsersAdminPanel.prototype.onAddClicked = function () {
});
};
+/**
+ *
+ * @param {string} login
+ * @returns {Promise}
+ */
UsersAdminPanel.prototype.removeUser = function (login) {
var self = this;
GuiConnector.showProcessing();
- return ServerConnector.removeUser(login).then(function () {
+ return self.getServerConnector().removeUser(login).then(function () {
return self.onRefreshClicked();
}).then(function () {
GuiConnector.hideProcessing();
diff --git a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
index 73fa48f126b94db5707701045588809b343fc77f..8d5c6d84f7e3159aeea25af7454d251187e11601 100644
--- a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
@@ -208,12 +208,12 @@ AbstractPanel.prototype.refreshSearchResults = function () {
promises.push(searchDb.getElementsByQuery(queries[i]));
}
return Promise.all(promises).then(function (results) {
- for (var i = 0; i < queries.length; i++) {
- self.addResultTab(queries[i], results[i]);
- }
+ return Promise.each(queries, function(query, index){
+ return self.addResultTab(query, results[index]);
+ });
+ }).then(function(){
self.onresize();
});
-
};
AbstractPanel.prototype.getAutocomplete = function () {
@@ -225,6 +225,7 @@ AbstractPanel.prototype.searchByQuery = function () {
};
AbstractPanel.prototype.addResultTab = function (query, elements) {
+ var self = this;
var name = JSON.parse(query).query;
var tabId = this.getPanelName() + "Tab_" + this._tabIdCount;
@@ -277,13 +278,29 @@ AbstractPanel.prototype.addResultTab = function (query, elements) {
var tableBody = document.createElement("tbody");
tableDiv.appendChild(tableBody);
- for (var i = 0; i < elements.length; i++) {
- var element = elements[i].element;
- var icon = elements[i].icon;
- tableBody.appendChild(this.createTableElement(element, icon));
- }
+ return Promise.each(elements, function (entry) {
+ var element = entry.element;
+ var icon = entry.icon;
+ return self.createTableElement(element, icon).then(function (div) {
+ return tableBody.appendChild(div);
+ });
+ });
+};
+
+/**
+ *
+ * @returns {Promise<HTMLTableRowElement>}
+ */
+AbstractPanel.prototype.createTableElement = function () {
+ throw new Error("Not implemented");
};
+/**
+ *
+ * @param {Target} target
+ * @param {string} icon
+ * @returns {Promise<HTMLTableRowElement>}
+ */
AbstractPanel.prototype.createTargetRow = function (target, icon) {
var self = this;
var guiUtils = self.getGuiUtils();
@@ -349,7 +366,7 @@ AbstractPanel.prototype.createTargetRow = function (target, icon) {
descColumn.appendChild(button);
}
}
- return result;
+ return Promise.resolve(result);
};
AbstractPanel.prototype.computeAutocompleteDictionary = function (queries) {
diff --git a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
index 931d88743cb4d3bbbc23cc1ed577d39d26de896d..e1b3d6fa419a879bf18c388d3bebeafea431b6ae 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
@@ -48,6 +48,12 @@ GenericSearchPanel.prototype.createSearchGui = function () {
searchDiv.appendChild(perfectMatchLabel);
};
+/**
+ *
+ * @param {SearchBioEntityGroup|BioEntity} element
+ * @param {string} icon
+ * @returns {Promise<HTMLTableRowElement>}
+ */
GenericSearchPanel.prototype.createTableElement = function (element, icon) {
if (element instanceof Alias) {
return this.createAliasElement(element, icon);
@@ -64,6 +70,11 @@ GenericSearchPanel.prototype.createPreamble = function () {
return document.createElement("div");
};
+/**
+ *
+ * @param {Reaction} reaction
+ * @returns {Promise<HTMLTableRowElement>}
+ */
GenericSearchPanel.prototype.createReactionElement = function (reaction) {
var self = this;
var guiUtils = self.getGuiUtils();
@@ -71,15 +82,19 @@ GenericSearchPanel.prototype.createReactionElement = function (reaction) {
var td = document.createElement("td");
result.appendChild(td);
- var div = guiUtils.createReactionElement({
- reaction: reaction
- });
-
- div.appendChild(guiUtils.createSeparator());
- td.appendChild(div);
- return result;
+ return guiUtils.createReactionElement({reaction: reaction}).then((function (div) {
+ div.appendChild(guiUtils.createSeparator());
+ td.appendChild(div);
+ return result;
+ }));
};
+/**
+ *
+ * @param {Alias} alias
+ * @param {string} icon
+ * @returns {Promise<HTMLTableRowElement>}
+ */
GenericSearchPanel.prototype.createAliasElement = function (alias, icon) {
var self = this;
var guiUtils = self.getGuiUtils();
@@ -87,30 +102,37 @@ GenericSearchPanel.prototype.createAliasElement = function (alias, icon) {
var result = document.createElement("tr");
var td = document.createElement("td");
result.appendChild(td);
- var div = guiUtils.createAliasElement({
+ return guiUtils.createAliasElement({
alias: alias,
icon: icon
- });
+ }).then(function (div) {
+ div.appendChild(guiUtils.createSeparator());
+ td.appendChild(div);
- div.appendChild(guiUtils.createSeparator());
- td.appendChild(div);
+ return result;
+ });
- return result;
};
-GenericSearchPanel.prototype.createSearchBioEntityGroupElement = function (group, icon) {
+/**
+ *
+ * @param {SearchBioEntityGroup} group
+ * @returns {Promise<HTMLTableRowElement>}
+ */
+GenericSearchPanel.prototype.createSearchBioEntityGroupElement = function (group) {
var self = this;
var guiUtils = self.getGuiUtils();
var result = document.createElement("tr");
var td = document.createElement("td");
result.appendChild(td);
- var div = guiUtils.createSearchBioEntityGroupElement(group);
+ return guiUtils.createSearchBioEntityGroupElement(group).then(function (div) {
+ div.appendChild(guiUtils.createSeparator());
+ td.appendChild(div);
- div.appendChild(guiUtils.createSeparator());
- td.appendChild(div);
+ return result;
+ });
- return result;
};
GenericSearchPanel.prototype.searchByQuery = function () {
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index 69fdb3189da3886e905e2d97aa212d47a9481715..37c7cb0f4c0e25753841dfdb4462072ee0cd6b74 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -4,6 +4,9 @@
var Alias = require('../../map/data/Alias');
var ConfigurationType = require('../../ConfigurationType');
+var IdentifiedElement = require('../../map/data/IdentifiedElement');
+var SearchBioEntityGroup = require('../../map/data/SearchBioEntityGroup');
+
var GuiConnector = require('../../GuiConnector');
var AbstractGuiElement = require('../AbstractGuiElement');
@@ -12,8 +15,15 @@ var Functions = require('../../Functions');
var logger = require('../../logger');
var xss = require('xss');
+var Promise = require('bluebird');
+
var tabIdCounter = 0;
+/**
+ *
+ * @param {Configuration} configuration
+ * @constructor
+ */
function GuiUtils(configuration) {
var self = this;
self.setConfiguration(configuration);
@@ -22,14 +32,27 @@ function GuiUtils(configuration) {
GuiUtils.prototype = Object.create(AbstractGuiElement.prototype);
GuiUtils.prototype.constructor = GuiUtils;
+/**
+ *
+ * @param {Configuration} configuration
+ */
GuiUtils.prototype.setConfiguration = function (configuration) {
this._configuration = configuration;
};
+/**
+ *
+ * @returns {Configuration}
+ */
GuiUtils.prototype.getConfiguration = function () {
return this._configuration;
};
+/**
+ *
+ * @param {string} value
+ * @returns {HTMLSpanElement}
+ */
GuiUtils.prototype.createLabel = function (value) {
var result = document.createElement("span");
result.innerHTML = value;
@@ -37,56 +60,117 @@ GuiUtils.prototype.createLabel = function (value) {
return result;
};
+/**
+ *
+ * @param {Object} modification
+ * @param {string} [modification.name]
+ * @param {string} modification.type
+ * @param {string} [modification.state]
+ *
+ * @returns {HTMLElement| null}
+ */
+GuiUtils.prototype.createModificationRow = function (modification) {
+ var self = this;
+ var row = null;
+ var name = modification.name;
+ var desc = undefined;
+ if (modification.state !== undefined && modification.state !== null) {
+ var modificationStateType = self.getConfiguration().getModificationStateTypeByName(modification.state);
+ var state = modificationStateType.getCommonName();
+
+ if (name !== null && name !== undefined && name !== "") {
+ desc = state + " at position " + name + ", ";
+ } else {
+ desc = state + ",";
+ }
+ } else if (name !== null && name !== undefined && name !== "" &&
+ (modification.type === "BINDING_REGION" ||
+ modification.type === "CODING_REGION" ||
+ modification.type === "PROTEIN_BINDING_DOMAIN" ||
+ modification.type === "TRANSCRIPTION_SITE_LEFT" ||
+ modification.type === "TRANSCRIPTION_SITE_RIGHT" ||
+ modification.type === "REGULATORY_REGION"
+ )) {
+ desc = name + ",";
+ }
+
+ if (desc !== undefined) {
+ row = Functions.createElement({
+ type: "li"
+ });
+ row.appendChild(self.createLabelText(desc));
+ }
+ return row;
+};
+
+/**
+ *
+ * @param {string} label
+ * @param {Object[]} value
+ * @returns {HTMLDivElement}
+ */
GuiUtils.prototype.createPostTranslationalModifications = function (label, value) {
var result = document.createElement("div");
+ var count = 0;
if (value !== undefined && value.length > 0) {
var self = this;
- result.appendChild(self.createLabel(label));
+ var userFriendlyLabel = label + ": ";
+ if (label === "RESIDUE") {
+ userFriendlyLabel = "Posttranslational modifications: "
+ } else if (label === "BINDING_REGION") {
+ userFriendlyLabel = "Binding regions: "
+ } else if (label === "CODING_REGION") {
+ userFriendlyLabel = "Coding regions: "
+ } else if (label === "PROTEIN_BINDING_DOMAIN") {
+ userFriendlyLabel = "Protein binding domains: "
+ } else if (label === "TRANSCRIPTION_SITE_LEFT") {
+ userFriendlyLabel = "Transcription sites (left): "
+ } else if (label === "TRANSCRIPTION_SITE_RIGHT") {
+ userFriendlyLabel = "Transcription sites (right): "
+ } else if (label === "TRANSCRIPTION_SITE") {
+ userFriendlyLabel = "Transcription sites: "
+ } else if (label === "MODIFICATION_SITE") {
+ userFriendlyLabel = "Modification sites: "
+ }
+ result.appendChild(self.createLabel(userFriendlyLabel));
result.appendChild(self.createNewLine());
var list = Functions.createElement({
type: "ul"
});
for (var i = 0; i < value.length; i++) {
- var name = value[i].name;
- var modificationStateType = self.getConfiguration().getModificationStateTypeByName(value[i].state);
- var state = modificationStateType.getCommonName();
- var desc;
- if (name !== null && name !== undefined && name !== "") {
- desc = state + " at position " + name + ", ";
- } else {
- desc = state + ",";
+ var modification = value[i];
+ var row = self.createModificationRow(modification, self);
+ if (row !== null) {
+ list.appendChild(row);
+ count++;
}
- var row = Functions.createElement({
- type: "li"
- });
- row.appendChild(self.createLabelText(desc));
- list.appendChild(row);
}
result.appendChild(list);
}
- return result;
-};
-
-GuiUtils.prototype.createCandidates = function (label, value) {
- var result = document.createElement("div");
- if (value !== undefined) {
- throw new Error("Not implemented");
+ if (count > 0) {
+ return result;
+ } else {
+ return document.createElement("div");
}
- return result;
};
-GuiUtils.prototype.createChebiTree = function (label, value) {
- var result = document.createElement("div");
- if (value !== undefined) {
- throw new Error("Not implemented");
- }
- return result;
-};
+/**
+ *
+ * @returns {HTMLHRElement}
+ */
GuiUtils.prototype.createSeparator = function () {
return document.createElement("hr");
};
+/**
+ *
+ * @param {number} [count]
+ * @returns {HTMLParagraphElement}
+ */
GuiUtils.prototype.createNewLine = function (count) {
+ if (count === undefined) {
+ count = 0;
+ }
var result = document.createElement("p");
if (count > 0) {
result.style.height = ((count - 1) * 10) + "px";
@@ -94,14 +178,16 @@ GuiUtils.prototype.createNewLine = function (count) {
return result;
};
+/**
+ *
+ * @param {string} [url]
+ * @param {string} name
+ * @returns {HTMLElement}
+ */
GuiUtils.prototype.createLink = function (url, name) {
if (url === null || url === undefined) {
logger.warn("URL not defined for: \"" + name + "\" link");
- return Functions.createElement(
- {
- type: "span",
- content: name
- });
+ return Functions.createElement({type: "span", content: name});
}
var link = document.createElement("a");
link.href = url;
@@ -111,6 +197,12 @@ GuiUtils.prototype.createLink = function (url, name) {
return link;
};
+/**
+ *
+ * @param {Annotation} annotation
+ * @param {boolean} [showType=false]
+ * @returns {HTMLElement}
+ */
GuiUtils.prototype.createAnnotationLink = function (annotation, showType) {
var self = this;
var name, type, hint;
@@ -148,6 +240,15 @@ GuiUtils.prototype.createAnnotationLink = function (annotation, showType) {
}
};
+/**
+ *
+ * @param {string} label
+ * @param {Annotation[]} [value]
+ * @param {Object} [options]
+ * @param {boolean} [options.inline]
+ *
+ * @returns {HTMLDivElement}
+ */
GuiUtils.prototype.createAnnotations = function (label, value, options) {
var self = this;
@@ -170,9 +271,16 @@ GuiUtils.prototype.createAnnotations = function (label, value, options) {
return result;
};
+/**
+ *
+ * @param {boolean} inline
+ * @param {string} annotatorClass
+ * @param {Object.<string, Annotator>} annotatorsClassMapping
+ * @param {boolean} groupAnnotations
+ * @returns {HTMLElement}
+ */
function createGroupContainer(inline, annotatorClass, annotatorsClassMapping, groupAnnotations) {
var automaticallyAnnotated = !(annotatorClass === undefined || annotatorClass === "undefined" || annotatorClass === null || annotatorClass === "");
-// var desc = grouppedAnnotations.keys()[i];
var groupContainer = (inline ? document.createElement("span") : document.createElement("div"));
var descContainer = (inline ? document.createElement("span") : document.createElement("div"));
@@ -332,6 +440,11 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
return result;
};
+/**
+ *
+ * @param {string} [value]
+ * @returns {HTMLSpanElement}
+ */
GuiUtils.prototype.createLabelText = function (value) {
var result = document.createElement("span");
if (value !== undefined) {
@@ -340,6 +453,11 @@ GuiUtils.prototype.createLabelText = function (value) {
return result;
};
+/**
+ *
+ * @param {string} [value]
+ * @returns {HTMLInputElement}
+ */
GuiUtils.prototype.createInputText = function (value) {
var result = document.createElement("input");
result.setAttribute('type', 'text');
@@ -350,6 +468,11 @@ GuiUtils.prototype.createInputText = function (value) {
return result;
};
+/**
+ *
+ * @param {string} [value]
+ * @returns {HTMLTextAreaElement}
+ */
GuiUtils.prototype.createTextArea = function (value) {
var result = document.createElement("textarea");
@@ -360,16 +483,12 @@ GuiUtils.prototype.createTextArea = function (value) {
return result;
};
-GuiUtils.prototype.createCheckbox = function (value) {
- var result = document.createElement("input");
- result.type = "checkbox";
-
- if (value) {
- result.checked = true;
- }
- return result;
-};
-
+/**
+ *
+ * @param {string} label
+ * @param {string|number} [value]
+ * @returns {HTMLDivElement}
+ */
GuiUtils.prototype.createParamLine = function (label, value) {
var result = document.createElement("div");
if (value !== undefined && value !== null && value !== "") {
@@ -380,6 +499,12 @@ GuiUtils.prototype.createParamLine = function (label, value) {
return result;
};
+/**
+ *
+ * @param {string} [icon]
+ * @param {function} [onclickFunction]
+ * @returns {HTMLDivElement}
+ */
GuiUtils.prototype.createIcon = function (icon, onclickFunction) {
var result = document.createElement("div");
if (icon !== undefined && icon !== null) {
@@ -395,6 +520,13 @@ GuiUtils.prototype.createIcon = function (icon, onclickFunction) {
return result;
};
+/**
+ *
+ * @param {string} label
+ * @param {string[]} [value]
+ *
+ * @returns {HTMLDivElement}
+ */
GuiUtils.prototype.createArrayParamLine = function (label, value) {
var result = document.createElement("div");
if (value !== undefined && value.length > 0) {
@@ -405,6 +537,12 @@ GuiUtils.prototype.createArrayParamLine = function (label, value) {
return result;
};
+/**
+ *
+ * @param {string} label
+ * @param {number} [modelId]
+ * @returns {HTMLDivElement}
+ */
GuiUtils.prototype.createSubMapLink = function (label, modelId) {
var self = this;
var result = document.createElement("div");
@@ -422,6 +560,11 @@ GuiUtils.prototype.createSubMapLink = function (label, modelId) {
return result;
};
+/**
+ *
+ * @param {Array<string|HTMLElement>} elements
+ * @returns {HTMLElement}
+ */
GuiUtils.prototype.createTableRow = function (elements) {
var row = Functions.createElement({
type: "div",
@@ -443,6 +586,14 @@ GuiUtils.prototype.createTableRow = function (elements) {
return row;
};
+/**
+ *
+ * @param {Reaction|SearchBioEntityGroup} params.reaction
+ * @param {string} [params.icon]
+ * @param {boolean} [params.showTitle]
+ *
+ * @returns {Promise<HTMLDivElement>}
+ */
GuiUtils.prototype.createReactionElement = function (params) {
var reaction = params.reaction;
var showTitle = ((params.showTitle === undefined) || params.showTitle);
@@ -477,9 +628,44 @@ GuiUtils.prototype.createReactionElement = function (params) {
div.appendChild(self.createArrayParamLine("Synonyms: ", reaction.getSynonyms()));
div.appendChild(self.createParamLine("Description: ", reaction.getDescription()));
div.appendChild(self.createAnnotations("Annotations: ", reaction.getReferences()));
- return div;
+ return Promise.resolve(div);
};
+/**
+ *
+ * @param {Object[]} modifications
+ *
+ * @returns {HTMLDivElement}
+ */
+GuiUtils.prototype.createModifications = function (modifications) {
+ var self = this;
+ var result = document.createElement("div");
+ var modificationsByType = [];
+ if (modifications !== undefined) {
+ for (var i = 0; i < modifications.length; i++) {
+ var modification = modifications[i];
+ if (modificationsByType[modification.type] === undefined) {
+ modificationsByType[modification.type] = [];
+ }
+ modificationsByType[modification.type].push(modification);
+ }
+ for (var key in modificationsByType) {
+ if (modificationsByType.hasOwnProperty(key)) {
+ result.appendChild(self.createPostTranslationalModifications(key, modificationsByType[key]));
+ }
+ }
+ }
+ return result;
+};
+
+/**
+ *
+ * @param {Alias|SearchBioEntityGroup} params.alias
+ * @param {string} [params.icon]
+ * @param {boolean} [params.showTitle]
+ *
+ * @returns {Promise<HTMLDivElement>}
+ */
GuiUtils.prototype.createAliasElement = function (params) {
var alias = params.alias;
var icon = params.icon;
@@ -505,27 +691,49 @@ GuiUtils.prototype.createAliasElement = function (params) {
div.appendChild(self.createSubMapLink("In submap: ", alias.getModelId()));
}
}
- if (alias.getLinkedSubmodelId() !== null && alias.getLinkedSubmodelId() !== undefined) {
+ if (alias.getLinkedSubmodelId() !== undefined) {
div.appendChild(self.createSubMapLink("Associated submap: ", alias.getLinkedSubmodelId()));
}
+ if (alias instanceof SearchBioEntityGroup && alias.getBioEntities().length > 1) {
+ div.appendChild(self.createLabelText("Group of " + alias.getBioEntities().length + " elements."));
+ }
if (showTitle) {
div.appendChild(self.createNewLine(3));
}
- div.appendChild(self.createParamLine("Full name: ", alias.getFullName()));
- div.appendChild(self.createParamLine("Symbol: ", alias.getSymbol()));
- div.appendChild(self.createParamLine("Abbreviation: ", alias.getAbbreviation()));
- div.appendChild(self.createParamLine("Formula: ", alias.getFormula()));
- div.appendChild(self.createArrayParamLine("Former symbols: ", alias.getFormerSymbols()));
- div.appendChild(self.createPostTranslationalModifications("PostTranslational modifications: ", alias
- .getOther('modifications')));
- div.appendChild(self.createParamLine("Charge: ", alias.getCharge()));
- div.appendChild(self.createArrayParamLine("Synonyms: ", alias.getSynonyms()));
- div.appendChild(self.createLabelText(alias.getDescription()));
- // div.appendChild(self.createChebiTree("Chebi ontology: ", alias.getOther('chebiTree')));
- div.appendChild(self.createAnnotations("Annotations: ", alias.getReferences()));
- return div;
+ var promise = Promise.resolve();
+ if (alias.getCompartmentId() !== undefined) {
+ promise = self.getMap().getModel().getByIdentifiedElement(new IdentifiedElement({
+ type: "ALIAS",
+ id: alias.getCompartmentId(),
+ modelId: alias.getModelId()
+ }), true).then(function (compartment) {
+ div.appendChild(self.createParamLine("Compartment: ", compartment.getName()));
+ })
+ }
+
+ return promise.then(function () {
+
+ div.appendChild(self.createParamLine("Full name: ", alias.getFullName()));
+ div.appendChild(self.createParamLine("Symbol: ", alias.getSymbol()));
+ div.appendChild(self.createParamLine("Abbreviation: ", alias.getAbbreviation()));
+ div.appendChild(self.createParamLine("Formula: ", alias.getFormula()));
+ div.appendChild(self.createArrayParamLine("Former symbols: ", alias.getFormerSymbols()));
+ div.appendChild(self.createModifications(alias.getOther('modifications')));
+ div.appendChild(self.createParamLine("Charge: ", alias.getCharge()));
+ div.appendChild(self.createArrayParamLine("Synonyms: ", alias.getSynonyms()));
+ div.appendChild(self.createLabelText(alias.getDescription()));
+ div.appendChild(self.createAnnotations("Annotations: ", alias.getReferences()));
+
+ return div;
+ })
};
+
+/**
+ *
+ * @param {SearchBioEntityGroup} group
+ * @returns {Promise<HTMLDivElement>}
+ */
GuiUtils.prototype.createSearchBioEntityGroupElement = function (group) {
if (group.getBioEntities()[0] instanceof Alias) {
return this.createAliasElement({alias: group, icon: group.getIcon()});
@@ -534,6 +742,10 @@ GuiUtils.prototype.createSearchBioEntityGroupElement = function (group) {
}
};
+/**
+ *
+ * @returns {HTMLAnchorElement}
+ */
GuiUtils.prototype.createLogoutLink = function () {
var logoutLink = document.createElement("a");
logoutLink.href = "#";
@@ -545,6 +757,14 @@ GuiUtils.prototype.createLogoutLink = function () {
return logoutLink;
};
+/**
+ *
+ * @param {string} params.name
+ * @param {string} params.id
+ * @param {HTMLElement} params.navigationBar
+ *
+ * @returns {HTMLLIElement}
+ */
GuiUtils.prototype.createTabMenuObject = function (params) {
var name = params.name;
var id = params.id;
@@ -573,6 +793,13 @@ GuiUtils.prototype.createTabMenuObject = function (params) {
return navLi;
};
+/**
+ *
+ * @param {string} params.id
+ * @param {HTMLElement} params.navigationObject
+ *
+ * @returns {HTMLDivElement}
+ */
GuiUtils.prototype.createTabContentObject = function (params) {
var navigationObject = params.navigationObject;
var tabId = params.id;
@@ -589,6 +816,13 @@ GuiUtils.prototype.createTabContentObject = function (params) {
return result;
};
+/**
+ *
+ * @param {HTMLElement} [params.element]
+ * @param {string} params.id
+ *
+ * @returns {{element: HTMLElement, menu: HTMLElement, content: HTMLElement, tabId: *}}
+ */
GuiUtils.prototype.createTabDiv = function (params) {
var tabDiv = Functions.createElement({
type: "div",
@@ -608,7 +842,7 @@ GuiUtils.prototype.createTabDiv = function (params) {
});
tabDiv.appendChild(tabContentDiv);
- if (params !== undefined && params.element !== undefined) {
+ if (params.element !== undefined) {
params.element.appendChild(tabDiv);
}
@@ -621,7 +855,6 @@ GuiUtils.prototype.createTabDiv = function (params) {
};
GuiUtils.prototype.createTab = function (params) {
- var self = this;
var tabData = params.tabData;
var tabId = tabData.tabId + "_tab_" + tabIdCounter;
@@ -669,6 +902,12 @@ GuiUtils.prototype.createTab = function (params) {
}
};
+/**
+ *
+ * @param {string} toolTip
+ * @param {boolean} [useXss=false]
+ * @returns {HTMLElement}
+ */
GuiUtils.prototype.createHelpButton = function (toolTip, useXss) {
var helpContent;
if (useXss) {
diff --git a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
index 2b19d922e08d63f12ab54a814bee478ed133f4f7..7a6942a1f5717649a9d6315bc0cac209373ca2bc 100644
--- a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
@@ -20,6 +20,19 @@ var SubmapPanel = require('./SubmapPanel');
var Functions = require('../../Functions');
var logger = require('../../logger');
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
function LeftPanel(params) {
AbstractGuiElement.call(this, params);
var self = this;
@@ -174,9 +187,13 @@ LeftPanel.prototype.showElementDetails = function (element) {
if (element !== undefined && openTabName !== undefined && (openTabName.indexOf("SEARCH") === -1 || searchTabName !== "GENERIC")) {
var model = self.getMap().getSubmapById(element.getModelId()).getModel();
- return model.getByIdentifiedElement(element, true).then(function (bioEntity) {
+ var bioEntity;
+ return model.getByIdentifiedElement(element, true).then(function (result) {
+ bioEntity=result;
+ return self.prepareElementDetailsContent(bioEntity);
+ }).then(function(elementDetailsDiv){
div.innerHTML = "";
- div.appendChild(self.prepareElementDetailsContent(bioEntity));
+ div.appendChild(elementDetailsDiv);
$(div).dialog("open");
$(div).dialog("option", "title", self.getElementTitle(bioEntity));
$(div).scrollTop(0);
@@ -187,6 +204,12 @@ LeftPanel.prototype.showElementDetails = function (element) {
}
};
+/**
+ *
+ * @param {BioEntity} bioEntity
+ *
+ * @returns {Promise<HTMLDivElement>}
+ */
LeftPanel.prototype.prepareElementDetailsContent = function (bioEntity) {
var guiUtils = this.getGuiUtils();
if (bioEntity instanceof Reaction) {
@@ -200,14 +223,18 @@ LeftPanel.prototype.prepareElementDetailsContent = function (bioEntity) {
showTitle: false
});
} else if (bioEntity instanceof PointData) {
- return Functions.createElement({
+ return Promise.resolve(Functions.createElement({
type: "div"
- });
+ }));
} else {
throw new Error("Unknown element type:" + bioEntity);
}
};
+/**
+ *
+ * @returns {GuiUtils}
+ */
LeftPanel.prototype.getGuiUtils = function () {
var self = this;
if (self._guiUtils === undefined) {
@@ -217,6 +244,11 @@ LeftPanel.prototype.getGuiUtils = function () {
return self._guiUtils;
};
+/**
+ *
+ * @param {BioEntity} bioEntity
+ * @returns {string}
+ */
LeftPanel.prototype.getElementTitle = function (bioEntity) {
if (bioEntity instanceof Reaction) {
return bioEntity.getType() + ": " + bioEntity.getReactionId();
@@ -255,6 +287,7 @@ LeftPanel.prototype.addTab = function (params, tabData) {
this._panels.push(new params.panelClass({
element: data.content,
customMap: self.getMap(),
+ configuration: self.getConfiguration(),
parent: self
}));
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index 4c9637d4d214f24ed873af3045610f3a38840892..862b8f9f46349a84796d866ffea8f3016e8cca71 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -16,11 +16,12 @@ var Promise = require('bluebird');
/**
*
* @param {Object} params
- * @param {Configuration} [params.configuration]
* @param {HTMLElement} params.element
- * @param {Project} params.project
* @param {CustomMap} params.customMap
+ * @param {Configuration} [params.configuration]
+ * @param {Project} [params.project]
* @param params.parent
+ *
* @constructor
* @extends Panel
*/
@@ -30,6 +31,9 @@ function OverlayPanel(params) {
params["helpTip"] = "<p>Overlays tab allows to display or generate custom coloring of elements and interactions in the map.</p>"
+ "<p>General overlays are overlays accessible for every user viewing the content.</p>"
+ "<p>Custom overlays are user-provided overlays, this menu becomes available upon login (see below).</p>";
+ if (params.project === undefined) {
+ params.project = params.customMap.getProject();
+ }
Panel.call(this, params);
//overflow is defined in minerva-overlay-panel, so remove the one that is already there
@@ -211,8 +215,8 @@ OverlayPanel.prototype.createTableHeader = function (edit) {
/**
*
* @param {DataOverlay} overlay
- * @param {boolean} checked
- * @param {boolean} disabled
+ * @param {boolean} [checked=false]
+ * @param {boolean} [disabled=false]
* @returns {HTMLElement}
*/
OverlayPanel.prototype.createOverlayRow = function (overlay, checked, disabled) {
@@ -549,7 +553,8 @@ OverlayPanel.prototype.openAddOverlayDialog = function () {
self._addOverlayDialog = new AddOverlayDialog({
project: self.getProject(),
customMap: self.getMap(),
- element: document.createElement("div")
+ element: document.createElement("div"),
+ configuration: self.getConfiguration()
});
self._addOverlayDialog.addListener("onAddOverlay", function (e) {
self.getProject().addDataOverlay(e.arg);
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index 967fff2cb0a0ce4e92bdb9664a8decb529c778e7..03f7119a22234b8e84ddcd4af47f08c9e4ce3627 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -9,6 +9,7 @@ var AliasInfoWindow = require('./window/AliasInfoWindow');
var AliasSurface = require('./surface/AliasSurface');
var GuiConnector = require('../GuiConnector');
var IdentifiedElement = require('./data/IdentifiedElement');
+var LayoutAlias = require('./data/LayoutAlias');
var ObjectWithListeners = require('../ObjectWithListeners');
var MapModel = require('./data/MapModel');
var Point = require('./canvas/Point');
@@ -362,65 +363,127 @@ AbstractCustomMap.prototype._showSelectedDataOverlay = function (overlayId, inde
// end ratio
var endX = (index + 1) * (1.0 / length);
- var overlayAliases;
- var overlayReactions;
-
return self.getProject().getDataOverlayById(overlayId).then(function (overlay) {
- overlayAliases = overlay.getAliases();
- overlayReactions = overlay.getReactions();
+ return Promise.all([self._showDataOverlayAliases(overlay, startX, endX),
+ self._showDataOverlayReactions(overlay, length === 1)
+ ]);
+ });
+};
- var i, identifiedElements = [];
- for (i = 0; i < overlayAliases.length; i++) {
- if (overlayAliases[i].getModelId() === self.getId()) {
- identifiedElements.push(new IdentifiedElement(overlayAliases[i]));
- }
+/**
+ *
+ * @param {DataOverlay} overlay
+ * @param {number} startX
+ * @param {number} endX
+ *
+ * @returns {Promise|PromiseLike}
+ * @private
+ */
+AbstractCustomMap.prototype._showDataOverlayAliases = function (overlay, startX, endX) {
+ var self = this;
+ var overlayAliases = overlay.getAliases();
+ var overlayAliasesOnMap = [];
+
+ var i, identifiedElements = [];
+ var usedAliasIds = [];
+ var overlayMapIds = [];
+ for (i = 0; i < overlayAliases.length; i++) {
+ if (overlayMapIds[overlayAliases[i].getModelId()] === undefined) {
+ overlayMapIds[overlayAliases[i].getModelId()] = [];
}
- for (i = 0; i < overlayReactions.length; i++) {
- if (overlayReactions[i].getModelId() === self.getId()) {
- identifiedElements.push(new IdentifiedElement(overlayReactions[i]));
+ overlayMapIds[overlayAliases[i].getModelId()].push(overlayAliases[i]);
+
+ if (overlayAliases[i].getModelId() === self.getId()) {
+ identifiedElements.push(new IdentifiedElement(overlayAliases[i]));
+ overlayAliasesOnMap.push(overlayAliases[i]);
+ usedAliasIds[overlayAliases[i].getId()] = true;
+ }
+ }
+ var elementsPointingToSubmapPromises = [];
+ for (var mapId in overlayMapIds) {
+ elementsPointingToSubmapPromises.push(self.getProject().getElementsPointingToSubmap(parseInt(mapId)));
+ }
+ return Promise.all(elementsPointingToSubmapPromises).then(function (elementsPointingToSubmap) {
+ for (var i = 0; i < elementsPointingToSubmap.length; i++) {
+ var row = elementsPointingToSubmap[i];
+ for (var j = 0; j < row.length; j++) {
+ var identifiedElement = row[j];
+ if (identifiedElement.getModelId() === self.getId() && !usedAliasIds[identifiedElement.getId()]) {
+ usedAliasIds[identifiedElement.getId()] = true;
+ overlayAliasesOnMap.push(new LayoutAlias({
+ idObject: identifiedElement.getId(),
+ modelId: identifiedElement.getModelId(),
+ value: 0
+ }));
+ }
}
}
- return self.getModel().getByIdentifiedElements(identifiedElements, false);
+ return self.getModel().getByIdentifiedElements(identifiedElements, false)
}).then(function () {
- return Promise.each(overlayAliases, function (overlayAlias) {
- if (overlayAlias.getModelId() === self.getId()) {
- return self.getModel().getAliasById(overlayAlias.getId()).then(function (aliasData) {
- var surface = new AliasSurface({
- overlayAlias: overlayAlias,
- alias: aliasData,
- map: self,
- startX: startX,
- endX: endX,
- onClick: [function () {
- return self.getTopMap().getOverlayByName("search").searchByTarget(new IdentifiedElement(aliasData));
- }, function () {
- return self.getTopMap().callListeners("onBioEntityClick", new IdentifiedElement(aliasData));
- }]
- });
- self.selectedLayoutOverlays[overlayId].push(surface);
- return surface.show();
+ return Promise.each(overlayAliasesOnMap, function (overlayAlias) {
+ return self.getModel().getAliasById(overlayAlias.getId()).then(function (aliasData) {
+ var overlayData;
+ if (aliasData.getLinkedSubmodelId() !== undefined && overlayMapIds[aliasData.getLinkedSubmodelId()] !== undefined) {
+ overlayData = overlayMapIds[aliasData.getLinkedSubmodelId()];
+ } else {
+ overlayData = [overlayAlias];
+ }
+ var surface = new AliasSurface({
+ overlayData: overlayData,
+ alias: aliasData,
+ map: self,
+ startX: startX,
+ endX: endX,
+ onClick: [function () {
+ return self.getTopMap().getOverlayByName("search").searchByTarget(new IdentifiedElement(aliasData));
+ }, function () {
+ return self.getTopMap().callListeners("onBioEntityClick", new IdentifiedElement(aliasData));
+ }]
});
- }
+ self.selectedLayoutOverlays[overlay.getId()].push(surface);
+ return surface.show();
+ });
});
- }).then(function () {
- return Promise.each(overlayReactions, function (overlayReaction) {
- if (overlayReaction.getModelId() === self.getId()) {
- return self.getModel().getReactionById(overlayReaction.getId()).then(function (reactionData) {
- var surface = new ReactionSurface({
- layoutReaction: overlayReaction,
- reaction: reactionData,
- map: self,
- onClick: [function () {
- return self.getTopMap().getOverlayByName("search").searchByTarget(new IdentifiedElement(reactionData));
- }, function () {
- return self.getTopMap().callListeners("onBioEntityClick", new IdentifiedElement(reactionData));
- }],
- customized: (length === 1)
- });
- self.selectedLayoutOverlays[overlayId].push(surface);
- return surface.show();
+ });
+};
+
+/**
+ *
+ * @param {DataOverlay} overlay
+ * @param {boolean} customized
+ *
+ * @returns {Promise}
+ * @private
+ */
+AbstractCustomMap.prototype._showDataOverlayReactions = function (overlay, customized) {
+ var self = this;
+ var overlayReactions = overlay.getReactions();
+ var overlayReactionsOnMap = [];
+
+ var i, identifiedElements = [];
+ for (i = 0; i < overlayReactions.length; i++) {
+ if (overlayReactions[i].getModelId() === self.getId()) {
+ identifiedElements.push(new IdentifiedElement(overlayReactions[i]));
+ overlayReactionsOnMap.push(overlayReactions[i]);
+ }
+ }
+ return self.getModel().getByIdentifiedElements(identifiedElements, false).then(function () {
+ return Promise.each(overlayReactionsOnMap, function (overlayReaction) {
+ return self.getModel().getReactionById(overlayReaction.getId()).then(function (reactionData) {
+ var surface = new ReactionSurface({
+ layoutReaction: overlayReaction,
+ reaction: reactionData,
+ map: self,
+ onClick: [function () {
+ return self.getTopMap().getOverlayByName("search").searchByTarget(new IdentifiedElement(reactionData));
+ }, function () {
+ return self.getTopMap().callListeners("onBioEntityClick", new IdentifiedElement(reactionData));
+ }],
+ customized: customized
});
- }
+ self.selectedLayoutOverlays[overlay.getId()].push(surface);
+ return surface.show();
+ });
});
});
};
@@ -440,7 +503,7 @@ AbstractCustomMap.prototype._hideSelectedLayout = function (overlayId) {
return Promise.resolve();
}
- var promises =[];
+ var promises = [];
for (var i = 0; i < this.selectedLayoutOverlays[overlayId].length; i++) {
promises.push(this.selectedLayoutOverlays[overlayId][i].hide());
}
@@ -508,27 +571,6 @@ AbstractCustomMap.prototype._openInfoWindowForAlias = function (alias, marker) {
}
};
-/**
- * Returns promise of a list of {@link LayoutAlias} information for a given
- * {@link Alias} in all currently visualized overlays.
- *
- * @param {number} aliasId
- * identifier of the {@link Alias}
- * @returns {PromiseLike<LayoutAlias[]>| Promise<LayoutAlias[]>} promise of an {Array} with list of {@link LayoutAlias} information
- * for a given {@link Alias} in all currently visualized overlays
- */
-AbstractCustomMap.prototype.getAliasVisibleLayoutsData = function (aliasId) {
- var self = this;
- return self.getTopMap().getVisibleDataOverlays().then(function (visibleDataOverlays) {
- var result = [];
- for (var i = 0; i < visibleDataOverlays.length; i++) {
- var overlay = visibleDataOverlays[i];
- result.push(overlay.getFullAliasById(aliasId));
- }
- return Promise.all(result);
- });
-};
-
/**
* Opens {@link ReactionInfoWindow} for given reaction identifier.
*
diff --git a/frontend-js/src/main/js/map/OverlayParser.js b/frontend-js/src/main/js/map/OverlayParser.js
index 72fc466358ac3bc06fb988402834959eca341687..320c0b936c4e09eedceea040c4c5f88e58eb7541 100644
--- a/frontend-js/src/main/js/map/OverlayParser.js
+++ b/frontend-js/src/main/js/map/OverlayParser.js
@@ -7,6 +7,11 @@ var TextDecoder = require('text-encoding').TextDecoder;
function OverlayParser() {
}
+/**
+ *
+ * @param {string| Uint8Array|ArrayBuffer} content
+ * @returns {DataOverlay}
+ */
OverlayParser.prototype.parse = function (content) {
if (content instanceof Uint8Array || content instanceof ArrayBuffer) {
content = new TextDecoder("UTF8").decode(content);
diff --git a/frontend-js/src/main/js/map/canvas/Bounds.js b/frontend-js/src/main/js/map/canvas/Bounds.js
index 210e7484774d27156809bd26498fa32e75cb9352..0cbc6b1f2c88c2616b0248973d5c194bae2bee46 100644
--- a/frontend-js/src/main/js/map/canvas/Bounds.js
+++ b/frontend-js/src/main/js/map/canvas/Bounds.js
@@ -73,4 +73,16 @@ Bounds.prototype.contains = function (point) {
};
+/**
+ *
+ * @returns {string}
+ */
+Bounds.prototype.toString = function () {
+ if (this._topLeft === undefined) {
+ return "[NaN]";
+ } else {
+ return "[" + this._topLeft.x + "," + this._topLeft.y + "]-[" + this._rightBottom.x + "," + this._rightBottom.y + "]";
+ }
+};
+
module.exports = Bounds;
diff --git a/frontend-js/src/main/js/map/canvas/GoogleMaps/GoogleMapsApiCanvas.js b/frontend-js/src/main/js/map/canvas/GoogleMaps/GoogleMapsApiCanvas.js
index 60fb32554f4e23ad3d96ca0f92effd87d5ff3821..2e465b34a8d719c99c9ab9127745803fb3f875e3 100644
--- a/frontend-js/src/main/js/map/canvas/GoogleMaps/GoogleMapsApiCanvas.js
+++ b/frontend-js/src/main/js/map/canvas/GoogleMaps/GoogleMapsApiCanvas.js
@@ -232,9 +232,9 @@ GoogleMapsApiCanvas.prototype.createMarker = function (options) {
/**
*
* @param {Bounds} options.bounds
- * @param {string} options.id
- * @param {number} options.fillOpacity
* @param {string} options.fillColor
+ * @param {number} options.fillOpacity
+ * @param {string} options.id
* @param {string} options.strokeColor
* @param {number} options.strokeOpacity
* @param {number} options.strokeWeight
diff --git a/frontend-js/src/main/js/map/canvas/GoogleMaps/GoogleMapsApiRectangle.js b/frontend-js/src/main/js/map/canvas/GoogleMaps/GoogleMapsApiRectangle.js
index 97ac9369942a054c256d233fc99e2d10c6ee237a..4490ef861d517ddaf4ce19f58270f3e6fa497c62 100644
--- a/frontend-js/src/main/js/map/canvas/GoogleMaps/GoogleMapsApiRectangle.js
+++ b/frontend-js/src/main/js/map/canvas/GoogleMaps/GoogleMapsApiRectangle.js
@@ -1,21 +1,23 @@
"use strict";
-var Rectangle = require('../Rectangle');
var Bounds = require('../Bounds');
+var Point = require('../Point');
+var Rectangle = require('../Rectangle');
// noinspection JSUnusedLocalSymbols
var logger = require('../../../logger');
/**
*
- * @param {MapCanvas} options.map
+ * @param {GoogleMapsApiCanvas} options.map
* @param {Bounds} options.bounds
- * @param {MapCanvas} options.fillOpacity
- * @param {number} options.id
- * @param {number} options.strokeWeight
- * @param {string} options.fillColor
+ * @param {string} [options.fillColor]
+ * @param {{color: string, amount: number}[]} [options.fillGradient]
+ * @param {number} options.fillOpacity
+ * @param {string} options.id
* @param {string} options.strokeColor
* @param {number} options.strokeOpacity
+ * @param {number} options.strokeWeight
*
* @constructor
* @extends Rectangle
@@ -24,24 +26,67 @@ function GoogleMapsApiRectangle(options) {
Rectangle.call(this, options);
var self = this;
+ self._rectangles = [];
+
+
+ var i;
+ var bounds;
+ if (options.fillGradient !== undefined) {
+ var totalAmount = 0;
+ for (i = 0; i < options.fillGradient.length; i++) {
+ totalAmount += options.fillGradient[i].amount;
+ }
+ var y = options.bounds.getTopLeft().y;
+ for (i = 0; i < options.fillGradient.length; i++) {
+ var x1 = options.bounds.getTopLeft().x;
+ var x2 = options.bounds.getRightBottom().x;
+ var y1 = y;
+ var ratio = options.fillGradient[i].amount / totalAmount;
+
+ var y2 = y1 + ratio * (options.bounds.getRightBottom().y - options.bounds.getTopLeft().y);
+ y = y2;
+ bounds = new google.maps.LatLngBounds();
+ bounds.extend(self.getMap().fromPointToLatLng(new Point(x1, y1)));
+ bounds.extend(self.getMap().fromPointToLatLng(new Point(x2, y2)));
+ self.addGoogleRectangle(new google.maps.Rectangle({
+ bounds: bounds,
+ fillOpacity: options.fillOpacity,
+ strokeWeight: 0.0,
+ fillColor: options.fillGradient[i].color
+ }));
+ }
+ bounds = new google.maps.LatLngBounds();
+ bounds.extend(self.getMap().fromPointToLatLng(options.bounds.getTopLeft()));
+ bounds.extend(self.getMap().fromPointToLatLng(options.bounds.getRightBottom()));
+ self.addGoogleRectangle(new google.maps.Rectangle({
+ bounds: bounds,
+ fillOpacity: 0.0,
+ id: options.id,
+ strokeWeight: options.strokeWeight,
+ strokeColor: options.strokeColor,
+ strokeOpacity: options.strokeOpacity
+ }));
+ } else {
+ bounds = new google.maps.LatLngBounds();
+ bounds.extend(self.getMap().fromPointToLatLng(options.bounds.getTopLeft()));
+ bounds.extend(self.getMap().fromPointToLatLng(options.bounds.getRightBottom()));
+ self.addGoogleRectangle(new google.maps.Rectangle({
+ bounds: bounds,
+ fillOpacity: options.fillOpacity,
+ id: options.id,
+ strokeWeight: options.strokeWeight,
+ fillColor: options.fillColor,
+ strokeColor: options.strokeColor,
+ strokeOpacity: options.strokeOpacity
+ }));
+ }
- var bounds = new google.maps.LatLngBounds();
- bounds.extend(this.getMap().fromPointToLatLng(options.bounds.getTopLeft()));
- bounds.extend(this.getMap().fromPointToLatLng(options.bounds.getRightBottom()));
-
- this.setGoogleRectangle(new google.maps.Rectangle({
- bounds: bounds,
- fillOpacity: options.fillOpacity,
- id: options.id,
- strokeWeight: options.strokeWeight,
- fillColor: options.fillColor,
- strokeColor: options.strokeColor,
- strokeOpacity: options.strokeOpacity
- }));
-
- google.maps.event.addListener(this.getGoogleRectangle(), "click", function(){
- return self.callListeners("click");
- });
+ var rectangles = self.getGoogleRectangles();
+ for (i = 0; i < rectangles.length; i++) {
+ google.maps.event.addListener(rectangles[i], "click", function () {
+ return self.callListeners("click");
+ });
+ }
}
GoogleMapsApiRectangle.prototype = Object.create(Rectangle.prototype);
@@ -51,33 +96,31 @@ GoogleMapsApiRectangle.prototype.constructor = GoogleMapsApiRectangle;
*
* @param {google.maps.Rectangle} rectangle
*/
-GoogleMapsApiRectangle.prototype.setGoogleRectangle = function (rectangle) {
- this._rectangle = rectangle;
+GoogleMapsApiRectangle.prototype.addGoogleRectangle = function (rectangle) {
+ this._rectangles.push(rectangle);
};
/**
*
- * @returns {google.maps.Rectangle}
+ * @returns {google.maps.Rectangle[]}
*/
-GoogleMapsApiRectangle.prototype.getGoogleRectangle = function () {
- return this._rectangle;
+GoogleMapsApiRectangle.prototype.getGoogleRectangles = function () {
+ return this._rectangles;
};
GoogleMapsApiRectangle.prototype.show = function () {
- var googleRectangle = this.getGoogleRectangle();
- if (googleRectangle.getMap() !== undefined && googleRectangle.getMap() !== null) {
- logger.warn("Rectangle is already shown");
- }
- else {
- googleRectangle.setMap(this.getMap().getGoogleMap());
+ var rectangles = this.getGoogleRectangles();
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ rectangle.setMap(this.getMap().getGoogleMap());
}
};
GoogleMapsApiRectangle.prototype.hide = function () {
- if (!this.isShown()) {
- logger.warn("Rectangle is already invisible");
- } else {
- this.getGoogleRectangle().setMap(null);
+ var rectangles = this.getGoogleRectangles();
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ rectangle.setMap(null);
}
};
@@ -86,19 +129,40 @@ GoogleMapsApiRectangle.prototype.hide = function () {
* @returns {boolean}
*/
GoogleMapsApiRectangle.prototype.isShown = function () {
- var googleRectangle = this.getGoogleRectangle();
- return googleRectangle.getMap() !== null && googleRectangle.getMap() !== undefined;
+ var rectangles = this.getGoogleRectangles();
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ if (rectangle.getMap() !== null && rectangle.getMap() !== undefined) {
+ return true;
+ }
+ }
+ return false;
};
/**
*
- * @param bounds {Bounds}
+ * @param newBounds {Bounds}
*/
-GoogleMapsApiRectangle.prototype.setBounds = function (bounds) {
- var latLngBounds = new google.maps.LatLngBounds();
- latLngBounds.extend(this.getMap().fromPointToLatLng(bounds.getTopLeft()));
- latLngBounds.extend(this.getMap().fromPointToLatLng(bounds.getRightBottom()));
- this.getGoogleRectangle().setBounds(latLngBounds);
+GoogleMapsApiRectangle.prototype.setBounds = function (newBounds) {
+ var oldBounds = this.getBounds();
+
+ var rectangles = this.getGoogleRectangles();
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ var rectangleLatLngBounds = rectangle.getBounds();
+ var currentBounds = new Bounds();
+ currentBounds.extend(this.getMap().fromLatLngToPoint(rectangleLatLngBounds.getSouthWest()));
+ currentBounds.extend(this.getMap().fromLatLngToPoint(rectangleLatLngBounds.getNorthEast()));
+
+ var latLngBounds = new google.maps.LatLngBounds();
+
+ var topLeft = this._transformCoordinates(currentBounds.getTopLeft(), oldBounds, newBounds);
+ var rightBottom = this._transformCoordinates(currentBounds.getRightBottom(), oldBounds, newBounds);
+
+ latLngBounds.extend(this.getMap().fromPointToLatLng(topLeft));
+ latLngBounds.extend(this.getMap().fromPointToLatLng(rightBottom));
+ rectangle.setBounds(latLngBounds);
+ }
};
/**
@@ -106,10 +170,15 @@ GoogleMapsApiRectangle.prototype.setBounds = function (bounds) {
* @returns {Bounds}
*/
GoogleMapsApiRectangle.prototype.getBounds = function () {
- var latLngBounds = this.getGoogleRectangle().getBounds();
var result = new Bounds();
- result.extend(this.getMap().fromLatLngToPoint(latLngBounds.getSouthWest()));
- result.extend(this.getMap().fromLatLngToPoint(latLngBounds.getNorthEast()));
+
+ var rectangles = this.getGoogleRectangles();
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ var latLngBounds = rectangle.getBounds();
+ result.extend(this.getMap().fromLatLngToPoint(latLngBounds.getSouthWest()));
+ result.extend(this.getMap().fromLatLngToPoint(latLngBounds.getNorthEast()));
+ }
return result;
};
@@ -118,7 +187,11 @@ GoogleMapsApiRectangle.prototype.getBounds = function () {
* @param {Object} options
*/
GoogleMapsApiRectangle.prototype.setOptions = function (options) {
- this.getGoogleRectangle().setOptions(options);
+ var rectangles = this.getGoogleRectangles();
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ rectangle.setOptions(options);
+ }
};
diff --git a/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerRectangle.js b/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerRectangle.js
index eb0b859ee61e9a8156d3eea4eb6e9f2028ae3841..b9037203fc91b3ca670297309d81ca687f3a8839 100644
--- a/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerRectangle.js
+++ b/frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerRectangle.js
@@ -27,29 +27,84 @@ function OpenLayersRectangle(options) {
options.strokeWeight = 1;
}
this._options = options;
+ this._rectangles = [];
+
+ if (options.fillGradient !== undefined) {
+ var totalAmount = 0;
+ for (var i = 0; i < options.fillGradient.length; i++) {
+ totalAmount += options.fillGradient[i].amount;
+ }
+ var y = options.bounds.getTopLeft().y;
+ for (i = 0; i < options.fillGradient.length; i++) {
+ var x1 = options.bounds.getTopLeft().x;
+ var x2 = options.bounds.getRightBottom().x;
+ var y1 = y;
+ var ratio = options.fillGradient[i].amount / totalAmount;
+
+ var y2 = y1 + ratio * (options.bounds.getRightBottom().y - options.bounds.getTopLeft().y);
+ y = y2;
+
+ var bounds = new Bounds(new Point(x1, y1), new Point(x2, y2));
+
+ self.addOpenLayersRectangle(self._createFeature({
+ strokeWeight: 0.5,
+ strokeColor: options.fillGradient[i].color,
+ strokeOpacity: options.fillOpacity,
+ bounds: bounds,
+ fillOpacity: options.fillOpacity,
+ fillColor: options.fillGradient[i].color,
+ source: options.source
+ }));
+ }
+ self.addOpenLayersRectangle(self._createFeature({
+ strokeWeight: options.strokeWeight,
+ strokeColor: options.strokeColor,
+ strokeOpacity: options.strokeOpacity,
+ bounds: options.bounds,
+ fillOpacity: 0.0,
+ id: options.id,
+ fillColor: "#000000",
+ source: options.source
+ }));
+ } else {
+ self.addOpenLayersRectangle(self._createFeature(options));
+ }
- var style = self.createStyle(options);
+}
+
+OpenLayersRectangle.prototype = Object.create(Rectangle.prototype);
+OpenLayersRectangle.prototype.constructor = OpenLayersRectangle;
- var polygon = this.createPolygon(options.bounds);
+OpenLayersRectangle.prototype._createFeature = function (options) {
+ var self = this;
+ var style = self.createStyle(options);
+ var polygon;
+ polygon = self.createPolygon(options.bounds);
var feature = new ol.Feature({
geometry: polygon,
id: options.id
});
- this.setOpenLayersRectangle(feature);
feature.setStyle(new ol.style.Style({}));
options.source.addFeature(feature);
feature.__openLayerRectangle = this;
+ /**
+ *
+ * @type {style.Style}
+ * @private
+ */
+ feature.__style = style;
+ return feature;
+};
- this._style = style;
-
-}
-
-OpenLayersRectangle.prototype = Object.create(Rectangle.prototype);
-OpenLayersRectangle.prototype.constructor = OpenLayersRectangle;
+/**
+ *
+ * @param {Bounds} bounds
+ * @returns {geom.Polygon}
+ */
OpenLayersRectangle.prototype.createPolygon = function (bounds) {
var self = this;
@@ -68,6 +123,16 @@ OpenLayersRectangle.prototype.createPolygon = function (bounds) {
return new ol.geom.Polygon([points]);
};
+/**
+ *
+ * @param {string} options.strokeColor
+ * @param {number} options.strokeOpacity
+ * @param {number} options.strokeWeight
+ * @param {string} options.fillColor
+ * @param {number} options.fillOpacity
+ *
+ * @returns {style.Style}
+ */
OpenLayersRectangle.prototype.createStyle = function (options) {
return new ol.style.Style({
stroke: new ol.style.Stroke({
@@ -80,54 +145,110 @@ OpenLayersRectangle.prototype.createStyle = function (options) {
});
};
-
-OpenLayersRectangle.prototype.setOpenLayersRectangle = function (rectangle) {
- this._rectangle = rectangle;
+OpenLayersRectangle.prototype.addOpenLayersRectangle = function (rectangle) {
+ this._rectangles.push(rectangle);
};
-OpenLayersRectangle.prototype.getOpenLayersRectangle = function () {
- return this._rectangle;
+/**
+ *
+ * @returns {Array}
+ */
+OpenLayersRectangle.prototype.getOpenLayersRectangles = function () {
+ return this._rectangles;
};
+/**
+ *
+ */
OpenLayersRectangle.prototype.show = function () {
- return this.getOpenLayersRectangle().setStyle(this._style);
+ var rectangles = this.getOpenLayersRectangles();
+
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ rectangle.setStyle(rectangle.__style);
+ }
};
OpenLayersRectangle.prototype.hide = function () {
- return this.getOpenLayersRectangle().setStyle(new ol.style.Style({}));
+ var rectangles = this.getOpenLayersRectangles();
+ var hiddenStyle = new ol.style.Style({});
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ rectangle.setStyle(hiddenStyle);
+ }
};
OpenLayersRectangle.prototype.isShown = function () {
- return this.getOpenLayersRectangle().getStyle().getFill() !== null;
+ var rectangles = this.getOpenLayersRectangles();
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ if (rectangle.getStyle().getFill() !== null) {
+ return true;
+ }
+ }
};
/**
*
- * @param bounds {Bounds}
+ * @param newBounds {Bounds}
*/
-OpenLayersRectangle.prototype.setBounds = function (bounds) {
- this._options.bounds = bounds;
- this.getOpenLayersRectangle().setGeometry(this.createPolygon(bounds));
+OpenLayersRectangle.prototype.setBounds = function (newBounds) {
+ var self = this;
+
+ self._options.bounds = newBounds;
+ var oldBounds = self.getBounds();
+
+ var rectangles = self.getOpenLayersRectangles();
+
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ var currentBounds = new Bounds();
+ var extent = rectangle.getGeometry().getExtent();
+
+ var projection1 = [extent[0], extent[1]];
+ currentBounds.extend(self.getMap().fromProjectionToPoint(projection1));
+ var projection2 = [extent[2], extent[3]];
+ currentBounds.extend(self.getMap().fromProjectionToPoint(projection2));
+
+ var topLeft = self._transformCoordinates(currentBounds.getTopLeft(), oldBounds, newBounds);
+ var rightBottom = self._transformCoordinates(currentBounds.getRightBottom(), oldBounds, newBounds);
+
+ rectangle.setGeometry(self.createPolygon(new Bounds(topLeft, rightBottom)));
+ }
+
};
OpenLayersRectangle.prototype.getBounds = function () {
var self = this;
- var extent = self.getOpenLayersRectangle().getGeometry().getExtent();
-
- var projection1 = [extent[0], extent[1]];
- var p1 = self.getMap().fromProjectionToPoint(projection1);
- var projection2 = [extent[2], extent[3]];
- var p2 = self.getMap().fromProjectionToPoint(projection2);
- return new Bounds(p1, p2);
+ var bounds = new Bounds();
+ var rectangles = this.getOpenLayersRectangles();
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ var extent = rectangle.getGeometry().getExtent();
+
+ var projection1 = [extent[0], extent[1]];
+ bounds.extend(self.getMap().fromProjectionToPoint(projection1));
+ var projection2 = [extent[2], extent[3]];
+ bounds.extend(self.getMap().fromProjectionToPoint(projection2));
+ }
+ return bounds;
};
OpenLayersRectangle.prototype.setOptions = function (options) {
var self = this;
self._options = Object.assign(self._options, options);
- var style = self.createStyle(self._options);
- if (self.isShown()) {
- self.getOpenLayersRectangle().setStyle(style);
+ var rectangles = this.getOpenLayersRectangles();
+ for (var i = 0; i < rectangles.length; i++) {
+ var rectangle = rectangles[i];
+ var style = rectangle.__style;
+ if (self._options.fillColor !== undefined) {
+ style.getFill().setColor(Functions.colorToRgbaString(self._options.fillColor, self._options.fillOpacity));
+ }
+
+ if (i === rectangles.length - 1) {
+ style.getStroke().setWidth(self._options.strokeWeight);
+ style.getStroke().setColor(Functions.colorToRgbaString(self._options.strokeColor, self._options.strokeOpacity));
+ }
}
- self._style = style;
};
module.exports = OpenLayersRectangle;
diff --git a/frontend-js/src/main/js/map/canvas/Point.js b/frontend-js/src/main/js/map/canvas/Point.js
index 5d382661af887724b11bc53ea262b2524c9085d0..dcec9a39f16137179e68feeb6ddfe2699aff3113 100644
--- a/frontend-js/src/main/js/map/canvas/Point.js
+++ b/frontend-js/src/main/js/map/canvas/Point.js
@@ -30,4 +30,12 @@ Point.prototype.toString = function () {
return "[" + this.x + ", " + this.y + "]";
};
+/**
+ * @param {Point} otherPoint
+ * @returns {number}
+ */
+Point.prototype.distanceTo = function (otherPoint) {
+ return Math.sqrt((otherPoint.x - this.x) * (otherPoint.x - this.x) + (otherPoint.y - this.y) * (otherPoint.y - this.y));
+};
+
module.exports = Point;
diff --git a/frontend-js/src/main/js/map/canvas/Rectangle.js b/frontend-js/src/main/js/map/canvas/Rectangle.js
index b30ec9c9ea811cd02685665975a8009a7a960260..9da655253c42dc1842b7902122b70d50ea0f67da 100644
--- a/frontend-js/src/main/js/map/canvas/Rectangle.js
+++ b/frontend-js/src/main/js/map/canvas/Rectangle.js
@@ -1,6 +1,7 @@
"use strict";
var MapCanvas = require('./MapCanvas');
+var Point = require('./Point');
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
@@ -74,4 +75,19 @@ Rectangle.prototype.getMap = function () {
return this._map;
};
+/**
+ *
+ * @param {Point} point
+ * @param {Bounds} oldBounds
+ * @param {Bounds} newBounds
+ *
+ * @returns {Point}
+ * @protected
+ */
+Rectangle.prototype._transformCoordinates = function (point, oldBounds, newBounds) {
+ var x = newBounds.getTopLeft().x + (point.x - oldBounds.getTopLeft().x) / (oldBounds.getRightBottom().x - oldBounds.getTopLeft().x) * (newBounds.getRightBottom().x - newBounds.getTopLeft().x);
+ var y = newBounds.getTopLeft().y + (point.y - oldBounds.getTopLeft().y) / (oldBounds.getRightBottom().y - oldBounds.getTopLeft().y) * (newBounds.getRightBottom().y - newBounds.getTopLeft().y);
+ return new Point(x, y);
+};
+
module.exports = Rectangle;
diff --git a/frontend-js/src/main/js/map/data/Alias.js b/frontend-js/src/main/js/map/data/Alias.js
index c1207a70457ce3f9d17a5db9a55274b46667d811..1bfd76989315b1d645d6a6438a4fad8556fbe213 100644
--- a/frontend-js/src/main/js/map/data/Alias.js
+++ b/frontend-js/src/main/js/map/data/Alias.js
@@ -26,6 +26,7 @@ function Alias(javaObject) {
this.setWidth(javaObject.bounds.width);
this.setHeight(javaObject.bounds.height);
}
+ this.setLinkedSubmodelId(javaObject.linkedSubmodel);
if (this._modelId === undefined) {
throw new Error("ModelId is not defined for alias" + javaObject);
@@ -341,7 +342,7 @@ Alias.prototype.setFullName = function (fullName) {
/**
*
- * @returns {number}
+ * @returns {number|undefined}
*/
Alias.prototype.getCompartmentId = function () {
return this._compartmentId;
diff --git a/frontend-js/src/main/js/map/data/Annotation.js b/frontend-js/src/main/js/map/data/Annotation.js
index 748eff92445c3ccd2e9bc33a806652a206279760..7b6f82bef9bf4a6518da736cb18df40c06c23303 100644
--- a/frontend-js/src/main/js/map/data/Annotation.js
+++ b/frontend-js/src/main/js/map/data/Annotation.js
@@ -11,10 +11,10 @@ var logger = require('../../logger');
* @typedef {Object} AnnotationOptions
* @property {string} link
* @property {number} id
- * @property {Article|ArticleOptions} article
+ * @property {Article|ArticleOptions} [article]
* @property {string} type
* @property {string} resource
- * @property {string} annotatorClassName
+ * @property {string} [annotatorClassName]
*/
/**
@@ -140,7 +140,7 @@ Annotation.prototype.setAnnotatorClassName = function (annotatorClassName) {
/**
*
- * @returns {string}
+ * @returns {string|undefined}
*/
Annotation.prototype.getAnnotatorClassName = function () {
return this._annotatorClassName;
diff --git a/frontend-js/src/main/js/map/data/BioEntity.js b/frontend-js/src/main/js/map/data/BioEntity.js
index f5e5a8370645e2cff368bca1356317948e9aafb5..f2deb9b7686a2f9fc60e57f141c172d0b665ebba 100644
--- a/frontend-js/src/main/js/map/data/BioEntity.js
+++ b/frontend-js/src/main/js/map/data/BioEntity.js
@@ -1,10 +1,11 @@
"use strict";
var Annotation = require("./Annotation");
+var Functions = require("../../Functions");
/**
* Class representing BioEntity.
- *
+ *
* @constructor
*/
function BioEntity() {
@@ -12,9 +13,9 @@ function BioEntity() {
/**
*
- * @returns {number}
+ * @returns {number|undefined}
*/
-BioEntity.prototype.getLinkedSubmodelId = function() {
+BioEntity.prototype.getLinkedSubmodelId = function () {
return this._linkedSubmodelId;
};
@@ -22,16 +23,16 @@ BioEntity.prototype.getLinkedSubmodelId = function() {
*
* @param {number} linkedSubmodelId
*/
-BioEntity.prototype.setLinkedSubmodelId = function(linkedSubmodelId) {
- this._linkedSubmodelId = linkedSubmodelId;
+BioEntity.prototype.setLinkedSubmodelId = function (linkedSubmodelId) {
+ this._linkedSubmodelId = Functions.getIntOrUndefined(linkedSubmodelId);
};
/**
* Returns identifier of the BioEntity.
- *
+ *
* @returns {number} identifier of the BioEntity
*/
-BioEntity.prototype.getId = function() {
+BioEntity.prototype.getId = function () {
return this.id;
};
@@ -39,16 +40,16 @@ BioEntity.prototype.getId = function() {
*
* @param {number} id
*/
-BioEntity.prototype.setId = function(id) {
+BioEntity.prototype.setId = function (id) {
this.id = id;
};
/**
* Returns model identifier where {@link BioEntity} is located.
- *
+ *
* @returns {number} model identifier where {@link BioEntity} is located
*/
-BioEntity.prototype.getModelId = function() {
+BioEntity.prototype.getModelId = function () {
return this._modelId;
};
@@ -56,7 +57,7 @@ BioEntity.prototype.getModelId = function() {
*
* @param {number} modelId
*/
-BioEntity.prototype.setModelId = function(modelId) {
+BioEntity.prototype.setModelId = function (modelId) {
this._modelId = modelId;
};
@@ -64,7 +65,7 @@ BioEntity.prototype.setModelId = function(modelId) {
*
* @returns {boolean}
*/
-BioEntity.prototype.isComplete = function() {
+BioEntity.prototype.isComplete = function () {
return this._complete;
};
@@ -72,7 +73,7 @@ BioEntity.prototype.isComplete = function() {
*
* @param {boolean} complete
*/
-BioEntity.prototype.setIsComplete = function(complete) {
+BioEntity.prototype.setIsComplete = function (complete) {
this._complete = complete;
};
@@ -80,7 +81,7 @@ BioEntity.prototype.setIsComplete = function(complete) {
*
* @returns {string}
*/
-BioEntity.prototype.getSymbol = function() {
+BioEntity.prototype.getSymbol = function () {
return this.symbol;
};
@@ -88,7 +89,7 @@ BioEntity.prototype.getSymbol = function() {
*
* @param {string} symbol
*/
-BioEntity.prototype.setSymbol = function(symbol) {
+BioEntity.prototype.setSymbol = function (symbol) {
this.symbol = symbol;
};
@@ -96,7 +97,7 @@ BioEntity.prototype.setSymbol = function(symbol) {
*
* @returns {string}
*/
-BioEntity.prototype.getAbbreviation = function() {
+BioEntity.prototype.getAbbreviation = function () {
return this._abbreviation;
};
@@ -104,7 +105,7 @@ BioEntity.prototype.getAbbreviation = function() {
*
* @param {string} abbreviation
*/
-BioEntity.prototype.setAbbreviation = function(abbreviation) {
+BioEntity.prototype.setAbbreviation = function (abbreviation) {
this._abbreviation = abbreviation;
};
@@ -112,7 +113,7 @@ BioEntity.prototype.setAbbreviation = function(abbreviation) {
*
* @returns {string}
*/
-BioEntity.prototype.getFormula = function() {
+BioEntity.prototype.getFormula = function () {
return this._formula;
};
@@ -120,7 +121,7 @@ BioEntity.prototype.getFormula = function() {
*
* @param {string} formula
*/
-BioEntity.prototype.setFormula = function(formula) {
+BioEntity.prototype.setFormula = function (formula) {
this._formula = formula;
};
@@ -128,7 +129,7 @@ BioEntity.prototype.setFormula = function(formula) {
*
* @param {string[]} synonyms
*/
-BioEntity.prototype.setSynonyms = function(synonyms) {
+BioEntity.prototype.setSynonyms = function (synonyms) {
this._synonyms = synonyms;
};
@@ -136,7 +137,7 @@ BioEntity.prototype.setSynonyms = function(synonyms) {
*
* @returns {string[]}
*/
-BioEntity.prototype.getSynonyms = function() {
+BioEntity.prototype.getSynonyms = function () {
return this._synonyms;
};
@@ -144,7 +145,7 @@ BioEntity.prototype.getSynonyms = function() {
*
* @param {string} description
*/
-BioEntity.prototype.setDescription = function(description) {
+BioEntity.prototype.setDescription = function (description) {
this._description = description;
};
@@ -152,7 +153,7 @@ BioEntity.prototype.setDescription = function(description) {
*
* @returns {string}
*/
-BioEntity.prototype.getDescription = function() {
+BioEntity.prototype.getDescription = function () {
return this._description;
};
@@ -160,7 +161,7 @@ BioEntity.prototype.getDescription = function() {
*
* @param {string} type
*/
-BioEntity.prototype.setType = function(type) {
+BioEntity.prototype.setType = function (type) {
if (type === undefined) {
throw new Error("type cannot be undefined");
}
@@ -171,7 +172,7 @@ BioEntity.prototype.setType = function(type) {
*
* @returns {string}
*/
-BioEntity.prototype.getType = function() {
+BioEntity.prototype.getType = function () {
return this._type;
};
@@ -180,7 +181,7 @@ BioEntity.prototype.getType = function() {
* @param {string} type
* @returns {Object}
*/
-BioEntity.prototype.getOther = function(type) {
+BioEntity.prototype.getOther = function (type) {
if (this._other !== undefined) {
return (type === undefined) ? this._other : this._other[type];
}
@@ -190,7 +191,7 @@ BioEntity.prototype.getOther = function(type) {
*
* @param {Object} other
*/
-BioEntity.prototype.setOther = function(other) {
+BioEntity.prototype.setOther = function (other) {
this._other = other;
};
@@ -198,7 +199,7 @@ BioEntity.prototype.setOther = function(other) {
*
* @returns {number}
*/
-BioEntity.prototype.getHierarchyVisibilityLevel = function() {
+BioEntity.prototype.getHierarchyVisibilityLevel = function () {
return this._hierarchyVisibilityLevel;
};
@@ -206,7 +207,7 @@ BioEntity.prototype.getHierarchyVisibilityLevel = function() {
*
* @param {number} hierarchyVisibilityLevel
*/
-BioEntity.prototype.setHierarchyVisibilityLevel = function(hierarchyVisibilityLevel) {
+BioEntity.prototype.setHierarchyVisibilityLevel = function (hierarchyVisibilityLevel) {
this._hierarchyVisibilityLevel = hierarchyVisibilityLevel;
};
@@ -214,7 +215,7 @@ BioEntity.prototype.setHierarchyVisibilityLevel = function(hierarchyVisibilityLe
*
* @returns {Annotation[]}
*/
-BioEntity.prototype.getReferences = function() {
+BioEntity.prototype.getReferences = function () {
return this.references;
};
@@ -222,8 +223,8 @@ BioEntity.prototype.getReferences = function() {
*
* @param {Annotation[]} references
*/
-BioEntity.prototype.setReferences = function(references) {
- if (references=== undefined) {
+BioEntity.prototype.setReferences = function (references) {
+ if (references === undefined) {
throw new Error("references must be defined");
}
this.references = [];
@@ -235,7 +236,7 @@ BioEntity.prototype.setReferences = function(references) {
/**
* @returns {Point}
*/
-BioEntity.prototype.getCenter = function() {
+BioEntity.prototype.getCenter = function () {
throw new Error("Not implemented");
};
diff --git a/frontend-js/src/main/js/map/data/DataOverlay.js b/frontend-js/src/main/js/map/data/DataOverlay.js
index e508d179054d5a283b94d2db58239b0b64a87985..c957147c37c78b05fc84220366908b2f2aa5ab7f 100644
--- a/frontend-js/src/main/js/map/data/DataOverlay.js
+++ b/frontend-js/src/main/js/map/data/DataOverlay.js
@@ -210,7 +210,7 @@ DataOverlay.prototype.getFullAliasById = function (id) {
var self = this;
var alias = self.getAliasById(id);
if (alias !== undefined) {
- if (alias.getType() === LayoutAlias.LIGTH) {
+ if (alias.getType() === LayoutAlias.LIGHT) {
return ServerConnector.getFullOverlayElement({
element: new IdentifiedElement(alias),
overlay: self
diff --git a/frontend-js/src/main/js/map/data/GeneVariant.js b/frontend-js/src/main/js/map/data/GeneVariant.js
index 1b4a6e0d7665ad84944c75b1468a6c6919c545c4..50fa4462f2eecc232ad702e927cdd6dfbed6928b 100644
--- a/frontend-js/src/main/js/map/data/GeneVariant.js
+++ b/frontend-js/src/main/js/map/data/GeneVariant.js
@@ -1,5 +1,19 @@
"use strict";
+/**
+ *
+ * @param {Object} javaObject
+ * @param {number} javaObject.position
+ * @param {string} javaObject.originalDna
+ * @param {string} javaObject.modifiedDna
+ * @param {string} javaObject.referenceGenomeType
+ * @param {string} javaObject.referenceGenomeVersion
+ * @param {string} javaObject.contig
+ * @param {null|number} [javaObject.allelFrequency]
+ * @param {null|string} [javaObject.variantIdentifier]
+ *
+ * @constructor
+ */
function GeneVariant(javaObject) {
this.setPosition(javaObject.position);
this.setOriginalDna(javaObject.originalDna);
@@ -11,68 +25,139 @@ function GeneVariant(javaObject) {
this.setVariantIdentifier(javaObject.variantIdentifier);
}
-GeneVariant.prototype.setPosition = function(position) {
+/**
+ *
+ * @param {number} position
+ */
+GeneVariant.prototype.setPosition = function (position) {
this._position = position;
};
-GeneVariant.prototype.getPosition = function() {
+/**
+ *
+ * @returns {number}
+ */
+GeneVariant.prototype.getPosition = function () {
return this._position;
};
-GeneVariant.prototype.setOriginalDna = function(originalDna) {
+/**
+ *
+ * @param {string} originalDna
+ */
+GeneVariant.prototype.setOriginalDna = function (originalDna) {
this._original = originalDna;
};
-GeneVariant.prototype.getOriginalDna = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getOriginalDna = function () {
return this._original;
};
-GeneVariant.prototype.setModifiedDna = function(modifiedDna) {
+/**
+ *
+ * @param {string} modifiedDna
+ */
+GeneVariant.prototype.setModifiedDna = function (modifiedDna) {
this._modifiedDna = modifiedDna;
};
-GeneVariant.prototype.getModifiedDna = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getModifiedDna = function () {
return this._modifiedDna;
};
-GeneVariant.prototype.setContig = function(contig) {
+/**
+ *
+ * @param {string} contig
+ */
+GeneVariant.prototype.setContig = function (contig) {
this._contig = contig;
};
-GeneVariant.prototype.getContig = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getContig = function () {
return this._contig;
};
-GeneVariant.prototype.setAllelFrequency = function(allelFrequency) {
- this._allelFrequency = allelFrequency;
+/**
+ *
+ * @param {number} allelFrequency
+ */
+GeneVariant.prototype.setAllelFrequency = function (allelFrequency) {
+ if (allelFrequency === null) {
+ this._allelFrequency = undefined;
+ } else {
+ this._allelFrequency = allelFrequency;
+ }
};
-GeneVariant.prototype.getAllelFrequency = function() {
+/**
+ *
+ * @returns {number}
+ */
+GeneVariant.prototype.getAllelFrequency = function () {
return this._allelFrequency;
};
-GeneVariant.prototype.setVariantIdentifier = function(variantIdentifier) {
- this._variantIdentifier = variantIdentifier;
+/**
+ *
+ * @param {string} variantIdentifier
+ */
+GeneVariant.prototype.setVariantIdentifier = function (variantIdentifier) {
+ if (variantIdentifier === null) {
+ this._variantIdentifier = undefined;
+ } else {
+ this._variantIdentifier = variantIdentifier;
+ }
};
-GeneVariant.prototype.getVariantIdentifier = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getVariantIdentifier = function () {
return this._variantIdentifier;
};
-GeneVariant.prototype.setReferenceGenomeType = function(referenceGenomeType) {
+/**
+ *
+ * @param {string} referenceGenomeType
+ */
+GeneVariant.prototype.setReferenceGenomeType = function (referenceGenomeType) {
this._referenceGenomeType = referenceGenomeType;
};
-GeneVariant.prototype.getReferenceGenomeType = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getReferenceGenomeType = function () {
return this._referenceGenomeType;
};
-GeneVariant.prototype.setReferenceGenomeVersion = function(
- referenceGenomeVersion) {
+/**
+ *
+ * @param {string} referenceGenomeVersion
+ */
+GeneVariant.prototype.setReferenceGenomeVersion = function (referenceGenomeVersion) {
this._referenceGenomeVersion = referenceGenomeVersion;
};
-GeneVariant.prototype.getReferenceGenomeVersion = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getReferenceGenomeVersion = function () {
return this._referenceGenomeVersion;
};
diff --git a/frontend-js/src/main/js/map/data/LayoutAlias.js b/frontend-js/src/main/js/map/data/LayoutAlias.js
index d41d52b7bc5f173f05a86fd859876b6fafb04646..e82336b0ce6f72c0e25549a5a4bb2367ec430ee8 100644
--- a/frontend-js/src/main/js/map/data/LayoutAlias.js
+++ b/frontend-js/src/main/js/map/data/LayoutAlias.js
@@ -1,111 +1,116 @@
-"use strict";
-
-var GeneVariant = require('./GeneVariant');
-
-/**
- * Class representing alias visualized in a overlay.
- *
- * @param javaObject
- * object de-serialized ajax query to the server side
- */
-function LayoutAlias(javaObject) {
- this.setId(javaObject.idObject);
- this.setValue(javaObject.value);
- this.setColor(javaObject.color);
- this.setModelId(javaObject.modelId);
- this.setDescription(javaObject.description);
- if (javaObject.type === undefined) {
- this.setType(LayoutAlias.LIGTH);
- } else if (javaObject.type === LayoutAlias.GENETIC_VARIANT) {
- this.setType(LayoutAlias.GENETIC_VARIANT);
- } else if (javaObject.type === LayoutAlias.GENERIC) {
- this.setType(LayoutAlias.GENERIC);
- } else {
- throw new Error("Unknown type: " + javaObject.type);
- }
-
- this.setGeneVariants([]);
- if (javaObject.geneVariations !== undefined) {
- for (var i = 0; i < javaObject.geneVariations.length; i++) {
- this.addGeneVariant(new GeneVariant(javaObject.geneVariations[i]));
- }
- }
-}
-
-LayoutAlias.LIGHT = "LIGHT";
-LayoutAlias.GENETIC_VARIANT = "GENETIC_VARIANT";
-LayoutAlias.GENERIC = "GENERIC";
-
-LayoutAlias.prototype.getId = function () {
- return this.id;
-};
-
-LayoutAlias.prototype.setId = function (id) {
- this.id = parseInt(id);
-};
-
-LayoutAlias.prototype.getModelId = function () {
- return this._modelId;
-};
-
-LayoutAlias.prototype.setModelId = function (modelId) {
- this._modelId = parseInt(modelId);
-};
-
-LayoutAlias.prototype.getValue = function () {
- return this.value;
-};
-
-LayoutAlias.prototype.getColor = function () {
- return this.color;
-};
-
-LayoutAlias.prototype.getType = function () {
- return this._type;
-};
-
-LayoutAlias.prototype.getGeneVariants = function () {
- return this._geneVariants;
-};
-
-LayoutAlias.prototype.setValue = function (newValue) {
- this.value = newValue;
-};
-
-LayoutAlias.prototype.setColor = function (newColor) {
- this.color = newColor;
-};
-
-LayoutAlias.prototype.setType = function (newType) {
- this._type = newType;
-};
-
-LayoutAlias.prototype.setGeneVariants = function (newGeneVariants) {
- this._geneVariants = newGeneVariants;
-};
-
-LayoutAlias.prototype.update = function (alias) {
- if (!(alias instanceof LayoutAlias)) {
- throw new Error("Unknown parameter type: " + alias);
- }
-
- this.setValue(alias.getValue());
- this.setColor(alias.getColor());
- this.setGeneVariants(alias.getGeneVariants());
- this.setType(alias.getType());
- this.setDescription(alias.getDescription());
-};
-
-LayoutAlias.prototype.addGeneVariant = function (geneVariant) {
- this._geneVariants.push(geneVariant);
-};
-
-LayoutAlias.prototype.getDescription = function () {
- return this._description;
-};
-
-LayoutAlias.prototype.setDescription = function (description) {
- this._description = description;
-};
-
-module.exports = LayoutAlias;
+"use strict";
+
+var GeneVariant = require('./GeneVariant');
+
+/**
+ * Class representing alias visualized in a overlay.
+ *
+ * @param {number} javaObject.idObject
+ * @param {number} [javaObject.value]
+ * @param {string} [javaObject.color]
+ * @param {number} javaObject.modelId
+ * @param {string} [javaObject.description]
+ * @param {string} [javaObject.type=LayoutAlias.LIGHT]
+ * @param {Array} [javaObject.geneVariations]
+ */
+function LayoutAlias(javaObject) {
+ this.setId(javaObject.idObject);
+ this.setValue(javaObject.value);
+ this.setColor(javaObject.color);
+ this.setModelId(javaObject.modelId);
+ this.setDescription(javaObject.description);
+ if (javaObject.type === undefined) {
+ this.setType(LayoutAlias.LIGHT);
+ } else if (javaObject.type === LayoutAlias.GENETIC_VARIANT) {
+ this.setType(LayoutAlias.GENETIC_VARIANT);
+ } else if (javaObject.type === LayoutAlias.GENERIC) {
+ this.setType(LayoutAlias.GENERIC);
+ } else {
+ throw new Error("Unknown type: " + javaObject.type);
+ }
+
+ this.setGeneVariants([]);
+ if (javaObject.geneVariations !== undefined) {
+ for (var i = 0; i < javaObject.geneVariations.length; i++) {
+ this.addGeneVariant(new GeneVariant(javaObject.geneVariations[i]));
+ }
+ }
+}
+
+LayoutAlias.LIGHT = "LIGHT";
+LayoutAlias.GENETIC_VARIANT = "GENETIC_VARIANT";
+LayoutAlias.GENERIC = "GENERIC";
+
+LayoutAlias.prototype.getId = function () {
+ return this.id;
+};
+
+LayoutAlias.prototype.setId = function (id) {
+ this.id = parseInt(id);
+};
+
+LayoutAlias.prototype.getModelId = function () {
+ return this._modelId;
+};
+
+LayoutAlias.prototype.setModelId = function (modelId) {
+ this._modelId = parseInt(modelId);
+};
+
+LayoutAlias.prototype.getValue = function () {
+ return this.value;
+};
+
+LayoutAlias.prototype.getColor = function () {
+ return this.color;
+};
+
+LayoutAlias.prototype.getType = function () {
+ return this._type;
+};
+
+LayoutAlias.prototype.getGeneVariants = function () {
+ return this._geneVariants;
+};
+
+LayoutAlias.prototype.setValue = function (newValue) {
+ this.value = newValue;
+};
+
+LayoutAlias.prototype.setColor = function (newColor) {
+ this.color = newColor;
+};
+
+LayoutAlias.prototype.setType = function (newType) {
+ this._type = newType;
+};
+
+LayoutAlias.prototype.setGeneVariants = function (newGeneVariants) {
+ this._geneVariants = newGeneVariants;
+};
+
+LayoutAlias.prototype.update = function (alias) {
+ if (!(alias instanceof LayoutAlias)) {
+ throw new Error("Unknown parameter type: " + alias);
+ }
+
+ this.setValue(alias.getValue());
+ this.setColor(alias.getColor());
+ this.setGeneVariants(alias.getGeneVariants());
+ this.setType(alias.getType());
+ this.setDescription(alias.getDescription());
+};
+
+LayoutAlias.prototype.addGeneVariant = function (geneVariant) {
+ this._geneVariants.push(geneVariant);
+};
+
+LayoutAlias.prototype.getDescription = function () {
+ return this._description;
+};
+
+LayoutAlias.prototype.setDescription = function (description) {
+ this._description = description;
+};
+
+module.exports = LayoutAlias;
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index 81a5dae53e5580ab0fa912bd3b7df2be7257ad81..2173114711ad26566674abb7edb539d4d5d8f0c3 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -256,7 +256,7 @@ MapModel.prototype.getMissingElements = function (elements) {
} else {
aliasPromise = ServerConnector.getAliases({
ids: aliasIds,
- columns: "id,bounds,modelId"
+ columns: "id,bounds,modelId,linkedSubmodel"
});
}
diff --git a/frontend-js/src/main/js/map/data/PrivilegeType.js b/frontend-js/src/main/js/map/data/PrivilegeType.js
index 54e528f1214a998043abe0eccb4fcc2a46ad4b9f..45af426283985ab02e2165bc19cd799600a71254 100644
--- a/frontend-js/src/main/js/map/data/PrivilegeType.js
+++ b/frontend-js/src/main/js/map/data/PrivilegeType.js
@@ -17,8 +17,9 @@ PrivilegeType.prototype = Object.create(ObjectWithListeners.prototype);
PrivilegeType.prototype.constructor = PrivilegeType;
PrivilegeType.CONFIGURATION_MANAGE = 'CONFIGURATION_MANAGE';
-PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
+PrivilegeType.MANAGE_GENOMES = 'MANAGE_GENOMES';
PrivilegeType.PROJECT_MANAGEMENT = 'PROJECT_MANAGEMENT';
+PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
PrivilegeType.prototype.setObjectType = function (objectType) {
this._objectType = objectType;
diff --git a/frontend-js/src/main/js/map/data/ReferenceGenome.js b/frontend-js/src/main/js/map/data/ReferenceGenome.js
index 38756a6bd0341c76e46c6266e6d0ce0b7c225891..8ed9b5445016bb0b1a922580129e125079e4c7be 100644
--- a/frontend-js/src/main/js/map/data/ReferenceGenome.js
+++ b/frontend-js/src/main/js/map/data/ReferenceGenome.js
@@ -1,50 +1,192 @@
"use strict";
+var Annotation = require('./Annotation');
var ReferenceGenomeGeneMapping = require('./ReferenceGenomeGeneMapping');
function ReferenceGenome(javaObject) {
if (javaObject !== undefined && javaObject !== null) {
+ this.setId(javaObject.idObject);
this.setType(javaObject.type);
this.setVersion(javaObject.version);
+ this.setLocalUrl(javaObject.localUrl);
+ this.setSourceUrl(javaObject.sourceUrl);
if (javaObject.localUrl !== undefined) {
this.setUrl(javaObject.localUrl);
} else {
this.setUrl(javaObject.sourceUrl);
}
+ this.setOrganism(new Annotation(javaObject.organism));
+ this.setDownloadProgress(javaObject.downloadProgress);
this._geneMapping = [];
if (javaObject.geneMapping !== undefined) {
for (var i = 0; i < javaObject.geneMapping.length; i++) {
this._geneMapping.push(new ReferenceGenomeGeneMapping(javaObject.geneMapping[i]));
}
}
+ } else {
+ this._geneMapping = [];
}
}
-ReferenceGenome.prototype.setType = function(type) {
+/**
+ *
+ * @param {string} type
+ */
+ReferenceGenome.prototype.setType = function (type) {
this._type = type;
};
-ReferenceGenome.prototype.getType = function() {
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getType = function () {
return this._type;
};
-ReferenceGenome.prototype.setUrl = function(url) {
+/**
+ *
+ * @param {number} id
+ */
+ReferenceGenome.prototype.setId = function (id) {
+ this._id = id;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenome.prototype.getId = function () {
+ return this._id;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenome.prototype.getDownloadProgress = function () {
+ return this._downloadProgress;
+};
+
+/**
+ *
+ * @param {number} downloadProgress
+ */
+ReferenceGenome.prototype.setDownloadProgress = function (downloadProgress) {
+ this._downloadProgress = downloadProgress;
+};
+
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getDownloadProgressStatus = function () {
+ if (this.getDownloadProgress() === 100) {
+ if (this.getLocalUrl() !== undefined) {
+ return "READY";
+ } else {
+ return "ERROR";
+ }
+ } else {
+ if (this.getDownloadProgress() === undefined) {
+ return "N/A";
+ } else {
+ return this.getDownloadProgress().toString();
+ }
+ }
+};
+
+
+/**
+ *
+ * @param {Annotation} organism
+ */
+ReferenceGenome.prototype.setOrganism = function (organism) {
+ this._organism = organism;
+};
+
+/**
+ *
+ * @returns {Annotation}
+ */
+ReferenceGenome.prototype.getOrganism = function () {
+ return this._organism;
+};
+
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenome.prototype.setUrl = function (url) {
this._url = url;
};
-ReferenceGenome.prototype.getUrl = function() {
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getUrl = function () {
return this._url;
};
-ReferenceGenome.prototype.setVersion = function(version) {
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getSourceUrl = function () {
+ return this._sourceUrl;
+};
+
+/**
+ *
+ * @param {string} sourceUrl
+ */
+ReferenceGenome.prototype.setSourceUrl = function (sourceUrl) {
+ this._sourceUrl = sourceUrl;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getLocalUrl = function () {
+ return this._localUrl;
+};
+
+/**
+ *
+ * @param {string} localUrl
+ */
+ReferenceGenome.prototype.setLocalUrl = function (localUrl) {
+ if (localUrl === null) {
+ this._localUrl = undefined;
+ } else {
+ this._localUrl = localUrl;
+ }
+};
+
+/**
+ *
+ * @param {string} version
+ */
+ReferenceGenome.prototype.setVersion = function (version) {
this._version = version;
};
-ReferenceGenome.prototype.getVersion = function() {
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getVersion = function () {
return this._version;
};
-ReferenceGenome.prototype.getGeneMappings = function() {
+/**
+ *
+ * @returns {ReferenceGenomeGeneMapping[]}
+ */
+ReferenceGenome.prototype.getGeneMappings = function () {
return this._geneMapping;
};
diff --git a/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js b/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
index 5b6ad8744b16c438f3150de669ea07540636dffa..b28f702bb5667b2d93d8672502bb26faa1b602a8 100644
--- a/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
+++ b/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
@@ -7,19 +7,106 @@ function ReferenceGenomeGeneMapping(javaObject) {
} else {
this.setUrl(javaObject.sourceUrl);
}
+ this.setLocalUrl(javaObject.localUrl);
+ this.setSourceUrl(javaObject.sourceUrl);
+ this.setProgress(javaObject.downloadProgress);
+ this.setId(javaObject.idObject);
}
-ReferenceGenomeGeneMapping.prototype.setName = function(name) {
+/**
+ *
+ * @param {string} name
+ */
+ReferenceGenomeGeneMapping.prototype.setName = function (name) {
this._name = name;
};
-ReferenceGenomeGeneMapping.prototype.setUrl = function(url) {
- this._url = url;
-};
-ReferenceGenomeGeneMapping.prototype.getName = function() {
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getName = function () {
return this._name;
};
-ReferenceGenomeGeneMapping.prototype.getUrl = function() {
+
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenomeGeneMapping.prototype.setUrl = function (url) {
+ this._url = url;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getUrl = function () {
return this._url;
};
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenomeGeneMapping.prototype.setLocalUrl = function (url) {
+ this._localUrl = url;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getLocalUrl = function () {
+ return this._localUrl;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getSourceUrl = function () {
+ return this._sourceUrl;
+};
+
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenomeGeneMapping.prototype.setSourceUrl = function (url) {
+ this._sourceUrl = url;
+};
+
+/**
+ *
+ * @param {number} progress
+ */
+ReferenceGenomeGeneMapping.prototype.setProgress = function (progress) {
+ this._progress = progress;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenomeGeneMapping.prototype.getProgress = function () {
+ return this._progress;
+};
+
+/**
+ *
+ * @param {number} id
+ */
+ReferenceGenomeGeneMapping.prototype.setId = function (id) {
+ this._id = id;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenomeGeneMapping.prototype.getId = function () {
+ return this._id;
+};
+
module.exports = ReferenceGenomeGeneMapping;
diff --git a/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js b/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
index bee43aa1ad2488796144079fca8f2670d7253723..16e07a3fe3d759e763ed2b449944a8e7fd57e0ac 100644
--- a/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
+++ b/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
@@ -13,14 +13,14 @@ var logger = require('../../logger');
* @param bioEntity
* initial bioEntity from which group is created
*/
-function SearchAliasGroup(bioEntity) {
+function SearchBioEntityGroup(bioEntity) {
if (!(bioEntity instanceof BioEntity)) {
throw new Error("Invalid argument");
}
this._bioEntites = [bioEntity];
}
-SearchAliasGroup.prototype.bioEntityMatch = function (newBioEntity) {
+SearchBioEntityGroup.prototype.bioEntityMatch = function (newBioEntity) {
var result = true;
var self = this;
@@ -33,15 +33,15 @@ SearchAliasGroup.prototype.bioEntityMatch = function (newBioEntity) {
return result;
};
-SearchAliasGroup.prototype.addBioEntity = function (newBioEntity) {
+SearchBioEntityGroup.prototype.addBioEntity = function (newBioEntity) {
this._bioEntites.push(newBioEntity);
};
-SearchAliasGroup.prototype.getBioEntities = function () {
+SearchBioEntityGroup.prototype.getBioEntities = function () {
return this._bioEntites;
};
-SearchAliasGroup.prototype.bioEntityComparator = function (bioEntity1, bioEntity2) {
+SearchBioEntityGroup.prototype.bioEntityComparator = function (bioEntity1, bioEntity2) {
if (bioEntity1 instanceof Alias && bioEntity2 instanceof Alias) {
if (bioEntity1.getName() !== bioEntity2.getName()) {
return -1;
@@ -92,89 +92,93 @@ SearchAliasGroup.prototype.bioEntityComparator = function (bioEntity1, bioEntity
return -9;
};
-SearchAliasGroup.prototype.setIcon = function (icon) {
+SearchBioEntityGroup.prototype.setIcon = function (icon) {
this._icon = icon;
};
-SearchAliasGroup.prototype.getIcon = function () {
+SearchBioEntityGroup.prototype.getIcon = function () {
return this._icon;
};
//aggregated data
-SearchAliasGroup.prototype.getType = function () {
+SearchBioEntityGroup.prototype.getType = function () {
return this._bioEntites[0].getType();
};
-SearchAliasGroup.prototype.getName = function () {
+SearchBioEntityGroup.prototype.getName = function () {
return this._bioEntites[0].getName();
};
-SearchAliasGroup.prototype.getModelId = function () {
+SearchBioEntityGroup.prototype.getModelId = function () {
return this._bioEntites[0].getModelId();
};
-SearchAliasGroup.prototype.getReactants = function () {
+SearchBioEntityGroup.prototype.getCompartmentId = function () {
+ return this._bioEntites[0].getCompartmentId();
+};
+
+SearchBioEntityGroup.prototype.getReactants = function () {
return this._bioEntites[0].getReactants();
};
-SearchAliasGroup.prototype.getProducts = function () {
+SearchBioEntityGroup.prototype.getProducts = function () {
return this._bioEntites[0].getProducts();
};
-SearchAliasGroup.prototype.getModifiers = function () {
+SearchBioEntityGroup.prototype.getModifiers = function () {
return this._bioEntites[0].getModifiers();
};
-SearchAliasGroup.prototype.getFullName = function () {
+SearchBioEntityGroup.prototype.getFullName = function () {
return this.getMergedParameterByFunction("getFullName");
};
-SearchAliasGroup.prototype.getReactionId = function () {
+SearchBioEntityGroup.prototype.getReactionId = function () {
return this.getMergedParameterByFunction("getReactionId");
};
-SearchAliasGroup.prototype.getLinkedSubmodelId = function () {
+SearchBioEntityGroup.prototype.getLinkedSubmodelId = function () {
return this.getMergedParameterByFunction("getLinkedSubmodelId");
};
-SearchAliasGroup.prototype.getSymbol = function () {
+SearchBioEntityGroup.prototype.getSymbol = function () {
return this.getMergedParameterByFunction("getSymbol");
};
-SearchAliasGroup.prototype.getAbbreviation = function () {
+SearchBioEntityGroup.prototype.getAbbreviation = function () {
return this.getMergedParameterByFunction("getAbbreviation");
};
-SearchAliasGroup.prototype.getFormula = function () {
+SearchBioEntityGroup.prototype.getFormula = function () {
return this.getMergedParameterByFunction("getFormula");
};
-SearchAliasGroup.prototype.getMechanicalConfidenceScore = function () {
+SearchBioEntityGroup.prototype.getMechanicalConfidenceScore = function () {
return this.getMergedParameterByFunction("getMechanicalConfidenceScore");
};
-SearchAliasGroup.prototype.getLowerBound = function () {
+SearchBioEntityGroup.prototype.getLowerBound = function () {
return this.getMergedParameterByFunction("getLowerBound");
};
-SearchAliasGroup.prototype.getUpperBound = function () {
+SearchBioEntityGroup.prototype.getUpperBound = function () {
return this.getMergedParameterByFunction("getUpperBound");
};
-SearchAliasGroup.prototype.getGeneProteinReaction = function () {
+SearchBioEntityGroup.prototype.getGeneProteinReaction = function () {
return this.getMergedParameterByFunction("getGeneProteinReaction");
};
-SearchAliasGroup.prototype.getSubsystem = function () {
+SearchBioEntityGroup.prototype.getSubsystem = function () {
return this.getMergedParameterByFunction("getSubsystem");
};
-SearchAliasGroup.prototype.getDescription = function () {
+SearchBioEntityGroup.prototype.getDescription = function () {
return this.getMergedParameterByFunction("getDescription");
};
-SearchAliasGroup.prototype.getCharge = function () {
+SearchBioEntityGroup.prototype.getCharge = function () {
return this.getMergedParameterByFunction("getCharge");
};
-SearchAliasGroup.prototype.getSynonyms = function () {
+SearchBioEntityGroup.prototype.getSynonyms = function () {
return this.getIntersectionListByFunction("getSynonyms");
};
-SearchAliasGroup.prototype.getFormerSymbols = function () {
+SearchBioEntityGroup.prototype.getFormerSymbols = function () {
return this.getIntersectionListByFunction("getFormerSymbols");
};
-SearchAliasGroup.prototype.getReferences = function () {
+SearchBioEntityGroup.prototype.getReferences = function () {
return this.getIntersectionListByFunction("getReferences");
};
-SearchAliasGroup.prototype.getOther = function (param) {
+SearchBioEntityGroup.prototype.getOther = function (param) {
if (param === "modifications") {
return this.getIntersectionListByFunction(function (alias) {
return alias.getOther(param)
@@ -184,7 +188,7 @@ SearchAliasGroup.prototype.getOther = function (param) {
}
};
-SearchAliasGroup.prototype.getMergedParameterByFunction = function (functionName) {
+SearchBioEntityGroup.prototype.getMergedParameterByFunction = function (functionName) {
var bioEntities = this.getBioEntities();
var result = bioEntities[0][functionName]();
for (var i = 1; i < bioEntities.length; i++) {
@@ -196,7 +200,7 @@ SearchAliasGroup.prototype.getMergedParameterByFunction = function (functionName
return result;
};
-SearchAliasGroup.prototype.getIntersectionListByFunction = function (functionName) {
+SearchBioEntityGroup.prototype.getIntersectionListByFunction = function (functionName) {
var bioEntities = this.getBioEntities();
var result;
if (typeof functionName === "function") {
@@ -220,4 +224,4 @@ SearchAliasGroup.prototype.getIntersectionListByFunction = function (functionNam
};
-module.exports = SearchAliasGroup;
+module.exports = SearchBioEntityGroup;
diff --git a/frontend-js/src/main/js/map/data/User.js b/frontend-js/src/main/js/map/data/User.js
index fdccd92f982a38273718678650934804e9f0f9e6..8c129f086c3f34238fc1b46169f8458b21b4398d 100644
--- a/frontend-js/src/main/js/map/data/User.js
+++ b/frontend-js/src/main/js/map/data/User.js
@@ -2,11 +2,17 @@
/* exported logger */
+// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
var UserPreferences = require('./UserPreferences');
var ObjectWithListeners = require('../../ObjectWithListeners');
+/**
+ *
+ * @param javaObject
+ * @constructor
+ */
function User(javaObject) {
// call super constructor
ObjectWithListeners.call(this);
@@ -25,6 +31,8 @@ function User(javaObject) {
this.setNeutralColor(javaObject.neutralColor);
this.setSimpleColor(javaObject.simpleColor);
this.setTermsOfUseConsent(javaObject.termsOfUseConsent);
+ this.setLdapAccountAvailable(javaObject.ldapAccountAvailable);
+ this.setConnectedToLdap(javaObject.connectedToLdap);
}
// this class inherits from ObjectWithListeners class where generic methods for
@@ -32,86 +40,170 @@ function User(javaObject) {
User.prototype = Object.create(ObjectWithListeners.prototype);
User.prototype.constructor = User;
+/**
+ *
+ * @param {string} login
+ */
User.prototype.setLogin = function (login) {
this._login = login;
};
+/**
+ *
+ * @returns {string}
+ */
User.prototype.getLogin = function () {
return this._login;
};
+/**
+ *
+ * @param {string} name
+ */
User.prototype.setName = function (name) {
this._name = name;
};
+/**
+ *
+ * @returns {string}
+ */
User.prototype.getName = function () {
return this._name;
};
+/**
+ *
+ * @param {string} surname
+ */
User.prototype.setSurname = function (surname) {
this._surname = surname;
};
+/**
+ *
+ * @returns {string}
+ */
User.prototype.getSurname = function () {
return this._surname;
};
+/**
+ *
+ * @param {string} email
+ */
User.prototype.setEmail = function (email) {
this._email = email;
};
+/**
+ *
+ * @returns {string}
+ */
User.prototype.getEmail = function () {
return this._email;
};
+/**
+ *
+ * @param {boolean} removed
+ */
User.prototype.setRemoved = function (removed) {
this._removed = removed;
};
+/**
+ *
+ * @returns {boolean}
+ */
User.prototype.getRemoved = function () {
return this._removed;
};
+/**
+ *
+ * @param {string} minColor
+ */
User.prototype.setMinColor = function (minColor) {
this._minColor = minColor;
};
+/**
+ *
+ * @returns {string}
+ */
User.prototype.getMinColor = function () {
return this._minColor;
};
+/**
+ *
+ * @param {string} simpleColor
+ */
User.prototype.setSimpleColor = function (simpleColor) {
this._simpleColor = simpleColor;
};
+/**
+ *
+ * @returns {string}
+ */
User.prototype.getSimpleColor = function () {
return this._simpleColor;
};
+/**
+ *
+ * @param {string} neutralColor
+ */
User.prototype.setNeutralColor = function (neutralColor) {
this._neutralColor = neutralColor;
};
+/**
+ *
+ * @returns {string}
+ */
User.prototype.getNeutralColor = function () {
return this._neutralColor;
};
+/**
+ *
+ * @param {string} maxColor
+ */
User.prototype.setMaxColor = function (maxColor) {
this._maxColor = maxColor;
};
+/**
+ *
+ * @returns {string}
+ */
User.prototype.getMaxColor = function () {
return this._maxColor;
};
+/**
+ *
+ * @param {string} password
+ */
User.prototype.setPassword = function (password) {
this._password = password;
};
+/**
+ *
+ * @returns {string}
+ */
User.prototype.getPassword = function () {
return this._password;
};
+/**
+ *
+ * @param {Object[]} privileges
+ */
User.prototype.setPrivileges = function (privileges) {
this._privileges = privileges;
if (this._privileges === undefined) {
@@ -119,10 +211,18 @@ User.prototype.setPrivileges = function (privileges) {
}
};
+/**
+ *
+ * @returns {Array}
+ */
User.prototype.getPrivileges = function () {
return this._privileges;
};
+/**
+ *
+ * @param {UserPreferences|Object} preferences
+ */
User.prototype.setPreferences = function (preferences) {
if (!(preferences instanceof UserPreferences)) {
preferences = new UserPreferences(preferences);
@@ -130,14 +230,31 @@ User.prototype.setPreferences = function (preferences) {
this._preferences = preferences;
};
+/**
+ *
+ * @returns {UserPreferences}
+ */
User.prototype.getPreferences = function () {
return this._preferences;
};
+/**
+ *
+ * @param {PrivilegeType} type
+ * @param {number} [objectId]
+ * @returns {boolean}
+ */
User.prototype.hasPrivilege = function (type, objectId) {
return this.getPrivilegeValue(type, objectId) > 0;
};
+/**
+ *
+ * @param {Object} params
+ * @param {number} params.objectId
+ * @param {PrivilegeType} params.type
+ * @param {number} [params.value=1]
+ */
User.prototype.setPrivilege = function (params) {
var objectId = params.objectId;
var type = params.type;
@@ -165,6 +282,13 @@ User.prototype.setPrivilege = function (params) {
});
};
+/**
+ *
+ * @param {PrivilegeType} type
+ * @param {number} [objectId]
+ *
+ * @returns {number}
+ */
User.prototype.getPrivilegeValue = function (type, objectId) {
for (var i = 0; i < this._privileges.length; i++) {
var privilege = this._privileges[i];
@@ -177,6 +301,12 @@ User.prototype.getPrivilegeValue = function (type, objectId) {
return 0;
};
+/**
+ *
+ * @param {Configuration} configuration
+ *
+ * @returns {Object}
+ */
User.prototype.privilegesToExport = function (configuration) {
var self = this;
var result = {};
@@ -201,6 +331,11 @@ User.prototype.privilegesToExport = function (configuration) {
return result;
};
+/**
+ *
+ * @param {User} user
+ * @returns {PromiseLike}
+ */
User.prototype.update = function (user) {
var self = this;
self.setLogin(user.getLogin());
@@ -217,12 +352,52 @@ User.prototype.update = function (user) {
return self.callListeners("onreload");
};
+/**
+ *
+ * @param {boolean} termsOfUseConsent
+ */
User.prototype.setTermsOfUseConsent = function (termsOfUseConsent) {
this._termsOfUseConsent = termsOfUseConsent;
};
+/**
+ *
+ * @returns {boolean}
+ */
User.prototype.isTermsOfUseConsent = function () {
return this._termsOfUseConsent;
};
+/**
+ *
+ * @param {boolean} ldapAccountAvailable
+ */
+User.prototype.setLdapAccountAvailable = function (ldapAccountAvailable) {
+ this._ldapAccountAvailable = ldapAccountAvailable;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+User.prototype.isLdapAccountAvailable = function () {
+ return this._ldapAccountAvailable;
+};
+
+/**
+ *
+ * @param {boolean} connectedToLdap
+ */
+User.prototype.setConnectedToLdap = function (connectedToLdap) {
+ this._connectedToLdap = connectedToLdap;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+User.prototype.isConnectedToLdap = function () {
+ return this._connectedToLdap;
+};
+
module.exports = User;
diff --git a/frontend-js/src/main/js/map/surface/AliasSurface.js b/frontend-js/src/main/js/map/surface/AliasSurface.js
index f7dc2968bc2c47f7f20d80ad3847b9fc11c9ecdc..b80391ef416accf3cd996390e639767efd78f6d5 100644
--- a/frontend-js/src/main/js/map/surface/AliasSurface.js
+++ b/frontend-js/src/main/js/map/surface/AliasSurface.js
@@ -1,260 +1,291 @@
-"use strict";
-
-/* exported logger */
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-var functions = require('../../Functions');
-
-var AbstractSurfaceElement = require('./AbstractSurfaceElement');
-var ConfigurationType = require('../../ConfigurationType');
-var IdentifiedElement = require('../data/IdentifiedElement');
-var Bounds = require('../canvas/Bounds');
-var Point = require('../canvas/Point');
-
-/**
- * Class representing overlay of the alias on the map relevant for a specific
- * layout.
- *
- * @param {LayoutAlias} [params.overlayAlias] - {@link LayoutAlias} for which overlay is created
- * @param {number} [params.startX] - this is the ratio on OX axis that should be use as a
- * starting point of the overlay. For instance when there are three
- * overlays to visualize then
- * <ul>
- * <li>the first layout have startX=0.0; endX=0.33333</li>
- * <li>second layout have startX=0.33333; endX=0.66666</li>
- * <li>the last layout have startX=0.66666; endX=1.0</li>
- * </ul>
- * @param {number} [params.endX] this is the ratio on OX axis that should be use as a
- * starting point of the overlay
-
- * @param {IdentifiedElement} [params.element]
- * @param {Alias} params.alias
- * @param {AbstractCustomMap} params.map
- * @param {function|function[]} [params.onClick]
- * @constructor
- * @extends AbstractSurfaceElement
- */
-function AliasSurface(params) {
- // call super constructor
- AbstractSurfaceElement.call(this, params);
-
- this.setOverlayData(params.overlayAlias);
- this.setStartX(params.startX);
- this.setEndX(params.endX);
-
- this.setColor(params.color);
- this.setFillOpacity(params.opacity);
- this.setStrokeWeight(params.strokeWeight);
- this.setStrokeColor(params.strokeColor);
- this.setStrokeOpacity(params.strokeOpacity);
-
- // original data
- this.setBioEntity(params.alias);
- this.setIdentifiedElement(new IdentifiedElement(params.alias));
-}
-
-AliasSurface.prototype = Object.create(AbstractSurfaceElement.prototype);
-AliasSurface.prototype.constructor = AliasSurface;
-
-/**
- *
- * @param {string} color
- */
-AliasSurface.prototype.setColor = function (color) {
- if (color === undefined) {
- color = "#FF0000";
- }
-
- this._color = color;
- var mapCanvasObjects = this.getMapCanvasObjects();
- for (var i = 0; i < mapCanvasObjects.length; i++) {
- mapCanvasObjects[i].setOptions({
- strokeColor: color
- });
- }
-};
-
-/**
- *
- * @param {number} opacity
- */
-AliasSurface.prototype.setFillOpacity = function (opacity) {
- this._fillOpacity = opacity;
-};
-
-/**
- *
- * @returns {number|undefined}
- */
-AliasSurface.prototype.getFillOpacity = function () {
- return this._fillOpacity;
-};
-
-/**
- *
- * @param {number} weight
- */
-AliasSurface.prototype.setStrokeWeight = function (weight) {
- if (weight === undefined) {
- weight = 1;
- }
- this._strokeWeight = weight;
-};
-
-/**
- *
- * @returns {number}
- */
-AliasSurface.prototype.getStrokeWeight = function () {
- return this._strokeWeight;
-};
-
-/**
- *
- * @param {string} color
- */
-AliasSurface.prototype.setStrokeColor = function (color) {
- if (color === undefined) {
- color = "#000000";
- }
- this._strokeColor = color;
-};
-
-/**
- *
- * @returns {string}
- */
-AliasSurface.prototype.getStrokeColor = function () {
- return this._strokeColor;
-};
-
-/**
- *
- * @param {number} opacity
- */
-AliasSurface.prototype.setStrokeOpacity = function (opacity) {
- if (opacity === undefined) {
- opacity = 1;
- }
- this._strokeOpacity = opacity;
-};
-
-AliasSurface.prototype.getStrokeOpacity = function () {
- return this._strokeOpacity;
-};
-
-/**
- * Function used to recalculate boundaries of the {@link AliasSurface}.
- * Boundaries define how big part of original alias is taken by this layout
- * visualization.
- *
- * @param {number} startX
- * value between 0..1 defining where should be the start on OX axis
- * @param {number} endX
- * value between 0..1 defining where should be the end on OX axis
- */
-AliasSurface.prototype.setBoundsForAlias = function (startX, endX) {
- var alias = this.getBioEntity();
- var pointA = new Point(alias.getX() + startX * alias.getWidth(), alias.getY());
- var pointB = new Point(alias.getX() + endX * alias.getWidth(), alias.getY() + alias.getHeight());
-
- var bounds = new Bounds(pointA, pointB);
- this.getMapCanvasObjects()[0].setBounds(bounds);
-};
-
-/**
- *
- * @returns {PromiseLike<any>}
- */
-AliasSurface.prototype.init = function () {
- var self = this;
- var overlayData = self.getOverlayData();
- var alias = self.getBioEntity();
- var map = self.getCustomMap();
- var startX = self.getStartX();
- var endX = self.getEndX();
-
- var pointA = new Point(alias.getX() + startX * alias.getWidth(), alias.getY());
- var pointB = new Point(alias.getX() + endX * alias.getWidth(), alias.getY() + alias.getHeight());
-
- var bounds = new Bounds(pointA, pointB);
- var fillOpacity;
- return ServerConnector.getConfigurationParam(ConfigurationType.OVERLAY_OPACITY).then(function (result) {
- fillOpacity = self.getFillOpacity();
- if (fillOpacity === undefined) {
- fillOpacity = result;
- }
- if (overlayData !== undefined) {
- return functions.overlayToColor(overlayData);
- } else {
- return "#FF0000";
- }
- }).then(function (color) {
- self.addMapCanvasObject(map.getMapCanvas().createRectangle({
- fillOpacity: fillOpacity,
- strokeColor: self.getStrokeColor(),
- strokeOpacity: self.getStrokeOpacity(),
- strokeWeight: self.getStrokeWeight(),
- fillColor: color,
- bounds: bounds
- }));
- });
-};
-
-/**
- *
- * @returns {LayoutAlias}
- */
-AliasSurface.prototype.getOverlayData = function () {
- return this._overlayData;
-};
-
-/**
- *
- * @param {LayoutAlias} overlayData
- */
-AliasSurface.prototype.setOverlayData = function (overlayData) {
- this._overlayData = overlayData;
-};
-
-/**
- *
- * @returns {number}
- */
-AliasSurface.prototype.getStartX = function () {
- return this._startX;
-};
-
-/**
- *
- * @param {number} startX
- */
-AliasSurface.prototype.setStartX = function (startX) {
- if (startX === undefined) {
- startX = 0;
- }
- this._startX = startX;
-};
-
-/**
- *
- * @returns {number}
- */
-AliasSurface.prototype.getEndX = function () {
- return this._endX;
-};
-
-/**
- *
- * @param {number} endX
- */
-AliasSurface.prototype.setEndX = function (endX) {
- if (endX === undefined) {
- endX = 1;
- }
- this._endX = endX;
-};
-
-
-module.exports = AliasSurface;
+"use strict";
+
+/* exported logger */
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+var functions = require('../../Functions');
+
+var AbstractSurfaceElement = require('./AbstractSurfaceElement');
+var ConfigurationType = require('../../ConfigurationType');
+var IdentifiedElement = require('../data/IdentifiedElement');
+var Bounds = require('../canvas/Bounds');
+var Point = require('../canvas/Point');
+
+/**
+ * Class representing overlay of the alias on the map relevant for a specific
+ * layout.
+ *
+ * @param {LayoutAlias[]} [params.overlayData] - {@link LayoutAlias} for which overlay is created
+ * @param {number} [params.startX] - this is the ratio on OX axis that should be use as a
+ * starting point of the overlay. For instance when there are three
+ * overlays to visualize then
+ * <ul>
+ * <li>the first layout have startX=0.0; endX=0.33333</li>
+ * <li>second layout have startX=0.33333; endX=0.66666</li>
+ * <li>the last layout have startX=0.66666; endX=1.0</li>
+ * </ul>
+ * @param {number} [params.endX] this is the ratio on OX axis that should be use as a
+ * starting point of the overlay
+
+ * @param {IdentifiedElement} [params.element]
+ * @param {Alias} params.alias
+ * @param {AbstractCustomMap} params.map
+ * @param {function|function[]} [params.onClick]
+ * @constructor
+ * @extends AbstractSurfaceElement
+ */
+function AliasSurface(params) {
+ // call super constructor
+ AbstractSurfaceElement.call(this, params);
+ if (params.overlayAlias !== undefined) {
+ throw new Error();
+ }
+
+ this.setOverlayData(params.overlayData);
+ this.setStartX(params.startX);
+ this.setEndX(params.endX);
+
+ this.setColor(params.color);
+ this.setFillOpacity(params.opacity);
+ this.setStrokeWeight(params.strokeWeight);
+ this.setStrokeColor(params.strokeColor);
+ this.setStrokeOpacity(params.strokeOpacity);
+
+ // original data
+ this.setBioEntity(params.alias);
+ this.setIdentifiedElement(new IdentifiedElement(params.alias));
+}
+
+AliasSurface.prototype = Object.create(AbstractSurfaceElement.prototype);
+AliasSurface.prototype.constructor = AliasSurface;
+
+/**
+ *
+ * @param {string} color
+ */
+AliasSurface.prototype.setColor = function (color) {
+ if (color === undefined) {
+ color = "#FF0000";
+ }
+
+ this._color = color;
+ var mapCanvasObjects = this.getMapCanvasObjects();
+ for (var i = 0; i < mapCanvasObjects.length; i++) {
+ mapCanvasObjects[i].setOptions({
+ strokeColor: color
+ });
+ }
+};
+
+/**
+ *
+ * @returns {string}
+ */
+AliasSurface.prototype.getColor = function () {
+ return this._color;
+};
+
+/**
+ *
+ * @param {number} opacity
+ */
+AliasSurface.prototype.setFillOpacity = function (opacity) {
+ this._fillOpacity = opacity;
+};
+
+/**
+ *
+ * @returns {number|undefined}
+ */
+AliasSurface.prototype.getFillOpacity = function () {
+ return this._fillOpacity;
+};
+
+/**
+ *
+ * @param {number} weight
+ */
+AliasSurface.prototype.setStrokeWeight = function (weight) {
+ if (weight === undefined) {
+ weight = 1;
+ }
+ this._strokeWeight = weight;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+AliasSurface.prototype.getStrokeWeight = function () {
+ return this._strokeWeight;
+};
+
+/**
+ *
+ * @param {string} color
+ */
+AliasSurface.prototype.setStrokeColor = function (color) {
+ if (color === undefined) {
+ color = "#000000";
+ }
+ this._strokeColor = color;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+AliasSurface.prototype.getStrokeColor = function () {
+ return this._strokeColor;
+};
+
+/**
+ *
+ * @param {number} opacity
+ */
+AliasSurface.prototype.setStrokeOpacity = function (opacity) {
+ if (opacity === undefined) {
+ opacity = 1;
+ }
+ this._strokeOpacity = opacity;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+AliasSurface.prototype.getStrokeOpacity = function () {
+ return this._strokeOpacity;
+};
+
+/**
+ * Function used to recalculate boundaries of the {@link AliasSurface}.
+ * Boundaries define how big part of original alias is taken by this layout
+ * visualization.
+ *
+ * @param {number} startX
+ * value between 0..1 defining where should be the start on OX axis
+ * @param {number} endX
+ * value between 0..1 defining where should be the end on OX axis
+ */
+AliasSurface.prototype.setBoundsForAlias = function (startX, endX) {
+ var alias = this.getBioEntity();
+ var pointA = new Point(alias.getX() + startX * alias.getWidth(), alias.getY());
+ var pointB = new Point(alias.getX() + endX * alias.getWidth(), alias.getY() + alias.getHeight());
+
+ var bounds = new Bounds(pointA, pointB);
+ this.getMapCanvasObjects()[0].setBounds(bounds);
+};
+
+AliasSurface.prototype._computeColors = function () {
+ var self = this;
+ var overlayData = self.getOverlayData();
+ if (overlayData === undefined || overlayData.length === 0) {
+ return self.getColor();
+ } else {
+ return functions.overlaysToColorDataStructure(overlayData);
+ }
+
+};
+/**
+ *
+ * @returns {PromiseLike<any>}
+ */
+AliasSurface.prototype.init = function () {
+ var self = this;
+ var alias = self.getBioEntity();
+ var map = self.getCustomMap();
+ var startX = self.getStartX();
+ var endX = self.getEndX();
+
+ var pointA = new Point(alias.getX() + startX * alias.getWidth(), alias.getY());
+ var pointB = new Point(alias.getX() + endX * alias.getWidth(), alias.getY() + alias.getHeight());
+
+ var bounds = new Bounds(pointA, pointB);
+ var fillOpacity;
+ return map.getServerConnector().getConfigurationParam(ConfigurationType.OVERLAY_OPACITY).then(function (result) {
+ fillOpacity = self.getFillOpacity();
+ if (fillOpacity === undefined) {
+ fillOpacity = result;
+ }
+ return self._computeColors();
+ }).then(function (color) {
+ if (typeof color === 'string' || color instanceof String) {
+ self.addMapCanvasObject(map.getMapCanvas().createRectangle({
+ fillOpacity: fillOpacity,
+ strokeColor: self.getStrokeColor(),
+ strokeOpacity: self.getStrokeOpacity(),
+ strokeWeight: self.getStrokeWeight(),
+ fillColor: color,
+ bounds: bounds
+ }));
+ } else {
+ self.addMapCanvasObject(map.getMapCanvas().createRectangle({
+ fillOpacity: fillOpacity,
+ strokeColor: self.getStrokeColor(),
+ strokeOpacity: self.getStrokeOpacity(),
+ strokeWeight: self.getStrokeWeight(),
+ fillGradient: color,
+ bounds: bounds
+ }));
+ }
+ });
+};
+
+/**
+ *
+ * @returns {LayoutAlias[]}
+ */
+AliasSurface.prototype.getOverlayData = function () {
+ return this._overlayData;
+};
+
+/**
+ *
+ * @param {LayoutAlias[]} overlayData
+ */
+AliasSurface.prototype.setOverlayData = function (overlayData) {
+ this._overlayData = overlayData;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+AliasSurface.prototype.getStartX = function () {
+ return this._startX;
+};
+
+/**
+ *
+ * @param {number} startX
+ */
+AliasSurface.prototype.setStartX = function (startX) {
+ if (startX === undefined) {
+ startX = 0;
+ }
+ this._startX = startX;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+AliasSurface.prototype.getEndX = function () {
+ return this._endX;
+};
+
+/**
+ *
+ * @param {number} endX
+ */
+AliasSurface.prototype.setEndX = function (endX) {
+ if (endX === undefined) {
+ endX = 1;
+ }
+ this._endX = endX;
+};
+
+
+module.exports = AliasSurface;
diff --git a/frontend-js/src/main/js/map/window/AbstractInfoWindow.js b/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
index c174f946a93fbf7a57590a1c94d5a0e60b53f37e..63a91ad29070633a007e64f983e726c8df451051 100644
--- a/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
@@ -1,743 +1,743 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var logger = require('../../logger');
-var Functions = require('../../Functions');
-
-var Comment = require('../data/Comment');
-var GuiConnector = require('../../GuiConnector');
-var GuiUtils = require('../../gui/leftPanel/GuiUtils');
-var IdentifiedElement = require('../data/IdentifiedElement');
-var ObjectWithListeners = require('../../ObjectWithListeners');
-var TargettingStructure = require('../data/TargettingStructure');
-
-/**
- * Class representing any info window in our map.
- *
- * @param {IdentifiedElement} params.identifiedElement
- * @param {AbstractCustomMap} params.map
- * @param {Marker} params.marker
- *
- * @constructor
- */
-function AbstractInfoWindow(params) {
- // call super constructor
- ObjectWithListeners.call(this);
-
- var self = this;
-
- self.setIdentifiedElement(params.identifiedElement);
-
- self.setCustomMap(params.map);
- self.setMarker(params.marker);
-
- self.setContent(this.createWaitingContentDiv());
-
- self._overlayFullView = [];
-
- self.registerPropertyType("overlayFullView");
-
- self.registerListenerType("onShow");
- self.registerListenerType("onUpdate");
-
- self.setGuiUtils(new GuiUtils());
-
- var dbOverlaySearchChanged = function () {
- return self.update();
- };
- var searchDbOverlay = params.map.getTopMap().getOverlayByName("search");
- if (searchDbOverlay !== undefined) {
- searchDbOverlay.addListener("onSearch", dbOverlaySearchChanged);
- }
- var commentDbOverlay = params.map.getTopMap().getOverlayByName("comment");
- if (commentDbOverlay !== undefined) {
- commentDbOverlay.addListener("onSearch", dbOverlaySearchChanged);
- }
-}
-
-AbstractInfoWindow.prototype = Object.create(ObjectWithListeners.prototype);
-AbstractInfoWindow.prototype.constructor = AbstractInfoWindow;
-
-/**
- * Returns <code>true</code> if overlay should visualize all possible values.
- *
- * @param {string} overlayName
- * name of the overlay
- * @returns {boolean}, <code>true</code> if overlay should visualize all possible values
- */
-AbstractInfoWindow.prototype.isOverlayFullView = function (overlayName) {
- if (this._overlayFullView[overlayName] === undefined) {
- this._overlayFullView[overlayName] = false;
- }
- return this._overlayFullView[overlayName];
-};
-
-/**
- * Returns associative array with information if specific overlay should present
- * all possible results or only specified by the data searched by user.
- *
- * @returns {Object.<string,boolean>} with information if specific overlay should present all
- * possible results or only specified by the data searched by user
- */
-AbstractInfoWindow.prototype.getOverlayFullViewArray = function () {
- return this._overlayFullView;
-};
-
-/**
- *
- * @param {string} overlayName
- * @param {boolean} value
- * @returns {Promise}
- */
-AbstractInfoWindow.prototype.setOverlayFullView = function (overlayName, value) {
- var oldVal = this._overlayFullView[overlayName];
- this._overlayFullView[overlayName] = value;
- if (oldVal !== value) {
- return this.firePropertyChangeListener("overlayFullView", overlayName + "," + oldVal, value);
- } else {
- return Promise.resolve();
- }
-};
-
-/**
- * This method checks if {@link AbstractInfoWindow} is opened.
- *
- * @returns {Boolean} <code>true</code> if window is opened,
- * <code>false</code> otherwise
- */
-AbstractInfoWindow.prototype.isOpened = function () {
- if (this._infoWindow === undefined) {
- return false;
- }
- return this._infoWindow.isOpened();
-};
-
-/**
- * Opens Info Window.
- *
- * @param {Marker} [newMarker]
- *
- * @returns {PromiseLike<any> | Promise<any>}
- */
-AbstractInfoWindow.prototype.open = function (newMarker) {
- var self = this;
- var infoWindow = self._infoWindow;
- if (infoWindow === null || infoWindow === undefined) {
- logger.warn("Cannot open window.");
- return Promise.resolve();
- }
- if (newMarker !== undefined) {
- infoWindow.setMarker(newMarker);
- }
- infoWindow.open();
-
- return self.update().then(function () {
- return self.callListeners("onShow");
- });
-};
-
-/**
- * Sets new content of the info window.
- *
- * @param {HTMLElement|string} content
- * new content of the window
- */
-AbstractInfoWindow.prototype.setContent = function (content) {
- var self = this;
- self._content = content;
- if (self._infoWindow !== undefined) {
- self._infoWindow.setContent(content);
- }
-};
-
-/**
- * Returns content visualized in the info window.
- *
- * @returns {string|HTMLElement} content visualized in the info window
- */
-AbstractInfoWindow.prototype.getContent = function () {
- return this._content;
-};
-
-/**
- * Creates div for an overlay data.
- *
- * @param {AbstractDbOverlay} overlay
- * corresponding overlay
- * @param {BioEntity[]|Comment[]|Drug[]|MiRna[]|Chemical[]} data
- * data taken from overlay
- * @returns {HTMLElement} div for given overlay data
- */
-AbstractInfoWindow.prototype.createOverlayInfoDiv = function (overlay, data) {
- var alias = this.alias;
- if (alias !== undefined) {
- if (alias.getType() !== undefined) {
- if (overlay.name === "drug") {
- if (alias.getType().toUpperCase() === "RNA" || //
- alias.getType().toUpperCase() === "PROTEIN" || //
- alias.getType().toUpperCase() === "GENE") {
- return this._createDrugInfoDiv(overlay, data);
- } else {
- return null;
- }
- } else if (overlay.name === "chemical") {
- if (this.alias.getType().toUpperCase() === "RNA" || //
- alias.getType().toUpperCase() === "PROTEIN" || //
- alias.getType().toUpperCase() === "GENE") {
- return this._createChemicalInfoDiv(overlay, data);
- } else {
- return null;
- }
- } else if (overlay.name === "mirna") {
- if (alias.getType().toUpperCase() === "RNA" || //
- alias.getType().toUpperCase() === "PROTEIN" || //
- alias.getType().toUpperCase() === "GENE") {
- return this._createMiRnaInfoDiv(overlay, data);
- } else {
- return null;
- }
-
- } else if (overlay.name === "comment") {
- return this._createCommentInfoDiv(overlay, data);
- } else {
- logger.warn("Unknown overlay data for AliasInfoWindow: " + overlay.name);
- return this._createDefaultInfoDiv(overlay, data);
- }
- } else {
- logger.debug(alias);
- throw new Error("Cannot customize info window. Alias type is unknown ");
- }
- } else {
- if (overlay.getName() === "comment") {
- return this._createCommentInfoDiv(overlay, data);
- } else {
- logger.debug("Cannot customize info window. Alias not defined. Overlay: " + overlay.getName());
- return null;
- }
- }
-};
-
-/**
- * Creates and returns div for drug overlay information.
- *
- * @param {AbstractDbOverlay} overlay
- * @param {Drug[]} data
- * data taken from drug overlay
- * @returns {HTMLElement} div for drug overlay information
- * @private
- */
-AbstractInfoWindow.prototype._createDrugInfoDiv = function (overlay, data) {
- return this._createTargetInfoDiv({
- overlay: overlay,
- data: data,
- name: "Interacting drugs"
- });
-};
-
-/**
- * Creates and returns div for comment overlay information.
- *
- * @param {AbstractDbOverlay} overlay
- * @param {Comment[]} data
- * data taken from comment overlay
- * @returns {HTMLElement} div for comment overlay information
- */
-AbstractInfoWindow.prototype._createCommentInfoDiv = function (overlay, data) {
- if (data.length === 0 || data[0] === undefined) {
- return null;
- }
- var result = document.createElement("div");
-
- var titleElement = document.createElement("h3");
- titleElement.innerHTML = "Comments";
- result.appendChild(titleElement);
- for (var i = 0; i < data.length; i++) {
- var comment = data[i];
- if (comment instanceof Comment) {
- if (!comment.isRemoved()) {
- result.appendChild(document.createElement("hr"));
- var commentId = document.createElement("div");
- commentId.innerHTML = '#' + comment.getId();
- result.appendChild(commentId);
- result.appendChild(document.createElement("br"));
- var commentContent = Functions.createElement({type: "div", content: comment.getContent(), xss: true});
-
- result.appendChild(commentContent);
- }
- } else {
- throw new Error("Invalid comment data: " + comment);
- }
- }
-
- return result;
-};
-
-/**
- * Creates and returns div for unknown overlay.
- *
- * @param {AbstractDbOverlay} overlay
- * @param {Array} data
- * data taken from overlay
- * @returns {HTMLElement} div for overlay information
- */
-
-AbstractInfoWindow.prototype._createDefaultInfoDiv = function (overlay, data) {
- var divElement = document.createElement("div");
- var count = 0;
-
- var titleElement = document.createElement("h3");
- var title = document.createTextNode(overlay.getName());
- titleElement.appendChild(title);
- divElement.appendChild(titleElement);
- for (var searchId in data) {
- if (data.hasOwnProperty(searchId) && data[searchId] !== undefined && data[searchId] !== null) {
- count++;
- var resultTitleElement = document.createElement("h4");
- var resultTitle = document.createTextNode(searchId);
- resultTitleElement.appendChild(resultTitle);
- divElement.appendChild(resultTitleElement);
-
- var keys = Object.keys(data[searchId]);
- for (var i = 0; i < keys.length; i++) {
- var resultValElement = document.createElement("p");
- var resultVal = document.createTextNode(keys[i] + ": " + data[searchId][keys[i]]);
- resultValElement.appendChild(resultVal);
- divElement.appendChild(resultValElement);
- }
- }
- }
-
- if (count === 0) {
- divElement = null;
- }
- return divElement;
-};
-
-/**
- * Returns Marker object where this info window is attached.
- *
- * @returns {Marker} object where this info window is attached
- */
-AbstractInfoWindow.prototype.getMarker = function () {
- return this._marker;
-};
-
-/**
- *
- * @param {Marker} marker
- */
-AbstractInfoWindow.prototype.setMarker = function (marker) {
- this._marker = marker;
- if (this._infoWindow !== undefined) {
- this._infoWindow.setMarker(marker);
- }
-};
-
-/**
- * Returns {@link AbstractCustomMap} where this window is presented.
- *
- * @returns {AbstractCustomMap} where this window is presented
- */
-AbstractInfoWindow.prototype.getCustomMap = function () {
- return this.customMap;
-};
-
-/**
- *
- * @param {AbstractCustomMap} map
- */
-AbstractInfoWindow.prototype.setCustomMap = function (map) {
- if (map === undefined) {
- throw new Error("Map must be defined");
- }
- this.customMap = map;
-};
-
-/**
- * Returns html DOM object with content that should presented when waiting for
- * some data from server.
- *
- * @returns {HTMLElement} html with content that should presented when waiting for
- * some data from server
- */
-AbstractInfoWindow.prototype.createWaitingContentDiv = function () {
- var result = document.createElement("div");
- var img = document.createElement("img");
- img.src = GuiConnector.getImgPrefix() + GuiConnector.getLoadingImg();
- var message = document.createElement("h4");
- message.innerHTML = "loading...";
- result.appendChild(img);
- result.appendChild(message);
- return result;
-};
-
-/**
- * This is a generic method that updates content of the window.
- *
- * @returns {Promise|PromiseLike}
- * @private
- */
-AbstractInfoWindow.prototype._updateContent = function () {
- var contentDiv = null;
- var self = this;
-
- if (!self.isOpened()) {
- return Promise.resolve();
- } else {
- self.setContent(self.createWaitingContentDiv());
-
- return self.createContentDiv().then(function (content) {
- contentDiv = content;
- return self.createOverlaysDiv();
- }).then(function (overlaysDiv) {
- if (overlaysDiv !== undefined && overlaysDiv !== null) {
- contentDiv.appendChild(overlaysDiv);
- }
- self.setContent(contentDiv);
- return self.callListeners("onUpdate");
- }).then(function () {
- return contentDiv;
- });
- }
-};
-
-/**
- * Creates and returns div with overlays content.
- *
- * @returns {Promise<HTMLElement>} with html representing data taken from
- * {@link AbstractDbOverlay} for this window
- */
-AbstractInfoWindow.prototype.createOverlaysDiv = function () {
- var self = this;
- var result = document.createElement("div");
- return this.getOverlaysData(self.getOverlayFullViewArray()).then(function (overlayData) {
- for (var i = 0; i < overlayData.length; i++) {
- var overlay = overlayData[i].overlay;
- var data = overlayData[i].data;
- var overlayInfo = self.createOverlayInfoDiv(overlay, data);
- if (overlayInfo !== null) {
- result.appendChild(overlayInfo);
- }
- }
- return result;
- });
-};
-
-// noinspection JSUnusedLocalSymbols
-/**
- * Returns array with data taken from all known {@link AbstractDbOverlay}.
- *
- * @param {Object.<string,boolean>} general
- * if true then all elements will be returned, if false then only ones
- * available right now in the overlay
- *
- * @returns {Promise} array with data from {@link AbstractDbOverlay}
- */
-AbstractInfoWindow.prototype.getOverlaysData = function (general) {
- throw new Error("Not implemented");
-};
-
-/**
- * Abstract method (to be implemented by subclasses) for updating content.
- *
- * @returns {Promise}
- */
-AbstractInfoWindow.prototype.update = function () {
- return this._updateContent();
-};
-
-/**
- *
- * @param {string} params.name
- * @param {AbstractDbOverlay} params.overlay
- * @param {Array} params.data
- * @returns {HTMLElement}
- * @private
- */
-AbstractInfoWindow.prototype._createTargetInfoDiv = function (params) {
- var overlay = params.overlay;
- var data = params.data;
- var name = params.name;
-
- var self = this;
- var result = document.createElement("div");
-
- var titleElement = document.createElement("h3");
- titleElement.innerHTML = name;
- result.appendChild(titleElement);
- if (overlay.allowGeneralSearch()) {
- var checkboxDiv = document.createElement("div");
- checkboxDiv.style.float = "right";
-
- var checkbox = document.createElement("input");
- checkbox.id = "checkbox-" + name + "-" + this.getElementType() + "-" + this.getElementId();
- checkbox.type = "checkbox";
- checkbox.checked = self.isOverlayFullView(overlay.getName());
- checkbox.onclick = function () {
- return self.setOverlayFullView(overlay.getName(), this.checked).then(null, GuiConnector.alert);
- };
-
- checkboxDiv.appendChild(checkbox);
-
- var description = document.createElement("div");
- description.style.float = "right";
- description.innerHTML = "Show all";
- checkboxDiv.appendChild(description);
- result.appendChild(checkboxDiv);
- }
- var count = 0;
- for (var dataId in data) {
- if (data.hasOwnProperty(dataId)) {
- count++;
- }
- }
-
- var table = self._createTableForTargetDiv(data, overlay);
-
- if (count === 0 && !overlay.allowGeneralSearch() && !this.isOverlayFullView(overlay.getName())) {
- result = null;
- }
- if (result !== null) {
- result.appendChild(table);
- }
- return result;
-};
-
-/**
- *
- * @param {Array} data
- * @param {AbstractDbOverlay} overlay
- * @returns {HTMLElement}
- * @private
- */
-AbstractInfoWindow.prototype._createTableForTargetDiv = function (data, overlay) {
- var self = this;
- var table = document.createElement("table");
- table.className = "minerva-window-drug-table";
- var header = document.createElement("tr");
- var headerCol = document.createElement("th");
- headerCol.innerHTML = "Name";
- header.appendChild(headerCol);
- headerCol = document.createElement("th");
- headerCol.innerHTML = "References";
- header.appendChild(headerCol);
-
- var cell;
- table.appendChild(header);
- var row;
-
- var onclick = function () {
- // ';' enforces single query (in case there are ',' characters in the name)
- return overlay.searchByQuery(this.innerHTML + ";");
- };
-
- var count = 0;
- for (var searchId in data) {
- if (data.hasOwnProperty(searchId)) {
-
- row = document.createElement("tr");
- var nameContent = searchId;
- var annotations = [];
- if (typeof data[searchId] === "string") {
- nameContent = data[searchId];
- } else if (data[searchId] instanceof TargettingStructure) {
- nameContent = data[searchId].getName();
- var targets = data[searchId].getTargetsForIdentifiedElement(self.getIdentifiedElement());
- for (var i = 0; i < targets.length; i++) {
- var references = targets[i].getReferences();
- for (var j = 0; j < references.length; j++) {
- annotations.push(references[j]);
- }
- }
- }
- var link = Functions.createElement({
- type: "a",
- onclick: onclick,
- href: "#",
- content: nameContent
- });
-
- var nameTd = Functions.createElement({
- type: "td"
- });
- nameTd.appendChild(link);
- row.appendChild(nameTd);
-
- var referencesCell = Functions.createElement({
- type: "td"
- });
- referencesCell.appendChild(self.getGuiUtils().createAnnotationList(annotations, {groupAnnotations: false}));
-
- row.appendChild(referencesCell);
-
- table.appendChild(row);
- count++;
- }
- }
-
- if (self.isOverlayFullView(overlay.getName()) && count === 0) {
- row = document.createElement("tr");
- cell = document.createElement("td");
- cell.colSpan = 2;
- cell.innerHTML = "No results available";
- row.appendChild(cell);
- table.appendChild(row);
- }
-
- if (!self.isOverlayFullView(overlay.getName()) && count === 0 && overlay.allowGeneralSearch()) {
- row = document.createElement("tr");
- cell = document.createElement("td");
- cell.colSpan = 2;
- cell.innerHTML = "Search for available targets";
- row.appendChild(cell);
- table.appendChild(row);
- }
- return table;
-};
-
-/**
- *
- * @returns {PromiseLike<any> | Promise<any>}
- */
-AbstractInfoWindow.prototype.init = function () {
- var self = this;
- var promises = [
- // default settings of visualizing full information about elements
- this.setOverlayFullView("drug", false),
- this.setOverlayFullView("chemical", false),
- this.setOverlayFullView("mirna", false),
- this.setOverlayFullView("search", false),
- // only all comments should be visible from the beginning
- this.setOverlayFullView("comment", true)
- ];
-
- return Promise.all(promises).then(function () {
- // listener called when user want to see all data about specific data overlay
- var onOverlayFullViewChanged = function (e) {
- var self = e.object;
- // first change the content of the element
- return self.update().then(function () {
- if (e.newVal) {
- var element = new IdentifiedElement({
- objectId: self.getElementId(),
- modelId: self.getCustomMap().getId(),
- type: self.getElementType()
- });
- var topMap = self.getCustomMap().getTopMap();
- return topMap.retrieveOverlayDetailDataForElement(element, self.getOverlayFullViewArray());
- }
- });
-
- };
-
- self.addPropertyChangeListener("overlayFullView", onOverlayFullViewChanged);
-
- self._infoWindow = self.getCustomMap().getMapCanvas().createInfoWindow({
- content: self.content,
- position: self.getPosition(),
- marker: self._marker
- });
-
- return ServerConnector.getConfiguration();
- }).then(function (configuration) {
- self.getGuiUtils().setConfiguration(configuration);
- self.getGuiUtils().setMap(self.getCustomMap());
- });
-};
-
-/**
- *
- * @param {GuiUtils} guiUtils
- */
-AbstractInfoWindow.prototype.setGuiUtils = function (guiUtils) {
- this._guiUtils = guiUtils;
-};
-
-/**
- *
- * @returns {GuiUtils}
- */
-AbstractInfoWindow.prototype.getGuiUtils = function () {
- return this._guiUtils;
-};
-
-/**
- * Creates and returns DOM div for chemical overlay information.
- *
- * @param {AbstractDbOverlay} overlay
- * @param {Chemical[]} data
- * data taken from chemical overlay
- * @returns {HTMLElement} element with a div for comment overlay information
- * @private
- */
-AbstractInfoWindow.prototype._createChemicalInfoDiv = function (overlay, data) {
- return this._createTargetInfoDiv({
- overlay: overlay,
- data: data,
- name: "Interacting chemicals"
- });
-};
-
-/**
- * Creates and returns DOM div for mi rna overlay information.
- *
- * @param {AbstractDbOverlay} overlay
- * @param {MiRna[]} data
- * data taken from mi rna overlay
- * @returns {HTMLElement} DOM element with a div for comment overlay information
- */
-AbstractInfoWindow.prototype._createMiRnaInfoDiv = function (overlay, data) {
- return this._createTargetInfoDiv({
- overlay: overlay,
- data: data,
- name: "Interacting Micro RNAs"
- });
-};
-
-/**
- *
- * @param {IdentifiedElement} identifiedElement
- */
-AbstractInfoWindow.prototype.setIdentifiedElement = function (identifiedElement) {
- if (identifiedElement === undefined) {
- throw new Error("identifiedElement cannot be undefined");
- }
- this._identifiedElement = identifiedElement;
-};
-
-/**
- *
- * @returns {IdentifiedElement}
- */
-AbstractInfoWindow.prototype.getIdentifiedElement = function () {
- return this._identifiedElement;
-};
-
-
-/**
- * Method returning identifier of the object for which this window was created.
- *
- * @returns {string|number}
- */
-AbstractInfoWindow.prototype.getElementId = function () {
- return this.getIdentifiedElement().getId();
-};
-
-/**
- * Method returning type of the object for which this window was created.
- *
- * @returns {string}
- */
-AbstractInfoWindow.prototype.getElementType = function () {
- return this.getIdentifiedElement().getType();
-};
-
-/**
- * @returns {Point}
- */
-AbstractInfoWindow.prototype.getPosition = function () {
- throw new Error("Not Implemented");
-};
-
-module.exports = AbstractInfoWindow;
+"use strict";
+
+var Promise = require("bluebird");
+
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+
+var Comment = require('../data/Comment');
+var GuiConnector = require('../../GuiConnector');
+var GuiUtils = require('../../gui/leftPanel/GuiUtils');
+var IdentifiedElement = require('../data/IdentifiedElement');
+var ObjectWithListeners = require('../../ObjectWithListeners');
+var TargettingStructure = require('../data/TargettingStructure');
+
+/**
+ * Class representing any info window in our map.
+ *
+ * @param {IdentifiedElement} params.identifiedElement
+ * @param {AbstractCustomMap} params.map
+ * @param {Marker} params.marker
+ *
+ * @constructor
+ */
+function AbstractInfoWindow(params) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ var self = this;
+
+ self.setIdentifiedElement(params.identifiedElement);
+
+ self.setCustomMap(params.map);
+ self.setMarker(params.marker);
+
+ self.setContent(this.createWaitingContentDiv());
+
+ self._overlayFullView = [];
+
+ self.registerPropertyType("overlayFullView");
+
+ self.registerListenerType("onShow");
+ self.registerListenerType("onUpdate");
+
+ self.setGuiUtils(new GuiUtils());
+
+ var dbOverlaySearchChanged = function () {
+ return self.update();
+ };
+ var searchDbOverlay = params.map.getTopMap().getOverlayByName("search");
+ if (searchDbOverlay !== undefined) {
+ searchDbOverlay.addListener("onSearch", dbOverlaySearchChanged);
+ }
+ var commentDbOverlay = params.map.getTopMap().getOverlayByName("comment");
+ if (commentDbOverlay !== undefined) {
+ commentDbOverlay.addListener("onSearch", dbOverlaySearchChanged);
+ }
+}
+
+AbstractInfoWindow.prototype = Object.create(ObjectWithListeners.prototype);
+AbstractInfoWindow.prototype.constructor = AbstractInfoWindow;
+
+/**
+ * Returns <code>true</code> if overlay should visualize all possible values.
+ *
+ * @param {string} overlayName
+ * name of the overlay
+ * @returns {boolean}, <code>true</code> if overlay should visualize all possible values
+ */
+AbstractInfoWindow.prototype.isOverlayFullView = function (overlayName) {
+ if (this._overlayFullView[overlayName] === undefined) {
+ this._overlayFullView[overlayName] = false;
+ }
+ return this._overlayFullView[overlayName];
+};
+
+/**
+ * Returns associative array with information if specific overlay should present
+ * all possible results or only specified by the data searched by user.
+ *
+ * @returns {Object.<string,boolean>} with information if specific overlay should present all
+ * possible results or only specified by the data searched by user
+ */
+AbstractInfoWindow.prototype.getOverlayFullViewArray = function () {
+ return this._overlayFullView;
+};
+
+/**
+ *
+ * @param {string} overlayName
+ * @param {boolean} value
+ * @returns {Promise}
+ */
+AbstractInfoWindow.prototype.setOverlayFullView = function (overlayName, value) {
+ var oldVal = this._overlayFullView[overlayName];
+ this._overlayFullView[overlayName] = value;
+ if (oldVal !== value) {
+ return this.firePropertyChangeListener("overlayFullView", overlayName + "," + oldVal, value);
+ } else {
+ return Promise.resolve();
+ }
+};
+
+/**
+ * This method checks if {@link AbstractInfoWindow} is opened.
+ *
+ * @returns {Boolean} <code>true</code> if window is opened,
+ * <code>false</code> otherwise
+ */
+AbstractInfoWindow.prototype.isOpened = function () {
+ if (this._infoWindow === undefined) {
+ return false;
+ }
+ return this._infoWindow.isOpened();
+};
+
+/**
+ * Opens Info Window.
+ *
+ * @param {Marker} [newMarker]
+ *
+ * @returns {PromiseLike<any> | Promise<any>}
+ */
+AbstractInfoWindow.prototype.open = function (newMarker) {
+ var self = this;
+ var infoWindow = self._infoWindow;
+ if (infoWindow === null || infoWindow === undefined) {
+ logger.warn("Cannot open window.");
+ return Promise.resolve();
+ }
+ if (newMarker !== undefined) {
+ infoWindow.setMarker(newMarker);
+ }
+ infoWindow.open();
+
+ return self.update().then(function () {
+ return self.callListeners("onShow");
+ });
+};
+
+/**
+ * Sets new content of the info window.
+ *
+ * @param {HTMLElement|string} content
+ * new content of the window
+ */
+AbstractInfoWindow.prototype.setContent = function (content) {
+ var self = this;
+ self._content = content;
+ if (self._infoWindow !== undefined) {
+ self._infoWindow.setContent(content);
+ }
+};
+
+/**
+ * Returns content visualized in the info window.
+ *
+ * @returns {string|HTMLElement} content visualized in the info window
+ */
+AbstractInfoWindow.prototype.getContent = function () {
+ return this._content;
+};
+
+/**
+ * Creates div for an overlay data.
+ *
+ * @param {AbstractDbOverlay} overlay
+ * corresponding overlay
+ * @param {BioEntity[]|Comment[]|Drug[]|MiRna[]|Chemical[]} data
+ * data taken from overlay
+ * @returns {HTMLElement} div for given overlay data
+ */
+AbstractInfoWindow.prototype.createOverlayInfoDiv = function (overlay, data) {
+ var alias = this.alias;
+ if (alias !== undefined) {
+ if (alias.getType() !== undefined) {
+ if (overlay.name === "drug") {
+ if (alias.getType().toUpperCase() === "RNA" || //
+ alias.getType().toUpperCase() === "PROTEIN" || //
+ alias.getType().toUpperCase() === "GENE") {
+ return this._createDrugInfoDiv(overlay, data);
+ } else {
+ return null;
+ }
+ } else if (overlay.name === "chemical") {
+ if (this.alias.getType().toUpperCase() === "RNA" || //
+ alias.getType().toUpperCase() === "PROTEIN" || //
+ alias.getType().toUpperCase() === "GENE") {
+ return this._createChemicalInfoDiv(overlay, data);
+ } else {
+ return null;
+ }
+ } else if (overlay.name === "mirna") {
+ if (alias.getType().toUpperCase() === "RNA" || //
+ alias.getType().toUpperCase() === "PROTEIN" || //
+ alias.getType().toUpperCase() === "GENE") {
+ return this._createMiRnaInfoDiv(overlay, data);
+ } else {
+ return null;
+ }
+
+ } else if (overlay.name === "comment") {
+ return this._createCommentInfoDiv(overlay, data);
+ } else {
+ logger.warn("Unknown overlay data for AliasInfoWindow: " + overlay.name);
+ return this._createDefaultInfoDiv(overlay, data);
+ }
+ } else {
+ logger.debug(alias);
+ throw new Error("Cannot customize info window. Alias type is unknown ");
+ }
+ } else {
+ if (overlay.getName() === "comment") {
+ return this._createCommentInfoDiv(overlay, data);
+ } else {
+ logger.debug("Cannot customize info window. Alias not defined. Overlay: " + overlay.getName());
+ return null;
+ }
+ }
+};
+
+/**
+ * Creates and returns div for drug overlay information.
+ *
+ * @param {AbstractDbOverlay} overlay
+ * @param {Drug[]} data
+ * data taken from drug overlay
+ * @returns {HTMLElement} div for drug overlay information
+ * @private
+ */
+AbstractInfoWindow.prototype._createDrugInfoDiv = function (overlay, data) {
+ return this._createTargetInfoDiv({
+ overlay: overlay,
+ data: data,
+ name: "Interacting drugs"
+ });
+};
+
+/**
+ * Creates and returns div for comment overlay information.
+ *
+ * @param {AbstractDbOverlay} overlay
+ * @param {Comment[]} data
+ * data taken from comment overlay
+ * @returns {HTMLElement} div for comment overlay information
+ */
+AbstractInfoWindow.prototype._createCommentInfoDiv = function (overlay, data) {
+ if (data.length === 0 || data[0] === undefined) {
+ return null;
+ }
+ var result = document.createElement("div");
+
+ var titleElement = document.createElement("h3");
+ titleElement.innerHTML = "Comments";
+ result.appendChild(titleElement);
+ for (var i = 0; i < data.length; i++) {
+ var comment = data[i];
+ if (comment instanceof Comment) {
+ if (!comment.isRemoved()) {
+ result.appendChild(document.createElement("hr"));
+ var commentId = document.createElement("div");
+ commentId.innerHTML = '#' + comment.getId();
+ result.appendChild(commentId);
+ result.appendChild(document.createElement("br"));
+ var commentContent = Functions.createElement({type: "div", content: comment.getContent(), xss: true});
+
+ result.appendChild(commentContent);
+ }
+ } else {
+ throw new Error("Invalid comment data: " + comment);
+ }
+ }
+
+ return result;
+};
+
+/**
+ * Creates and returns div for unknown overlay.
+ *
+ * @param {AbstractDbOverlay} overlay
+ * @param {Array} data
+ * data taken from overlay
+ * @returns {HTMLElement} div for overlay information
+ */
+
+AbstractInfoWindow.prototype._createDefaultInfoDiv = function (overlay, data) {
+ var divElement = document.createElement("div");
+ var count = 0;
+
+ var titleElement = document.createElement("h3");
+ var title = document.createTextNode(overlay.getName());
+ titleElement.appendChild(title);
+ divElement.appendChild(titleElement);
+ for (var searchId in data) {
+ if (data.hasOwnProperty(searchId) && data[searchId] !== undefined && data[searchId] !== null) {
+ count++;
+ var resultTitleElement = document.createElement("h4");
+ var resultTitle = document.createTextNode(searchId);
+ resultTitleElement.appendChild(resultTitle);
+ divElement.appendChild(resultTitleElement);
+
+ var keys = Object.keys(data[searchId]);
+ for (var i = 0; i < keys.length; i++) {
+ var resultValElement = document.createElement("p");
+ var resultVal = document.createTextNode(keys[i] + ": " + data[searchId][keys[i]]);
+ resultValElement.appendChild(resultVal);
+ divElement.appendChild(resultValElement);
+ }
+ }
+ }
+
+ if (count === 0) {
+ divElement = null;
+ }
+ return divElement;
+};
+
+/**
+ * Returns Marker object where this info window is attached.
+ *
+ * @returns {Marker} object where this info window is attached
+ */
+AbstractInfoWindow.prototype.getMarker = function () {
+ return this._marker;
+};
+
+/**
+ *
+ * @param {Marker} marker
+ */
+AbstractInfoWindow.prototype.setMarker = function (marker) {
+ this._marker = marker;
+ if (this._infoWindow !== undefined) {
+ this._infoWindow.setMarker(marker);
+ }
+};
+
+/**
+ * Returns {@link AbstractCustomMap} where this window is presented.
+ *
+ * @returns {AbstractCustomMap} where this window is presented
+ */
+AbstractInfoWindow.prototype.getCustomMap = function () {
+ return this.customMap;
+};
+
+/**
+ *
+ * @param {AbstractCustomMap} map
+ */
+AbstractInfoWindow.prototype.setCustomMap = function (map) {
+ if (map === undefined) {
+ throw new Error("Map must be defined");
+ }
+ this.customMap = map;
+};
+
+/**
+ * Returns html DOM object with content that should presented when waiting for
+ * some data from server.
+ *
+ * @returns {HTMLElement} html with content that should presented when waiting for
+ * some data from server
+ */
+AbstractInfoWindow.prototype.createWaitingContentDiv = function () {
+ var result = document.createElement("div");
+ var img = document.createElement("img");
+ img.src = GuiConnector.getImgPrefix() + GuiConnector.getLoadingImg();
+ var message = document.createElement("h4");
+ message.innerHTML = "loading...";
+ result.appendChild(img);
+ result.appendChild(message);
+ return result;
+};
+
+/**
+ * This is a generic method that updates content of the window.
+ *
+ * @returns {Promise|PromiseLike}
+ * @private
+ */
+AbstractInfoWindow.prototype._updateContent = function () {
+ var contentDiv = null;
+ var self = this;
+
+ if (!self.isOpened()) {
+ return Promise.resolve();
+ } else {
+ self.setContent(self.createWaitingContentDiv());
+
+ return self.createContentDiv().then(function (content) {
+ contentDiv = content;
+ return self.createDbOverlaysDiv();
+ }).then(function (overlaysDiv) {
+ if (overlaysDiv !== undefined && overlaysDiv !== null) {
+ contentDiv.appendChild(overlaysDiv);
+ }
+ self.setContent(contentDiv);
+ return self.callListeners("onUpdate");
+ }).then(function () {
+ return contentDiv;
+ });
+ }
+};
+
+/**
+ * Creates and returns div with overlays content.
+ *
+ * @returns {Promise<HTMLElement>} with html representing data taken from
+ * {@link AbstractDbOverlay} for this window
+ */
+AbstractInfoWindow.prototype.createDbOverlaysDiv = function () {
+ var self = this;
+ var result = document.createElement("div");
+ return this.getDbOverlaysData(self.getOverlayFullViewArray()).then(function (overlayData) {
+ for (var i = 0; i < overlayData.length; i++) {
+ var overlay = overlayData[i].overlay;
+ var data = overlayData[i].data;
+ var overlayInfo = self.createOverlayInfoDiv(overlay, data);
+ if (overlayInfo !== null) {
+ result.appendChild(overlayInfo);
+ }
+ }
+ return result;
+ });
+};
+
+// noinspection JSUnusedLocalSymbols
+/**
+ * Returns array with data taken from all known {@link AbstractDbOverlay}.
+ *
+ * @param {Object.<string,boolean>} general
+ * if true then all elements will be returned, if false then only ones
+ * available right now in the overlay
+ *
+ * @returns {Promise} array with data from {@link AbstractDbOverlay}
+ */
+AbstractInfoWindow.prototype.getDbOverlaysData = function (general) {
+ throw new Error("Not implemented");
+};
+
+/**
+ * Abstract method (to be implemented by subclasses) for updating content.
+ *
+ * @returns {Promise}
+ */
+AbstractInfoWindow.prototype.update = function () {
+ return this._updateContent();
+};
+
+/**
+ *
+ * @param {string} params.name
+ * @param {AbstractDbOverlay} params.overlay
+ * @param {Array} params.data
+ * @returns {HTMLElement}
+ * @private
+ */
+AbstractInfoWindow.prototype._createTargetInfoDiv = function (params) {
+ var overlay = params.overlay;
+ var data = params.data;
+ var name = params.name;
+
+ var self = this;
+ var result = document.createElement("div");
+
+ var titleElement = document.createElement("h3");
+ titleElement.innerHTML = name;
+ result.appendChild(titleElement);
+ if (overlay.allowGeneralSearch()) {
+ var checkboxDiv = document.createElement("div");
+ checkboxDiv.style.float = "right";
+
+ var checkbox = document.createElement("input");
+ checkbox.id = "checkbox-" + name + "-" + this.getElementType() + "-" + this.getElementId();
+ checkbox.type = "checkbox";
+ checkbox.checked = self.isOverlayFullView(overlay.getName());
+ checkbox.onclick = function () {
+ return self.setOverlayFullView(overlay.getName(), this.checked).then(null, GuiConnector.alert);
+ };
+
+ checkboxDiv.appendChild(checkbox);
+
+ var description = document.createElement("div");
+ description.style.float = "right";
+ description.innerHTML = "Show all";
+ checkboxDiv.appendChild(description);
+ result.appendChild(checkboxDiv);
+ }
+ var count = 0;
+ for (var dataId in data) {
+ if (data.hasOwnProperty(dataId)) {
+ count++;
+ }
+ }
+
+ var table = self._createTableForTargetDiv(data, overlay);
+
+ if (count === 0 && !overlay.allowGeneralSearch() && !this.isOverlayFullView(overlay.getName())) {
+ result = null;
+ }
+ if (result !== null) {
+ result.appendChild(table);
+ }
+ return result;
+};
+
+/**
+ *
+ * @param {Array} data
+ * @param {AbstractDbOverlay} overlay
+ * @returns {HTMLElement}
+ * @private
+ */
+AbstractInfoWindow.prototype._createTableForTargetDiv = function (data, overlay) {
+ var self = this;
+ var table = document.createElement("table");
+ table.className = "minerva-window-drug-table";
+ var header = document.createElement("tr");
+ var headerCol = document.createElement("th");
+ headerCol.innerHTML = "Name";
+ header.appendChild(headerCol);
+ headerCol = document.createElement("th");
+ headerCol.innerHTML = "References";
+ header.appendChild(headerCol);
+
+ var cell;
+ table.appendChild(header);
+ var row;
+
+ var onclick = function () {
+ // ';' enforces single query (in case there are ',' characters in the name)
+ return overlay.searchByQuery(this.innerHTML + ";");
+ };
+
+ var count = 0;
+ for (var searchId in data) {
+ if (data.hasOwnProperty(searchId)) {
+
+ row = document.createElement("tr");
+ var nameContent = searchId;
+ var annotations = [];
+ if (typeof data[searchId] === "string") {
+ nameContent = data[searchId];
+ } else if (data[searchId] instanceof TargettingStructure) {
+ nameContent = data[searchId].getName();
+ var targets = data[searchId].getTargetsForIdentifiedElement(self.getIdentifiedElement());
+ for (var i = 0; i < targets.length; i++) {
+ var references = targets[i].getReferences();
+ for (var j = 0; j < references.length; j++) {
+ annotations.push(references[j]);
+ }
+ }
+ }
+ var link = Functions.createElement({
+ type: "a",
+ onclick: onclick,
+ href: "#",
+ content: nameContent
+ });
+
+ var nameTd = Functions.createElement({
+ type: "td"
+ });
+ nameTd.appendChild(link);
+ row.appendChild(nameTd);
+
+ var referencesCell = Functions.createElement({
+ type: "td"
+ });
+ referencesCell.appendChild(self.getGuiUtils().createAnnotationList(annotations, {groupAnnotations: false}));
+
+ row.appendChild(referencesCell);
+
+ table.appendChild(row);
+ count++;
+ }
+ }
+
+ if (self.isOverlayFullView(overlay.getName()) && count === 0) {
+ row = document.createElement("tr");
+ cell = document.createElement("td");
+ cell.colSpan = 2;
+ cell.innerHTML = "No results available";
+ row.appendChild(cell);
+ table.appendChild(row);
+ }
+
+ if (!self.isOverlayFullView(overlay.getName()) && count === 0 && overlay.allowGeneralSearch()) {
+ row = document.createElement("tr");
+ cell = document.createElement("td");
+ cell.colSpan = 2;
+ cell.innerHTML = "Search for available targets";
+ row.appendChild(cell);
+ table.appendChild(row);
+ }
+ return table;
+};
+
+/**
+ *
+ * @returns {PromiseLike<any> | Promise<any>}
+ */
+AbstractInfoWindow.prototype.init = function () {
+ var self = this;
+ var promises = [
+ // default settings of visualizing full information about elements
+ this.setOverlayFullView("drug", false),
+ this.setOverlayFullView("chemical", false),
+ this.setOverlayFullView("mirna", false),
+ this.setOverlayFullView("search", false),
+ // only all comments should be visible from the beginning
+ this.setOverlayFullView("comment", true)
+ ];
+
+ return Promise.all(promises).then(function () {
+ // listener called when user want to see all data about specific data overlay
+ var onOverlayFullViewChanged = function (e) {
+ var self = e.object;
+ // first change the content of the element
+ return self.update().then(function () {
+ if (e.newVal) {
+ var element = new IdentifiedElement({
+ objectId: self.getElementId(),
+ modelId: self.getCustomMap().getId(),
+ type: self.getElementType()
+ });
+ var topMap = self.getCustomMap().getTopMap();
+ return topMap.retrieveOverlayDetailDataForElement(element, self.getOverlayFullViewArray());
+ }
+ });
+
+ };
+
+ self.addPropertyChangeListener("overlayFullView", onOverlayFullViewChanged);
+
+ self._infoWindow = self.getCustomMap().getMapCanvas().createInfoWindow({
+ content: self.content,
+ position: self.getPosition(),
+ marker: self._marker
+ });
+
+ return ServerConnector.getConfiguration();
+ }).then(function (configuration) {
+ self.getGuiUtils().setConfiguration(configuration);
+ self.getGuiUtils().setMap(self.getCustomMap());
+ });
+};
+
+/**
+ *
+ * @param {GuiUtils} guiUtils
+ */
+AbstractInfoWindow.prototype.setGuiUtils = function (guiUtils) {
+ this._guiUtils = guiUtils;
+};
+
+/**
+ *
+ * @returns {GuiUtils}
+ */
+AbstractInfoWindow.prototype.getGuiUtils = function () {
+ return this._guiUtils;
+};
+
+/**
+ * Creates and returns DOM div for chemical overlay information.
+ *
+ * @param {AbstractDbOverlay} overlay
+ * @param {Chemical[]} data
+ * data taken from chemical overlay
+ * @returns {HTMLElement} element with a div for comment overlay information
+ * @private
+ */
+AbstractInfoWindow.prototype._createChemicalInfoDiv = function (overlay, data) {
+ return this._createTargetInfoDiv({
+ overlay: overlay,
+ data: data,
+ name: "Interacting chemicals"
+ });
+};
+
+/**
+ * Creates and returns DOM div for mi rna overlay information.
+ *
+ * @param {AbstractDbOverlay} overlay
+ * @param {MiRna[]} data
+ * data taken from mi rna overlay
+ * @returns {HTMLElement} DOM element with a div for comment overlay information
+ */
+AbstractInfoWindow.prototype._createMiRnaInfoDiv = function (overlay, data) {
+ return this._createTargetInfoDiv({
+ overlay: overlay,
+ data: data,
+ name: "Interacting Micro RNAs"
+ });
+};
+
+/**
+ *
+ * @param {IdentifiedElement} identifiedElement
+ */
+AbstractInfoWindow.prototype.setIdentifiedElement = function (identifiedElement) {
+ if (identifiedElement === undefined) {
+ throw new Error("identifiedElement cannot be undefined");
+ }
+ this._identifiedElement = identifiedElement;
+};
+
+/**
+ *
+ * @returns {IdentifiedElement}
+ */
+AbstractInfoWindow.prototype.getIdentifiedElement = function () {
+ return this._identifiedElement;
+};
+
+
+/**
+ * Method returning identifier of the object for which this window was created.
+ *
+ * @returns {string|number}
+ */
+AbstractInfoWindow.prototype.getElementId = function () {
+ return this.getIdentifiedElement().getId();
+};
+
+/**
+ * Method returning type of the object for which this window was created.
+ *
+ * @returns {string}
+ */
+AbstractInfoWindow.prototype.getElementType = function () {
+ return this.getIdentifiedElement().getType();
+};
+
+/**
+ * @returns {Point}
+ */
+AbstractInfoWindow.prototype.getPosition = function () {
+ throw new Error("Not Implemented");
+};
+
+module.exports = AbstractInfoWindow;
diff --git a/frontend-js/src/main/js/map/window/AliasInfoWindow.js b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
index 5f9957d418f073468ce95763fe133a99d75c6df2..f80f8bfc7eeb1635491e921e36b5f9c8329ae146 100644
--- a/frontend-js/src/main/js/map/window/AliasInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
@@ -36,10 +36,7 @@ function AliasInfoWindow(params) {
this.setAlias(params.alias);
var overlayListChanged = function () {
- return self.getCustomMap().getAliasVisibleLayoutsData(self.getAlias().getId()).then(function (layoutAliases) {
- self.layoutAliases = layoutAliases;
- return self.update();
- });
+ return self.update();
};
var dbOverlaySearchChanged = function () {
@@ -97,99 +94,147 @@ AliasInfoWindow.prototype.init = function () {
* Creates and returns chart representing data related to alias on different
* overlays.
*
+ * @param {DataOverlay[]} params.overlays
+ *
* @returns {PromiseLike<HTMLElement>} html element representing chart with data related to alias
* on different overlays
*/
-AliasInfoWindow.prototype.createChartDiv = function () {
+AliasInfoWindow.prototype.createChartDiv = function (params) {
+ var overlays = params.overlays;
+
var result = document.createElement("div");
- var rows = [];
+ var promises = [];
var self = this;
- return Promise.each(self.layoutAliases, function (data, i) {
- var rowDiv = document.createElement("div");
- if (i % 2 === 0) {
- rowDiv.className = "mapChartRowEvenDiv";
- } else {
- rowDiv.className = "mapChartRowOddDiv";
- }
- rowDiv.style.position = "relative";
- var nameDiv = document.createElement("div");
- nameDiv.className = "mapChartNameDiv";
- nameDiv.innerHTML = self.layoutNames[i] + " ";
- rowDiv.appendChild(nameDiv);
-
- rows[i] = rowDiv;
- if (data !== undefined && data !== null) {
- return Functions.overlayToColor(data).then(function (color) {
- var value = parseFloat(data.value);
- var description = data.description;
- if (description === null || description === undefined || description === "") {
- description = "";
- if (!isNaN(value)) {
- description = value.toFixed(2);
+
+ overlays.forEach(function (overlay, i) {
+ promises.push(overlay.getFullAliasById(self.getAlias().getId()).then(function (data) {
+ var rowDiv = document.createElement("div");
+ if (i % 2 === 0 || self.getAlias().getLinkedSubmodelId() !== undefined) {
+ rowDiv.className = "minerva-chart-row-even";
+ } else {
+ rowDiv.className = "minerva-chart-row-odd";
+ }
+ var nameDiv = document.createElement("div");
+ nameDiv.className = "minerva-chart-name";
+ nameDiv.innerHTML = overlays[i].getName() + " ";
+ rowDiv.appendChild(nameDiv);
+
+ if (data !== undefined && data !== null) {
+ return Functions.overlayToColor(data).then(function (color) {
+ var value = parseFloat(data.value);
+ var description = data.description;
+ if (description === null || description === undefined || description === "") {
+ description = "";
+ if (!isNaN(value)) {
+ description = value.toFixed(2);
+ }
}
- }
- var leftMarginDiv = document.createElement("div");
- leftMarginDiv.innerHTML = " ";
- leftMarginDiv.style.float = "left";
- var centerBarDiv = document.createElement("div");
- centerBarDiv.style.width = "1px";
- centerBarDiv.style.float = "left";
- centerBarDiv.style.background = "#000000";
- centerBarDiv.innerHTML = " ";
-
- var rightBarDiv = document.createElement("div");
- rightBarDiv.innerHTML = " ";
- rightBarDiv.style.float = "left";
- rightBarDiv.style.background = color;
- rightBarDiv.style.width = Math.abs(value * 100) + "px";
- var offset = 100;
- var descDiv = document.createElement("div");
- descDiv.style.float = "right";
- descDiv.style.textAlign = "right";
- descDiv.style.position = "absolute";
- descDiv.style.right = "0";
- descDiv.innerHTML = "<span>" + description + "</span>";
- if (!isNaN(value)) {
- if (value > 0) {
- offset = 100;
- leftMarginDiv.style.width = offset + "px";
+ var leftMarginDiv = document.createElement("div");
+ leftMarginDiv.innerHTML = " ";
+ leftMarginDiv.style.float = "left";
+ var centerBarDiv = document.createElement("div");
+ centerBarDiv.style.width = "1px";
+ centerBarDiv.style.float = "left";
+ centerBarDiv.style.background = "#000000";
+ centerBarDiv.innerHTML = " ";
+
+ var rightBarDiv = document.createElement("div");
+ rightBarDiv.innerHTML = " ";
+ rightBarDiv.style.float = "left";
+ rightBarDiv.style.background = color;
+ rightBarDiv.style.width = Math.abs(value * 100) + "px";
+ var offset = 100;
+ var descDiv = document.createElement("div");
+ descDiv.style.float = "right";
+ descDiv.style.textAlign = "right";
+ descDiv.style.position = "absolute";
+ descDiv.style.right = "0";
+ descDiv.innerHTML = "<span>" + description + "</span>";
+ if (!isNaN(value)) {
+ if (value > 0) {
+ offset = 100;
+ leftMarginDiv.style.width = offset + "px";
- rightBarDiv.style.textAlign = "right";
+ rightBarDiv.style.textAlign = "right";
+
+ rowDiv.appendChild(leftMarginDiv);
+ rowDiv.appendChild(centerBarDiv);
+ rowDiv.appendChild(rightBarDiv);
+ } else {
+ offset = 100 + (value * 100);
+ leftMarginDiv.style.width = offset + "px";
+
+ rowDiv.appendChild(leftMarginDiv);
+ rowDiv.appendChild(rightBarDiv);
+ rowDiv.appendChild(centerBarDiv);
+ }
- rowDiv.appendChild(leftMarginDiv);
- rowDiv.appendChild(centerBarDiv);
- rowDiv.appendChild(rightBarDiv);
} else {
- offset = 100 + (value * 100);
+ offset = 100;
leftMarginDiv.style.width = offset + "px";
-
+ leftMarginDiv.style.background = color;
+ rightBarDiv.style.width = offset + "px";
+ rightBarDiv.style.background = color;
+ rightBarDiv.style.textAlign = "right";
rowDiv.appendChild(leftMarginDiv);
- rowDiv.appendChild(rightBarDiv);
rowDiv.appendChild(centerBarDiv);
+ rowDiv.appendChild(rightBarDiv);
+ }
+ rowDiv.appendChild(descDiv);
+ return rowDiv;
+ });
+ } else {
+ var emptyDiv = document.createElement("div");
+ emptyDiv.innerHTML = " ";
+ emptyDiv.style.float = "left";
+ emptyDiv.style.width = "201px";
+ rowDiv.appendChild(emptyDiv);
+ return rowDiv;
+ }
+ }));
+ if (self.getAlias().getLinkedSubmodelId() !== undefined) {
+ promises.push(new Promise.resolve(overlay).then(function (overlay) {
+ var overlayData = overlay.getAliases();
+ var overlayDataOnSubmap = [];
+ for (var j = 0; j < overlayData.length; j++) {
+ var data = overlayData[j];
+ if (data.getModelId() === self.getAlias().getLinkedSubmodelId()) {
+ overlayDataOnSubmap.push(data);
}
-
- } else {
- offset = 100;
- leftMarginDiv.style.width = offset + "px";
- leftMarginDiv.style.background = color;
- rightBarDiv.style.width = offset + "px";
- rightBarDiv.style.background = color;
- rightBarDiv.style.textAlign = "right";
- rowDiv.appendChild(leftMarginDiv);
- rowDiv.appendChild(centerBarDiv);
- rowDiv.appendChild(rightBarDiv);
}
- rowDiv.appendChild(descDiv);
- });
- } else {
- var emptyDiv = document.createElement("div");
- emptyDiv.innerHTML = " ";
- emptyDiv.style.float = "left";
- emptyDiv.style.width = "201px";
- rowDiv.appendChild(emptyDiv);
- return Promise.resolve();
+ return Functions.overlaysToColorDataStructure(overlayDataOnSubmap).then(function (colors) {
+ var rowDiv = document.createElement("div");
+ rowDiv.className = "minerva-chart-row-odd";
+ var nameDiv = document.createElement("div");
+ nameDiv.className = "minerva-chart-name";
+ var submapName = self.getCustomMap().getTopMap().getSubmapById(self.getAlias().getLinkedSubmodelId()).getModel().getName();
+ nameDiv.innerHTML = "Submap " + submapName;
+ rowDiv.appendChild(nameDiv);
+
+ var emptyDiv = document.createElement("div");
+ emptyDiv.style.float = "left";
+ emptyDiv.style.width = "201px";
+ rowDiv.appendChild(emptyDiv);
+
+ var totalAmount = 0;
+ for (var j = 0; j < colors.length; j++) {
+ totalAmount += colors[j].amount;
+ }
+
+ for (j = 0; j < colors.length; j++) {
+ var overlayDataDiv = document.createElement("div");
+ overlayDataDiv.innerHTML = " ";
+ overlayDataDiv.style.float = "left";
+ overlayDataDiv.style.width = Math.floor(100*colors[j].amount / totalAmount) + "%";
+ overlayDataDiv.style.background = colors[j].color;
+ emptyDiv.appendChild(overlayDataDiv);
+ }
+ return rowDiv;
+ });
+ }));
}
- }).then(function () {
+ });
+ return Promise.all(promises).then(function (rows) {
for (var i = 0; i < rows.length; i++) {
result.appendChild(rows[i]);
}
@@ -215,18 +260,14 @@ AliasInfoWindow.prototype.createContentDiv = function () {
result.appendChild(overlayDiv);
- return self.getCustomMap().getAliasVisibleLayoutsData(alias.getId()).then(function (layoutAliases) {
- self.layoutAliases = layoutAliases;
- return self.getCustomMap().getTopMap().getVisibleDataOverlays();
- }).then(function (dataOverlays) {
- self.layoutNames = [];
- for (var i = 0; i < dataOverlays.length; i++) {
- self.layoutNames.push(dataOverlays[i].getName());
- }
- return self.createChartDiv();
+ var overlays;
+
+ return self.getCustomMap().getTopMap().getVisibleDataOverlays().then(function (dataOverlays) {
+ overlays = dataOverlays;
+ return self.createChartDiv({overlays: overlays});
}).then(function (chartDiv) {
overlayDiv.appendChild(chartDiv);
- return self.createGenomicDiv();
+ return self.createGenomicDiv({overlays: overlays});
}).then(function (genomicDiv) {
overlayDiv.appendChild(genomicDiv);
return result;
@@ -245,15 +286,19 @@ AliasInfoWindow.prototype.createContentDiv = function () {
*
* @returns {Promise} array with data from {@link AbstractDbOverlay}
*/
-AliasInfoWindow.prototype.getOverlaysData = function (general) {
+AliasInfoWindow.prototype.getDbOverlaysData = function (general) {
return this.getCustomMap().getTopMap().getOverlayDataForAlias(this.getAlias(), general);
};
/**
*
- * @returns {PromiseLike<HTMLElement>}
+ * @param {DataOverlay[]} params.overlays
+ *
+ * @returns {Promise|PromiseLike}
*/
-AliasInfoWindow.prototype.createGenomicDiv = function () {
+AliasInfoWindow.prototype.createGenomicDiv = function (params) {
+ var overlays = params.overlays;
+
var self = this;
var result = document.createElement("div");
@@ -285,34 +330,41 @@ AliasInfoWindow.prototype.createGenomicDiv = function () {
var globalGeneVariants = [];
- return Promise.each(
- self.layoutAliases,
- function (data) {
+ var promises = [];
+ var overlaysData = [];
+
+ overlays.forEach(function (overlay) {
+ promises.push(overlay.getFullAliasById(self.getAlias().getId()));
+ });
+ return Promise.all(promises).then(function (result) {
+ promises = [];
+ overlaysData = result;
+ for (var i = 0; i < overlaysData.length; i++) {
+ var data = overlaysData[i];
if (data !== null && data !== undefined && data.getType() === LayoutAlias.GENETIC_VARIANT) {
geneticInformation = true;
- return Promise.each(data.getGeneVariants(), function (variant) {
- return self.getCustomMap().getReferenceGenome(variant.getReferenceGenomeType(),
- variant.getReferenceGenomeVersion()).then(
- function (genome) {
- if (genome.getUrl() !== null && genome.getUrl() !== undefined) {
- if (genomes[genome.getUrl()] === undefined) {
- genomes[genome.getUrl()] = genome;
- genomeUrls.push(genome.getUrl());
- }
- } else {
- logger.warn("Genome for " + variant.getReferenceGenomeType() + ","
- + variant.getReferenceGenomeVersion() + " not loaded");
+ promises.push(Promise.each(data.getGeneVariants(), function (variant) {
+ return self.getCustomMap().getTopMap().getReferenceGenome(variant.getReferenceGenomeType(),
+ variant.getReferenceGenomeVersion()).then(function (genome) {
+ if (genome.getUrl() !== null && genome.getUrl() !== undefined) {
+ if (genomes[genome.getUrl()] === undefined) {
+ genomes[genome.getUrl()] = genome;
+ genomeUrls.push(genome.getUrl());
}
- },
- function () {
+ } else {
logger.warn("Genome for " + variant.getReferenceGenomeType() + ","
+ variant.getReferenceGenomeVersion() + " not loaded");
+ }
+ }, function () {
+ logger.warn("Genome for " + variant.getReferenceGenomeType() + ","
+ + variant.getReferenceGenomeVersion() + " not loaded");
- });
- });
-
+ });
+ }));
}
- }).then(function () {
+ }
+ return Promise.all(promises);
+ }).then(function () {
for (var i = 0; i < genomeUrls.length; i++) {
var genome = genomes[genomeUrls[i]];
pileupSource.splice(0, 0, {
@@ -334,7 +386,8 @@ AliasInfoWindow.prototype.createGenomicDiv = function () {
});
}
}
- return Promise.each(self.layoutAliases, function (data, i) {
+ for (i = 0; i < overlaysData.length; i++) {
+ var data = overlaysData[i];
globalGeneVariants[i] = [];
if (data !== null && data !== undefined && data.getType() === LayoutAlias.GENETIC_VARIANT) {
var geneVariants = data.getGeneVariants();
@@ -349,21 +402,20 @@ AliasInfoWindow.prototype.createGenomicDiv = function () {
pileupRange.stop = Math.max(pileupRange.stop, variant.getPosition() + length);
}
}
- });
- }).then(function () {
+ }
if (geneticInformation) {
if (genomeUrls.length === 0) {
contentElement.innerHTML = "No reference genome data available on minerva platform";
} else {
- for (var iter = 0; iter < self.layoutAliases.length; iter++) {
- if (globalGeneVariants[iter].length > 0) {
- var vcfContent = self.createVcfString(globalGeneVariants[iter]);
+ for (i = 0; i < overlaysData.length; i++) {
+ if (globalGeneVariants[i].length > 0) {
+ var vcfContent = self.createVcfString(globalGeneVariants[i]);
pileupSource.push({
viz: pileup.viz.variants(),
data: pileup.formats.vcf({
content: vcfContent
}),
- name: self.layoutNames[iter] + ' - Variants',
+ name: overlays[i].getName() + ' - Variants',
options: {
variantHeightByFrequency: true
}
@@ -385,6 +437,40 @@ AliasInfoWindow.prototype.createGenomicDiv = function () {
range: pileupRange,
tracks: pileupSource
});
+
+
+ //Code below is a workaround - for some reason on openlayers events bound by pileup are not working properly...
+ var zoomControls = $(".zoom-controls", contentElement);
+
+ zoomControls.children().hide();
+
+ var zoomIn = $('<input type="button" value="+" class="btn-zoom-in"/>');
+ zoomIn.on("click", function () {
+ var range = self.pileup.getRange();
+ var distDiff = parseInt((range.stop - range.start + 1) / 4);
+ range.start += distDiff;
+ range.stop -= distDiff;
+
+ self.pileup.setRange(range);
+ });
+ zoomIn.appendTo(zoomControls);
+ var zoomOut = $('<input type="button" value="-" class="btn-zoom-out"/>');
+ zoomOut.on("click", function () {
+ var range = self.pileup.getRange();
+ var distDiff = parseInt((range.stop - range.start) / 2);
+ if (distDiff === 0) {
+ distDiff = 1;
+ }
+ range.start -= distDiff;
+ range.stop += distDiff;
+ if (range.start < 0) {
+ range.stop -= range.start;
+ range.start = 0;
+ }
+
+ self.pileup.setRange(range);
+ });
+ zoomOut.appendTo(zoomControls);
}
return result;
@@ -459,5 +545,4 @@ AliasInfoWindow.prototype.getPosition = function () {
return new Point(alias.x + alias.width / 2, alias.y + alias.height / 2);
};
-
module.exports = AliasInfoWindow;
diff --git a/frontend-js/src/main/js/map/window/PointInfoWindow.js b/frontend-js/src/main/js/map/window/PointInfoWindow.js
index dc1c2d7f8bb90b04f783ce2ebd63acbad6f380ba..bf263c8e7a751e2e94ac1497e077cc2614c78f02 100644
--- a/frontend-js/src/main/js/map/window/PointInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/PointInfoWindow.js
@@ -1,63 +1,63 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var AbstractInfoWindow = require('./AbstractInfoWindow');
-var IdentifiedElement = require('../data/IdentifiedElement');
-
-/**
- *
- * @param {IdentifiedElement} [params.identifiedElement]
- * @param {AbstractCustomMap} params.map
- * @param {Marker} params.marker
- * @param {PointData} params.point
- *
- * @constructor
- * @extends AbstractInfoWindow
- */
-function PointInfoWindow(params) {
- if (params.identifiedElement === undefined) {
- params.identifiedElement = new IdentifiedElement(params.point);
- }
- // call super constructor
- AbstractInfoWindow.call(this, params);
-
- this.pointData = params.point;
-
-}
-
-PointInfoWindow.prototype = Object.create(AbstractInfoWindow.prototype);
-PointInfoWindow.prototype.constructor = PointInfoWindow;
-
-/**
- *
- * @returns {PromiseLike<HTMLElement>}
- */
-PointInfoWindow.prototype.createContentDiv = function () {
- var result = document.createElement("div");
- var title = document.createElement("h3");
- title.innerHTML = "Point: " + this.pointData.getPoint();
- result.appendChild(title);
-
- return Promise.resolve(result);
-};
-
-/**
- *
- * @param {Object.<string,boolean>} general
- * @returns {Promise}
- */
-PointInfoWindow.prototype.getOverlaysData = function (general) {
- return this.getCustomMap().getTopMap().getOverlayDataForPoint(this.pointData, general);
-};
-
-/**
- *
- * @returns {Point}
- */
-PointInfoWindow.prototype.getPosition = function () {
- return this.pointData.getPoint();
-};
-
-
-module.exports = PointInfoWindow;
+"use strict";
+
+var Promise = require("bluebird");
+
+var AbstractInfoWindow = require('./AbstractInfoWindow');
+var IdentifiedElement = require('../data/IdentifiedElement');
+
+/**
+ *
+ * @param {IdentifiedElement} [params.identifiedElement]
+ * @param {AbstractCustomMap} params.map
+ * @param {Marker} params.marker
+ * @param {PointData} params.point
+ *
+ * @constructor
+ * @extends AbstractInfoWindow
+ */
+function PointInfoWindow(params) {
+ if (params.identifiedElement === undefined) {
+ params.identifiedElement = new IdentifiedElement(params.point);
+ }
+ // call super constructor
+ AbstractInfoWindow.call(this, params);
+
+ this.pointData = params.point;
+
+}
+
+PointInfoWindow.prototype = Object.create(AbstractInfoWindow.prototype);
+PointInfoWindow.prototype.constructor = PointInfoWindow;
+
+/**
+ *
+ * @returns {PromiseLike<HTMLElement>}
+ */
+PointInfoWindow.prototype.createContentDiv = function () {
+ var result = document.createElement("div");
+ var title = document.createElement("h3");
+ title.innerHTML = "Point: " + this.pointData.getPoint();
+ result.appendChild(title);
+
+ return Promise.resolve(result);
+};
+
+/**
+ *
+ * @param {Object.<string,boolean>} general
+ * @returns {Promise}
+ */
+PointInfoWindow.prototype.getDbOverlaysData = function (general) {
+ return this.getCustomMap().getTopMap().getOverlayDataForPoint(this.pointData, general);
+};
+
+/**
+ *
+ * @returns {Point}
+ */
+PointInfoWindow.prototype.getPosition = function () {
+ return this.pointData.getPoint();
+};
+
+
+module.exports = PointInfoWindow;
diff --git a/frontend-js/src/main/js/map/window/ReactionInfoWindow.js b/frontend-js/src/main/js/map/window/ReactionInfoWindow.js
index cca0f9d2c820e3e6b6ebe8ed31a42415f8ffc07d..bd6b7c493c9be2b3b0d3539a3829c76b95bd7db0 100644
--- a/frontend-js/src/main/js/map/window/ReactionInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/ReactionInfoWindow.js
@@ -1,264 +1,264 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var AbstractInfoWindow = require('./AbstractInfoWindow');
-var GuiUtils = require('../../gui/leftPanel/GuiUtils');
-var IdentifiedElement = require('../data/IdentifiedElement');
-var Reaction = require('../data/Reaction');
-var Functions = require('../../Functions');
-var logger = require('../../logger');
-
-/**
- * Class representing info window that should be opened when clicking on
- * reaction.
- */
-/**
- *
- * @param {IdentifiedElement} [params.identifiedElement]
- * @param {AbstractCustomMap} params.map
- * @param {Marker} params.marker
- * @param {Reaction} params.reaction
- *
- * @constructor
- * @extends AbstractInfoWindow
- */
-function ReactionInfoWindow(params) {
- if (params.identifiedElement === undefined) {
- params.identifiedElement = new IdentifiedElement(params.reaction);
- }
- // call super constructor
- AbstractInfoWindow.call(this, params);
-
- var self = this;
-
- self.setReactionData(params.reaction);
- if (params.reaction.getKineticLaw() !== undefined) {
- self.addListener("onShow", function () {
- return MathJax.Hub.Queue(["Typeset", MathJax.Hub]);
- });
- }
-}
-
-ReactionInfoWindow.prototype = Object.create(AbstractInfoWindow.prototype);
-ReactionInfoWindow.prototype.constructor = ReactionInfoWindow;
-
-/**
- * Methods that creates and return html code with the content of the window.
- *
- * @returns {Promise} representing html code for content of the info window
- */
-ReactionInfoWindow.prototype.createContentDiv = function () {
- var self = this;
- var reaction = self.getReactionData();
- var result = document.createElement("div");
- var title = document.createElement("h3");
- title.innerHTML = "Reaction: " + reaction.getReactionId();
- result.appendChild(title);
-
- return self.createKineticsDiv(reaction, result).then(function () {
- result.appendChild(self.createElementsDiv(reaction));
- return result;
- });
-};
-
-/**
- *
- * @param {Reaction} reaction
- * @param {HTMLElement} result
- * @returns {Promise}
- */
-ReactionInfoWindow.prototype.createKineticsDiv = function (reaction, result) {
- var self = this;
- if (reaction.getKineticLaw() === undefined) {
- return Promise.resolve();
- } else {
- var kineticLaw = reaction.getKineticLaw();
- return Functions.loadScript('https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/MathJax.js?config=TeX-MML-AM_CHTML').then(function () {
- return MathJax.Hub.Config({
- tex2jax: {
- skipTags: ["script", "noscript", "style", "textarea", "pre", "code"]
- }
- });
- }).then(function () {
-
- result.appendChild(Functions.createElement({type: "h4", content: "Kinetic law"}));
-
- if (kineticLaw.getMathMlPresentation() !== undefined) {
- result.appendChild(Functions.createElement({
- type: "div",
- content: kineticLaw.getMathMlPresentation(),
- xss: false
- }));
- } else {
-
- result.appendChild(Functions.createElement({
- type: "div",
- content: "<p>Problematic MathML</p>"
- }));
- logger.warn("Problematic MathML: " + kineticLaw.getDefinition());
- }
- var promises = [];
- for (var i = 0; i < kineticLaw.getFunctionIds().length; i++) {
- promises.push(self.getCustomMap().getModel().getSbmlFunctionById(kineticLaw.getFunctionIds()[i]));
- }
- return Promise.all(promises);
- }).then(function (functions) {
- result.appendChild(self.createSbmlFunctionDiv(functions));
-
- var promises = [];
- for (var i = 0; i < kineticLaw.getParameterIds().length; i++) {
- promises.push(self.getCustomMap().getModel().getSbmlParameterById(kineticLaw.getParameterIds()[i]));
- }
- return Promise.all(promises);
- }).then(function (parameters) {
- result.appendChild(self.createSbmlParameterDiv(parameters));
- });
- }
-};
-
-/**
- *
- * @param {SbmlFunction[]} functions
- * @returns {HTMLElement}
- */
-ReactionInfoWindow.prototype.createSbmlFunctionDiv = function (functions) {
- var result = Functions.createElement({type: "div"});
- if (functions.length > 0) {
- result.appendChild(Functions.createElement({type: "h5", content: "Functions: "}));
- var guiUtils = new GuiUtils();
- var table = Functions.createElement({type: "div", style: "display: table;", className: "borderTable"});
- table.appendChild(guiUtils.createTableRow(["Name", "Definition", "Arguments"]));
- for (var i = 0; i < functions.length; i++) {
- var sbmlFunction = functions[i];
- var mathML;
- if (sbmlFunction.getMathMlPresentation() !== undefined) {
- mathML = sbmlFunction.getMathMlPresentation();
- } else {
- mathML = "<p>Problematic MathML</p>";
- logger.warn("Problematic MathML: " + sbmlFunction.getDefinition());
- }
- var functionArguments = sbmlFunction.getArguments().join(", ");
- table.appendChild(guiUtils.createTableRow([sbmlFunction.getName(), mathML, functionArguments]));
- }
- result.appendChild(table);
- }
- return result;
-};
-
-/**
- *
- * @param {SbmlParameter[]} parameters
- * @returns {HTMLElement}
- */
-ReactionInfoWindow.prototype.createSbmlParameterDiv = function (parameters) {
- var result = Functions.createElement({type: "div"});
- if (parameters.length > 0) {
- result.appendChild(Functions.createElement({type: "h5", content: "Parameters: "}));
- var guiUtils = new GuiUtils();
- var table = Functions.createElement({type: "div", style: "display: table;", className: "borderTable"});
- table.appendChild(guiUtils.createTableRow(["Name", "parameterId", "Value", "Global"]));
- for (var i = 0; i < parameters.length; i++) {
- var sbmlFunction = parameters[i];
- table.appendChild(guiUtils.createTableRow([sbmlFunction.getName(), sbmlFunction.getParameterId(), sbmlFunction.getValue(), sbmlFunction.getGlobal()]));
- }
- result.appendChild(table);
- }
- return result;
-};
-
-/**
- *
- * @param {Reaction} reaction
- * @returns {HTMLElement}
- */
-ReactionInfoWindow.prototype.createElementsDiv = function (reaction) {
- var result = Functions.createElement({type: "div"});
- result.appendChild(Functions.createElement({type: "h5", content: "Elements: "}));
- var guiUtils = new GuiUtils();
- var table = Functions.createElement({type: "div", style: "display: table;", className: "borderTable"});
- table.appendChild(guiUtils.createTableRow(["Name", "Role", "elementId", "Constant", "Boundary condition", "Initial concentration", "Initial amount", "Stoichiometry"]));
- var elements = reaction.getReactants();
- var i, element;
-
- function createRow(node, title) {
- var element = node.getAlias();
- var stoichiometry = node.getStoichiometry();
- if (stoichiometry === undefined) {
- stoichiometry = "";
- }
- return guiUtils.createTableRow([element.getName(), title, element.getElementId(), element.getConstant(), element.getBoundaryCondition(), element.getInitialConcentration(), element.getInitialAmount(), stoichiometry])
- }
-
- for (i = 0; i < elements.length; i++) {
- element = elements[i].getAlias();
- table.appendChild(createRow(elements[i], "Reactant"));
- }
- elements = reaction.getProducts();
- for (i = 0; i < elements.length; i++) {
- element = elements[i].getAlias();
- table.appendChild(createRow(elements[i], "Product"));
- }
- elements = reaction.getModifiers();
- for (i = 0; i < elements.length; i++) {
- element = elements[i].getAlias();
- table.appendChild(createRow(elements[i], "Modifier"));
- }
- result.appendChild(table);
- return result;
-};
-
-/**
- *
- * @returns {PromiseLike<any> | Promise<any>}
- */
-ReactionInfoWindow.prototype.init = function () {
- var self = this;
- return Promise.resolve().then(function () {
- return AbstractInfoWindow.prototype.init.call(self);
- }).then(function () {
- return self.update();
- });
-};
-
-/**
- * Returns array with data taken from all known {@link AbstractDbOverlay}.
- *
- * @param {Object.<string,boolean>} general
- * @returns {Promise} of an array with data from {@link AbstractDbOverlay}
- */
-ReactionInfoWindow.prototype.getOverlaysData = function (general) {
- return this.getCustomMap().getTopMap().getOverlayDataForReaction(this.getReactionData(), general);
-};
-
-/**
- *
- * @returns {Reaction}
- */
-ReactionInfoWindow.prototype.getReactionData = function () {
- return this._reactionData;
-};
-
-/**
- *
- * @param {Reaction} reactionData
- */
-ReactionInfoWindow.prototype.setReactionData = function (reactionData) {
- if (reactionData === undefined || reactionData === null) {
- throw new Error("Reaction must be specified");
- } else if (reactionData instanceof Reaction) {
- this._reactionData = reactionData;
- } else {
- throw new Error("Parameter must be of Reaction type, but found" + reactionData);
- }
-};
-
-/**
- *
- * @returns {Point}
- */
-ReactionInfoWindow.prototype.getPosition = function () {
- return this.getReactionData().getCenter();
-};
-
-module.exports = ReactionInfoWindow;
+"use strict";
+
+var Promise = require("bluebird");
+
+var AbstractInfoWindow = require('./AbstractInfoWindow');
+var GuiUtils = require('../../gui/leftPanel/GuiUtils');
+var IdentifiedElement = require('../data/IdentifiedElement');
+var Reaction = require('../data/Reaction');
+var Functions = require('../../Functions');
+var logger = require('../../logger');
+
+/**
+ * Class representing info window that should be opened when clicking on
+ * reaction.
+ */
+/**
+ *
+ * @param {IdentifiedElement} [params.identifiedElement]
+ * @param {AbstractCustomMap} params.map
+ * @param {Marker} params.marker
+ * @param {Reaction} params.reaction
+ *
+ * @constructor
+ * @extends AbstractInfoWindow
+ */
+function ReactionInfoWindow(params) {
+ if (params.identifiedElement === undefined) {
+ params.identifiedElement = new IdentifiedElement(params.reaction);
+ }
+ // call super constructor
+ AbstractInfoWindow.call(this, params);
+
+ var self = this;
+
+ self.setReactionData(params.reaction);
+ if (params.reaction.getKineticLaw() !== undefined) {
+ self.addListener("onShow", function () {
+ return MathJax.Hub.Queue(["Typeset", MathJax.Hub]);
+ });
+ }
+}
+
+ReactionInfoWindow.prototype = Object.create(AbstractInfoWindow.prototype);
+ReactionInfoWindow.prototype.constructor = ReactionInfoWindow;
+
+/**
+ * Methods that creates and return html code with the content of the window.
+ *
+ * @returns {Promise} representing html code for content of the info window
+ */
+ReactionInfoWindow.prototype.createContentDiv = function () {
+ var self = this;
+ var reaction = self.getReactionData();
+ var result = document.createElement("div");
+ var title = document.createElement("h3");
+ title.innerHTML = "Reaction: " + reaction.getReactionId();
+ result.appendChild(title);
+
+ return self.createKineticsDiv(reaction, result).then(function () {
+ result.appendChild(self.createElementsDiv(reaction));
+ return result;
+ });
+};
+
+/**
+ *
+ * @param {Reaction} reaction
+ * @param {HTMLElement} result
+ * @returns {Promise}
+ */
+ReactionInfoWindow.prototype.createKineticsDiv = function (reaction, result) {
+ var self = this;
+ if (reaction.getKineticLaw() === undefined) {
+ return Promise.resolve();
+ } else {
+ var kineticLaw = reaction.getKineticLaw();
+ return Functions.loadScript('https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/MathJax.js?config=TeX-MML-AM_CHTML').then(function () {
+ return MathJax.Hub.Config({
+ tex2jax: {
+ skipTags: ["script", "noscript", "style", "textarea", "pre", "code"]
+ }
+ });
+ }).then(function () {
+
+ result.appendChild(Functions.createElement({type: "h4", content: "Kinetic law"}));
+
+ if (kineticLaw.getMathMlPresentation() !== undefined) {
+ result.appendChild(Functions.createElement({
+ type: "div",
+ content: kineticLaw.getMathMlPresentation(),
+ xss: false
+ }));
+ } else {
+
+ result.appendChild(Functions.createElement({
+ type: "div",
+ content: "<p>Problematic MathML</p>"
+ }));
+ logger.warn("Problematic MathML: " + kineticLaw.getDefinition());
+ }
+ var promises = [];
+ for (var i = 0; i < kineticLaw.getFunctionIds().length; i++) {
+ promises.push(self.getCustomMap().getModel().getSbmlFunctionById(kineticLaw.getFunctionIds()[i]));
+ }
+ return Promise.all(promises);
+ }).then(function (functions) {
+ result.appendChild(self.createSbmlFunctionDiv(functions));
+
+ var promises = [];
+ for (var i = 0; i < kineticLaw.getParameterIds().length; i++) {
+ promises.push(self.getCustomMap().getModel().getSbmlParameterById(kineticLaw.getParameterIds()[i]));
+ }
+ return Promise.all(promises);
+ }).then(function (parameters) {
+ result.appendChild(self.createSbmlParameterDiv(parameters));
+ });
+ }
+};
+
+/**
+ *
+ * @param {SbmlFunction[]} functions
+ * @returns {HTMLElement}
+ */
+ReactionInfoWindow.prototype.createSbmlFunctionDiv = function (functions) {
+ var result = Functions.createElement({type: "div"});
+ if (functions.length > 0) {
+ result.appendChild(Functions.createElement({type: "h5", content: "Functions: "}));
+ var guiUtils = new GuiUtils();
+ var table = Functions.createElement({type: "div", style: "display: table;", className: "borderTable"});
+ table.appendChild(guiUtils.createTableRow(["Name", "Definition", "Arguments"]));
+ for (var i = 0; i < functions.length; i++) {
+ var sbmlFunction = functions[i];
+ var mathML;
+ if (sbmlFunction.getMathMlPresentation() !== undefined) {
+ mathML = sbmlFunction.getMathMlPresentation();
+ } else {
+ mathML = "<p>Problematic MathML</p>";
+ logger.warn("Problematic MathML: " + sbmlFunction.getDefinition());
+ }
+ var functionArguments = sbmlFunction.getArguments().join(", ");
+ table.appendChild(guiUtils.createTableRow([sbmlFunction.getName(), mathML, functionArguments]));
+ }
+ result.appendChild(table);
+ }
+ return result;
+};
+
+/**
+ *
+ * @param {SbmlParameter[]} parameters
+ * @returns {HTMLElement}
+ */
+ReactionInfoWindow.prototype.createSbmlParameterDiv = function (parameters) {
+ var result = Functions.createElement({type: "div"});
+ if (parameters.length > 0) {
+ result.appendChild(Functions.createElement({type: "h5", content: "Parameters: "}));
+ var guiUtils = new GuiUtils();
+ var table = Functions.createElement({type: "div", style: "display: table;", className: "borderTable"});
+ table.appendChild(guiUtils.createTableRow(["Name", "parameterId", "Value", "Global"]));
+ for (var i = 0; i < parameters.length; i++) {
+ var sbmlFunction = parameters[i];
+ table.appendChild(guiUtils.createTableRow([sbmlFunction.getName(), sbmlFunction.getParameterId(), sbmlFunction.getValue(), sbmlFunction.getGlobal()]));
+ }
+ result.appendChild(table);
+ }
+ return result;
+};
+
+/**
+ *
+ * @param {Reaction} reaction
+ * @returns {HTMLElement}
+ */
+ReactionInfoWindow.prototype.createElementsDiv = function (reaction) {
+ var result = Functions.createElement({type: "div"});
+ result.appendChild(Functions.createElement({type: "h5", content: "Elements: "}));
+ var guiUtils = new GuiUtils();
+ var table = Functions.createElement({type: "div", style: "display: table;", className: "borderTable"});
+ table.appendChild(guiUtils.createTableRow(["Name", "Role", "elementId", "Constant", "Boundary condition", "Initial concentration", "Initial amount", "Stoichiometry"]));
+ var elements = reaction.getReactants();
+ var i, element;
+
+ function createRow(node, title) {
+ var element = node.getAlias();
+ var stoichiometry = node.getStoichiometry();
+ if (stoichiometry === undefined) {
+ stoichiometry = "";
+ }
+ return guiUtils.createTableRow([element.getName(), title, element.getElementId(), element.getConstant(), element.getBoundaryCondition(), element.getInitialConcentration(), element.getInitialAmount(), stoichiometry])
+ }
+
+ for (i = 0; i < elements.length; i++) {
+ element = elements[i].getAlias();
+ table.appendChild(createRow(elements[i], "Reactant"));
+ }
+ elements = reaction.getProducts();
+ for (i = 0; i < elements.length; i++) {
+ element = elements[i].getAlias();
+ table.appendChild(createRow(elements[i], "Product"));
+ }
+ elements = reaction.getModifiers();
+ for (i = 0; i < elements.length; i++) {
+ element = elements[i].getAlias();
+ table.appendChild(createRow(elements[i], "Modifier"));
+ }
+ result.appendChild(table);
+ return result;
+};
+
+/**
+ *
+ * @returns {PromiseLike<any> | Promise<any>}
+ */
+ReactionInfoWindow.prototype.init = function () {
+ var self = this;
+ return Promise.resolve().then(function () {
+ return AbstractInfoWindow.prototype.init.call(self);
+ }).then(function () {
+ return self.update();
+ });
+};
+
+/**
+ * Returns array with data taken from all known {@link AbstractDbOverlay}.
+ *
+ * @param {Object.<string,boolean>} general
+ * @returns {Promise} of an array with data from {@link AbstractDbOverlay}
+ */
+ReactionInfoWindow.prototype.getDbOverlaysData = function (general) {
+ return this.getCustomMap().getTopMap().getOverlayDataForReaction(this.getReactionData(), general);
+};
+
+/**
+ *
+ * @returns {Reaction}
+ */
+ReactionInfoWindow.prototype.getReactionData = function () {
+ return this._reactionData;
+};
+
+/**
+ *
+ * @param {Reaction} reactionData
+ */
+ReactionInfoWindow.prototype.setReactionData = function (reactionData) {
+ if (reactionData === undefined || reactionData === null) {
+ throw new Error("Reaction must be specified");
+ } else if (reactionData instanceof Reaction) {
+ this._reactionData = reactionData;
+ } else {
+ throw new Error("Parameter must be of Reaction type, but found" + reactionData);
+ }
+};
+
+/**
+ *
+ * @returns {Point}
+ */
+ReactionInfoWindow.prototype.getPosition = function () {
+ return this.getReactionData().getCenter();
+};
+
+module.exports = ReactionInfoWindow;
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index 8a5570401657857cd9c6d0f53cc7920d16e49b28..88c4a9baf3c732deb5eaa3f16b0fa6050360b402 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/frontend-js/src/main/js/minerva.js
@@ -335,7 +335,8 @@ function create(params) {
leftPanel = new LeftPanel({
element: functions.getElementByClassName(element, "minerva-left-panel"),
- customMap: customMap
+ customMap: customMap,
+ configuration: params.getConfiguration()
});
var pluginManager = new PluginManager({
diff --git a/frontend-js/src/test/js/gui/AddOverlayDialog-test.js b/frontend-js/src/test/js/gui/AddOverlayDialog-test.js
index e238c5c36a8df527f130e501022c11f1b25ee935..c823a626721cbb594ba62dc30139dc1e0d652ea4 100644
--- a/frontend-js/src/test/js/gui/AddOverlayDialog-test.js
+++ b/frontend-js/src/test/js/gui/AddOverlayDialog-test.js
@@ -17,7 +17,9 @@ describe('AddOverlayDialog', function () {
dialog = new AddOverlayDialog({
element: testDiv,
project: project,
- customMap: null
+ customMap: null,
+ configuration: helper.getConfiguration(),
+ serverConnector: ServerConnector
});
dialog.setFileContent("s1\n");
diff --git a/frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js b/frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..36be57ba12a2bba3917ae2b59fa8bdc66bcf0a53
--- /dev/null
+++ b/frontend-js/src/test/js/gui/admin/EditGenomeDialog-test.js
@@ -0,0 +1,153 @@
+"use strict";
+
+require("../../mocha-config");
+
+var EditGenomeDialog = require('../../../../main/js/gui/admin/EditGenomeDialog');
+var ReferenceGenome = require('../../../../main/js/map/data/ReferenceGenome');
+var ValidationError = require('../../../../main/js/ValidationError');
+var ServerConnector = require('../../ServerConnector-mock');
+
+var logger = require('../../logger');
+var Promise = require('bluebird');
+
+var chai = require('chai');
+var assert = chai.assert;
+var expect = chai.expect;
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @returns {EditGenomeDialog}
+ */
+function createDialog(genome) {
+ return new EditGenomeDialog({
+ element: testDiv,
+ referenceGenome: genome,
+ customMap: null,
+ serverConnector: ServerConnector
+ });
+}
+
+describe('EditGenomeDialog', function () {
+
+ describe('init', function () {
+ it('new genome', function () {
+ var genome = new ReferenceGenome();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ return dialog.destroy();
+ });
+ });
+ it('existing', function () {
+ helper.loginAsAdmin();
+ var dialog;
+ return ServerConnector.getReferenceGenome({genomeId: 154}).then(function (genome) {
+ dialog = createDialog(genome);
+ return dialog.init();
+ }).then(function () {
+ return dialog.destroy();
+ });
+ });
+ });
+
+ it('removeMapping', function () {
+ helper.loginAsAdmin();
+ var dialog;
+ return ServerConnector.getReferenceGenome({genomeId: 154}).then(function (genome) {
+ dialog = createDialog(genome);
+ return dialog.init();
+ }).then(function () {
+ dialog.askConfirmRemoval = function () {
+ return Promise.resolve({status: true});
+ };
+ assert.equal(0, logger.getWarnings().length);
+
+ var element = $("[name='removeMapping']")[0];
+ return helper.triggerJqueryEvent(element, "click");
+ }).then(function () {
+ return dialog.destroy();
+ });
+ });
+
+
+ it('on organism change', function () {
+ var genome = new ReferenceGenome();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ var element = $("[name='genomeOrganismSelect']")[0];
+ return helper.triggerJqueryEvent(element, "change");
+ }).then(function () {
+ return dialog.destroy();
+ });
+ });
+
+ it('on type change', function () {
+ var genome = new ReferenceGenome();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ var element = $("[name='genomeTypeSelect']")[0];
+ return helper.triggerJqueryEvent(element, "change");
+ }).then(function () {
+ return dialog.destroy();
+ });
+ });
+
+ it('on version change', function () {
+ var genome = new ReferenceGenome();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ var element = $("[name='genomeVersionSelect']")[0];
+ return helper.triggerJqueryEvent(element, "change");
+ }).then(function () {
+ return dialog.destroy();
+ });
+ });
+
+ describe('click cancel', function () {
+ it('new genome', function () {
+ var genome = new ReferenceGenome();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ return dialog.open();
+ }).then(function () {
+ return $("[name=cancelGenome]", testDiv)[0].onclick();
+ }).then(function () {
+ dialog.destroy();
+ });
+ });
+ });
+
+ describe('click save', function () {
+ it('existing genome', function () {
+ var dialog;
+ return ServerConnector.getReferenceGenome({
+ organism: "9606",
+ type: "UCSC",
+ version: "hg38"
+ }).then(function (genome) {
+ dialog = createDialog(genome);
+ return dialog.init();
+ }).then(function () {
+ return dialog.open();
+ }).then(function () {
+ return $("[name=saveGenome]", testDiv)[0].onclick();
+ }).then(function () {
+ dialog.destroy();
+ });
+ });
+
+ it('new genome', function () {
+ helper.loginAsAdmin();
+ var genome = new ReferenceGenome();
+ var dialog = createDialog(genome);
+ return dialog.init().then(function () {
+ return dialog.open();
+ }).then(function () {
+ return $("[name=saveGenome]", testDiv)[0].onclick();
+ }).then(function () {
+ dialog.destroy();
+ });
+ });
+ });
+
+});
diff --git a/frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js b/frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..3eb0ab70904372ca41b409736354bc6271f0b08e
--- /dev/null
+++ b/frontend-js/src/test/js/gui/admin/GenomeAdminPanel-test.js
@@ -0,0 +1,91 @@
+"use strict";
+
+require("../../mocha-config");
+
+var GenomeAdminPanel = require('../../../../main/js/gui/admin/GenomeAdminPanel');
+var ConfigurationType = require('../../../../main/js/ConfigurationType');
+var ServerConnector = require('../../ServerConnector-mock');
+var logger = require('../../logger');
+var Promise = require('bluebird');
+
+var chai = require('chai');
+var assert = chai.assert;
+
+describe('GenomeAdminPanel', function () {
+ describe('init', function () {
+ it('admin', function () {
+ helper.loginAsAdmin();
+ var mapTab;
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ mapTab = new GenomeAdminPanel({
+ element: testDiv,
+ configuration: configuration,
+ serverConnector: ServerConnector
+ });
+ return mapTab.init();
+ }).then(function () {
+ assert.equal(0, logger.getWarnings().length);
+ return mapTab.destroy();
+ });
+ });
+ });
+ it('open edit dialog', function () {
+ helper.loginAsAdmin();
+ var mapTab;
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ mapTab = new GenomeAdminPanel({
+ element: testDiv,
+ configuration: configuration,
+ serverConnector: ServerConnector
+ });
+ return mapTab.init();
+ }).then(function () {
+ assert.equal(0, logger.getWarnings().length);
+ var element = $("[name='editGenome']")[0];
+ return helper.triggerJqueryEvent(element, "click");
+ }).then(function () {
+ return mapTab.destroy();
+ });
+ });
+
+ it('open add genome dialog', function () {
+ helper.loginAsAdmin();
+ var mapTab;
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ mapTab = new GenomeAdminPanel({
+ element: testDiv,
+ configuration: configuration,
+ serverConnector: ServerConnector
+ });
+ return mapTab.init();
+ }).then(function () {
+ assert.equal(0, logger.getWarnings().length);
+ var element = $("[name='addGenome']")[0];
+ return element.onclick();
+ }).then(function () {
+ return mapTab.destroy();
+ });
+ });
+
+ it('remove genome', function () {
+ helper.loginAsAdmin();
+ var mapTab;
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ mapTab = new GenomeAdminPanel({
+ element: testDiv,
+ configuration: configuration,
+ serverConnector: ServerConnector
+ });
+ return mapTab.init();
+ }).then(function () {
+ mapTab.askConfirmRemoval = function () {
+ return Promise.resolve({status: true});
+ };
+ assert.equal(0, logger.getWarnings().length);
+ var element = $("[name='removeGenome']")[0];
+ return helper.triggerJqueryEvent(element, "click");
+ }).then(function () {
+ return mapTab.destroy();
+ });
+ });
+});
diff --git a/frontend-js/src/test/js/gui/admin/UserAdminPanel-test.js b/frontend-js/src/test/js/gui/admin/UserAdminPanel-test.js
index 494f438fb552101f4ff552f6f98f493676bc5dbe..fb675b9525b9a984701bf5569cc54b48577afd6f 100644
--- a/frontend-js/src/test/js/gui/admin/UserAdminPanel-test.js
+++ b/frontend-js/src/test/js/gui/admin/UserAdminPanel-test.js
@@ -11,6 +11,14 @@ var logger = require('../../logger');
var assert = require('assert');
+function createUserAdminPanel(configuration) {
+ return new UsersAdminPanel({
+ element: testDiv,
+ configuration: configuration,
+ serverConnector: ServerConnector
+ });
+}
+
describe('UsersAdminPanel', function () {
describe('init', function () {
@@ -18,10 +26,7 @@ describe('UsersAdminPanel', function () {
helper.loginAsAdmin();
var usersTab;
return ServerConnector.getConfiguration().then(function (configuration) {
- usersTab = new UsersAdminPanel({
- element: testDiv,
- configuration: configuration
- });
+ usersTab = createUserAdminPanel(configuration);
return usersTab.init();
}).then(function () {
assert.equal(0, logger.getWarnings().length);
@@ -35,10 +40,7 @@ describe('UsersAdminPanel', function () {
return Promise.reject(new SecurityError("Access denied."));
};
return ServerConnector.getConfiguration().then(function (configuration) {
- usersTab = new UsersAdminPanel({
- element: testDiv,
- configuration: configuration
- });
+ usersTab = createUserAdminPanel(configuration);
return usersTab.init();
}).then(function () {
assert.equal(0, logger.getWarnings().length);
@@ -52,48 +54,39 @@ describe('UsersAdminPanel', function () {
it('refresh', function () {
helper.loginAsAdmin();
- var mapTab;
+ var usersTab;
return ServerConnector.getConfiguration().then(function (configuration) {
- mapTab = new UsersAdminPanel({
- element: testDiv,
- configuration: configuration
- });
- return mapTab.init();
+ usersTab = createUserAdminPanel(configuration);
+ return usersTab.init();
}).then(function () {
- return mapTab.onRefreshClicked();
+ return usersTab.onRefreshClicked();
}).then(function () {
- return mapTab.destroy();
+ return usersTab.destroy();
});
});
it('showEditDialog', function () {
helper.loginAsAdmin();
- var mapTab;
+ var usersTab;
return ServerConnector.getConfiguration().then(function (configuration) {
- mapTab = new UsersAdminPanel({
- element: testDiv,
- configuration: configuration
- });
- return mapTab.init();
+ usersTab = createUserAdminPanel(configuration);
+ return usersTab.init();
}).then(function () {
- return mapTab.showEditDialog("anonymous");
+ return usersTab.showEditDialog("anonymous");
}).then(function () {
- return mapTab.destroy();
+ return usersTab.destroy();
});
});
it('onAddClicked', function () {
helper.loginAsAdmin();
- var mapTab;
+ var usersTab;
return ServerConnector.getConfiguration().then(function (configuration) {
- mapTab = new UsersAdminPanel({
- element: testDiv,
- configuration: configuration
- });
- return mapTab.init();
+ usersTab = createUserAdminPanel(configuration);
+ return usersTab.init();
}).then(function () {
- return mapTab.onAddClicked();
+ return usersTab.onAddClicked();
}).then(function () {
- return mapTab.destroy();
+ return usersTab.destroy();
});
});
diff --git a/frontend-js/src/test/js/gui/leftPanel/AbstractPanel-test.js b/frontend-js/src/test/js/gui/leftPanel/AbstractPanel-test.js
index da4594bbe8ea2f47df94566bbec6cb457eb25442..86f750982033c36c38f073cdd85960e07ab05f56 100644
--- a/frontend-js/src/test/js/gui/leftPanel/AbstractPanel-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/AbstractPanel-test.js
@@ -57,9 +57,10 @@ describe('AbstractDbPanel', function () {
references: [],
targetParticipants: []
});
- var htmlTag = panel.createTargetRow(target, "empty.png");
- assert.ok(htmlTag);
- assert.equal(1, $(".minerva-open-submap-button", $(htmlTag)).length);
+ return panel.createTargetRow(target, "empty.png").then(function (htmlTag) {
+ assert.ok(htmlTag);
+ assert.equal(1, $(".minerva-open-submap-button", $(htmlTag)).length);
+ });
});
});
});
diff --git a/frontend-js/src/test/js/gui/leftPanel/GenericSearchPanel-test.js b/frontend-js/src/test/js/gui/leftPanel/GenericSearchPanel-test.js
index 5ed0a92606e7ee4375a595a98059100d9981bd24..557e044d5c3b44f91365e1465569d9b846148857 100644
--- a/frontend-js/src/test/js/gui/leftPanel/GenericSearchPanel-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/GenericSearchPanel-test.js
@@ -7,7 +7,7 @@ var Alias = require('../../../../main/js/map/data/Alias');
var ConfigurationType = require('../../../../main/js/ConfigurationType');
var GenericSearchPanel = require('../../../../main/js/gui/leftPanel/GenericSearchPanel');
var PanelControlElementType = require('../../../../main/js/gui/PanelControlElementType');
-var Point= require('../../../../main/js/map/canvas/Point');
+var Point = require('../../../../main/js/map/canvas/Point');
var ServerConnector = require('../../ServerConnector-mock');
var chai = require('chai');
@@ -95,23 +95,44 @@ describe('GenericSearchPanel', function () {
describe('createReactionElement', function () {
- it('type in desc', function () {
- helper.getConfiguration().getOption(ConfigurationType.SHOW_REACTION_TYPE).setValue("true");
- var map = helper.createCustomMap();
- helper.createSearchDbOverlay(map);
-
- var panel = new GenericSearchPanel({
- element: testDiv,
- customMap: map
+ describe('type in desc', function () {
+ it('visible', function () {
+ helper.getConfiguration().getOption(ConfigurationType.SHOW_REACTION_TYPE).setValue("true");
+ var map = helper.createCustomMap();
+ helper.createSearchDbOverlay(map);
+
+ var panel = new GenericSearchPanel({
+ element: testDiv,
+ customMap: map
+ });
+ var reaction = helper.createReaction(map);
+ var reactionType = "XX TYPE";
+ reaction.setType(reactionType);
+
+ return panel.createReactionElement(reaction).then(function (div) {
+ assert.ok(div.innerHTML.indexOf(reactionType) >= 0);
+ });
});
- var reaction = helper.createReaction(map);
- var reactionType = "XX TYPE";
- reaction.setType(reactionType);
- assert.ok(panel.createReactionElement(reaction).innerHTML.indexOf(reactionType) >= 0);
+ it('invisible', function () {
+ helper.getConfiguration().getOption(ConfigurationType.SHOW_REACTION_TYPE).setValue("true");
+ var map = helper.createCustomMap();
+ helper.createSearchDbOverlay(map);
+
+ var panel = new GenericSearchPanel({
+ element: testDiv,
+ customMap: map
+ });
+ var reaction = helper.createReaction(map);
+ var reactionType = "XX TYPE";
+ reaction.setType(reactionType);
+
+ helper.getConfiguration().getOption(ConfigurationType.SHOW_REACTION_TYPE).setValue("false");
+ return panel.createReactionElement(reaction).then(function (div) {
+ assert.notOk(div.innerHTML.indexOf(reactionType) >= 0);
+ });
+ });
- helper.getConfiguration().getOption(ConfigurationType.SHOW_REACTION_TYPE).setValue("false");
- assert.notOk(panel.createReactionElement(reaction).innerHTML.indexOf(reactionType) >= 0);
});
});
@@ -148,26 +169,46 @@ describe('GenericSearchPanel', function () {
customMap: map
});
- var aliasDiv = panel.createAliasElement(alias);
- assert.ok(aliasDiv.innerHTML);
+ return panel.createAliasElement(alias).then(function (aliasDiv) {
+ assert.ok(aliasDiv.innerHTML);
+ });
});
- it('full name in desc', function () {
- var map = helper.createCustomMap();
- helper.createSearchDbOverlay(map);
+ describe('full name in desc', function () {
+ it('visible', function () {
+ var map = helper.createCustomMap();
+ helper.createSearchDbOverlay(map);
- var panel = new GenericSearchPanel({
- element: testDiv,
- customMap: map
+ var panel = new GenericSearchPanel({
+ element: testDiv,
+ customMap: map
+ });
+ var alias = helper.createAlias(map);
+
+ alias.setFullName("xxx");
+ return panel.createAliasElement(alias).then(function (div) {
+
+ assert.ok(div.innerHTML.indexOf("Full name") >= 0);
+ });
});
- var alias = helper.createAlias(map);
- alias.setFullName("xxx");
- assert.ok(panel.createAliasElement(alias).innerHTML.indexOf("Full name") >= 0);
+ it('invisible', function () {
+ var map = helper.createCustomMap();
+ helper.createSearchDbOverlay(map);
+
+ var panel = new GenericSearchPanel({
+ element: testDiv,
+ customMap: map
+ });
+ var alias = helper.createAlias(map);
- alias.setFullName("");
- assert.ok(panel.createAliasElement(alias).innerHTML.indexOf("Full name") === -1);
+ alias.setFullName("");
+ return panel.createAliasElement(alias).then(function (div) {
+ assert.ok(div.innerHTML.indexOf("Full name") === -1);
+ });
+
+ });
});
});
diff --git a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
index 078ec940fa008fa23dee36574751b8779acfe3b1..93f55f5850b2867e0295e4ea34d38c6a1de1588a 100644
--- a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
@@ -23,7 +23,7 @@ describe('GuiUtils', function () {
var map = helper.createCustomMap();
helper.createSearchDbOverlay(map);
- new GuiUtils();
+ new GuiUtils(helper.getConfiguration());
assert.equal(logger.getWarnings().length, 0);
});
@@ -56,17 +56,15 @@ describe('GuiUtils', function () {
var guiUtils = createGuiUtils();
guiUtils.setMap(map);
- var aliasDiv = guiUtils.createAliasElement({
- alias: alias
+ return guiUtils.createAliasElement({alias: alias}).then(function (aliasDiv) {
+ assert.ok(aliasDiv.innerHTML);
});
- assert.ok(aliasDiv.innerHTML);
});
it('createLabelText for undefined', function () {
var map = helper.createCustomMap();
- var guiUtils = new GuiUtils();
- guiUtils.setMap(map);
+ var guiUtils = createGuiUtils(map);
var res = guiUtils.createLabelText();
assert.notOk(res.innerHTML);
@@ -75,8 +73,7 @@ describe('GuiUtils', function () {
it('createSubMapLink', function () {
var map = helper.createCustomMap();
- var guiUtils = new GuiUtils();
- guiUtils.setMap(map);
+ var guiUtils = createGuiUtils(map);
var res = guiUtils.createSubMapLink("TEST", map.getId());
assert.ok(res.innerHTML);
@@ -117,62 +114,85 @@ describe('GuiUtils', function () {
var reactionId = "XX ID";
reaction.setReactionId(reactionId);
- assert.ok(guiUtils.createReactionElement({
- reaction: reaction
- }).innerHTML.indexOf(reactionId) >= 0);
+ return guiUtils.createReactionElement({reaction: reaction}).then(function (div) {
+ assert.ok(div.innerHTML.indexOf(reactionId) >= 0);
+ })
});
});
describe('createAliasElement', function () {
- it('full name in desc', function () {
+ it('full name in desc visible', function () {
var map = helper.createCustomMap();
helper.createSearchDbOverlay(map);
- var guiUtils = new GuiUtils();
- guiUtils.setMap(map);
+ var guiUtils = createGuiUtils(map);
var alias = helper.createAlias(map);
alias.setFullName("xxx");
- assert.ok(guiUtils.createAliasElement({
- alias: alias
- }).innerHTML.indexOf("Full name") >= 0);
+ return guiUtils.createAliasElement({alias: alias}).then(function (div) {
+ assert.ok(div.innerHTML.indexOf("Full name") >= 0);
+ });
+ });
+
+ it('compartment visible', function () {
+ var map = helper.createCustomMap();
+ helper.createSearchDbOverlay(map);
+
+ var guiUtils = createGuiUtils(map);
+ var alias = helper.createAlias(map);
+ var compartment = helper.createAlias(map);
+ alias.setCompartmentId(compartment.getId());
+
+ compartment.setName("compartment_name");
+ return guiUtils.createAliasElement({alias: alias}).then(function (div) {
+ assert.ok(div.innerHTML.indexOf("compartment_name") >= 0);
+ });
+ });
+
+
+ it('full name in desc invisible', function () {
+ var map = helper.createCustomMap();
+ helper.createSearchDbOverlay(map);
+
+ var guiUtils = createGuiUtils(map);
+ var alias = helper.createAlias(map);
alias.setFullName("");
- assert.ok(guiUtils.createAliasElement({
- alias: alias
- }).innerHTML.indexOf("Full name") === -1);
+ return guiUtils.createAliasElement({alias: alias}).then(function (div) {
+ assert.ok(div.innerHTML.indexOf("Full name") === -1);
+ });
});
it('onclick function', function () {
var map = helper.createCustomMap();
helper.createSearchDbOverlay(map);
- var guiUtils = new GuiUtils();
- guiUtils.setMap(map);
+ var guiUtils = createGuiUtils(map);
var alias = helper.createAlias(map);
alias.setFullName("xxx");
- var htmlElement = guiUtils.createAliasElement({
+ return guiUtils.createAliasElement({
alias: alias,
icon: "empty.png"
- });
-
- var img = $("img", htmlElement)[0];
+ }).then(function (htmlElement) {
+ var img = $("img", htmlElement)[0];
- return img.onclick();
+ return img.onclick();
+ });
});
});
describe('createLink', function () {
it('normal', function () {
- var guiUtils = new GuiUtils();
+ var guiUtils = createGuiUtils();
var link = guiUtils.createLink("http://www.minerva.uni.lu", "PD map");
assert.ok(link);
assert.equal(0, logger.getWarnings().length);
});
it('with null link', function () {
- var guiUtils = new GuiUtils();
+ var guiUtils = createGuiUtils();
+ // noinspection JSCheckFunctionSignatures
var link = guiUtils.createLink(null, "PD map");
assert.ok(link);
assert.ok(logger.getWarnings().length > 0);
@@ -231,5 +251,92 @@ describe('GuiUtils', function () {
});
});
+ describe('createModificationRow', function () {
+ describe('PTM', function () {
+ it('default', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({name: "n", type: "RESIDUE", state: "PHOSPHORYLATED"});
+ assert.ok(li);
+ });
+ it('empty PTM', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({name: "n", type: "RESIDUE"});
+ assert.notOk(li);
+ });
+ });
+ describe('Modification Site', function () {
+ it('default', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({name: "n", type: "MODIFICATION_SITE", state: "PHOSPHORYLATED"});
+ assert.ok(li);
+ });
+ it('empty', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({name: "n", type: "MODIFICATION_SITE"});
+ assert.notOk(li);
+ });
+ });
+ describe('Binding Region', function () {
+ it('default', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({name: "n", type: "BINDING_REGION"});
+ assert.ok(li);
+ });
+ it('empty', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({type: "BINDING_REGION"});
+ assert.notOk(li);
+ });
+ });
+ describe('Coding Region', function () {
+ it('default', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({name: "n", type: "CODING_REGION"});
+ assert.ok(li);
+ });
+ it('empty', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({type: "CODING_REGION"});
+ assert.notOk(li);
+ });
+ });
+ describe('Protein binding region', function () {
+ it('default', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({name: "n", type: "PROTEIN_BINDING_DOMAIN"});
+ assert.ok(li);
+ });
+ it('empty', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({type: "PROTEIN_BINDING_DOMAIN"});
+ assert.notOk(li);
+ });
+ });
+ describe('Regulatory region', function () {
+ it('default', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({name: "n", type: "REGULATORY_REGION"});
+ assert.ok(li);
+ });
+ it('empty', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({type: "REGULATORY_REGION"});
+ assert.notOk(li);
+ });
+ });
+ describe('Transcription sites', function () {
+ it('default', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({name: "n", type: "TRANSCRIPTION_SITE_LEFT"});
+ assert.ok(li);
+ });
+ it('empty', function () {
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var li = guiUtils.createModificationRow({type: "TRANSCRIPTION_SITE_LEFT"});
+ assert.notOk(li);
+ });
+ });
+ });
+
});
diff --git a/frontend-js/src/test/js/gui/leftPanel/LeftPanel-test.js b/frontend-js/src/test/js/gui/leftPanel/LeftPanel-test.js
index 49e5d1811c9f9126f641863e9885e4512b86c2e2..24f4f694cb023e1e617fb0969d42a5c5e8c9f914 100644
--- a/frontend-js/src/test/js/gui/leftPanel/LeftPanel-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/LeftPanel-test.js
@@ -154,6 +154,37 @@ describe('LeftPanel', function () {
return panel.destroy();
});
});
+ it('when different tab is active', function () {
+ var map;
+ var panel;
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+
+ helper.createSearchDbOverlay(map);
+ helper.createDrugDbOverlay(map);
+ helper.createChemicalDbOverlay(map);
+ helper.createMiRnaDbOverlay(map);
+
+ panel = new LeftPanel({
+ element: testDiv,
+ customMap: map
+ });
+ return panel.init();
+ }).then(function () {
+ return $('a:contains("DRUG")').click();
+ }).then(function () {
+
+ var element = new IdentifiedElement({
+ id: 329163,
+ type: "ALIAS",
+ modelId: map.getId()
+ });
+ return panel.showElementDetails(element);
+ }).then(function () {
+ assert.ok($(panel.elementInfoDiv).dialog('isOpen'));
+ return panel.destroy();
+ });
+ });
});
});
diff --git a/frontend-js/src/test/js/gui/leftPanel/OverlayPanel-test.js b/frontend-js/src/test/js/gui/leftPanel/OverlayPanel-test.js
index eaf001bb281285a649d62753e1e24a814cc89afb..e36f55db5a9818a299e1d224a32e934e2cd5459f 100644
--- a/frontend-js/src/test/js/gui/leftPanel/OverlayPanel-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/OverlayPanel-test.js
@@ -9,6 +9,19 @@ var chai = require('chai');
var assert = chai.assert;
var logger = require('../../logger');
+/**
+ *
+ * @param {CustomMap} map
+ * @returns {OverlayPanel}
+ */
+function createOverlayPanel(map) {
+ return new OverlayPanel({
+ element: testDiv,
+ customMap: map,
+ configuration: helper.getConfiguration()
+ });
+}
+
describe('OverlayPanel', function () {
it('constructor', function () {
@@ -138,10 +151,7 @@ describe('OverlayPanel', function () {
it('open', function () {
var map = helper.createCustomMap();
- var panel = new OverlayPanel({
- element: testDiv,
- customMap: map
- });
+ var panel = createOverlayPanel(map);
return panel.openAddOverlayDialog().then(function () {
return panel.destroy();
@@ -150,11 +160,7 @@ describe('OverlayPanel', function () {
it('trigger onAddOverlay event handler', function () {
var map = helper.createCustomMap();
-
- var panel = new OverlayPanel({
- element: testDiv,
- customMap: map
- });
+ var panel = createOverlayPanel(map);
return panel.init().then(function () {
return panel.openAddOverlayDialog();
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index bb886842375a076532515e8536e94d5b89f3d109..11fc0efa1884a43783a7801b84373de106a9b633 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/frontend-js/src/test/js/helper.js
@@ -220,7 +220,14 @@ Helper.prototype.createAlias = function (map) {
return result;
};
-Helper.prototype.createLayoutAlias = function (alias) {
+/**
+ *
+ * @param {Alias} [alias]
+ * @param {string} [type]
+ *
+ * @returns {LayoutAlias}
+ */
+Helper.prototype.createLayoutAlias = function (alias, type) {
var id;
var modelId;
if (alias instanceof Alias) {
@@ -237,7 +244,8 @@ Helper.prototype.createLayoutAlias = function (alias) {
a: 23
},
modelId: modelId,
- geneVariations: [{}]
+ geneVariations: [],
+ type: type
});
};
@@ -488,6 +496,12 @@ Helper.prototype.loginWithoutAccess = function () {
};
+/**
+ *
+ * @param {HTMLElement} element
+ * @param {string} eventType
+ * @returns {Promise}
+ */
Helper.prototype.triggerJqueryEvent = function (element, eventType) {
var domElements = $("*");
var promises = [];
diff --git a/frontend-js/src/test/js/map/CustomMap-test.js b/frontend-js/src/test/js/map/CustomMap-test.js
index 9c8cf3654a232c44fa8853d325fd2631a9d73fda..880efabfaac797fc04af47722fd81ac9caf3c0b3 100644
--- a/frontend-js/src/test/js/map/CustomMap-test.js
+++ b/frontend-js/src/test/js/map/CustomMap-test.js
@@ -1,1037 +1,1021 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-require("../mocha-config.js");
-
-var AliasMarker = require('../../../main/js/map/marker/AliasMarker');
-var AliasSurface = require('../../../main/js/map/surface/AliasSurface');
-var Comment = require('../../../main/js/map/data/Comment');
-var ControlType = require('../../../main/js/map/ControlType');
-var CustomMap = require('../../../main/js/map/CustomMap');
-var IdentifiedElement = require('../../../main/js/map/data/IdentifiedElement');
-var MapContextMenu = require('../../../main/js/gui/MapContextMenu');
-var MolArt = require('../../../main/js/map/structure/MolArt');
-var Point = require('../../../main/js/map/canvas/Point');
-var PointData = require('../../../main/js/map/data/PointData');
-var PointMarker = require('../../../main/js/map/marker/PointMarker');
-var ReactionMarker = require('../../../main/js/map/marker/ReactionMarker');
-var ReactionSurface = require('../../../main/js/map/surface/ReactionSurface');
-
-var ServerConnector = require('./../ServerConnector-mock');
-
-var logger = require('./../logger');
-
-var chai = require('chai');
-var assert = chai.assert;
-
-describe('CustomMap', function () {
- describe("constructor", function () {
- it("default", function () {
- var options = helper.createCustomMapOptions();
- var map = new CustomMap(options);
- assert.ok(map);
- });
-
- it("with submaps", function () {
- var options = helper.createCustomMapOptions();
-
- options.getProject().addModel(helper.createModel());
-
- var map = new CustomMap(options);
- assert.ok(map);
- });
-
- it("with session data pointing to not existing overlay", function () {
- var options = helper.createCustomMapOptions();
-
- ServerConnector.getSessionData(options.getProject()).setSelectedBackgroundOverlay("-1");
-
- var map = new CustomMap(options);
- assert.ok(map);
- });
- });
-
- it("getSubmapById", function () {
- var map = helper.createCustomMap();
- assert.ok(map.getSubmapById(map.getId()));
- });
-
- it("getSubmapById (invalid)", function () {
- var map = helper.createCustomMap();
- assert.equal(map.getSubmapById(-1), null);
- });
-
- it("getSubmapById (string id)", function () {
- var map = helper.createCustomMap();
- assert.ok(map.getSubmapById(map.getId() + ""));
- });
-
- describe("openDataOverlay", function () {
- it("for not existing id", function () {
- var map = helper.createCustomMap();
- try {
- map.openDataOverlay(-1);
- assert.ok(false);
- } catch (exception) {
- assert.ok(exception.message.indexOf("You have no privileges") >= 0);
- }
- });
-
- it("for int id", function () {
- var options = helper.createCustomMapOptions();
- var layout = options.getProject().getDataOverlays()[0];
- var map = new CustomMap(options);
- map.openDataOverlay(layout.getId());
- assert.equal(logger.getErrors().length, 0);
- });
-
- it("for overlay object", function () {
- var options = helper.createCustomMapOptions();
- var layout = options.getProject().getDataOverlays()[0];
- var map = new CustomMap(options);
- map.openDataOverlay(layout);
- assert.equal(logger.getErrors().length, 0);
- });
-
- it("for string id", function () {
- var options = helper.createCustomMapOptions();
- var layout = options.getProject().getDataOverlays()[0];
- var map = new CustomMap(options);
- map.openDataOverlay(layout.getId() + "");
- assert.equal(logger.getErrors().length, 0);
- });
-
- it("with background overlay", function () {
- var map = helper.createCustomMap();
- var layout = helper.createOverlay();
- layout.setInitialized(true);
- layout.setInputDataAvailable(false);
- map.getProject().addDataOverlay(layout);
-
- return map.openDataOverlay(layout.getId()).then(function () {
- var vLayouts = ServerConnector.getSessionData(map.getProject()).getVisibleOverlays();
- assert.equal(0, vLayouts.length);
- });
- });
-
- it("with non background overlay", function () {
- var project = helper.createProject();
- var layout = helper.createOverlay();
- layout.setInitialized(true);
- layout.setInputDataAvailable(true);
- project.addDataOverlay(layout);
-
- var emptyBackground = helper.createOverlay();
- emptyBackground.setInputDataAvailable(false);
- emptyBackground.setName("Empty");
- project.addDataOverlay(emptyBackground);
-
- var map = helper.createCustomMap(project);
-
-
- return map.openDataOverlay(layout.getId()).then(function () {
- var backgroundId = ServerConnector.getSessionData(project).getSelectedBackgroundOverlay();
- assert.equal(backgroundId, emptyBackground.getId());
- });
- });
-
- it("check backgroundChangeListener", function () {
- var project = helper.createProject();
- var overlay = helper.createOverlay();
- overlay.setInitialized(true);
- overlay.setInputDataAvailable(true);
- project.addDataOverlay(overlay);
-
- var overlay2 = helper.createOverlay();
- overlay2.setInitialized(true);
- overlay2.setInputDataAvailable(true);
- project.addDataOverlay(overlay2);
-
- var emptyBackground = helper.createOverlay();
- emptyBackground.setInputDataAvailable(false);
- emptyBackground.setName("Empty");
- project.addDataOverlay(emptyBackground);
-
- var map = helper.createCustomMap(project);
-
- var counter = 0;
- map.addListener("onBackgroundOverlayChange", function () {
- counter++;
- });
-
- return map.openDataOverlay(overlay.getId()).then(function () {
- assert.equal(1, counter, "listener wasn't fired");
- return map.openDataOverlay(overlay2.getId());
- }).then(function () {
- assert.equal(1, counter, "listener shouldn't be fired again because nothing changed");
- });
- });
-
- it("simple", function () {
- var map = helper.createCustomMap();
- var alias = helper.createAlias(map);
- map.getModel().addAlias(alias);
-
- var reaction = helper.createReaction(map);
- map.getModel().addReaction(reaction);
-
- var layout = helper.createOverlay();
- layout.setInputDataAvailable(true);
- layout.setInitialized(true);
- var layoutAlias = helper.createLayoutAlias(alias);
- layout.addAlias(layoutAlias);
-
- var layoutReaction = helper.createLayoutReaction(reaction);
- layout.addReaction(layoutReaction);
-
- map.getProject().addDataOverlay(layout);
-
- return map.openDataOverlay(layout.getId()).then(function () {
- return map._showSelectedDataOverlay(layout.getId(), 0, 1);
- }).then(function () {
- var vLayouts = ServerConnector.getSessionData(map.getProject()).getVisibleOverlays();
- assert.equal(1, vLayouts.length);
- assert.equal(layout.getId(), vLayouts[0]);
-
- assert.equal(2, map.selectedLayoutOverlays[layout.getId()].length);
- assert.ok(map.selectedLayoutOverlays[layout.getId()][0] instanceof AliasSurface);
- assert.ok(map.selectedLayoutOverlays[layout.getId()][1] instanceof ReactionSurface);
-
- // now hide the layout
- return map._hideSelectedLayout(layout.getId());
- }).then(function () {
- assert.ok(map.selectedLayoutOverlays[layout.getId()]);
- assert.equal(0, map.selectedLayoutOverlays[layout.getId()].length);
- });
-
- });
-
- it("with submaps", function () {
- var projectId = "complex_model_with_submaps";
- helper.setUrl("http://test/?id=" + projectId);
- var customMap;
- var emptySubmodelId = 16730;
- var filledSubmodelId = 16731;
- var overlayId = 18083;
-
- return ServerConnector.getProject(projectId).then(function (project) {
- var options = helper.createCustomMapOptions(project);
- customMap = new CustomMap(options);
-
- return customMap.openSubmap(emptySubmodelId);
- }).then(function () {
- return customMap.openSubmap(filledSubmodelId);
- }).then(function () {
-
- var emptySubmap = customMap.getSubmapById(emptySubmodelId);
- var filledSubmap = customMap.getSubmapById(filledSubmodelId);
-
- return customMap.openDataOverlay(overlayId).then(function () {
-
- assert.equal(1, customMap.selectedLayoutOverlays[overlayId].length);
- assert.equal(1, filledSubmap.selectedLayoutOverlays[overlayId].length);
- assert.equal(0, emptySubmap.selectedLayoutOverlays[overlayId].length);
-
- // now hide the layout
-
- return customMap.hideSelectedLayout(overlayId);
- }).then(function () {
- assert.equal(0, customMap.selectedLayoutOverlays[overlayId].length);
- assert.equal(0, filledSubmap.selectedLayoutOverlays[overlayId].length);
- assert.equal(0, emptySubmap.selectedLayoutOverlays[overlayId].length);
- });
-
- }).then(function () {
- return customMap.destroy();
- });
- });
-
- it("with submap double opened", function () {
- var projectId = "complex_model_with_submaps";
- helper.setUrl("http://test/?id=" + projectId);
- var customMap, filledSubmap;
- var filledSubmodelId = 16731;
- var overlayId = 18083;
-
- return ServerConnector.getProject(projectId).then(function (project) {
- customMap = helper.createCustomMap(project);
- return customMap.openSubmap(filledSubmodelId);
- }).then(function () {
- filledSubmap = customMap.getSubmapById(filledSubmodelId);
- return customMap.openDataOverlay(overlayId);
- }).then(function () {
- assert.equal(1, filledSubmap.selectedLayoutOverlays[overlayId].length);
- return customMap.openSubmap(filledSubmodelId);
- }).then(function () {
- //after opening submap nothing should change
- assert.equal(1, filledSubmap.selectedLayoutOverlays[overlayId].length);
- }).finally(function () {
- return customMap.destroy();
- });
- });
-
- it("check if info window content changed", function () {
- var project = helper.createProject();
- var layout = helper.createOverlay();
- layout.setInitialized(true);
- layout.setInputDataAvailable(true);
- project.addDataOverlay(layout);
-
- var map = helper.createCustomMap(project);
-
- var alias = helper.createAlias(map);
- var ie = helper.createIdentifiedElement(alias);
- var marker = map.getMapCanvas().createMarker({icon: "empty.png", position: new Point(0, 0)});
- var infoWindow;
- return map.openInfoWindowForIdentifiedElement(ie, marker).then(function (result) {
- infoWindow = result;
- assert.notOk(infoWindow.getContent().innerHTML.indexOf(layout.getName()) >= 0);
- return map.openDataOverlay(layout.getId());
- }).then(function () {
- assert.ok(infoWindow.getContent().innerHTML.indexOf(layout.getName()) >= 0);
- assert.equal(logger.getErrors().length, 0);
- });
- });
- });
-
- describe("hideDataOverlay", function () {
- it("default", function () {
- var map = helper.createCustomMap();
- var layout = helper.createOverlay();
- layout.setInitialized(true);
- layout.setInputDataAvailable(true);
- map.getProject().addDataOverlay(layout);
-
- return map.openDataOverlay(layout.getId()).then(function () {
- return map.hideDataOverlay(layout.getId());
- }).then(function () {
- var vLayouts = ServerConnector.getSessionData(map.getProject()).getVisibleOverlays();
- assert.equal(0, vLayouts.length);
- });
- });
- it("check if info window content changed", function () {
- var project = helper.createProject();
- var layout = helper.createOverlay();
- layout.setInitialized(true);
- layout.setInputDataAvailable(true);
- project.addDataOverlay(layout);
-
- var map = helper.createCustomMap(project);
-
- var alias = helper.createAlias(map);
- var ie = helper.createIdentifiedElement(alias);
- var marker = map.getMapCanvas().createMarker({icon: "empty.png", position: new Point(0, 0)});
- var infoWindow;
- return map.openInfoWindowForIdentifiedElement(ie, marker).then(function (result) {
- infoWindow = result;
- return map.openDataOverlay(layout.getId());
- }).then(function () {
- assert.ok(infoWindow.getContent().innerHTML.indexOf(layout.getName()) >= 0);
- return map.hideDataOverlay(layout.getId());
- }).then(function () {
- assert.notOk(infoWindow.getContent().innerHTML.indexOf(layout.getName()) >= 0);
- assert.equal(logger.getErrors().length, 0);
- });
- });
- });
-
-
- describe("renderOverlayCollection", function () {
- it("for alias", function () {
- var map = helper.createCustomMap();
- var alias = helper.createAlias(map);
-
- var oc = helper.createDbOverlay(map);
-
- oc.getIdentifiedElements = function () {
- return Promise.resolve([new IdentifiedElement({
- objectId: alias.getId(),
- icon: "empty.png",
- modelId: map.getId(),
- type: "Alias"
- })]);
- };
- return map.renderOverlayCollection({
- overlayCollection: oc
- }).then(function () {
- var markers = map.getMarkerSurfaceCollection().getMarkers();
- assert.equal(1, markers.length);
- });
- });
-
- it("alias re-rendering with different icon", function () {
- var map = helper.createCustomMap();
- var reaction = helper.createReaction(map, true);
- var alias = helper.createAlias(map);
- map.getModel().addAlias(alias);
- map.getModel().addReaction(reaction);
-
- var identifiedElement = new IdentifiedElement(alias);
- identifiedElement.setIcon("empty.png");
- var identifiedElement2 = new IdentifiedElement(alias);
- identifiedElement2.setIcon("new_icon.png");
-
- var marker;
- var oc = helper.createDbOverlay(map);
-
- oc.getIdentifiedElements = function () {
- return Promise.resolve([identifiedElement, new IdentifiedElement(reaction)]);
- };
- return map.renderOverlayCollection({
- overlayCollection: oc
- }).then(function () {
- marker = map.getMarkerSurfaceCollection().getMarker(identifiedElement);
- oc.getIdentifiedElements = function () {
- return Promise.resolve([identifiedElement2]);
- };
- assert.ok(map.getMarkerSurfaceCollection().getSurface({element: reaction, overlay: oc}));
-
- return map.renderOverlayCollection({
- overlayCollection: oc
- });
- }).then(function () {
- assert.equal(marker.getIcon(), "new_icon.png");
-
- assert.notOk(oc.mapOverlays["REACTION"][reaction.getId()]);
- });
- });
-
- it("for set of aliases", function () {
- var map = helper.createCustomMap();
-
- var oc = helper.createDbOverlay(map);
-
- var identifiedElements = [];
- for (var i = 0; i < 3; i++) {
- var alias = helper.createAlias(map);
- map.getModel().addAlias(alias);
- var ie = helper.createIdentifiedElement(alias);
- ie.setIcon("");
- identifiedElements.push(ie);
- }
-
- oc.getIdentifiedElements = function () {
- return Promise.resolve(identifiedElements);
- };
-
- return map.renderOverlayCollection({
- overlayCollection: oc
- }).then(function () {
- var markers = map.getMarkerSurfaceCollection().getMarkers();
- assert.equal(3, markers.length);
- });
- });
-
- it("for point", function () {
- var map = helper.createCustomMap();
-
- var oc = helper.createDbOverlay(map);
-
- var javaObj = {
- objectId: "Point2D.Double[117.685546875, 204.6923828125001]",
- modelId: map.getId(),
- type: "POINT",
- icon: "marker/empty.png"
- };
-
- oc.getIdentifiedElements = function () {
- return Promise.resolve([new IdentifiedElement(javaObj)]);
- };
-
- return map.renderOverlayCollection({
- overlayCollection: oc
- }).then(function () {
- var markers = map.getMarkerSurfaceCollection().getMarkers();
- assert.equal(1, markers.length);
- });
- });
-
- it("for reaction", function () {
- var map = helper.createCustomMap();
- var reaction = helper.createReaction(map, true);
- map.getModel().addReaction(reaction);
-
- var oc = helper.createDbOverlay(map);
-
- oc.getIdentifiedElements = function () {
- return Promise.resolve([new IdentifiedElement(reaction)]);
- };
-
- return map.renderOverlayCollection({
- overlayCollection: oc
- }).then(function () {
- var surfaces = map.getMarkerSurfaceCollection().getSurfaces();
- assert.equal(1, surfaces.length);
- });
- });
- });
-
- it("refreshMarkers", function () {
- var map = helper.createCustomMap();
- var alias = helper.createAlias(map);
- map.getModel().addAlias(alias);
-
- var oc = helper.createDbOverlay(map);
-
- oc.getIdentifiedElements = function () {
- var element = new IdentifiedElement(alias);
- element.setIcon("icon");
- return Promise.resolve([element]);
- };
- return map.renderOverlayCollection({
- overlayCollection: oc
- }).then(function () {
- return map.refreshMarkers(true);
- }).then(function () {
- var markers = map.getMarkerSurfaceCollection().getMarkers();
- assert.equal(1, markers.length);
- });
- });
-
- it("clearDbOverlays", function () {
- var map = helper.createCustomMap();
-
- var oc = helper.createDbOverlay(map);
-
- var javaObj = {
- objectId: "Point2D.Double[117.685546875, 204.6923828125001]",
- modelId: map.getId(),
- type: "POINT",
- icon: "marker/empty.png"
- };
- var searchResults = [new IdentifiedElement(javaObj)];
-
- oc.getIdentifiedElements = function () {
- return Promise.resolve(searchResults);
- };
- oc.clear = function () {
- searchResults = [];
- return this.callListeners("onSearch", searchResults);
- };
-
- return map.renderOverlayCollection({
- overlayCollection: oc
- }).then(function () {
-
- return map.clearDbOverlays();
- }).then(function () {
- var markerCount = 0;
- for (var id in oc.pointMarkers) {
- if (oc.pointMarkers.hasOwnProperty(id)) {
- markerCount++;
- }
- }
-
- assert.equal(0, markerCount);
- });
-
- });
-
- it("getInfoWindowForIdentifiedElement ( reaction)", function () {
- var map = helper.createCustomMap();
- var reaction = helper.createReaction(map, true);
- map.getModel().addReaction(reaction);
-
- var ie = helper.createIdentifiedElement(reaction);
- var marker = map.getMapCanvas().createMarker({icon: "empty.png", position: new Point(0, 0)});
-
- var infoWindow = map.getInfoWindowForIdentifiedElement(ie);
-
- assert.equal(null, infoWindow);
- return map.openInfoWindowForIdentifiedElement(ie, marker).then(function () {
- infoWindow = map.getInfoWindowForIdentifiedElement(ie);
-
- assert.ok(infoWindow);
- });
-
- });
-
- it("right click on map", function () {
- var map = helper.createCustomMap();
- map.setContextMenu(new MapContextMenu({
- customMap: map,
- element: testDiv,
- molArt: new MolArt(map.getElement(), map)
- }));
-
- return map.getContextMenu().init().then(function () {
- var data = {
- stop: null,
- point: new Point(10.0, 20.0)
- };
-
- assert.notOk(map.getActiveSubmapId());
- return map.triggerEvent("map-rightclick", data);
- }).then(function () {
- //we need to wait because some implementations don't use promises...
- return Promise.delay(100);
- }).then(function () {
- assert.equal(map.getId(), map.getActiveSubmapId());
- return map.destroy();
- });
-
- });
-
- it("left click on map", function () {
- var map;
- var searchOverlay;
- return ServerConnector.getProject().then(function (project) {
- map = helper.createCustomMap(project);
- searchOverlay = helper.createSearchDbOverlay(map);
-
- var data = {
- stop: null,
- point: new Point(184.79, 365.76)
- };
- map.setZoom(4);
-
- assert.notOk(map.getActiveSubmapId());
- return map.triggerEvent("map-click", data);
- }).then(function () {
- //we need to wait because some implementations don't use promises...
- return Promise.delay(100);
- }).then(function () {
- assert.equal(map.getId(), map.getActiveSubmapId());
- var element = new IdentifiedElement({id: 329171, type: "ALIAS", modelId: map.getId()});
- assert.ok(map.getMarkerSurfaceCollection().getMarker(element));
- });
-
- });
-
- it("left click on reaction", function () {
- var map;
- var searchOverlay;
- return ServerConnector.getProject().then(function (project) {
- map = helper.createCustomMap(project);
- searchOverlay = helper.createSearchDbOverlay(map);
-
- var data = {
- stop: null,
- point: new Point(457.51, 356.84)
- };
- map.setZoom(4);
-
- assert.notOk(map.getActiveSubmapId());
- return map.triggerEvent("map-click", data);
- }).then(function () {
- //we need to wait because some implementations don't use promises...
- return Promise.delay(100);
- }).then(function () {
- assert.equal(map.getId(), map.getActiveSubmapId());
-
- var reaction = new IdentifiedElement({id: 153521, type: "REACTION", modelId: map.getId()});
- var surface = map.getMarkerSurfaceCollection().getSurface({element: reaction, overlay: searchOverlay});
-
- assert.ok(surface);
- assert.ok(surface.isShown());
-
- var element = new IdentifiedElement({id: 329165, type: "ALIAS", modelId: map.getId()});
- var marker = map.getMarkerSurfaceCollection().getMarker(element);
- assert.ok(marker);
- });
- });
-
- it("getAliasVisibleLayoutsData", function () {
- var mockObject = helper.createCustomMap();
-
- var alias = helper.createAlias();
- mockObject.getModel().addAlias(alias);
-
- var layout = helper.createOverlay();
- layout.setInputDataAvailable(true);
- layout.setInitialized(true);
- mockObject.getProject().addDataOverlay(layout);
-
- return mockObject.openDataOverlay(layout.getId()).then(function () {
- return mockObject.getAliasVisibleLayoutsData(alias.getId());
- }).then(function (layoutAliases) {
- assert.equal(layoutAliases.length, 1);
- });
- });
-
- it("changed coordinates in map", function () {
- var map = helper.createCustomMap();
- var oldCenter = map.getCenter();
- var newCenter = new Point(3, 87);
- map.setCenter(newCenter);
- map.triggerEvent("map-center_changed");
-
- var center = ServerConnector.getSessionData(map.getProject()).getCenter(map.getModel());
- assert.ok(center !== oldCenter);
- assert.ok(center instanceof Point);
- });
-
- it("refreshComments", function () {
- var map = helper.createCustomMap();
- map.getModel().setId(15781);
- helper.createCommentDbOverlay(map);
-
- ServerConnector.getSessionData().setShowComments(true);
- return map.refreshComments().then(function () {
- assert.notOk(map.getMarkerSurfaceCollection().getMarker(new IdentifiedElement({
- id: '(241.01,372.35)',
- modelId: map.getId(),
- type: "POINT"
- })));
- assert.ok(map.getMarkerSurfaceCollection().getMarker(new IdentifiedElement({
- id: '(643.96,144.09)',
- modelId: map.getId(),
- type: "POINT"
- })));
- assert.notOk(map.getMarkerSurfaceCollection().getMarker(new IdentifiedElement({
- id: '(216.65,370.00)',
- modelId: map.getId(),
- type: "POINT"
- })));
- assert.notOk(map.getMarkerSurfaceCollection().getMarker(new IdentifiedElement({
- id: 'unkId',
- modelId: map.getId(),
- type: "POINT"
- })));
- });
- });
-
- it("hide comments", function () {
- var map = helper.createCustomMap();
- map.getModel().setId(15781);
- helper.createCommentDbOverlay(map);
-
- ServerConnector.getSessionData().setShowComments(true);
- return map.refreshComments().then(function () {
- ServerConnector.getSessionData().setShowComments(false);
- return map.refreshComments();
- }).then(function () {
- assert.notOk(map.getMarkerSurfaceCollection().getMarker(new IdentifiedElement({
- id: '(241.01, 372.35)',
- modelId: map.getId(),
- type: "POINT"
- })));
- });
- });
-
- it("openCommentDialog", function () {
- var map = helper.createCustomMap();
- map.getModel().setId(15781);
- map.setActiveSubmapId(15781);
- map.setActiveSubmapClickCoordinates(new Point(2, 12));
- return map.openCommentDialog().then(function () {
- var types = map.getCommentDialog().getTypes();
- assert.equal(types.length, 6);
- var selected = map.getCommentDialog().getSelectedType();
- assert.ok(selected === "<General>");
-
- map.getCommentDialog().setSelectedType(1);
- selected = map.getCommentDialog().getSelectedType();
- assert.notOk(selected === "<General>");
-
- map.getCommentDialog().setSelectedType(2);
- selected = map.getCommentDialog().getSelectedType();
- assert.notOk(selected === "<General>");
- }).then(function () {
- map.getCommentDialog().destroy();
- });
- });
-
- describe("addComment", function () {
- it("default", function () {
- var map;
- return ServerConnector.getProject().then(function (project) {
- map = helper.createCustomMap(project);
- helper.createCommentDbOverlay(map);
- map.setActiveSubmapId(map.getId());
- map.setActiveSubmapClickCoordinates(new Point(2, 12));
- return map.openCommentDialog();
- }).then(function () {
- return map.getCommentDialog().addComment();
- }).then(function (comments) {
- assert.equal(0, comments.length);
- map.getCommentDialog().destroy();
- });
- });
-
- it("when comments are visible", function () {
- var map;
- return ServerConnector.getProject().then(function (project) {
- map = helper.createCustomMap(project);
- helper.createCommentDbOverlay(map);
- map.setActiveSubmapId(map.getId());
- map.setActiveSubmapClickCoordinates(new Point(2, 12));
- return map.openCommentDialog();
- }).then(function () {
- ServerConnector.getSessionData().setShowComments(true);
- return map.getCommentDialog().addComment();
- }).then(function (comments) {
- assert.ok(comments.length > 0);
- map.getCommentDialog().destroy();
- });
- });
-
- it("add for protein", function () {
- var map;
- return ServerConnector.getProject().then(function (project) {
- map = helper.createCustomMap(project);
- helper.createCommentDbOverlay(map);
- map.setActiveSubmapId(map.getId());
- map.setActiveSubmapClickCoordinates(new Point(2, 12));
- return map.openCommentDialog();
- }).then(function () {
- var dialog = map.getCommentDialog();
- dialog.setSelectedType(1);
- return dialog.addComment();
- }).then(function () {
- map.getCommentDialog().destroy();
- });
- });
- });
-
- it("retrieveOverlayDetailDataForElement for comment", function () {
- var map = helper.createCustomMap();
- helper.createCommentDbOverlay(map);
-
- var alias = helper.createAlias(map);
- alias.setId(329157);
- map.getModel().addAlias(alias);
-
- var ie = new IdentifiedElement(alias);
-
- return map.retrieveOverlayDetailDataForElement(ie, {
- comment: true
- }).then(function (details) {
- assert.ok(details);
- assert.equal(details.length, 1);
- assert.equal(details[0].length, 1);
- assert.ok(details[0][0] instanceof Comment);
- });
- });
-
- it("getOverlayDataForIdentifiedElement", function () {
- var map = helper.createCustomMap();
- var commentOverlay = helper.createCommentDbOverlay(map);
-
- var alias = helper.createAlias(map);
- alias.setId(329157);
- map.getModel().addAlias(alias);
-
- var ie = new IdentifiedElement(alias);
-
- return map.getOverlayDataForIdentifiedElement(ie, {
- comment: true
- }).then(function (details) {
- assert.equal(details.length, 1);
-
- var overlayData = details[0];
- assert.equal(overlayData.overlay, commentOverlay);
- assert.ok(overlayData.data);
- assert.equal(overlayData.data.length, 1);
- assert.ok(overlayData.data[0] instanceof Comment);
- });
- });
-
- it("openSubmap", function () {
- var options = helper.createCustomMapOptions();
-
- var submodel = helper.createModel();
- options.getProject().addModel(submodel);
-
- var map = new CustomMap(options);
-
- map.openSubmap(submodel.getId());
- map.destroy();
- });
-
- describe("setCenter", function () {
- it("default", function () {
- var options = helper.createCustomMapOptions();
-
- var map = new CustomMap(options);
-
- map.setCenter(new Point(10, 20));
- assert.ok(ServerConnector.getSessionData().getCenter(map.getModel()));
- });
-
- it("on submap", function () {
- var options = helper.createCustomMapOptions();
-
- var submodel = helper.createModel();
- options.getProject().addModel(submodel);
-
- var map = new CustomMap(options);
- map.openSubmap(submodel.getId());
- var submap = map.getSubmapById(submodel.getId());
- submap.setCenter(new Point(10, 20));
- assert.ok(ServerConnector.getSessionData().getCenter(submodel));
- map.destroy();
- });
- });
-
- it("setZoom", function () {
- var options = helper.createCustomMapOptions();
-
- var map = new CustomMap(options);
-
- map.setZoom(3);
- assert.equal(3, ServerConnector.getSessionData().getZoomLevel(map.getModel()));
- });
-
- it("removeSelection when invalid model selected", function () {
- var options = helper.createCustomMapOptions();
-
- var map = new CustomMap(options);
- map.setActiveSubmapId(-1);
-
- try {
- map.removeSelection();
- assert.ok(false);
- } catch (e) {
- assert.ok(e.message.indexOf("Cannot find submap") >= 0);
- }
- });
-
- describe("_openInfoWindowForIdentifiedElement", function () {
- it("for AliasMarker", function () {
- var map;
- var alias, marker;
- return ServerConnector.getProject().then(function (project) {
- map = helper.createCustomMap(project);
- return map.getModel().getAliasById(329171);
- }).then(function (result) {
- alias = result;
-
- var identifiedElement = new IdentifiedElement(alias);
- identifiedElement.setIcon("empty.png");
-
- marker = new AliasMarker({
- element: identifiedElement,
- map: map
- });
-
- return marker.init();
- }).then(function () {
- assert.equal(null, map.getAliasInfoWindowById(alias.getId()));
- return map._openInfoWindowForIdentifiedElement(marker).then(function () {
- assert.ok(map.getAliasInfoWindowById(alias.getId()));
- });
- });
-
- });
- it("for ReactionMarker", function () {
- var map;
- var reaction, marker;
- return ServerConnector.getProject().then(function (project) {
- map = helper.createCustomMap(project);
- return map.getModel().getReactionById(153510);
- }).then(function (result) {
- reaction = result;
-
- marker = new ReactionMarker({
- element: new IdentifiedElement(reaction),
- map: map
- });
- return marker.init();
- }).then(function () {
- assert.equal(null, map.getReactionInfoWindowById(reaction.getId()));
- return map._openInfoWindowForIdentifiedElement(marker);
- }).then(function () {
- assert.ok(map.getReactionInfoWindowById(reaction.getId()));
- });
-
- });
- it("for PointMarker", function () {
-
- var mockObject = helper.createCustomMap();
-
- mockObject.getOverlayDataForPoint = function () {
- return Promise.resolve([]);
- };
-
- var point = new Point(2, 3.45);
- var pointData = new PointData(point, mockObject.getId());
-
- var pointMarker = new PointMarker({
- element: new IdentifiedElement(pointData),
- map: mockObject
- });
-
- return pointMarker.init().then(function () {
- assert.equal(null, mockObject.getPointInfoWindowById(pointData.getId()));
- return mockObject._openInfoWindowForIdentifiedElement(pointMarker.getIdentifiedElement());
- }).then(function () {
- assert.ok(mockObject.getPointInfoWindowById(pointData.getId()));
- });
- });
- });
-
- describe("init", function () {
- it("invalid background overlay", function () {
- var options = helper.createCustomMapOptions();
- ServerConnector.getSessionData(options.getProject()).setSelectedBackgroundOverlay("bla");
- var map = new CustomMap(options);
- return map.init().then(function () {
- assert.false("Error expected");
- }, function () {
- map.destroy();
- })
- });
-
- it("non-existing background overlay", function () {
- var options = helper.createCustomMapOptions();
- ServerConnector.getSessionData(options.getProject()).setSelectedBackgroundOverlay(-1);
- var map = new CustomMap(options);
- return map.init().then(function () {
- assert.ok(ServerConnector.getSessionData(options.getProject()).getSelectedBackgroundOverlay() > 0);
- return map.destroy();
- })
- });
-
- it("with session data overlays", function () {
- var project = helper.createProject();
- var overlay1 = helper.createOverlay();
- overlay1.setInputDataAvailable(true);
- project.addDataOverlay(overlay1);
-
- var options = helper.createCustomMapOptions(project);
- ServerConnector.getSessionData(options.getProject()).setVisibleOverlays([overlay1.getId()]);
- var map = new CustomMap(options);
- return map.init().then(function () {
- return map.getVisibleDataOverlays();
- }).then(function (overlays) {
- assert.equal(1, overlays.length);
- map.destroy();
- })
- });
-
- });
-
- describe("appendElementsPointingToSubmap", function () {
- it("point to reaction", function () {
- helper.setUrl("http://test/?id=complex_model_with_submaps");
- return ServerConnector.getProject().then(function (project) {
- var map = helper.createCustomMap(project);
- var oc = helper.createSearchDbOverlay(map);
-
- var reaction = new IdentifiedElement({id: 161955, modelId: 16729, type: "REACTION"});
-
- return map.appendElementsPointingToSubmap([reaction], oc).then(function (elements) {
- for (var i = 0; i < elements.length; i++) {
- var element = elements[i];
- //alias pointing to reaction should have an icon
- if (element.type === "ALIAS") {
- assert.ok(element.getIcon() !== undefined);
- }
- }
- });
- });
- });
- });
- describe("logo link", function () {
- it("left logo click", function () {
- var map = helper.createCustomMap();
- return map.getControl(ControlType.LOGO_2_IMG).onclick()
- });
- it("right logo click", function () {
- var map = helper.createCustomMap();
- return map.getControl(ControlType.LOGO_IMG).onclick()
- });
- });
-});
+"use strict";
+
+var Promise = require("bluebird");
+
+require("../mocha-config.js");
+
+var AliasMarker = require('../../../main/js/map/marker/AliasMarker');
+var AliasSurface = require('../../../main/js/map/surface/AliasSurface');
+var Comment = require('../../../main/js/map/data/Comment');
+var ControlType = require('../../../main/js/map/ControlType');
+var CustomMap = require('../../../main/js/map/CustomMap');
+var IdentifiedElement = require('../../../main/js/map/data/IdentifiedElement');
+var MapContextMenu = require('../../../main/js/gui/MapContextMenu');
+var MolArt = require('../../../main/js/map/structure/MolArt');
+var Point = require('../../../main/js/map/canvas/Point');
+var PointData = require('../../../main/js/map/data/PointData');
+var PointMarker = require('../../../main/js/map/marker/PointMarker');
+var ReactionMarker = require('../../../main/js/map/marker/ReactionMarker');
+var ReactionSurface = require('../../../main/js/map/surface/ReactionSurface');
+
+var ServerConnector = require('./../ServerConnector-mock');
+
+var logger = require('./../logger');
+
+var chai = require('chai');
+var assert = chai.assert;
+
+describe('CustomMap', function () {
+ describe("constructor", function () {
+ it("default", function () {
+ var options = helper.createCustomMapOptions();
+ var map = new CustomMap(options);
+ assert.ok(map);
+ });
+
+ it("with submaps", function () {
+ var options = helper.createCustomMapOptions();
+
+ options.getProject().addModel(helper.createModel());
+
+ var map = new CustomMap(options);
+ assert.ok(map);
+ });
+
+ it("with session data pointing to not existing overlay", function () {
+ var options = helper.createCustomMapOptions();
+
+ ServerConnector.getSessionData(options.getProject()).setSelectedBackgroundOverlay("-1");
+
+ var map = new CustomMap(options);
+ assert.ok(map);
+ });
+ });
+
+ it("getSubmapById", function () {
+ var map = helper.createCustomMap();
+ assert.ok(map.getSubmapById(map.getId()));
+ });
+
+ it("getSubmapById (invalid)", function () {
+ var map = helper.createCustomMap();
+ assert.equal(map.getSubmapById(-1), null);
+ });
+
+ it("getSubmapById (string id)", function () {
+ var map = helper.createCustomMap();
+ assert.ok(map.getSubmapById(map.getId() + ""));
+ });
+
+ describe("openDataOverlay", function () {
+ it("for not existing id", function () {
+ var map = helper.createCustomMap();
+ try {
+ map.openDataOverlay(-1);
+ assert.ok(false);
+ } catch (exception) {
+ assert.ok(exception.message.indexOf("You have no privileges") >= 0);
+ }
+ });
+
+ it("for int id", function () {
+ var options = helper.createCustomMapOptions();
+ var layout = options.getProject().getDataOverlays()[0];
+ var map = new CustomMap(options);
+ map.openDataOverlay(layout.getId());
+ assert.equal(logger.getErrors().length, 0);
+ });
+
+ it("for overlay object", function () {
+ var options = helper.createCustomMapOptions();
+ var layout = options.getProject().getDataOverlays()[0];
+ var map = new CustomMap(options);
+ map.openDataOverlay(layout);
+ assert.equal(logger.getErrors().length, 0);
+ });
+
+ it("for string id", function () {
+ var options = helper.createCustomMapOptions();
+ var layout = options.getProject().getDataOverlays()[0];
+ var map = new CustomMap(options);
+ map.openDataOverlay(layout.getId() + "");
+ assert.equal(logger.getErrors().length, 0);
+ });
+
+ it("with background overlay", function () {
+ var map = helper.createCustomMap();
+ var layout = helper.createOverlay();
+ layout.setInitialized(true);
+ layout.setInputDataAvailable(false);
+ map.getProject().addDataOverlay(layout);
+
+ return map.openDataOverlay(layout.getId()).then(function () {
+ var vLayouts = ServerConnector.getSessionData(map.getProject()).getVisibleOverlays();
+ assert.equal(0, vLayouts.length);
+ });
+ });
+
+ it("with non background overlay", function () {
+ var project = helper.createProject();
+ var layout = helper.createOverlay();
+ layout.setInitialized(true);
+ layout.setInputDataAvailable(true);
+ project.addDataOverlay(layout);
+
+ var emptyBackground = helper.createOverlay();
+ emptyBackground.setInputDataAvailable(false);
+ emptyBackground.setName("Empty");
+ project.addDataOverlay(emptyBackground);
+
+ var map = helper.createCustomMap(project);
+
+
+ return map.openDataOverlay(layout.getId()).then(function () {
+ var backgroundId = ServerConnector.getSessionData(project).getSelectedBackgroundOverlay();
+ assert.equal(backgroundId, emptyBackground.getId());
+ });
+ });
+
+ it("check backgroundChangeListener", function () {
+ var project = helper.createProject();
+ var overlay = helper.createOverlay();
+ overlay.setInitialized(true);
+ overlay.setInputDataAvailable(true);
+ project.addDataOverlay(overlay);
+
+ var overlay2 = helper.createOverlay();
+ overlay2.setInitialized(true);
+ overlay2.setInputDataAvailable(true);
+ project.addDataOverlay(overlay2);
+
+ var emptyBackground = helper.createOverlay();
+ emptyBackground.setInputDataAvailable(false);
+ emptyBackground.setName("Empty");
+ project.addDataOverlay(emptyBackground);
+
+ var map = helper.createCustomMap(project);
+
+ var counter = 0;
+ map.addListener("onBackgroundOverlayChange", function () {
+ counter++;
+ });
+
+ return map.openDataOverlay(overlay.getId()).then(function () {
+ assert.equal(1, counter, "listener wasn't fired");
+ return map.openDataOverlay(overlay2.getId());
+ }).then(function () {
+ assert.equal(1, counter, "listener shouldn't be fired again because nothing changed");
+ });
+ });
+
+ it("simple", function () {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+ map.getModel().addAlias(alias);
+
+ var reaction = helper.createReaction(map);
+ map.getModel().addReaction(reaction);
+
+ var layout = helper.createOverlay();
+ layout.setInputDataAvailable(true);
+ layout.setInitialized(true);
+ var layoutAlias = helper.createLayoutAlias(alias);
+ layout.addAlias(layoutAlias);
+
+ var layoutReaction = helper.createLayoutReaction(reaction);
+ layout.addReaction(layoutReaction);
+
+ map.getProject().addDataOverlay(layout);
+
+ return map.openDataOverlay(layout.getId()).then(function () {
+ return map._showSelectedDataOverlay(layout.getId(), 0, 1);
+ }).then(function () {
+ var vLayouts = ServerConnector.getSessionData(map.getProject()).getVisibleOverlays();
+ assert.equal(1, vLayouts.length);
+ assert.equal(layout.getId(), vLayouts[0]);
+
+ assert.equal(2, map.selectedLayoutOverlays[layout.getId()].length);
+ var surface1 = map.selectedLayoutOverlays[layout.getId()][0];
+ var surface2 = map.selectedLayoutOverlays[layout.getId()][1];
+ assert.ok(surface1 instanceof AliasSurface || surface2 instanceof AliasSurface);
+ assert.ok(surface1 instanceof ReactionSurface || surface2 instanceof ReactionSurface);
+
+ // now hide the layout
+ return map._hideSelectedLayout(layout.getId());
+ }).then(function () {
+ assert.ok(map.selectedLayoutOverlays[layout.getId()]);
+ assert.equal(0, map.selectedLayoutOverlays[layout.getId()].length);
+ });
+
+ });
+
+ it("with submaps", function () {
+ var projectId = "complex_model_with_submaps";
+ helper.setUrl("http://test/?id=" + projectId);
+ var customMap;
+ var emptySubmodelId = 16730;
+ var filledSubmodelId = 16731;
+ var overlayId = 18083;
+
+ return ServerConnector.getProject(projectId).then(function (project) {
+ var options = helper.createCustomMapOptions(project);
+ customMap = new CustomMap(options);
+
+ return customMap.openSubmap(emptySubmodelId);
+ }).then(function () {
+ return customMap.openSubmap(filledSubmodelId);
+ }).then(function () {
+
+ var emptySubmap = customMap.getSubmapById(emptySubmodelId);
+ var filledSubmap = customMap.getSubmapById(filledSubmodelId);
+
+ return customMap.openDataOverlay(overlayId).then(function () {
+
+ assert.equal(2, customMap.selectedLayoutOverlays[overlayId].length);
+ assert.equal(1, filledSubmap.selectedLayoutOverlays[overlayId].length);
+ assert.equal(0, emptySubmap.selectedLayoutOverlays[overlayId].length);
+
+ // now hide the layout
+
+ return customMap.hideSelectedLayout(overlayId);
+ }).then(function () {
+ assert.equal(0, customMap.selectedLayoutOverlays[overlayId].length);
+ assert.equal(0, filledSubmap.selectedLayoutOverlays[overlayId].length);
+ assert.equal(0, emptySubmap.selectedLayoutOverlays[overlayId].length);
+ });
+
+ }).then(function () {
+ return customMap.destroy();
+ });
+ });
+
+ it("with submap double opened", function () {
+ var projectId = "complex_model_with_submaps";
+ helper.setUrl("http://test/?id=" + projectId);
+ var customMap, filledSubmap;
+ var filledSubmodelId = 16731;
+ var overlayId = 18083;
+
+ return ServerConnector.getProject(projectId).then(function (project) {
+ customMap = helper.createCustomMap(project);
+ return customMap.openSubmap(filledSubmodelId);
+ }).then(function () {
+ filledSubmap = customMap.getSubmapById(filledSubmodelId);
+ return customMap.openDataOverlay(overlayId);
+ }).then(function () {
+ assert.equal(1, filledSubmap.selectedLayoutOverlays[overlayId].length);
+ return customMap.openSubmap(filledSubmodelId);
+ }).then(function () {
+ //after opening submap nothing should change
+ assert.equal(1, filledSubmap.selectedLayoutOverlays[overlayId].length);
+ }).finally(function () {
+ return customMap.destroy();
+ });
+ });
+
+ it("check if info window content changed", function () {
+ var project = helper.createProject();
+ var layout = helper.createOverlay();
+ layout.setInitialized(true);
+ layout.setInputDataAvailable(true);
+ project.addDataOverlay(layout);
+
+ var map = helper.createCustomMap(project);
+
+ var alias = helper.createAlias(map);
+ var ie = helper.createIdentifiedElement(alias);
+ var marker = map.getMapCanvas().createMarker({icon: "empty.png", position: new Point(0, 0)});
+ var infoWindow;
+ return map.openInfoWindowForIdentifiedElement(ie, marker).then(function (result) {
+ infoWindow = result;
+ assert.notOk(infoWindow.getContent().innerHTML.indexOf(layout.getName()) >= 0);
+ return map.openDataOverlay(layout.getId());
+ }).then(function () {
+ assert.ok(infoWindow.getContent().innerHTML.indexOf(layout.getName()) >= 0);
+ assert.equal(logger.getErrors().length, 0);
+ });
+ });
+ });
+
+ describe("hideDataOverlay", function () {
+ it("default", function () {
+ var map = helper.createCustomMap();
+ var layout = helper.createOverlay();
+ layout.setInitialized(true);
+ layout.setInputDataAvailable(true);
+ map.getProject().addDataOverlay(layout);
+
+ return map.openDataOverlay(layout.getId()).then(function () {
+ return map.hideDataOverlay(layout.getId());
+ }).then(function () {
+ var vLayouts = ServerConnector.getSessionData(map.getProject()).getVisibleOverlays();
+ assert.equal(0, vLayouts.length);
+ });
+ });
+ it("check if info window content changed", function () {
+ var project = helper.createProject();
+ var layout = helper.createOverlay();
+ layout.setInitialized(true);
+ layout.setInputDataAvailable(true);
+ project.addDataOverlay(layout);
+
+ var map = helper.createCustomMap(project);
+
+ var alias = helper.createAlias(map);
+ var ie = helper.createIdentifiedElement(alias);
+ var marker = map.getMapCanvas().createMarker({icon: "empty.png", position: new Point(0, 0)});
+ var infoWindow;
+ return map.openInfoWindowForIdentifiedElement(ie, marker).then(function (result) {
+ infoWindow = result;
+ return map.openDataOverlay(layout.getId());
+ }).then(function () {
+ assert.ok(infoWindow.getContent().innerHTML.indexOf(layout.getName()) >= 0);
+ return map.hideDataOverlay(layout.getId());
+ }).then(function () {
+ assert.notOk(infoWindow.getContent().innerHTML.indexOf(layout.getName()) >= 0);
+ assert.equal(logger.getErrors().length, 0);
+ });
+ });
+ });
+
+
+ describe("renderOverlayCollection", function () {
+ it("for alias", function () {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+
+ var oc = helper.createDbOverlay(map);
+
+ oc.getIdentifiedElements = function () {
+ return Promise.resolve([new IdentifiedElement({
+ objectId: alias.getId(),
+ icon: "empty.png",
+ modelId: map.getId(),
+ type: "Alias"
+ })]);
+ };
+ return map.renderOverlayCollection({
+ overlayCollection: oc
+ }).then(function () {
+ var markers = map.getMarkerSurfaceCollection().getMarkers();
+ assert.equal(1, markers.length);
+ });
+ });
+
+ it("alias re-rendering with different icon", function () {
+ var map = helper.createCustomMap();
+ var reaction = helper.createReaction(map, true);
+ var alias = helper.createAlias(map);
+ map.getModel().addAlias(alias);
+ map.getModel().addReaction(reaction);
+
+ var identifiedElement = new IdentifiedElement(alias);
+ identifiedElement.setIcon("empty.png");
+ var identifiedElement2 = new IdentifiedElement(alias);
+ identifiedElement2.setIcon("new_icon.png");
+
+ var marker;
+ var oc = helper.createDbOverlay(map);
+
+ oc.getIdentifiedElements = function () {
+ return Promise.resolve([identifiedElement, new IdentifiedElement(reaction)]);
+ };
+ return map.renderOverlayCollection({
+ overlayCollection: oc
+ }).then(function () {
+ marker = map.getMarkerSurfaceCollection().getMarker(identifiedElement);
+ oc.getIdentifiedElements = function () {
+ return Promise.resolve([identifiedElement2]);
+ };
+ assert.ok(map.getMarkerSurfaceCollection().getSurface({element: reaction, overlay: oc}));
+
+ return map.renderOverlayCollection({
+ overlayCollection: oc
+ });
+ }).then(function () {
+ assert.equal(marker.getIcon(), "new_icon.png");
+
+ assert.notOk(oc.mapOverlays["REACTION"][reaction.getId()]);
+ });
+ });
+
+ it("for set of aliases", function () {
+ var map = helper.createCustomMap();
+
+ var oc = helper.createDbOverlay(map);
+
+ var identifiedElements = [];
+ for (var i = 0; i < 3; i++) {
+ var alias = helper.createAlias(map);
+ map.getModel().addAlias(alias);
+ var ie = helper.createIdentifiedElement(alias);
+ ie.setIcon("");
+ identifiedElements.push(ie);
+ }
+
+ oc.getIdentifiedElements = function () {
+ return Promise.resolve(identifiedElements);
+ };
+
+ return map.renderOverlayCollection({
+ overlayCollection: oc
+ }).then(function () {
+ var markers = map.getMarkerSurfaceCollection().getMarkers();
+ assert.equal(3, markers.length);
+ });
+ });
+
+ it("for point", function () {
+ var map = helper.createCustomMap();
+
+ var oc = helper.createDbOverlay(map);
+
+ var javaObj = {
+ objectId: "Point2D.Double[117.685546875, 204.6923828125001]",
+ modelId: map.getId(),
+ type: "POINT",
+ icon: "marker/empty.png"
+ };
+
+ oc.getIdentifiedElements = function () {
+ return Promise.resolve([new IdentifiedElement(javaObj)]);
+ };
+
+ return map.renderOverlayCollection({
+ overlayCollection: oc
+ }).then(function () {
+ var markers = map.getMarkerSurfaceCollection().getMarkers();
+ assert.equal(1, markers.length);
+ });
+ });
+
+ it("for reaction", function () {
+ var map = helper.createCustomMap();
+ var reaction = helper.createReaction(map, true);
+ map.getModel().addReaction(reaction);
+
+ var oc = helper.createDbOverlay(map);
+
+ oc.getIdentifiedElements = function () {
+ return Promise.resolve([new IdentifiedElement(reaction)]);
+ };
+
+ return map.renderOverlayCollection({
+ overlayCollection: oc
+ }).then(function () {
+ var surfaces = map.getMarkerSurfaceCollection().getSurfaces();
+ assert.equal(1, surfaces.length);
+ });
+ });
+ });
+
+ it("refreshMarkers", function () {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+ map.getModel().addAlias(alias);
+
+ var oc = helper.createDbOverlay(map);
+
+ oc.getIdentifiedElements = function () {
+ var element = new IdentifiedElement(alias);
+ element.setIcon("icon");
+ return Promise.resolve([element]);
+ };
+ return map.renderOverlayCollection({
+ overlayCollection: oc
+ }).then(function () {
+ return map.refreshMarkers(true);
+ }).then(function () {
+ var markers = map.getMarkerSurfaceCollection().getMarkers();
+ assert.equal(1, markers.length);
+ });
+ });
+
+ it("clearDbOverlays", function () {
+ var map = helper.createCustomMap();
+
+ var oc = helper.createDbOverlay(map);
+
+ var javaObj = {
+ objectId: "Point2D.Double[117.685546875, 204.6923828125001]",
+ modelId: map.getId(),
+ type: "POINT",
+ icon: "marker/empty.png"
+ };
+ var searchResults = [new IdentifiedElement(javaObj)];
+
+ oc.getIdentifiedElements = function () {
+ return Promise.resolve(searchResults);
+ };
+ oc.clear = function () {
+ searchResults = [];
+ return this.callListeners("onSearch", searchResults);
+ };
+
+ return map.renderOverlayCollection({
+ overlayCollection: oc
+ }).then(function () {
+
+ return map.clearDbOverlays();
+ }).then(function () {
+ var markerCount = 0;
+ for (var id in oc.pointMarkers) {
+ if (oc.pointMarkers.hasOwnProperty(id)) {
+ markerCount++;
+ }
+ }
+
+ assert.equal(0, markerCount);
+ });
+
+ });
+
+ it("getInfoWindowForIdentifiedElement ( reaction)", function () {
+ var map = helper.createCustomMap();
+ var reaction = helper.createReaction(map, true);
+ map.getModel().addReaction(reaction);
+
+ var ie = helper.createIdentifiedElement(reaction);
+ var marker = map.getMapCanvas().createMarker({icon: "empty.png", position: new Point(0, 0)});
+
+ var infoWindow = map.getInfoWindowForIdentifiedElement(ie);
+
+ assert.equal(null, infoWindow);
+ return map.openInfoWindowForIdentifiedElement(ie, marker).then(function () {
+ infoWindow = map.getInfoWindowForIdentifiedElement(ie);
+
+ assert.ok(infoWindow);
+ });
+
+ });
+
+ it("right click on map", function () {
+ var map = helper.createCustomMap();
+ map.setContextMenu(new MapContextMenu({
+ customMap: map,
+ element: testDiv,
+ molArt: new MolArt(map.getElement(), map)
+ }));
+
+ return map.getContextMenu().init().then(function () {
+ var data = {
+ stop: null,
+ point: new Point(10.0, 20.0)
+ };
+
+ assert.notOk(map.getActiveSubmapId());
+ return map.triggerEvent("map-rightclick", data);
+ }).then(function () {
+ //we need to wait because some implementations don't use promises...
+ return Promise.delay(100);
+ }).then(function () {
+ assert.equal(map.getId(), map.getActiveSubmapId());
+ return map.destroy();
+ });
+
+ });
+
+ it("left click on map", function () {
+ var map;
+ var searchOverlay;
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ searchOverlay = helper.createSearchDbOverlay(map);
+
+ var data = {
+ stop: null,
+ point: new Point(184.79, 365.76)
+ };
+ map.setZoom(4);
+
+ assert.notOk(map.getActiveSubmapId());
+ return map.triggerEvent("map-click", data);
+ }).then(function () {
+ //we need to wait because some implementations don't use promises...
+ return Promise.delay(100);
+ }).then(function () {
+ assert.equal(map.getId(), map.getActiveSubmapId());
+ var element = new IdentifiedElement({id: 329171, type: "ALIAS", modelId: map.getId()});
+ assert.ok(map.getMarkerSurfaceCollection().getMarker(element));
+ });
+
+ });
+
+ it("left click on reaction", function () {
+ var map;
+ var searchOverlay;
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ searchOverlay = helper.createSearchDbOverlay(map);
+
+ var data = {
+ stop: null,
+ point: new Point(457.51, 356.84)
+ };
+ map.setZoom(4);
+
+ assert.notOk(map.getActiveSubmapId());
+ return map.triggerEvent("map-click", data);
+ }).then(function () {
+ //we need to wait because some implementations don't use promises...
+ return Promise.delay(100);
+ }).then(function () {
+ assert.equal(map.getId(), map.getActiveSubmapId());
+
+ var reaction = new IdentifiedElement({id: 153521, type: "REACTION", modelId: map.getId()});
+ var surface = map.getMarkerSurfaceCollection().getSurface({element: reaction, overlay: searchOverlay});
+
+ assert.ok(surface);
+ assert.ok(surface.isShown());
+
+ var element = new IdentifiedElement({id: 329165, type: "ALIAS", modelId: map.getId()});
+ var marker = map.getMarkerSurfaceCollection().getMarker(element);
+ assert.ok(marker);
+ });
+ });
+
+ it("changed coordinates in map", function () {
+ var map = helper.createCustomMap();
+ var oldCenter = map.getCenter();
+ var newCenter = new Point(3, 87);
+ map.setCenter(newCenter);
+ map.triggerEvent("map-center_changed");
+
+ var center = ServerConnector.getSessionData(map.getProject()).getCenter(map.getModel());
+ assert.ok(center !== oldCenter);
+ assert.ok(center instanceof Point);
+ });
+
+ it("refreshComments", function () {
+ var map = helper.createCustomMap();
+ map.getModel().setId(15781);
+ helper.createCommentDbOverlay(map);
+
+ ServerConnector.getSessionData().setShowComments(true);
+ return map.refreshComments().then(function () {
+ assert.notOk(map.getMarkerSurfaceCollection().getMarker(new IdentifiedElement({
+ id: '(241.01,372.35)',
+ modelId: map.getId(),
+ type: "POINT"
+ })));
+ assert.ok(map.getMarkerSurfaceCollection().getMarker(new IdentifiedElement({
+ id: '(643.96,144.09)',
+ modelId: map.getId(),
+ type: "POINT"
+ })));
+ assert.notOk(map.getMarkerSurfaceCollection().getMarker(new IdentifiedElement({
+ id: '(216.65,370.00)',
+ modelId: map.getId(),
+ type: "POINT"
+ })));
+ assert.notOk(map.getMarkerSurfaceCollection().getMarker(new IdentifiedElement({
+ id: 'unkId',
+ modelId: map.getId(),
+ type: "POINT"
+ })));
+ });
+ });
+
+ it("hide comments", function () {
+ var map = helper.createCustomMap();
+ map.getModel().setId(15781);
+ helper.createCommentDbOverlay(map);
+
+ ServerConnector.getSessionData().setShowComments(true);
+ return map.refreshComments().then(function () {
+ ServerConnector.getSessionData().setShowComments(false);
+ return map.refreshComments();
+ }).then(function () {
+ assert.notOk(map.getMarkerSurfaceCollection().getMarker(new IdentifiedElement({
+ id: '(241.01, 372.35)',
+ modelId: map.getId(),
+ type: "POINT"
+ })));
+ });
+ });
+
+ it("openCommentDialog", function () {
+ var map = helper.createCustomMap();
+ map.getModel().setId(15781);
+ map.setActiveSubmapId(15781);
+ map.setActiveSubmapClickCoordinates(new Point(2, 12));
+ return map.openCommentDialog().then(function () {
+ var types = map.getCommentDialog().getTypes();
+ assert.equal(types.length, 6);
+ var selected = map.getCommentDialog().getSelectedType();
+ assert.ok(selected === "<General>");
+
+ map.getCommentDialog().setSelectedType(1);
+ selected = map.getCommentDialog().getSelectedType();
+ assert.notOk(selected === "<General>");
+
+ map.getCommentDialog().setSelectedType(2);
+ selected = map.getCommentDialog().getSelectedType();
+ assert.notOk(selected === "<General>");
+ }).then(function () {
+ map.getCommentDialog().destroy();
+ });
+ });
+
+ describe("addComment", function () {
+ it("default", function () {
+ var map;
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ helper.createCommentDbOverlay(map);
+ map.setActiveSubmapId(map.getId());
+ map.setActiveSubmapClickCoordinates(new Point(2, 12));
+ return map.openCommentDialog();
+ }).then(function () {
+ return map.getCommentDialog().addComment();
+ }).then(function (comments) {
+ assert.equal(0, comments.length);
+ map.getCommentDialog().destroy();
+ });
+ });
+
+ it("when comments are visible", function () {
+ var map;
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ helper.createCommentDbOverlay(map);
+ map.setActiveSubmapId(map.getId());
+ map.setActiveSubmapClickCoordinates(new Point(2, 12));
+ return map.openCommentDialog();
+ }).then(function () {
+ ServerConnector.getSessionData().setShowComments(true);
+ return map.getCommentDialog().addComment();
+ }).then(function (comments) {
+ assert.ok(comments.length > 0);
+ map.getCommentDialog().destroy();
+ });
+ });
+
+ it("add for protein", function () {
+ var map;
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ helper.createCommentDbOverlay(map);
+ map.setActiveSubmapId(map.getId());
+ map.setActiveSubmapClickCoordinates(new Point(2, 12));
+ return map.openCommentDialog();
+ }).then(function () {
+ var dialog = map.getCommentDialog();
+ dialog.setSelectedType(1);
+ return dialog.addComment();
+ }).then(function () {
+ map.getCommentDialog().destroy();
+ });
+ });
+ });
+
+ it("retrieveOverlayDetailDataForElement for comment", function () {
+ var map = helper.createCustomMap();
+ helper.createCommentDbOverlay(map);
+
+ var alias = helper.createAlias(map);
+ alias.setId(329157);
+ map.getModel().addAlias(alias);
+
+ var ie = new IdentifiedElement(alias);
+
+ return map.retrieveOverlayDetailDataForElement(ie, {
+ comment: true
+ }).then(function (details) {
+ assert.ok(details);
+ assert.equal(details.length, 1);
+ assert.equal(details[0].length, 1);
+ assert.ok(details[0][0] instanceof Comment);
+ });
+ });
+
+ it("getOverlayDataForIdentifiedElement", function () {
+ var map = helper.createCustomMap();
+ var commentOverlay = helper.createCommentDbOverlay(map);
+
+ var alias = helper.createAlias(map);
+ alias.setId(329157);
+ map.getModel().addAlias(alias);
+
+ var ie = new IdentifiedElement(alias);
+
+ return map.getOverlayDataForIdentifiedElement(ie, {
+ comment: true
+ }).then(function (details) {
+ assert.equal(details.length, 1);
+
+ var overlayData = details[0];
+ assert.equal(overlayData.overlay, commentOverlay);
+ assert.ok(overlayData.data);
+ assert.equal(overlayData.data.length, 1);
+ assert.ok(overlayData.data[0] instanceof Comment);
+ });
+ });
+
+ it("openSubmap", function () {
+ var options = helper.createCustomMapOptions();
+
+ var submodel = helper.createModel();
+ options.getProject().addModel(submodel);
+
+ var map = new CustomMap(options);
+
+ map.openSubmap(submodel.getId());
+ map.destroy();
+ });
+
+ describe("setCenter", function () {
+ it("default", function () {
+ var options = helper.createCustomMapOptions();
+
+ var map = new CustomMap(options);
+
+ map.setCenter(new Point(10, 20));
+ assert.ok(ServerConnector.getSessionData().getCenter(map.getModel()));
+ });
+
+ it("on submap", function () {
+ var options = helper.createCustomMapOptions();
+
+ var submodel = helper.createModel();
+ options.getProject().addModel(submodel);
+
+ var map = new CustomMap(options);
+ map.openSubmap(submodel.getId());
+ var submap = map.getSubmapById(submodel.getId());
+ submap.setCenter(new Point(10, 20));
+ assert.ok(ServerConnector.getSessionData().getCenter(submodel));
+ map.destroy();
+ });
+ });
+
+ it("setZoom", function () {
+ var options = helper.createCustomMapOptions();
+
+ var map = new CustomMap(options);
+
+ map.setZoom(3);
+ assert.equal(3, ServerConnector.getSessionData().getZoomLevel(map.getModel()));
+ });
+
+ it("removeSelection when invalid model selected", function () {
+ var options = helper.createCustomMapOptions();
+
+ var map = new CustomMap(options);
+ map.setActiveSubmapId(-1);
+
+ try {
+ map.removeSelection();
+ assert.ok(false);
+ } catch (e) {
+ assert.ok(e.message.indexOf("Cannot find submap") >= 0);
+ }
+ });
+
+ describe("_openInfoWindowForIdentifiedElement", function () {
+ it("for AliasMarker", function () {
+ var map;
+ var alias, marker;
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ return map.getModel().getAliasById(329171);
+ }).then(function (result) {
+ alias = result;
+
+ var identifiedElement = new IdentifiedElement(alias);
+ identifiedElement.setIcon("empty.png");
+
+ marker = new AliasMarker({
+ element: identifiedElement,
+ map: map
+ });
+
+ return marker.init();
+ }).then(function () {
+ assert.equal(null, map.getAliasInfoWindowById(alias.getId()));
+ return map._openInfoWindowForIdentifiedElement(marker).then(function () {
+ assert.ok(map.getAliasInfoWindowById(alias.getId()));
+ });
+ });
+
+ });
+ it("for ReactionMarker", function () {
+ var map;
+ var reaction, marker;
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ return map.getModel().getReactionById(153510);
+ }).then(function (result) {
+ reaction = result;
+
+ marker = new ReactionMarker({
+ element: new IdentifiedElement(reaction),
+ map: map
+ });
+ return marker.init();
+ }).then(function () {
+ assert.equal(null, map.getReactionInfoWindowById(reaction.getId()));
+ return map._openInfoWindowForIdentifiedElement(marker);
+ }).then(function () {
+ assert.ok(map.getReactionInfoWindowById(reaction.getId()));
+ });
+
+ });
+ it("for PointMarker", function () {
+
+ var mockObject = helper.createCustomMap();
+
+ mockObject.getOverlayDataForPoint = function () {
+ return Promise.resolve([]);
+ };
+
+ var point = new Point(2, 3.45);
+ var pointData = new PointData(point, mockObject.getId());
+
+ var pointMarker = new PointMarker({
+ element: new IdentifiedElement(pointData),
+ map: mockObject
+ });
+
+ return pointMarker.init().then(function () {
+ assert.equal(null, mockObject.getPointInfoWindowById(pointData.getId()));
+ return mockObject._openInfoWindowForIdentifiedElement(pointMarker.getIdentifiedElement());
+ }).then(function () {
+ assert.ok(mockObject.getPointInfoWindowById(pointData.getId()));
+ });
+ });
+ });
+
+ describe("init", function () {
+ it("invalid background overlay", function () {
+ var options = helper.createCustomMapOptions();
+ ServerConnector.getSessionData(options.getProject()).setSelectedBackgroundOverlay("bla");
+ var map = new CustomMap(options);
+ return map.init().then(function () {
+ assert.false("Error expected");
+ }, function () {
+ map.destroy();
+ })
+ });
+
+ it("non-existing background overlay", function () {
+ var options = helper.createCustomMapOptions();
+ ServerConnector.getSessionData(options.getProject()).setSelectedBackgroundOverlay(-1);
+ var map = new CustomMap(options);
+ return map.init().then(function () {
+ assert.ok(ServerConnector.getSessionData(options.getProject()).getSelectedBackgroundOverlay() > 0);
+ return map.destroy();
+ })
+ });
+
+ it("with session data overlays", function () {
+ var project = helper.createProject();
+ var overlay1 = helper.createOverlay();
+ overlay1.setInputDataAvailable(true);
+ project.addDataOverlay(overlay1);
+
+ var options = helper.createCustomMapOptions(project);
+ ServerConnector.getSessionData(options.getProject()).setVisibleOverlays([overlay1.getId()]);
+ var map = new CustomMap(options);
+ return map.init().then(function () {
+ return map.getVisibleDataOverlays();
+ }).then(function (overlays) {
+ assert.equal(1, overlays.length);
+ map.destroy();
+ })
+ });
+
+ });
+
+ describe("appendElementsPointingToSubmap", function () {
+ it("point to reaction", function () {
+ helper.setUrl("http://test/?id=complex_model_with_submaps");
+ return ServerConnector.getProject().then(function (project) {
+ var map = helper.createCustomMap(project);
+ var oc = helper.createSearchDbOverlay(map);
+
+ var reaction = new IdentifiedElement({id: 161955, modelId: 16729, type: "REACTION"});
+
+ return map.appendElementsPointingToSubmap([reaction], oc).then(function (elements) {
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ //alias pointing to reaction should have an icon
+ if (element.type === "ALIAS") {
+ assert.ok(element.getIcon() !== undefined);
+ }
+ }
+ });
+ });
+ });
+ });
+ describe("logo link", function () {
+ it("left logo click", function () {
+ var map = helper.createCustomMap();
+ return map.getControl(ControlType.LOGO_2_IMG).onclick()
+ });
+ it("right logo click", function () {
+ var map = helper.createCustomMap();
+ return map.getControl(ControlType.LOGO_IMG).onclick()
+ });
+ });
+});
diff --git a/frontend-js/src/test/js/map/canvas/GoogleMaps/GoogleMapsApiCanvas-test.js b/frontend-js/src/test/js/map/canvas/GoogleMaps/GoogleMapsApiCanvas-test.js
index a95bd3d3adbf145d9ba74b55f38378bf4ac5eaaa..c91cf90576e5a09a1396eb0d8e05641f4c1e09f4 100644
--- a/frontend-js/src/test/js/map/canvas/GoogleMaps/GoogleMapsApiCanvas-test.js
+++ b/frontend-js/src/test/js/map/canvas/GoogleMaps/GoogleMapsApiCanvas-test.js
@@ -208,11 +208,41 @@ describe('GoogleMapsApiCanvas', function () {
strokeColor: "#330000",
strokeOpacity: 0.5,
strokeWeight: 1.0,
- id:"1",
+ id: "1",
fillColor: "#00FF00",
- bounds: new Bounds(new Point(0,0), new Point(2,2))
+ bounds: new Bounds(new Point(0, 0), new Point(2, 2))
+ });
+ return google.maps.event.trigger(rectangle.getGoogleRectangles()[0], "click");
+ });
+
+ it("set rectangle bounds", function () {
+ var canvas = new GoogleMapsApiCanvas(testDiv, testOptions);
+ var rectangle = canvas.createRectangle({
+ fillOpacity: 0.7,
+ strokeColor: "#330000",
+ strokeOpacity: 0.5,
+ strokeWeight: 1.0,
+ id: "1",
+ fillColor: "#00FF00",
+ bounds: new Bounds(new Point(10, 10), new Point(20, 200))
+ });
+ rectangle.setBounds(new Bounds(new Point(100, 10), new Point(150, 200)));
+ var newBounds = rectangle.getBounds();
+ assert.closeTo(newBounds.getTopLeft().distanceTo(new Point(100, 10)), 0, helper.EPSILON);
+ assert.closeTo(newBounds.getRightBottom().distanceTo(new Point(150, 200)), 0, helper.EPSILON);
+ });
+
+ it("create rectangle with gradient", function () {
+ var canvas = new GoogleMapsApiCanvas(testDiv, testOptions);
+ var rectangle = canvas.createRectangle({
+ fillOpacity: 0.7,
+ strokeColor: "#330000",
+ strokeOpacity: 0.5,
+ strokeWeight: 1.0,
+ id: "1",
+ fillGradient: [{color: "#00FF00", amount: 1}, {color: "#00aa00", amount: 5}],
+ bounds: new Bounds(new Point(10, 10), new Point(20, 200))
});
- return google.maps.event.trigger(rectangle.getGoogleRectangle(), "click");
});
});
diff --git a/frontend-js/src/test/js/map/canvas/Point-test.js b/frontend-js/src/test/js/map/canvas/Point-test.js
index 16da526d4eec5381fd92b33c906755d23b712362..cca9e5a71078120124a44476fcd6bb8dd344e47e 100644
--- a/frontend-js/src/test/js/map/canvas/Point-test.js
+++ b/frontend-js/src/test/js/map/canvas/Point-test.js
@@ -28,6 +28,19 @@ describe('Point', function () {
assert.equal(point.y, point2.y);
});
});
+ describe("distanceTo", function () {
+ it("the same", function () {
+ var point = new Point(12, 3);
+ assert.closeTo(point.distanceTo(point), 0, helper.EPSILON);
+ });
+ it("different", function () {
+ var point = new Point(12, 3);
+ var point2 = new Point(15, 7);
+ assert.closeTo(point.distanceTo(point2), 5, helper.EPSILON);
+ assert.closeTo(point.distanceTo(new Point(15, 3)), 3, helper.EPSILON);
+ assert.closeTo(point.distanceTo(new Point(12, -1)), 4, helper.EPSILON);
+ });
+ });
it("toString", function () {
var point = new Point(12, 3);
diff --git a/frontend-js/src/test/js/map/data/ReferenceGenome-test.js b/frontend-js/src/test/js/map/data/ReferenceGenome-test.js
index b001486d62b6f371b27916007a138f003e4ae8dc..204ff22eed48a35bf6068a6a7dd7badda613dc63 100644
--- a/frontend-js/src/test/js/map/data/ReferenceGenome-test.js
+++ b/frontend-js/src/test/js/map/data/ReferenceGenome-test.js
@@ -10,7 +10,16 @@ describe('ReferenceGenome', function () {
type: "TYP",
version: "v3",
localUrl: "http://google.pl/",
- sourceUrl: "http://google.pl/"
+ sourceUrl: "http://google.pl/",
+ organism: {
+ "annotatorClassName": "",
+ "descriptionByType": "",
+ "descriptionByTypeRelation": "",
+ "id": 517528,
+ "link": "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=8822",
+ "resource": "8822",
+ "type": "TAXONOMY"
+ }
};
var genome = new ReferenceGenome(data);
assert.equal(genome.getType(), data.type);
@@ -21,7 +30,16 @@ describe('ReferenceGenome', function () {
it("simple", function () {
var data = {
sourceUrl: "http://google.pl/",
- geneMapping: [{}]
+ geneMapping: [{}],
+ organism: {
+ "annotatorClassName": "",
+ "descriptionByType": "",
+ "descriptionByTypeRelation": "",
+ "id": 517528,
+ "link": "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=8822",
+ "resource": "8822",
+ "type": "TAXONOMY"
+ }
};
var genome = new ReferenceGenome(data);
assert.equal(genome.getUrl(), data.sourceUrl);
@@ -37,8 +55,5 @@ describe('ReferenceGenome', function () {
var genome = new ReferenceGenome(null);
assert.ok(genome);
});
-
});
-
-
});
diff --git a/frontend-js/src/test/js/map/surface/AliasSurface-test.js b/frontend-js/src/test/js/map/surface/AliasSurface-test.js
index 92ec4e60627ac61e2e6b09ae1a93b56ef40c7d48..4c98a6eb0db1934f67c8ddf5868744e2b0377a93 100644
--- a/frontend-js/src/test/js/map/surface/AliasSurface-test.js
+++ b/frontend-js/src/test/js/map/surface/AliasSurface-test.js
@@ -13,10 +13,9 @@ describe('AliasSurface', function () {
it("default", function () {
var map = helper.createCustomMap();
var alias = helper.createAlias(map);
- var layoutAlias = helper.createLayoutAlias(alias);
var result = new AliasSurface({
- overlayAlias: layoutAlias,
+ overlayData: [helper.createLayoutAlias(alias)],
alias: alias,
map: map,
startX: 1,
@@ -30,10 +29,9 @@ describe('AliasSurface', function () {
it("no bounds", function () {
var map = helper.createCustomMap();
var alias = helper.createAlias(map);
- var layoutAlias = helper.createLayoutAlias(alias);
var result = new AliasSurface({
- overlayAlias: layoutAlias,
+ overlayData: [helper.createLayoutAlias(alias)],
alias: alias,
map: map
});
@@ -55,6 +53,7 @@ describe('AliasSurface', function () {
alias = result;
surface = new AliasSurface({
alias: result,
+ overlayData: [helper.createLayoutAlias(alias)],
map: map
});
return surface.init();
@@ -71,7 +70,7 @@ describe('AliasSurface', function () {
var map = helper.createCustomMap();
var alias = helper.createAlias(map);
var surface = new AliasSurface({
- overlayAlias: helper.createLayoutAlias(alias),
+ overlayData: [helper.createLayoutAlias(alias)],
alias: alias,
map: map,
startX: 1,
@@ -97,6 +96,7 @@ describe('AliasSurface', function () {
alias = result;
surface = new AliasSurface({
alias: result,
+ overlayData: [helper.createLayoutAlias(result)],
map: map,
onClick: function () {
clicked = true;
diff --git a/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js b/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
index ab23b3e855eef90f8a7455d0b3485b5670fbcfe1..85c8f1ca153eba39ac234e5ed51849a6f58734da 100644
--- a/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
+++ b/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
@@ -7,7 +7,9 @@ var Promise = require("bluebird");
var functions = require('../../../../main/js/Functions');
var Alias = require('../../../../main/js/map/data/Alias');
+var LayoutAlias = require('../../../../main/js/map/data/LayoutAlias');
var Drug = require('../../../../main/js/map/data/Drug');
+var GeneVariant = require('../../../../main/js/map/data/GeneVariant');
var AliasInfoWindow = require('../../../../main/js/map/window/AliasInfoWindow');
var IdentifiedElement = require('../../../../main/js/map/data/IdentifiedElement');
var DataOverlay = require('../../../../main/js/map/data/DataOverlay');
@@ -219,107 +221,110 @@ describe('AliasInfoWindow', function () {
});
});
- xit("createGeneticsDiv", function () {
- var map;
- var overlay;
-
- var layoutAlias;
- var win;
-
- return ServerConnector.getProject().then(function (project) {
- map = helper.createCustomMap(project);
- overlay = new DataOverlay(18077, "xxx");
- return overlay.init();
- }).then(function () {
- return overlay.getFullAliasById(overlay.getAliases()[0].getId());
- }).then(function (data) {
- layoutAlias = data;
- return map.getModel().getAliasById(layoutAlias.getId());
- }).then(function (alias) {
- win = new AliasInfoWindow({
- alias: alias,
- map: map,
- marker: helper.createMarker({element: alias, map: map})
+ describe("createGeneticsDiv", function () {
+ it("on top map", function () {
+ var map;
+ var overlay;
+
+ var layoutAlias;
+ var win;
+
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ overlay = new DataOverlay(18077, "xxx");
+ return overlay.init();
+ }).then(function () {
+ return overlay.getFullAliasById(overlay.getAliases()[0].getId());
+ }).then(function (data) {
+ layoutAlias = data;
+ return map.getModel().getAliasById(layoutAlias.getId());
+ }).then(function (alias) {
+ win = new AliasInfoWindow({
+ alias: alias,
+ map: map,
+ marker: helper.createMarker({element: alias, map: map})
+ });
+ return win.init();
+ }).then(function () {
+ var overlay = helper.createOverlay();
+ overlay.addAlias(layoutAlias);
+ return win.createGenomicDiv({overlays: [overlay]});
+ }).then(function (div) {
+ assert.ok(div);
+ assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") === -1);
+ win.destroy();
});
- return win.init();
- }).then(function () {
- win.layoutAliases = [layoutAlias];
- win.layoutNames = ["xxx"];
- return win.createGenomicDiv();
- }).then(function (div) {
- assert.ok(div);
- assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") === -1);
- win.destroy();
- });
-
- });
-
- it("createGeneticsDiv with no genetic data", function () {
- var map;
- var win;
- var aliasId = 329173;
-
- return ServerConnector.getProject().then(function (project) {
- map = helper.createCustomMap(project);
- var overlay = new DataOverlay(18077, "xxx");
- return overlay.init();
- }).then(function () {
- return map.getModel().getAliasById(aliasId);
- }).then(function (alias) {
- win = new AliasInfoWindow({
- alias: alias,
- map: map,
- marker: helper.createMarker({element: alias, map: map})
- });
- return win.init();
- }).then(function () {
- win.layoutAliases = [undefined];
- return win.createGenomicDiv();
- }).then(function (div) {
- assert.ok(div);
- assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") === -1);
- win.destroy();
});
- });
-
- it("createGeneticsDivForUnknownOrganism", function () {
- var map;
- var overlay;
+ it("with no genetic data", function () {
+ var map;
+
+ var win;
+ var aliasId = 329173;
+
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ var overlay = new DataOverlay(18077, "xxx");
+ return overlay.init();
+ }).then(function () {
+ return map.getModel().getAliasById(aliasId);
+ }).then(function (alias) {
+ win = new AliasInfoWindow({
+ alias: alias,
+ map: map,
+ marker: helper.createMarker({element: alias, map: map})
+ });
+ return win.init();
+ }).then(function () {
+ var overlays = [helper.createOverlay()];
+ return win.createGenomicDiv({overlays: overlays});
+ }).then(function (div) {
+ assert.ok(div);
+ assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") === -1);
+ win.destroy();
+ });
- var layoutAlias;
- var win;
+ });
- return ServerConnector.getProject().then(function (project) {
- project.setOrganism({
- type: "TAXONOMY",
- resource: "123456"
+ it("for unknown organism", function () {
+ var map;
+ var overlay;
+
+ var layoutAlias;
+ var win;
+
+ return ServerConnector.getProject().then(function (project) {
+ project.setOrganism({
+ type: "TAXONOMY",
+ resource: "123456"
+ });
+ map = helper.createCustomMap(project);
+ overlay = new DataOverlay(18077, "xxx");
+ return overlay.init();
+ }).then(function () {
+ return overlay.getFullAliasById(overlay.getAliases()[0].getId());
+ }).then(function (data) {
+ layoutAlias = data;
+ return map.getModel().getAliasById(layoutAlias.getId());
+ }).then(function (alias) {
+ win = new AliasInfoWindow({
+ alias: alias,
+ map: map,
+ marker: helper.createMarker({element: alias, map: map})
+ });
+ return win.init();
+ }).then(function () {
+ var overlay = helper.createOverlay();
+ overlay.addAlias(layoutAlias);
+ return win.createGenomicDiv({overlays: [overlay]});
+ }).then(function (div) {
+ assert.ok(div);
+ assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") >= -1);
+ win.destroy();
});
- map = helper.createCustomMap(project);
- overlay = new DataOverlay(18077, "xxx");
- return overlay.init();
- }).then(function () {
- return overlay.getFullAliasById(overlay.getAliases()[0].getId());
- }).then(function (data) {
- layoutAlias = data;
- return map.getModel().getAliasById(layoutAlias.getId());
- }).then(function (alias) {
- win = new AliasInfoWindow({
- alias: alias,
- map: map,
- marker: helper.createMarker({element: alias, map: map})
- });
- return win.init();
- }).then(function () {
- win.layoutAliases = [layoutAlias];
- return win.createGenomicDiv();
- }).then(function (div) {
- assert.ok(div);
- assert.ok(div.innerHTML.indexOf("No reference genome data available on minerva platform") >= -1);
- win.destroy();
- });
+ });
});
it("createWaitingContentDiv", function () {
@@ -336,29 +341,104 @@ describe('AliasInfoWindow', function () {
assert.ok(functions.isDomElement(aliasWindow.createWaitingContentDiv()));
});
- it("createChartDiv ", function () {
- var map, ie, aliasWindow;
- return ServerConnector.getProject().then(function (project) {
- map = helper.createCustomMap(project);
- ie = new IdentifiedElement({
- id: 329170,
- modelId: map.getId(),
- type: "ALIAS"
+ describe("createChartDiv ", function () {
+ it("on submap map", function () {
+ helper.setUrl("http://test/?id=complex_model_with_submaps");
+
+ var map, submap, overlay, win, aliasOnSubmap, alias;
+
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ submap = map.getSubmapById(16731);
+ overlay = new DataOverlay(18077, "xxx");
+ overlay.setInitialized(true);
+ return map.openSubmap(submap.getId());
+ }).then(function () {
+ return map.getModel().getAliasById(345339);
+ }).then(function (data) {
+ alias = data;
+ return submap.getModel().getAliasById(345337);
+ }).then(function (data) {
+ aliasOnSubmap = data;
+ win = new AliasInfoWindow({
+ alias: alias,
+ map: map,
+ marker: helper.createMarker({element: alias, map: map})
+ });
+ return win.init();
+ }).then(function () {
+ var layoutAlias = helper.createLayoutAlias(aliasOnSubmap);
+ layoutAlias.setType(LayoutAlias.GENERIC);
+ var overlay = helper.createOverlay();
+ overlay.addAlias(layoutAlias);
+ return win.createChartDiv({overlays: [overlay]});
+ }).then(function (div) {
+ assert.ok(div);
+ win.destroy();
+ return map.destroy();
});
- return map.getModel().getByIdentifiedElement(ie, true);
- }).then(function (alias) {
- aliasWindow = new AliasInfoWindow({
- alias: alias,
- map: map,
- marker: helper.createMarker({element: alias, map: map})
+ });
+
+ it("default ", function () {
+ var map, ie, aliasWindow;
+ return ServerConnector.getProject().then(function (project) {
+ map = helper.createCustomMap(project);
+ ie = new IdentifiedElement({
+ id: 329170,
+ modelId: map.getId(),
+ type: "ALIAS"
+ });
+
+ return map.getModel().getByIdentifiedElement(ie, true);
+ }).then(function (alias) {
+ aliasWindow = new AliasInfoWindow({
+ alias: alias,
+ map: map,
+ marker: helper.createMarker({element: alias, map: map})
+ });
+ var overlay = helper.createOverlay();
+ overlay.addAlias(helper.createLayoutAlias(alias, LayoutAlias.GENERIC));
+ var overlays = [overlay, helper.createOverlay()];
+
+ return aliasWindow.createChartDiv({overlays: overlays});
+ }).then(function (div) {
+ assert.ok(div);
});
- aliasWindow.layoutAliases = [helper.createLayoutAlias(alias), null];
- aliasWindow.layoutNames = ["x", "y"];
- return aliasWindow.createChartDiv();
- }).then(function (div) {
- assert.ok(div);
});
});
+ it("createVcfString ", function () {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+ var aliasWindow = new AliasInfoWindow({
+ alias: alias,
+ map: map,
+ marker: helper.createMarker({element: alias, map: map})
+ });
+
+ var nullVal = null;
+
+ var variant = new GeneVariant({
+ contig: "11",
+ modifiedDna: "T",
+ originalDna: "C",
+ position: 233067,
+ referenceGenomeType: "UCSC",
+ referenceGenomeVersion: "hg19",
+ allelFrequency: nullVal,
+ variantIdentifier: nullVal
+ });
+ var variant2 = new GeneVariant({
+ contig: "11",
+ modifiedDna: "T",
+ originalDna: "C",
+ position: 233068,
+ referenceGenomeType: "UCSC",
+ referenceGenomeVersion: "hg19"
+ });
+ var str = aliasWindow.createVcfString([variant, variant2]);
+ assert.ok(str.indexOf("null") === -1, "null shouldn't appear in vcf format");
+ });
+
});
diff --git a/frontend-js/testFiles/apiCalls/genomics/154/DELETE_token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/154/DELETE_token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..9e26dfeeb6e641a33dae4961196235bdb965b21b
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/154/DELETE_token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+{}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/154/geneMapping/97/DELETE_token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/154/geneMapping/97/DELETE_token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..9e26dfeeb6e641a33dae4961196235bdb965b21b
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/154/geneMapping/97/DELETE_token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+{}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/43/DELETE_token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/43/DELETE_token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..9e26dfeeb6e641a33dae4961196235bdb965b21b
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/43/DELETE_token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+{}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/POST_organismId=9606&sourceUrl=ftp%3A%2F%2Fhgdownload.cse.ucsc.edu%2FgoldenPath%2Fhg18%2FbigZips%2Fhg18.2bit&type=UCSC&version=hg38&token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/POST_organismId=9606&sourceUrl=ftp%3A%2F%2Fhgdownload.cse.ucsc.edu%2FgoldenPath%2Fhg18%2FbigZips%2Fhg18.2bit&type=UCSC&version=hg38&token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..9e26dfeeb6e641a33dae4961196235bdb965b21b
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/POST_organismId=9606&sourceUrl=ftp%3A%2F%2Fhgdownload.cse.ucsc.edu%2FgoldenPath%2Fhg18%2FbigZips%2Fhg18.2bit&type=UCSC&version=hg38&token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+{}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/1570291/genomeTypes/UCSC/versions/eboVir3/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/1570291/genomeTypes/UCSC/versions/eboVir3/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..140c6ea04591e5dd06e8bb7c00d10d267cbaf709
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/1570291/genomeTypes/UCSC/versions/eboVir3/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+{"downloadProgress":100.0,"geneMapping":[],"idObject":1830,"localUrl":"../minerva-big//9395/eboVir3.2bit","organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1150730,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1570291","resource":"1570291","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/bigZips/eboVir3.2bit","type":"UCSC","version":"eboVir3"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/8822/genomeTypes/UCSC/versions/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/8822/genomeTypes/UCSC/versions/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..106569c7531bf23cc379e199e01d23a6e29dfbe4
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/8822/genomeTypes/UCSC/versions/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+[{"version":"aptMan1"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/8822/genomeTypes/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/8822/genomeTypes/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..239f1b00f1ba0895c5aaf49f1da4478b95881d7f
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/8822/genomeTypes/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+[{"type":"UCSC"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..c97ec2eab979ae2109713be27a6441842db4e0d3
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+[{"url":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..c97ec2eab979ae2109713be27a6441842db4e0d3
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38.getAvailableRemoteUrls/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"url":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..d6e3f651ae1e7ccd4ce1a774931527624d8eeb9a
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+{"downloadProgress":100.0,"geneMapping":[],"idObject":1563,"localUrl":"../minerva-big//5280/hg38.2bit","organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":927074,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit","type":"UCSC","version":"hg38"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..d6e3f651ae1e7ccd4ce1a774931527624d8eeb9a
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+{"downloadProgress":100.0,"geneMapping":[],"idObject":1563,"localUrl":"../minerva-big//5280/hg38.2bit","organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":927074,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit","type":"UCSC","version":"hg38"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..f885fbf47775e1a6cf8962609b34bb3a075acb1f
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+[{"version":"hg38"},{"version":"hg24may2000"},{"version":"hg19"},{"version":"hg18"},{"version":"hg17"},{"version":"hg16"},{"version":"hg15june2000"},{"version":"hg13"},{"version":"hg12"},{"version":"hg11"},{"version":"hg10"},{"version":"10april2003"},{"version":"hg8"},{"version":"hg7"},{"version":"hg6"},{"version":"hg5"},{"version":"hg4"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..f885fbf47775e1a6cf8962609b34bb3a075acb1f
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/UCSC/versions/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"version":"hg38"},{"version":"hg24may2000"},{"version":"hg19"},{"version":"hg18"},{"version":"hg17"},{"version":"hg16"},{"version":"hg15june2000"},{"version":"hg13"},{"version":"hg12"},{"version":"hg11"},{"version":"hg10"},{"version":"10april2003"},{"version":"hg8"},{"version":"hg7"},{"version":"hg6"},{"version":"hg5"},{"version":"hg4"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..239f1b00f1ba0895c5aaf49f1da4478b95881d7f
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+[{"type":"UCSC"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..239f1b00f1ba0895c5aaf49f1da4478b95881d7f
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/9606/genomeTypes/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"type":"UCSC"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..b386c9e5c8cf2a34248768230292b29582764ee8
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/taxonomies/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
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diff --git a/frontend-js/testFiles/apiCalls/genomics/taxonomies/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/taxonomies/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..b386c9e5c8cf2a34248768230292b29582764ee8
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\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/genomics/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/genomics/token=ADMIN_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..3d404fc2fc06ba770f05a5ef09943f23cfe110d5
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/genomics/token=ADMIN_TOKEN_ID&
@@ -0,0 +1 @@
+[{"downloadProgress":100.0,"geneMapping":[{"downloadProgress":100.0,"idObject":97,"localUrl":null,"name":"refGene","sourceUrl":"http://pg-sandbox.uni.lu/data/refGene.txt.bb"}],"idObject":154,"localUrl":null,"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":523719,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit","type":"UCSC","version":"hg19"},{"downloadProgress":100.0,"geneMapping":[],"idObject":1563,"localUrl":"../minerva-big//5280/hg38.2bit","organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":927074,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit","type":"UCSC","version":"hg38"},{"downloadProgress":100.0,"geneMapping":[],"idObject":1829,"localUrl":"../minerva-big//9387/hg18.2bit","organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1150729,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"sourceUrl":"ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit","type":"UCSC","version":"hg18"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345325&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345325&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345325&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345325&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345330&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345330&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330,345331,345337&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345330,345331,345337&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345330,345331,345337&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345330,345331,345337&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345331&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345331&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345331&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345331&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345334&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345334&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345334&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345334&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345337&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345337&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345337&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345337&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345339&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345339&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId&id=345339&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=345339&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/drug_target_sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=436152&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/drug_target_sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=436152&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/drug_target_sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=436152&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/drug_target_sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=436152&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/PATCH_project.disease.resource=D010300&project.disease.type=MESH_2012&project.mapCanvasType=OPEN_LAYERS&project.name=UNKNOWN DISEASE MAP&project.organism.resource=9606&project.organism.type=TAXONOMY&project.version=2.01&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/PATCH_project.disease.resource=D010300&project.disease.type=MESH_2012&project.mapCanvasType=OPEN_LAYERS&project.name=UNKNOWN DISEASE MAP&project.organism.resource=1570291&project.organism.type=TAXONOMY&project.version=2.01&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/PATCH_project.disease.resource=D010300&project.disease.type=MESH_2012&project.mapCanvasType=OPEN_LAYERS&project.name=UNKNOWN DISEASE MAP&project.organism.resource=9606&project.organism.type=TAXONOMY&project.version=2.01&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/PATCH_project.disease.resource=D010300&project.disease.type=MESH_2012&project.mapCanvasType=OPEN_LAYERS&project.name=UNKNOWN DISEASE MAP&project.organism.resource=1570291&project.organism.type=TAXONOMY&project.version=2.01&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=-1&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=-1&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=-1&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=-1&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329157&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329157&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329157&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329157&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329159&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329159&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329159&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329159&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329163&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329163&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329163&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329163&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329167&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329167&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329167&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329167&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329168,329173&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329168,329173&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329168,329173&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329168,329173&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329170&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329170&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329170&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329170&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329171&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329171&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329171&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329171&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329173&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329173&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&id=329173&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId,linkedSubmodel&id=329173&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/POST_fileId=6792&googleLicenseConsent=false&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/POST_fileId=6792&googleLicenseConsent=false&type=GENERIC&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/overlays/POST_fileId=6792&googleLicenseConsent=false&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/overlays/POST_fileId=6792&googleLicenseConsent=false&type=GENERIC&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/token=ADMIN_TOKEN_ID&
index 54a367141609387d8ebac9b32d849ccdf1fecf6d..d69e034815d9f87b6c3f02422e81e4f8730270a8 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/token=ADMIN_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/token=ADMIN_TOKEN_ID&
@@ -1 +1 @@
-{"version":"0","disease":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104479,"link":"http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300","resource":"D010300","type":"MESH_2012"},"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104480,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"idObject":14898,"status":"Ok","directory":"5e8ff9bf55ba3508199d22e984129be6","progress":100.0,"notifyEmail":"","warnings":true,"errors":false,"name":"UNKNOWN DISEASE MAP","projectId":"sample","mapCanvasType":"OPEN_LAYERS","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file
+{"version":"0","disease":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104479,"link":"http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300","resource":"D010300","type":"MESH_2012"},"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104480,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1570291","resource":"1570291","type":"TAXONOMY"},"idObject":14898,"status":"Ok","directory":"5e8ff9bf55ba3508199d22e984129be6","progress":100.0,"notifyEmail":"","warnings":true,"errors":false,"name":"UNKNOWN DISEASE MAP","projectId":"sample","mapCanvasType":"OPEN_LAYERS","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID&
index 54a367141609387d8ebac9b32d849ccdf1fecf6d..d69e034815d9f87b6c3f02422e81e4f8730270a8 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"version":"0","disease":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104479,"link":"http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300","resource":"D010300","type":"MESH_2012"},"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104480,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606","resource":"9606","type":"TAXONOMY"},"idObject":14898,"status":"Ok","directory":"5e8ff9bf55ba3508199d22e984129be6","progress":100.0,"notifyEmail":"","warnings":true,"errors":false,"name":"UNKNOWN DISEASE MAP","projectId":"sample","mapCanvasType":"OPEN_LAYERS","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file
+{"version":"0","disease":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104479,"link":"http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300","resource":"D010300","type":"MESH_2012"},"organism":{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":1104480,"link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1570291","resource":"1570291","type":"TAXONOMY"},"idObject":14898,"status":"Ok","directory":"5e8ff9bf55ba3508199d22e984129be6","progress":100.0,"notifyEmail":"","warnings":true,"errors":false,"name":"UNKNOWN DISEASE MAP","projectId":"sample","mapCanvasType":"OPEN_LAYERS","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index fc0c60226ee53ec1162bbe8ac3ba1857b1c2e037..e9c36488291281e137c013eb169494cc7b015b52 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -120,7 +120,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
Set<Species> elementToAlign = new HashSet<>();
Map<Compartment, Set<Element>> elementsByStaticCompartment = new HashMap<>();
for (Element element : elements) {
- if (element.getWidth() == 0) {
+ if (element.getWidth() == null || element.getWidth() == 0) {
element.setWidth(SPECIES_WIDTH);
element.setHeight(SPECIES_HEIGHT);
@@ -360,7 +360,9 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
protected Dimension2D estimateDimension(Collection<BioEntity> bioEntites) {
double suggestedSize = Math.max(100 * bioEntites.size() / 4,
Math.sqrt((SPECIES_WIDTH + 10) * (SPECIES_HEIGHT + 10) * bioEntites.size()));
- suggestedSize = Math.max(suggestedSize, 2 * (SPECIES_WIDTH + 10));
+ if (bioEntites.size() > 0) {
+ suggestedSize = Math.max(suggestedSize, 2 * (SPECIES_WIDTH + 10));
+ }
return new DoubleDimension(suggestedSize, suggestedSize);
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java b/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
index 8b883cd54a6e6b0a4db8e65d87d5fe9a01f5c220..71fece55e50d88007800b32758fccf88ecfc7090 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.commands;
+import lcsb.mapviewer.commands.layout.AllLayoutTests;
import lcsb.mapviewer.commands.properties.AllPropertyCommandTests;
import org.junit.runner.RunWith;
@@ -7,12 +8,13 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllPropertyCommandTests.class, //
- ColorModelCommandTest.class, //
- CopyCommandTest.class, //
- CreateHierarchyCommandTest.class, //
- MoveElementsCommandTest.class, //
- SubModelCommandTest.class,//
+@SuiteClasses({ AllLayoutTests.class, //
+ AllPropertyCommandTests.class, //
+ ColorModelCommandTest.class, //
+ CopyCommandTest.class, //
+ CreateHierarchyCommandTest.class, //
+ MoveElementsCommandTest.class, //
+ SubModelCommandTest.class,//
})
public class AllCommandsTests {
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
index 97eb95a6f99283ae3bffc29295bf0cdd4f7837f6..7047e094100318c2aba0bf6b41fe80272a288b7f 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
@@ -1,306 +1,307 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class CreateHierarchyCommandTest extends CommandTestFunctions {
- Logger logger = Logger.getLogger(CreateHierarchyCommandTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCyclicComplexes() throws Exception {
- try {
- Model model = getModelForFile("testFiles/cyclic_hierarchy_problem.xml", false);
-
- new CreateHierarchyCommand(model, 8, 80).execute();
-
- Species alias = model.getElementByElementId("sa5033");
-
- Set<Element> parents = new HashSet<Element>();
- while (alias.getComplex() != null) {
- assertFalse("Cyclic nesting", parents.contains(alias.getComplex()));
- alias = alias.getComplex();
- parents.add(alias);
- }
-
- Set<String> levels = new HashSet<>();
- for (Element a : model.getElements()) {
- levels.add(a.getVisibilityLevel());
- }
- assertTrue(levels.size() > 2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateHierachy() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- new CreateHierarchyCommand(model, 2, 2).execute();
- // check if second call will throw an exception...
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateHierachy2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- boolean artifitial = false;
- for (Compartment a : model.getCompartments()) {
- if (a instanceof PathwayCompartment) {
- artifitial = true;
- }
- }
- assertTrue("No hierarchical structure element found", artifitial);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRecreateHierachy() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- int aliasSize0 = model.getCompartments().size();
-
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- int aliasSize = model.getCompartments().size();
-
- assertTrue(aliasSize0 != aliasSize);
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- int aliasSize2 = model.getCompartments().size();
-
- assertEquals(aliasSize, aliasSize2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParenting() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- assertFalse(model.getElementByElementId("sa1").getCompartment() instanceof PathwayCompartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateComponentsMinVisibility() throws Exception {
- try {
- double zoomFactor = 39.0625;
- int levels = 6;
-
- Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
-
- new CreateHierarchyCommand(model, levels, zoomFactor).execute();
-
- for (Compartment compartment : model.getCompartments()) {
- if (compartment.getCompartment() == null) {
- int visibilityLevel = Integer.valueOf(compartment.getVisibilityLevel());
- assertTrue(
- "Alias " + compartment.getElementId() + " is not visible at levels highers than " + compartment.getVisibilityLevel(), visibilityLevel <= 1);
- }
- }
-
- for (Species species : model.getSpeciesList()) {
- if (species.getCompartment() == null) {
- int visibilityLevel = Integer.valueOf(species.getVisibilityLevel());
- assertTrue("Alias " + species.getElementId() + " is not visible at levels highers than " + species.getVisibilityLevel(), visibilityLevel <= 1);
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateComponentsMaxVisibility() throws Exception {
- try {
- double zoomFactor = 39.0625;
- int levels = 6;
-
- Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
-
- new CreateHierarchyCommand(model, levels, zoomFactor).execute();
-
- for (Element element : model.getElements()) {
- int visibilityLevel = Integer.valueOf(element.getVisibilityLevel());
- assertTrue(
- "Alias " + element.getElementId() + " is not visible even at the bottom level (visibility: " + element.getVisibilityLevel() + ") ",
- visibilityLevel <= levels);
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompactComplexesInNestedView() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/compact_complex_view_problem.xml", false);
- Element alias = model.getElementByElementId("sa1");
- Object parent1 = alias.getCompartment();
- new CreateHierarchyCommand(model, 3, 16).execute();
- Object parent2 = alias.getCompartment();
- assertEquals(parent1, parent2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRecallHierachyCreation() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
- command.execute();
- try {
- command.execute();
- fail("Exception expected");
- } catch (InvalidStateException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testClear() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
- command.clean();
- for (Element alias : model.getElements()) {
- assertNull(alias.getCompartment());
- }
- for (Compartment alias : model.getCompartments()) {
- assertNull(alias.getCompartment());
- assertTrue(alias.getElements().isEmpty());
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNestedProblem() throws Exception {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Model model = parser.createModel(new ConverterParams().filename("testFiles/nested_test.xml").sizeAutoAdjust(true));
-
- double zoomFactor = Math.max(model.getHeight(), model.getWidth()) / (256);
- int zoomLevels = (int) Math.ceil(Math.log(zoomFactor) / Math.log(2));
-
- CreateHierarchyCommand command = new CreateHierarchyCommand(model, zoomLevels, zoomFactor);
- command.execute();
-
- for (Element alias : model.getElements()) {
- Element parentAlias = alias.getCompartment();
- if (parentAlias != null) {
- int parentVisibilityLevel = Integer.valueOf(parentAlias.getVisibilityLevel());
- int aliasVisibilityLevel = Integer.valueOf(alias.getVisibilityLevel());
- assertTrue(aliasVisibilityLevel >= parentVisibilityLevel);
- }
- if (alias instanceof Species) {
- parentAlias = ((Species) alias).getComplex();
- if (parentAlias != null) {
- int parentVisibilityLevel = Integer.valueOf(parentAlias.getVisibilityLevel());
- int aliasVisibilityLevel = Integer.valueOf(alias.getVisibilityLevel());
- assertTrue(aliasVisibilityLevel >= parentVisibilityLevel);
- }
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDisconnectedChildInComplex() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/disconnected_child_in_complex.xml", false);
-
- new CreateHierarchyCommand(model, 8, 80).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xmlString = parser.toXml(model);
- // logger.debug(xmlString);
-
- InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
-
- parser.createModel(new ConverterParams().inputStream(stream));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class CreateHierarchyCommandTest extends CommandTestFunctions {
+ Logger logger = Logger.getLogger(CreateHierarchyCommandTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCyclicComplexes() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/cyclic_hierarchy_problem.xml", false);
+
+ new CreateHierarchyCommand(model, 8, 80).execute();
+
+ Species alias = model.getElementByElementId("sa5033");
+
+ Set<Element> parents = new HashSet<Element>();
+ while (alias.getComplex() != null) {
+ assertFalse("Cyclic nesting", parents.contains(alias.getComplex()));
+ alias = alias.getComplex();
+ parents.add(alias);
+ }
+
+ Set<String> levels = new HashSet<>();
+ for (Element a : model.getElements()) {
+ levels.add(a.getVisibilityLevel());
+ }
+ assertTrue(levels.size() > 2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateHierachy() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+ // check if second call will throw an exception...
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateHierachy2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ boolean artifitial = false;
+ for (Compartment a : model.getCompartments()) {
+ if (a instanceof PathwayCompartment) {
+ artifitial = true;
+ }
+ }
+ assertTrue("No hierarchical structure element found", artifitial);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRecreateHierachy() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ int aliasSize0 = model.getCompartments().size();
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ int aliasSize = model.getCompartments().size();
+
+ assertTrue(aliasSize0 != aliasSize);
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ int aliasSize2 = model.getCompartments().size();
+
+ assertEquals(aliasSize, aliasSize2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParenting() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ assertFalse(model.getElementByElementId("sa1").getCompartment() instanceof PathwayCompartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateComponentsMinVisibility() throws Exception {
+ try {
+ double zoomFactor = 39.0625;
+ int levels = 6;
+
+ Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
+
+ new CreateHierarchyCommand(model, levels, zoomFactor).execute();
+
+ for (Compartment compartment : model.getCompartments()) {
+ if (compartment.getCompartment() == null) {
+ int visibilityLevel = Integer.valueOf(compartment.getVisibilityLevel());
+ assertTrue("Alias " + compartment.getElementId() + " is not visible at levels highers than "
+ + compartment.getVisibilityLevel(), visibilityLevel <= 1);
+ }
+ }
+
+ for (Species species : model.getSpeciesList()) {
+ if (species.getCompartment() == null) {
+ int visibilityLevel = Integer.valueOf(species.getVisibilityLevel());
+ assertTrue("Alias " + species.getElementId() + " is not visible at levels highers than "
+ + species.getVisibilityLevel(), visibilityLevel <= 1);
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateComponentsMaxVisibility() throws Exception {
+ try {
+ double zoomFactor = 39.0625;
+ int levels = 6;
+
+ Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
+
+ new CreateHierarchyCommand(model, levels, zoomFactor).execute();
+
+ for (Element element : model.getElements()) {
+ int visibilityLevel = Integer.valueOf(element.getVisibilityLevel());
+ assertTrue("Alias " + element.getElementId() + " is not visible even at the bottom level (visibility: "
+ + element.getVisibilityLevel() + ") ", visibilityLevel <= levels);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompactComplexesInNestedView() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/compact_complex_view_problem.xml", false);
+ Element alias = model.getElementByElementId("sa1");
+ Object parent1 = alias.getCompartment();
+ new CreateHierarchyCommand(model, 3, 16).execute();
+ Object parent2 = alias.getCompartment();
+ assertEquals(parent1, parent2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRecallHierachyCreation() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
+ command.execute();
+ try {
+ command.execute();
+ fail("Exception expected");
+ } catch (InvalidStateException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testClear() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
+ command.clean();
+ for (Element alias : model.getElements()) {
+ assertNull(alias.getCompartment());
+ }
+ for (Compartment alias : model.getCompartments()) {
+ assertNull(alias.getCompartment());
+ assertTrue(alias.getElements().isEmpty());
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNestedProblem() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser
+ .createModel(new ConverterParams().filename("testFiles/nested_test.xml").sizeAutoAdjust(true));
+
+ double zoomFactor = Math.max(model.getHeight(), model.getWidth()) / (256);
+ int zoomLevels = (int) Math.ceil(Math.log(zoomFactor) / Math.log(2));
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, zoomLevels, zoomFactor);
+ command.execute();
+
+ for (Element alias : model.getElements()) {
+ Element parentAlias = alias.getCompartment();
+ if (parentAlias != null) {
+ int parentVisibilityLevel = Integer.valueOf(parentAlias.getVisibilityLevel());
+ int aliasVisibilityLevel = Integer.valueOf(alias.getVisibilityLevel());
+ assertTrue(aliasVisibilityLevel >= parentVisibilityLevel);
+ }
+ if (alias instanceof Species) {
+ parentAlias = ((Species) alias).getComplex();
+ if (parentAlias != null) {
+ int parentVisibilityLevel = Integer.valueOf(parentAlias.getVisibilityLevel());
+ int aliasVisibilityLevel = Integer.valueOf(alias.getVisibilityLevel());
+ assertTrue(aliasVisibilityLevel >= parentVisibilityLevel);
+ }
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDisconnectedChildInComplex() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/disconnected_child_in_complex.xml", false);
+
+ new CreateHierarchyCommand(model, 8, 80).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xmlString = parser.toXml(model);
+ // logger.debug(xmlString);
+
+ InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
+
+ parser.createModel(new ConverterParams().inputStream(stream));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index df278007811d37f0e1e98a41c87c472b6aef0b22..910ab16ccbbc81a2b71d3af5f628c83b8ab205a7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -373,6 +373,14 @@ public enum MiriamType {
"urn:miriam:refseq", //
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
+ /**
+ * Rhea: http://www.rhea-db.org/.
+ */
+ RHEA("Rhea", //
+ "http://www.rhea-db.org/", //
+ "urn:miriam:rhea", //
+ new Class<?>[] { Reaction.class }, "MIR:00000082"),
+
/**
* SGD: http://www.yeastgenome.org/.
*/
@@ -494,7 +502,7 @@ public enum MiriamType {
private String commonName;
/**
- * url to homepage of given resource type.
+ * url to home page of given resource type.
*/
private String dbHomepage;
@@ -504,9 +512,9 @@ public enum MiriamType {
private String registryIdentifier;
/**
- * Valid uris to this resource.
+ * Valid URIs to this resource.
*/
- private List<String> uris = new ArrayList<String>();
+ private List<String> uris = new ArrayList<>();
/**
* Classes that can be annotated by this resource.
@@ -523,7 +531,7 @@ public enum MiriamType {
* Constructor that initialize enum object.
*
* @param dbHomePage
- * homepage of the resource {@link #dbHomepage}
+ * home page of the resource {@link #dbHomepage}
* @param commonName
* {@link #commonName}
* @param uris
@@ -541,7 +549,7 @@ public enum MiriamType {
* Constructor that initialize enum object.
*
* @param dbHomePage
- * homepage of the resource {@link #dbHomepage}
+ * home page of the resource {@link #dbHomepage}
* @param commonName
* {@link #commonName}
* @param uris
@@ -573,7 +581,7 @@ public enum MiriamType {
* Constructor that initialize enum object.
*
* @param dbHomePage
- * homepage of the resource {@link #dbHomepage}
+ * home page of the resource {@link #dbHomepage}
* @param commonName
* {@link #commonName}
* @param uri
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
index 2208709e2dcc5975e740f76c339de0e5dedbf255..006ad5fb82dfa7268d4d17e02d6888ce551d257b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
@@ -1,113 +1,113 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-
-/**
- * Entity representing antisense rna element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("ANTISENSE_RNA_ALIAS")
-public class AntisenseRna extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of {@link AntisenseRnaRegion regions} related to this
- * {@link AntisenseRna}.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species")
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<AntisenseRnaRegion> regions = new ArrayList<>();
-
- /**
- * Empty constructor required by hibernate.
- */
- AntisenseRna() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public AntisenseRna(AntisenseRna original) {
- super(original);
- for (AntisenseRnaRegion region : original.getRegions()) {
- addRegion(new AntisenseRnaRegion(region));
- }
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public AntisenseRna(String elementId) {
- setElementId(elementId);
- }
-
- /**
- * Adds {@link AntisenseRnaRegion} to the object.
- *
- * @param antisenseRnaRegion
- * alement to be added
- */
- public void addRegion(AntisenseRnaRegion antisenseRnaRegion) {
- regions.add(antisenseRnaRegion);
- antisenseRnaRegion.setSpecies(this);
- }
-
- @Override
- public AntisenseRna copy() {
- if (this.getClass() == AntisenseRna.class) {
- return new AntisenseRna(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the regions
- * @see #regions
- */
- public List<AntisenseRnaRegion> getRegions() {
- return regions;
- }
-
- /**
- * @param regions
- * the regions to set
- * @see #regions
- */
- public void setRegions(List<AntisenseRnaRegion> regions) {
- this.regions = regions;
- }
-
- @Override
- public String getStringType() {
- return "Antisense RNA";
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.OneToMany;
+
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.LazyCollection;
+import org.hibernate.annotations.LazyCollectionOption;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Entity representing antisense rna element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("ANTISENSE_RNA_ALIAS")
+public class AntisenseRna extends Species {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * List of {@link AntisenseRnaRegion regions} related to this
+ * {@link AntisenseRna}.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "species")
+ @LazyCollection(LazyCollectionOption.FALSE)
+ private List<ModificationResidue> regions = new ArrayList<>();
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ AntisenseRna() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public AntisenseRna(AntisenseRna original) {
+ super(original);
+ for (ModificationResidue region : original.getRegions()) {
+ addRegion(region.copy());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * unique (within model) element identifier
+ */
+ public AntisenseRna(String elementId) {
+ setElementId(elementId);
+ }
+
+ /**
+ * Adds {@link AntisenseRnaRegion} to the object.
+ *
+ * @param antisenseRnaRegion
+ * region to be added
+ */
+ public void addRegion(ModificationResidue antisenseRnaRegion) {
+ regions.add(antisenseRnaRegion);
+ antisenseRnaRegion.setSpecies(this);
+ }
+
+ @Override
+ public AntisenseRna copy() {
+ if (this.getClass() == AntisenseRna.class) {
+ return new AntisenseRna(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the regions
+ * @see #regions
+ */
+ public List<ModificationResidue> getRegions() {
+ return regions;
+ }
+
+ /**
+ * @param regions
+ * the regions to set
+ * @see #regions
+ */
+ public void setRegions(List<ModificationResidue> regions) {
+ this.regions = regions;
+ }
+
+ @Override
+ public String getStringType() {
+ return "Antisense RNA";
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
index 95e2a358541cc7f2eec77865c0aeb23607793708..65f2b00630491ee2b5a9f73cece0e63ebe70906c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
@@ -8,7 +8,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
/**
* Comparator class used for comparing {@link AntisenseRna} objects.
@@ -56,18 +56,21 @@ public class AntisenseRnaComparator extends Comparator<AntisenseRna> {
protected int internalCompare(AntisenseRna arg0, AntisenseRna arg1) {
StringSetComparator stringSetComparator = new StringSetComparator();
- Set<String> set1 = new HashSet<String>();
- Set<String> set2 = new HashSet<String>();
+ Set<String> set1 = new HashSet<>();
+ Set<String> set2 = new HashSet<>();
- for (AntisenseRnaRegion region : arg0.getRegions()) {
+ for (ModificationResidue region : arg0.getRegions()) {
set1.add(region.toString());
}
- for (AntisenseRnaRegion region : arg1.getRegions()) {
+ for (ModificationResidue region : arg1.getRegions()) {
set2.add(region.toString());
}
if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.debug(set1);
+ logger.debug(set2);
+ logger.debug("Regions mismatch");
return stringSetComparator.compare(set1, set2);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
index db6c9cb8404aee7cbd002d25fd9ed5a30ce5e2ba..ae7a0cfc64e435a40828a9c69884e9822fb3a722 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
@@ -1,113 +1,113 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-/**
- * Entity representing gene element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("GENE_ALIAS")
-public class Gene extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of modifications for the Gene.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species", orphanRemoval = true)
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<ModificationResidue> modificationResidues = new ArrayList<>();
-
- /**
- * Empty constructor required by hibernate.
- */
- Gene() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public Gene(Gene original) {
- super(original);
- for (ModificationResidue mr : original.getModificationResidues()) {
- addModificationResidue(new ModificationResidue(mr));
- }
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public Gene(String elementId) {
- setElementId(elementId);
- }
-
- /**
- * Adds {@link ModificationResidue}.
- *
- * @param modificationResidue
- * {@link ModificationResidue} to be added
- */
- public void addModificationResidue(ModificationResidue modificationResidue) {
- modificationResidues.add(modificationResidue);
- modificationResidue.setSpecies(this);
-
- }
-
- @Override
- public Gene copy() {
- if (this.getClass() == Gene.class) {
- return new Gene(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the modificationResidues
- * @see #modificationResidues
- */
- public List<ModificationResidue> getModificationResidues() {
- return modificationResidues;
- }
-
- /**
- * @param modificationResidues
- * the modificationResidues to set
- * @see #modificationResidues
- */
- public void setModificationResidues(List<ModificationResidue> modificationResidues) {
- this.modificationResidues = modificationResidues;
- }
-
- @Override
- public String getStringType() {
- return "Gene";
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.OneToMany;
+
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.LazyCollection;
+import org.hibernate.annotations.LazyCollectionOption;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Entity representing gene element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("GENE_ALIAS")
+public class Gene extends Species {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * List of modifications for the Gene.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "species", orphanRemoval = true)
+ @LazyCollection(LazyCollectionOption.FALSE)
+ private List<ModificationResidue> modificationResidues = new ArrayList<>();
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Gene() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public Gene(Gene original) {
+ super(original);
+ for (ModificationResidue mr : original.getModificationResidues()) {
+ addModificationResidue(mr.copy());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Gene(String elementId) {
+ setElementId(elementId);
+ }
+
+ /**
+ * Adds {@link ModificationResidue}.
+ *
+ * @param modificationResidue
+ * {@link ModificationResidue} to be added
+ */
+ public void addModificationResidue(ModificationResidue modificationResidue) {
+ modificationResidues.add(modificationResidue);
+ modificationResidue.setSpecies(this);
+
+ }
+
+ @Override
+ public Gene copy() {
+ if (this.getClass() == Gene.class) {
+ return new Gene(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the modificationResidues
+ * @see #modificationResidues
+ */
+ public List<ModificationResidue> getModificationResidues() {
+ return modificationResidues;
+ }
+
+ /**
+ * @param modificationResidues
+ * the modificationResidues to set
+ * @see #modificationResidues
+ */
+ public void setModificationResidues(List<ModificationResidue> modificationResidues) {
+ this.modificationResidues = modificationResidues;
+ }
+
+ @Override
+ public String getStringType() {
+ return "Gene";
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
index 89b0aa38e0296cdd2206d121d925d35e6fafbfc5..95aa3b734ff7aea7c1473e60e1b462defbbf6bdd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
@@ -68,6 +68,10 @@ public class GeneComparator extends Comparator<Gene> {
}
if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.debug(set1);
+ logger.debug(set2);
+ logger.debug("Different modifications");
+ logger.debug("---");
return stringSetComparator.compare(set1, set2);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
index 9e891ddd9df99c9d85a2449c86e9a43128b29295..8f4cf0ecf0a03b4f32d08841098ae30bd48d7c3d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
@@ -58,7 +58,7 @@ public abstract class Protein extends Species {
super(original);
this.structuralState = original.getStructuralState();
for (ModificationResidue mr : original.getModificationResidues()) {
- addModificationResidue(new ModificationResidue(mr));
+ addModificationResidue(mr.copy());
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
index b397b9b4f3b38f956c0a93a9232b45cc6e9e5fb8..976ef785d5b84a01b76c804f4442627397036484 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
@@ -78,6 +78,8 @@ public class ProteinComparator extends Comparator<Protein> {
}
if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.debug(set1);
+ logger.debug(set2);
logger.debug("modification residues different");
return stringSetComparator.compare(set1, set2);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
index 7e3df3a906a00b7f102efc0839a795430a03405a..69c46c396d598d23cf6c6e6cf5f9571693dff6ee 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
@@ -1,113 +1,113 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-
-/**
- * Entity representing rna element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("RNA_ALIAS")
-public class Rna extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of rna regions (some rna sequences) in this object.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species", orphanRemoval = true)
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<RnaRegion> regions = new ArrayList<>();
-
- /**
- * Empty constructor required by hibernate.
- */
- Rna() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public Rna(Rna original) {
- super(original);
- for (RnaRegion region : original.getRegions()) {
- addRegion(new RnaRegion(region));
- }
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public Rna(String elementId) {
- super();
- setElementId(elementId);
- }
-
- /**
- * Adds {@link RnaRegion}.
- *
- * @param rnaRegion
- * object to be added
- */
- public void addRegion(RnaRegion rnaRegion) {
- regions.add(rnaRegion);
- rnaRegion.setSpecies(this);
- }
-
- @Override
- public Rna copy() {
- if (this.getClass() == Rna.class) {
- return new Rna(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the regions
- * @see #regions
- */
- public List<RnaRegion> getRegions() {
- return regions;
- }
-
- /**
- * @param regions
- * the regions to set
- * @see #regions
- */
- public void setRegions(List<RnaRegion> regions) {
- this.regions = regions;
- }
-
- @Override
- public String getStringType() {
- return "RNA";
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.OneToMany;
+
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.LazyCollection;
+import org.hibernate.annotations.LazyCollectionOption;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Entity representing rna element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("RNA_ALIAS")
+public class Rna extends Species {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * List of rna regions (some rna sequences) in this object.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "species", orphanRemoval = true)
+ @LazyCollection(LazyCollectionOption.FALSE)
+ private List<ModificationResidue> regions = new ArrayList<>();
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Rna() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public Rna(Rna original) {
+ super(original);
+ for (ModificationResidue region : original.getRegions()) {
+ addRegion(region.copy());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Rna(String elementId) {
+ super();
+ setElementId(elementId);
+ }
+
+ /**
+ * Adds {@link RnaRegion}.
+ *
+ * @param rnaRegion
+ * object to be added
+ */
+ public void addRegion(ModificationResidue rnaRegion) {
+ regions.add(rnaRegion);
+ rnaRegion.setSpecies(this);
+ }
+
+ @Override
+ public Rna copy() {
+ if (this.getClass() == Rna.class) {
+ return new Rna(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the regions
+ * @see #regions
+ */
+ public List<ModificationResidue> getRegions() {
+ return regions;
+ }
+
+ /**
+ * @param regions
+ * the regions to set
+ * @see #regions
+ */
+ public void setRegions(List<ModificationResidue> regions) {
+ this.regions = regions;
+ }
+
+ @Override
+ public String getStringType() {
+ return "RNA";
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
index a16fbb967e9cdc64cb31a4f67b8bb8aecb0c0f54..34efa599e5714460b60117568647c8ae2369cfd0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
@@ -8,7 +8,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
/**
* Comparator class used for comparing {@link Rna} objects.
@@ -59,15 +59,18 @@ public class RnaComparator extends Comparator<Rna> {
Set<String> set1 = new HashSet<>();
Set<String> set2 = new HashSet<>();
- for (RnaRegion region : arg0.getRegions()) {
+ for (ModificationResidue region : arg0.getRegions()) {
set1.add(region.toString());
}
- for (RnaRegion region : arg1.getRegions()) {
+ for (ModificationResidue region : arg1.getRegions()) {
set2.add(region.toString());
}
if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.debug("Regions different");
+ logger.debug(set1);
+ logger.debug(set2);
return stringSetComparator.compare(set1, set2);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractRegionModification.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractRegionModification.java
new file mode 100644
index 0000000000000000000000000000000000000000..ec63373addb301c960fba06c46a9b40a0b2e7219
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractRegionModification.java
@@ -0,0 +1,102 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import java.text.DecimalFormat;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+@Entity
+@DiscriminatorValue("ABSTRACT_REGION_MODIFICATION")
+public abstract class AbstractRegionModification extends ModificationResidue {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default size of the object (in graphical representation).
+ */
+ private static final double DEFAULT_SIZE = 10;
+
+ /**
+ * Width of the region in the graphic representation.
+ */
+ @Column(name = "width")
+ private double width = DEFAULT_SIZE;
+
+ /**
+ * Height of the region in the graphic representation.
+ */
+ @Column(name = "height")
+ private double height = DEFAULT_SIZE;
+
+ public AbstractRegionModification() {
+ super();
+ }
+
+ public AbstractRegionModification(AbstractRegionModification mr) {
+ super(mr);
+ this.width = mr.getWidth();
+ this.height = mr.getHeight();
+ }
+
+ @Override
+ public String toString() {
+ DecimalFormat format = new DecimalFormat("#.##");
+ String position;
+ if (getPosition() == null) {
+ position = null;
+ } else {
+ position = "Point2D[" + format.format(getPosition().getX()) + "," + format.format(getPosition().getY()) + "]";
+ }
+ String result = "[" + this.getClass().getSimpleName() + "]: " + getIdModificationResidue() + "," + getName() + ","
+ + getWidth() + "," + getHeight() + "," + position;
+ return result;
+ }
+
+ public double getWidth() {
+ return width;
+ }
+
+ public void setWidth(double width) {
+ this.width = width;
+ }
+
+ /**
+ * Update data in this object from parameter (only if values in parameter object
+ * are valid).
+ *
+ * @param mr
+ * object from which we are updating data
+ */
+ public void update(AbstractRegionModification mr) {
+ if (this.getIdModificationResidue() != null && !this.getIdModificationResidue().equals("")
+ && !this.getIdModificationResidue().equals(mr.getIdModificationResidue())) {
+ throw new InvalidArgumentException("Cannot update from mr with different id");
+ }
+ if (mr.getWidth() > 0 && mr.getWidth() != DEFAULT_SIZE) {
+ this.setWidth(mr.getWidth());
+ }
+ if (mr.getHeight() > 0 && mr.getHeight() != DEFAULT_SIZE) {
+ this.setHeight(mr.getHeight());
+ }
+ if (mr.getName() != null) {
+ this.setName(mr.getName());
+ }
+ if (mr.getPosition() != null) {
+ this.setPosition(mr.getPosition());
+ }
+ }
+
+ public double getHeight() {
+ return height;
+ }
+
+ public void setHeight(double height) {
+ this.height = height;
+ }
+}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
new file mode 100644
index 0000000000000000000000000000000000000000..d0249cea6281efb73da01a857a48fe80c72e932d
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
@@ -0,0 +1,51 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import java.text.DecimalFormat;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+
+@Entity
+@DiscriminatorValue("ABSTRACT_SITE_MODIFICATION")
+public abstract class AbstractSiteModification extends ModificationResidue {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * State in which this modification is.
+ */
+ @Enumerated(EnumType.STRING)
+ protected ModificationState state = null;
+
+ public AbstractSiteModification() {
+ super();
+ }
+
+ public AbstractSiteModification(AbstractSiteModification mr) {
+ super(mr);
+ this.state = mr.getState();
+ }
+
+ public ModificationState getState() {
+ return state;
+ }
+
+ public void setState(ModificationState state) {
+ this.state = state;
+ }
+
+ @Override
+ public String toString() {
+ DecimalFormat format = new DecimalFormat("#.##");
+ String result = getIdModificationResidue() + "," + getName() + "," + getState() + ",Point2D["
+ + format.format(getPosition().getX()) + "," + format.format(getPosition().getY()) + "]";
+ return result;
+ }
+
+
+}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
deleted file mode 100644
index ed51da8943b7682fb0ee357f8d9c5b7ee01377fc..0000000000000000000000000000000000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
+++ /dev/null
@@ -1,341 +0,0 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-
-/**
- * This structure contains information about antisense rna region (rna fragment
- * of interest) for a specific {@link AntisenseRna}.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "antisense_rna_region_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-public class AntisenseRnaRegion implements Serializable, ElementModification {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default size of the object (in graphical representation).
- */
- private static final double DEFAULT_SIZE = 0.1;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRnaRegion.class);
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "iddb", unique = true, nullable = false)
- private int id;
-
- /**
- * String identifier of the element. Unique in the model.
- */
- @Column(name = "idantisensernaregion")
- private String idAntisenseRnaRegion = "";
-
- /**
- * Name of the region.
- */
- @Column(name = "name")
- private String name = "";
-
- /**
- * Defines a state of the region (for instance ubiquitinated etc).
- *
- * @see ModificationState
- */
- @Column(name = "state")
- private ModificationState state = null;
-
- /**
- * Type of the region in the rna. There are three possible values:
- * <ul>
- * <li>Coding region,</li>
- * <li>Protein binding domain,</li>
- * <li>Modification site.</li>
- * </ul>
- */
- @Column(name = "type")
- private AntisenseRnaRegionType type;
-
- /**
- * Size of the region in the graphic representation.
- */
- @Column(name = "size")
- private double size = DEFAULT_SIZE;
-
- /**
- * Position on the species in graphic representation.
- */
- @Column(name = "pos")
- private Double pos;
-
- /**
- * Defines a species where the region belongs to.
- */
- @Cascade({ CascadeType.ALL })
- @ManyToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "idSpeciesDb")
- private AntisenseRna species;
-
- /**
- * Default constructor.
- */
- public AntisenseRnaRegion() {
-
- }
-
- /**
- * Constructor that initialize object with the data from the parameter.
- *
- * @param original
- * object from which we initialize data
- */
- public AntisenseRnaRegion(AntisenseRnaRegion original) {
- this.idAntisenseRnaRegion = original.idAntisenseRnaRegion;
- this.name = original.name;
- this.size = original.size;
- this.pos = original.pos;
- this.type = original.type;
- }
-
- /**
- * Creates a copy of current object.
- *
- * @return copy of the object
- */
- public AntisenseRnaRegion copy() {
- if (this.getClass() == AntisenseRnaRegion.class) {
- return new AntisenseRnaRegion(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
-
- }
-
- /**
- * Sets size from the string.
- *
- * @param text
- * size to parse and set
- * @see #size
- */
- public void setSize(String text) {
- try {
- size = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
- }
-
- /**
- * Sets position from the string.
- *
- * @param text
- * position to parse and set
- * @see #pos
- */
- public void setPos(String text) {
- try {
- pos = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid pos: " + text, e);
- }
- }
-
- /**
- * Update data in this object from parameter (only if values in parameter
- * object are valid).
- *
- * @param mr
- * object from which we are updating data
- */
- public void update(AntisenseRnaRegion mr) {
- if (this.idAntisenseRnaRegion != null && !this.idAntisenseRnaRegion.equals("") && !this.idAntisenseRnaRegion.equals(mr.getIdAntisenseRnaRegion())) {
- throw new InvalidArgumentException("Cannot update from mr with different id");
- }
- this.size = mr.getSize();
- if (mr.getState() != null) {
- this.state = mr.getState();
- }
- if (mr.getName() != null) {
- this.name = mr.getName();
- }
- if (mr.getPos() != null) {
- this.setPos(mr.getPos());
- }
-
- }
-
- @Override
- public String toString() {
- String result = getIdAntisenseRnaRegion() + "," + getName() + "," + getType() + "," + getPos() + "," + getSize() + ",";
- return result;
- }
-
- /**
- * @return the idAntisenseRnaRegion
- * @see #idAntisenseRnaRegion
- */
- public String getIdAntisenseRnaRegion() {
- return idAntisenseRnaRegion;
- }
-
- /**
- * @param idAntisenseRnaRegion
- * the id to set
- * @see #idAntisenseRnaRegion
- */
- public void setIdAntisenseRnaRegion(String idAntisenseRnaRegion) {
- this.idAntisenseRnaRegion = idAntisenseRnaRegion;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the state
- * @see #state
- */
- public ModificationState getState() {
- return state;
- }
-
- /**
- * @param state
- * the state to set
- * @see #state
- */
- public void setState(ModificationState state) {
- this.state = state;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public AntisenseRnaRegionType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(AntisenseRnaRegionType type) {
- this.type = type;
- }
-
- /**
- * @return the size
- * @see #size
- */
- public double getSize() {
- return size;
- }
-
- /**
- * @param size
- * the size to set
- * @see #size
- */
- public void setSize(double size) {
- this.size = size;
- }
-
- /**
- * @return the pos
- * @see #pos
- */
- public Double getPos() {
- return pos;
- }
-
- /**
- * @param pos
- * the pos to set
- * @see #pos
- */
- public void setPos(Double pos) {
- this.pos = pos;
- }
-
- /**
- * @return the species
- * @see #species
- */
- public AntisenseRna getSpecies() {
- return species;
- }
-
- /**
- * @param species
- * the species to set
- * @see #species
- */
- public void setSpecies(AntisenseRna species) {
- this.species = species;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionType.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionType.java
deleted file mode 100644
index 727ad5d4c831018249c9a185d943573f29d03f0e..0000000000000000000000000000000000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionType.java
+++ /dev/null
@@ -1,67 +0,0 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-
-/**
- * Enum that enlists types of available modification regions in
- * {@link AntisenseRna}.
- *
- * @author Piotr Gawron
- *
- */
-public enum AntisenseRnaRegionType {
-
- /**
- * Modification site.
- */
- MODIFICATION_SITE("Modification Site"), //
-
- /**
- * Coding region.
- */
- CODING_REGION("CodingRegion"), //
-
- /**
- * Protein binding domain.
- */
- PROTEIN_BINDING_DOMAIN("proteinBindingDomain");
-
- /**
- * Name of the type.
- */
- private String name;
-
- /**
- * Default constructor.
- *
- * @param name
- * name of the type
- */
- AntisenseRnaRegionType(String name) {
- this.name = name;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * Returns {@link AntisenseRnaRegionType} identified by name.
- *
- * @param name
- * name of the region
- * @return {@link AntisenseRnaRegionType} identified by name
- */
- public static AntisenseRnaRegionType getTypeByString(String name) {
- for (AntisenseRnaRegionType type : values()) {
- if (type.getName().equalsIgnoreCase(name)) {
- return type;
- }
- }
- return null;
- }
-}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java
new file mode 100644
index 0000000000000000000000000000000000000000..daa42fe4e3ddd4606d56a1ce00fad124a894af5b
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/BindingRegion.java
@@ -0,0 +1,69 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import java.io.Serializable;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This structure contains information about Binding Region for one of the
+ * following {@link Species}:
+ * <ul>
+ * <li>{@link Protein}</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("BINDING_REGION")
+public class BindingRegion extends AbstractRegionModification implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(BindingRegion.class);
+
+ /**
+ * Default constructor.
+ */
+ public BindingRegion() {
+
+ }
+
+ /**
+ * Constructor that initialize object with the data from the parameter.
+ *
+ * @param original
+ * object from which we initialize data
+ */
+ public BindingRegion(BindingRegion original) {
+ super(original);
+ }
+
+ /**
+ * Creates a copy of current object.
+ *
+ * @return copy of the object
+ */
+ public BindingRegion copy() {
+ if (this.getClass() == BindingRegion.class) {
+ return new BindingRegion(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java
new file mode 100644
index 0000000000000000000000000000000000000000..4a10b406425a8c4a391a12bc52174c1e704600a2
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/CodingRegion.java
@@ -0,0 +1,73 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import java.io.Serializable;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This structure contains information about Coding Region for one of the
+ * following {@link Species}:
+ * <ul>
+ * <li>{@link Rna}</li>
+ * <li>{@link AntisenseRna}</li>
+ * <li>{@link Gene}</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("CODING_REGION")
+public class CodingRegion extends AbstractRegionModification implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CodingRegion.class);
+
+ /**
+ * Default constructor.
+ */
+ public CodingRegion() {
+
+ }
+
+ /**
+ * Constructor that initialize object with the data from the parameter.
+ *
+ * @param original
+ * object from which we initialize data
+ */
+ public CodingRegion(CodingRegion original) {
+ super(original);
+ }
+
+ /**
+ * Creates a copy of current object.
+ *
+ * @return copy of the object
+ */
+ public CodingRegion copy() {
+ if (this.getClass() == CodingRegion.class) {
+ return new CodingRegion(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ElementModification.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ElementModification.java
deleted file mode 100644
index 97db98c8d9f2a005cfaf9a2d6b5715df44d8d3a4..0000000000000000000000000000000000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ElementModification.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package lcsb.mapviewer.model.map.species.field;
-
-public interface ElementModification {
- ModificationState getState();
-
- String getName();
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
index e0f7ef54909a29f5703805be25b011d87db2e966..4c8e7b3e37488f08699432ae4285de7fe39e745f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
@@ -1,266 +1,181 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class represent modification residue in protein and gene. However, it is
- * sometimes also used for storing information about AntisenseRna/Rna regions...
- * (due to CellDesigner xml strange structure).
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "modification_residue_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-public class ModificationResidue implements Serializable, ElementModification {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ModificationResidue.class.getName());
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "iddb", unique = true, nullable = false)
- private int id;
-
- /**
- * Identifier of the modification. Must be unique in single map model.
- */
- private String idModificationResidue = "";
-
- /**
- * Name of the modification.
- */
- private String name = "";
-
- /**
- * Some strange param in CellDesigner. No idea what is it for.
- */
- private String side = "";
-
- /**
- * State in which this modification is.
- */
- private ModificationState state = null;
-
- /**
- * Where this modification is located (on which side of the border).
- */
- private Double angle = null;
-
- /**
- * How big is this modification (used only for some types of the
- * modification).
- */
- private Double size = null;
-
- /**
- * Species to which this modification belong to.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "idSpeciesDb", nullable = false)
- private Species species;
-
- /**
- * Default constructor.
- */
- public ModificationResidue() {
- }
-
- /**
- * Constructor that initaize object with the data taken from the parameter.
- *
- * @param mr
- * original object from which data is taken
- */
- public ModificationResidue(ModificationResidue mr) {
- this.idModificationResidue = mr.idModificationResidue;
- this.name = mr.name;
- this.angle = mr.angle;
- this.size = mr.size;
- this.side = mr.side;
- this.state = mr.state;
- }
-
- @Override
- public String toString() {
- String result = getIdModificationResidue() + "," + getName() + "," + getState() + "," + getAngle() + "," + getSize() + "," + getSide() + ",";
- return result;
- }
-
- /**
- * Creates copy of the object.
- *
- * @return copy of the object.
- */
- public ModificationResidue copy() {
- if (this.getClass() == ModificationResidue.class) {
- return new ModificationResidue(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the idModificationResidue
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the idModificationResidue to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the id
- * @see #idModificationResidue
- */
- public String getIdModificationResidue() {
- return idModificationResidue;
- }
-
- /**
- * @param idModificationResidue
- * the id to set
- * @see #idModificationResidue
- */
- public void setIdModificationResidue(String idModificationResidue) {
- this.idModificationResidue = idModificationResidue;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the side
- * @see #side
- */
- public String getSide() {
- return side;
- }
-
- /**
- * @param side
- * the side to set
- * @see #side
- */
- public void setSide(String side) {
- this.side = side;
- }
-
- /**
- * @return the state
- * @see #state
- */
- public ModificationState getState() {
- return state;
- }
-
- /**
- * @param state
- * the state to set
- * @see #state
- */
- public void setState(ModificationState state) {
- this.state = state;
- }
-
- /**
- * @return the angle
- * @see #angle
- */
- public Double getAngle() {
- return angle;
- }
-
- /**
- * @param angle
- * the angle to set
- * @see #angle
- */
- public void setAngle(Double angle) {
- this.angle = angle;
- }
-
- /**
- * @return the size
- * @see #size
- */
- public Double getSize() {
- return size;
- }
-
- /**
- * @param size
- * the size to set
- * @see #size
- */
- public void setSize(Double size) {
- this.size = size;
- }
-
- /**
- * @return the species
- * @see #species
- */
- public Species getSpecies() {
- return species;
- }
-
- /**
- * @param species
- * the species to set
- * @see #species
- */
- public void setSpecies(Species species) {
- this.species = species;
- }
-
-}
+package lcsb.mapviewer.model.map.species.field;
+
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Type;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class represent modification residue in a {@link Species}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+@Entity
+@Table(name = "modification_residue_table")
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(name = "modification_type", discriminatorType = DiscriminatorType.STRING)
+@DiscriminatorValue("GENERIC_MODIFICATION_RESIDUE")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+public class ModificationResidue implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ModificationResidue.class.getName());
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "iddb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Identifier of the modification. Must be unique in single map model.
+ */
+ private String idModificationResidue = "";
+
+ /**
+ * Name of the modification.
+ */
+ private String name = "";
+
+ @Column(name = "position")
+ @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
+ private Point2D position = null;
+
+ /**
+ * Species to which this modification belong to.
+ */
+ @ManyToOne(fetch = FetchType.LAZY, cascade = CascadeType.ALL)
+ @JoinColumn(name = "idSpeciesDb", nullable = false)
+ private Species species;
+
+ /**
+ * Default constructor.
+ */
+ public ModificationResidue() {
+ }
+
+ /**
+ * Constructor that initialize object with the data taken from the parameter.
+ *
+ * @param mr
+ * original object from which data is taken
+ */
+ public ModificationResidue(ModificationResidue mr) {
+ this.idModificationResidue = mr.idModificationResidue;
+ this.name = mr.name;
+ this.position = mr.position;
+ }
+
+ /**
+ * @return the idModificationResidue
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the idModificationResidue to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the id
+ * @see #idModificationResidue
+ */
+ public String getIdModificationResidue() {
+ return idModificationResidue;
+ }
+
+ /**
+ * @param idModificationResidue
+ * the id to set
+ * @see #idModificationResidue
+ */
+ public void setIdModificationResidue(String idModificationResidue) {
+ this.idModificationResidue = idModificationResidue;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the species
+ * @see #species
+ */
+ public Species getSpecies() {
+ return species;
+ }
+
+ /**
+ * @param species
+ * the species to set
+ * @see #species
+ */
+ public void setSpecies(Species species) {
+ this.species = species;
+ }
+
+ public Point2D getPosition() {
+ return position;
+ }
+
+ public void setPosition(Point2D position) {
+ this.position = position;
+ }
+
+ public ModificationResidue copy() {
+ throw new NotImplementedException();
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java
new file mode 100644
index 0000000000000000000000000000000000000000..52b13b58659872ee34278be3e53a197531cf5fa7
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java
@@ -0,0 +1,54 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This structure contains information about Modification Site for one of the
+ * following {@link Species}:
+ * <ul>
+ * <li>{@link Rna}</li>
+ * <li>{@link AntisenseRna}</li>
+ * <li>{@link Gene}</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("MODIFICATION_SITE")
+public class ModificationSite extends AbstractSiteModification {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public ModificationSite() {
+ super();
+ }
+
+ public ModificationSite(ModificationSite site) {
+ super(site);
+ }
+
+ /**
+ * Creates copy of the object.
+ *
+ * @return copy of the object.
+ */
+ public ModificationSite copy() {
+ if (this.getClass() == ModificationSite.class) {
+ return new ModificationSite(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
index da3b3308eb7a20fc2ffceded6f2e4e184988d6c2..32184f55ee6f54583dc71029f7058f89e65c5872 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
@@ -1,152 +1,152 @@
-package lcsb.mapviewer.model.map.species.field;
-
-/**
- * Defines a type of modification (in protein or rna). Possible values are:
- * <ul>
- * <li>{@link ModificationState#ACETYLATED ACETYLATED},</li>
- * <li>{@link ModificationState#DONT_CARE DON'T CARE},</li>
- * <li>{@link ModificationState#EMPTY EMPTY},</li>
- * <li>{@link ModificationState#GLYCOSYLATED GLYCOSYLATED},</li>
- * <li>{@link ModificationState#HYDROXYLATED HYDROXYLATED},</li>
- * <li>{@link ModificationState#METHYLATED METHYLATED},</li>
- * <li>{@link ModificationState#MYRISTOYLATED MYRISTOYLATED},</li>
- * <li>{@link ModificationState#PALMYTOYLATED PALMYTOYLATED},</li>
- * <li>{@link ModificationState#PHOSPHORYLATED PHOSPHORYLATED},</li>
- * <li>{@link ModificationState#PRENYLATED PRENYLATED},</li>
- * <li>{@link ModificationState#PROTONATED PROTONATED},</li>
- * <li>{@link ModificationState#SULFATED SULFATED},</li>
- * <li>{@link ModificationState#UBIQUITINATED UBIQUITINATED},</li>
- * <li>{@link ModificationState#UNKNOWN UNKNOWN}.</li>
- * </ul>
- *
- * @author Piotr Gawron
- *
- */
-public enum ModificationState {
-
- /**
- * Phosporylated state.
- */
- PHOSPHORYLATED("phosphorylated", "P"), //
-
- /**
- * Acetylated state.
- */
- ACETYLATED("acetylated", "Ac"), //
-
- /**
- * Ubiquitinated state.
- */
- UBIQUITINATED("ubiquitinated", "Ub"), //
-
- /**
- * Methylated state.
- */
- METHYLATED("methylated", "Me"), //
-
- /**
- * Hydroxylated state.
- */
- HYDROXYLATED("hydroxylated", "OH"), //
-
- /**
- * Myristoylated state.
- */
- MYRISTOYLATED("myristoylated", "My"), //
-
- /**
- * Sulfated state.
- */
- SULFATED("sulfated", "S"), //
-
- /**
- * Prenylated state.
- */
- PRENYLATED("prenylated", "Pr"), //
-
- /**
- * Glycosylated state.
- */
- GLYCOSYLATED("glycosylated", "G"), //
-
- /**
- * Palmytoylated state.
- */
- PALMYTOYLATED("palmytoylated", "Pa"), //
-
- /**
- * Unknown state.
- */
- UNKNOWN("unknown", "?"), //
-
- /**
- * Empty state.
- */
- EMPTY("empty", ""), //
-
- /**
- * Protonated state.
- */
- PROTONATED("protonated", "H"), //
-
- /**
- * We don't care in which state it is.
- */
- DONT_CARE("don't care", "*");
-
- /**
- * Full name of the modification.
- */
-
- private String fullName;
- /**
- * Abbreviation used for the modification.
- */
- private String abbreviation;
-
- /**
- * Default constructor with the name and abbreviation.
- *
- * @param name
- * name used for this state
- * @param abbreviation
- * abbreviation used in this state
- */
- ModificationState(String name, String abbreviation) {
- this.fullName = name;
- this.abbreviation = abbreviation;
- }
-
- /**
- * @return the fullName
- * @see #fullName
- */
- public String getFullName() {
- return fullName;
- }
-
- /**
- * @return the abbreviation
- * @see #abbreviation
- */
- public String getAbbreviation() {
- return abbreviation;
- }
-
- /**
- * Returns {@link ModificationState} identified by the full name.
- *
- * @param name
- * full name of the state
- * @return {@link ModificationState} identified by the full name
- */
- public static ModificationState getByName(String name) {
- for (ModificationState state : values()) {
- if (state.getFullName().equalsIgnoreCase(name)) {
- return state;
- }
- }
- return null;
- }
-
-}
+package lcsb.mapviewer.model.map.species.field;
+
+/**
+ * Defines a type of modification (in protein or rna). Possible values are:
+ * <ul>
+ * <li>{@link ModificationState#ACETYLATED ACETYLATED},</li>
+ * <li>{@link ModificationState#DONT_CARE DON'T CARE},</li>
+ * <li>{@link ModificationState#EMPTY EMPTY},</li>
+ * <li>{@link ModificationState#GLYCOSYLATED GLYCOSYLATED},</li>
+ * <li>{@link ModificationState#HYDROXYLATED HYDROXYLATED},</li>
+ * <li>{@link ModificationState#METHYLATED METHYLATED},</li>
+ * <li>{@link ModificationState#MYRISTOYLATED MYRISTOYLATED},</li>
+ * <li>{@link ModificationState#PALMYTOYLATED PALMYTOYLATED},</li>
+ * <li>{@link ModificationState#PHOSPHORYLATED PHOSPHORYLATED},</li>
+ * <li>{@link ModificationState#PRENYLATED PRENYLATED},</li>
+ * <li>{@link ModificationState#PROTONATED PROTONATED},</li>
+ * <li>{@link ModificationState#SULFATED SULFATED},</li>
+ * <li>{@link ModificationState#UBIQUITINATED UBIQUITINATED},</li>
+ * <li>{@link ModificationState#UNKNOWN UNKNOWN}.</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ModificationState {
+
+ /**
+ * Phosporylated state.
+ */
+ PHOSPHORYLATED("phosphorylated", "P"), //
+
+ /**
+ * Acetylated state.
+ */
+ ACETYLATED("acetylated", "Ac"), //
+
+ /**
+ * Ubiquitinated state.
+ */
+ UBIQUITINATED("ubiquitinated", "Ub"), //
+
+ /**
+ * Methylated state.
+ */
+ METHYLATED("methylated", "Me"), //
+
+ /**
+ * Hydroxylated state.
+ */
+ HYDROXYLATED("hydroxylated", "OH"), //
+
+ /**
+ * Myristoylated state.
+ */
+ MYRISTOYLATED("myristoylated", "My"), //
+
+ /**
+ * Sulfated state.
+ */
+ SULFATED("sulfated", "S"), //
+
+ /**
+ * Prenylated state.
+ */
+ PRENYLATED("prenylated", "Pr"), //
+
+ /**
+ * Glycosylated state.
+ */
+ GLYCOSYLATED("glycosylated", "G"), //
+
+ /**
+ * Palmytoylated state.
+ */
+ PALMYTOYLATED("palmytoylated", "Pa"), //
+
+ /**
+ * Unknown state.
+ */
+ UNKNOWN("unknown", "?"), //
+
+ /**
+ * Empty state.
+ */
+ EMPTY("empty", ""), //
+
+ /**
+ * Protonated state.
+ */
+ PROTONATED("protonated", "H"), //
+
+ /**
+ * We don't care in which state it is.
+ */
+ DONT_CARE("don't care", "*");
+
+ /**
+ * Full name of the modification.
+ */
+
+ private String fullName;
+ /**
+ * Abbreviation used for the modification.
+ */
+ private String abbreviation;
+
+ /**
+ * Default constructor with the name and abbreviation.
+ *
+ * @param name
+ * name used for this state
+ * @param abbreviation
+ * abbreviation used in this state
+ */
+ ModificationState(String name, String abbreviation) {
+ this.fullName = name;
+ this.abbreviation = abbreviation;
+ }
+
+ /**
+ * @return the fullName
+ * @see #fullName
+ */
+ public String getFullName() {
+ return fullName;
+ }
+
+ /**
+ * @return the abbreviation
+ * @see #abbreviation
+ */
+ public String getAbbreviation() {
+ return abbreviation;
+ }
+
+ /**
+ * Returns {@link ModificationState} identified by the full name.
+ *
+ * @param name
+ * full name of the state
+ * @return {@link ModificationState} identified by the full name
+ */
+ public static ModificationState getByName(String name) {
+ for (ModificationState state : values()) {
+ if (state.getFullName().equalsIgnoreCase(name)) {
+ return state;
+ }
+ }
+ return null;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java
new file mode 100644
index 0000000000000000000000000000000000000000..92d9ea58f22dc937cbac59020022de6a79f51d43
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomain.java
@@ -0,0 +1,71 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import java.io.Serializable;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This structure contains information about Protein Binding Domain for one of
+ * the following {@link Species}:
+ * <ul>
+ * <li>{@link Rna}</li>
+ * <li>{@link AntisenseRna}</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("PROTEIN_BINDING_DOMAIN")
+public class ProteinBindingDomain extends AbstractRegionModification implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ProteinBindingDomain.class);
+
+ /**
+ * Default constructor.
+ */
+ public ProteinBindingDomain() {
+
+ }
+
+ /**
+ * Constructor that initialize object with the data from the parameter.
+ *
+ * @param original
+ * object from which we initialize data
+ */
+ public ProteinBindingDomain(ProteinBindingDomain original) {
+ super(original);
+ }
+
+ /**
+ * Creates a copy of current object.
+ *
+ * @return copy of the object
+ */
+ public ProteinBindingDomain copy() {
+ if (this.getClass() == ProteinBindingDomain.class) {
+ return new ProteinBindingDomain(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java
new file mode 100644
index 0000000000000000000000000000000000000000..fd47c43c8b6eeb0e806de8e8fcbba6be39abca89
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RegulatoryRegion.java
@@ -0,0 +1,69 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import java.io.Serializable;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This structure contains information about Regulatory Region for one of the
+ * following {@link Species}:
+ * <ul>
+ * <li>{@link Gene}</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("REGULATORY_REGION")
+public class RegulatoryRegion extends AbstractRegionModification implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(RegulatoryRegion.class);
+
+ /**
+ * Default constructor.
+ */
+ public RegulatoryRegion() {
+
+ }
+
+ /**
+ * Constructor that initialize object with the data from the parameter.
+ *
+ * @param original
+ * object from which we initialize data
+ */
+ public RegulatoryRegion(RegulatoryRegion original) {
+ super(original);
+ }
+
+ /**
+ * Creates a copy of current object.
+ *
+ * @return copy of the object
+ */
+ public RegulatoryRegion copy() {
+ if (this.getClass() == RegulatoryRegion.class) {
+ return new RegulatoryRegion(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java
new file mode 100644
index 0000000000000000000000000000000000000000..d93cc8956d07f82c5b61648d481c9d6de4c20b25
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java
@@ -0,0 +1,45 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Protein;
+
+/**
+ * This structure contains information about Residue for one of {@link Protein}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("RESIDUE")
+public class Residue extends AbstractSiteModification {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public Residue() {
+ super();
+ }
+
+ public Residue(Residue residue) {
+ super(residue);
+ }
+
+ /**
+ * Creates copy of the object.
+ *
+ * @return copy of the object.
+ */
+ public Residue copy() {
+ if (this.getClass() == Residue.class) {
+ return new Residue(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/RnaRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RnaRegion.java
deleted file mode 100644
index 9c5e32a201e2f8d6e4f84d40db4b6af0beab72e1..0000000000000000000000000000000000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/RnaRegion.java
+++ /dev/null
@@ -1,327 +0,0 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.Rna;
-
-/**
- * This structure contains information about rna region (rna fragment of
- * interest) for a specific {@link Rna}.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "rna_region_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-public class RnaRegion implements Serializable, ElementModification {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default {@link #size} of the region.
- */
- private static final double DEFAULT_SIZE = 0.1;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RnaRegion.class.getName());
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "iddb", unique = true, nullable = false)
- private int id;
-
- /**
- * Identifier of the region. Unique in the
- * {@link lcsb.mapviewer.model.map.model.Model}.
- */
- @Column(name = "idrnaregion")
- private String idRnaRegion = "";
- /**
- * Type of the region in the rna. There are three possible values:
- * <ul>
- * <li>Coding region,</li>
- * <li>Protein binding domain,</li>
- * <li>Modification site.</li>
- * </ul>
- */
-
- @Column(name = "type")
- private String type = "";
-
- /**
- * Defines a state of the region (for instance ubiquitinated etc).
- *
- * @see ModificationState
- */
- @Column(name = "state")
- private ModificationState state = null;
-
- /**
- * Name of the region.
- */
- @Column(name = "name")
- private String name = "";
-
- /**
- * Size of the region in the graphic representation.
- */
- @Column(name = "size")
- private double size = DEFAULT_SIZE;
-
- /**
- * Position on the species in graphic representation.
- */
- @Column(name = "pos")
- private Double pos;
-
- /**
- * Defines a species where the region belongs to.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "idSpeciesDb")
- private Rna species;
-
- /**
- * Default constructor.
- */
- public RnaRegion() {
-
- }
-
- /**
- * Creates object with the data taken from paramter region.
- *
- * @param mr
- * original {@link RnaRegion}
- */
- public RnaRegion(RnaRegion mr) {
- this.id = mr.id;
- this.idRnaRegion = mr.idRnaRegion;
- this.size = mr.size;
- setPos(mr.getPos());
- this.type = mr.type;
- this.state = mr.state;
- this.name = mr.name;
- }
-
- /**
- * Sets {@link #size}.
- *
- * @param text
- * new size value in string format
- */
- public void setSize(String text) {
- try {
- size = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
-
- }
-
- /**
- * Sets {@link #pos}.
- *
- * @param text
- * new {@link #pos} value in string format
- */
- public void setPos(String text) {
- try {
- setPos(Double.parseDouble(text));
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid pos: " + text, e);
- }
-
- }
-
- /**
- * Updates fields in the object with the data given in the parameter rna
- * region.
- *
- * @param mr
- * {@link RnaRegion} from which data will be used to update
- */
- public void update(RnaRegion mr) {
- if (this.idRnaRegion != null && !this.idRnaRegion.equals("") && !this.idRnaRegion.equals(mr.getIdRnaRegion())) {
- throw new InvalidArgumentException("Cannot update from mr with different id");
- }
- this.size = mr.getSize();
- if (mr.getState() != null) {
- this.state = mr.getState();
- }
- if (mr.getName() != null) {
- this.name = mr.getName();
- }
- if (mr.getPos() != null) {
- this.setPos(mr.getPos());
- }
-
- }
-
- @Override
- public String toString() {
- String result = "" + getIdRnaRegion() + "," + getType() + "," + getPos() + "," + getSize() + "," + getState() + ",";
- return result;
-
- }
-
- /**
- * @return the idRnaRegion
- * @see #idRnaRegion
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the idRnaRegion to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public String getIdRnaRegion() {
- return idRnaRegion;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setIdRnaRegion(String id) {
- this.idRnaRegion = id;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
- /**
- * @return the state
- * @see #state
- */
- public ModificationState getState() {
- return state;
- }
-
- /**
- * @param state
- * the state to set
- * @see #state
- */
- public void setState(ModificationState state) {
- this.state = state;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the size
- * @see #size
- */
- public double getSize() {
- return size;
- }
-
- /**
- * @param size
- * the size to set
- * @see #size
- */
- public void setSize(double size) {
- this.size = size;
- }
-
- /**
- * @return the pos
- * @see #pos
- */
- public Double getPos() {
- return pos;
- }
-
- /**
- * @param pos
- * the pos to set
- * @see #pos
- */
- public void setPos(Double pos) {
- this.pos = pos;
- }
-
- /**
- * @return the species
- * @see #species
- */
- public Rna getSpecies() {
- return species;
- }
-
- /**
- * @param species
- * the species to set
- * @see #species
- */
- public void setSpecies(Rna species) {
- this.species = species;
- }
-
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/TranscriptionSite.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/TranscriptionSite.java
new file mode 100644
index 0000000000000000000000000000000000000000..e878a893d5d2c8efbb0a7221af064282ae113313
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/TranscriptionSite.java
@@ -0,0 +1,107 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import java.io.Serializable;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This structure contains information about Transcription Site for one of the
+ * following {@link Species}:
+ * <ul>
+ * <li>{@link Gene}</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("TRANSCRIPTION_SITE")
+public class TranscriptionSite extends AbstractRegionModification implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(TranscriptionSite.class);
+
+ private String direction = null;
+
+ private Boolean active = false;
+
+ /**
+ * Default constructor.
+ */
+ public TranscriptionSite() {
+
+ }
+
+ /**
+ * Constructor that initialize object with the data from the parameter.
+ *
+ * @param original
+ * object from which we initialize data
+ */
+ public TranscriptionSite(TranscriptionSite original) {
+ super(original);
+ this.direction = original.getDirection();
+ this.active = original.getActive();
+ }
+
+ @Override
+ public void update(AbstractRegionModification mr) {
+ TranscriptionSite original = (TranscriptionSite) mr;
+ if (original.getDirection() != null) {
+ this.direction = original.getDirection();
+ }
+ if (original.getActive() != null) {
+ this.active = original.getActive();
+ }
+ }
+
+ /**
+ * Creates a copy of current object.
+ *
+ * @return copy of the object
+ */
+ public TranscriptionSite copy() {
+ if (this.getClass() == TranscriptionSite.class) {
+ return new TranscriptionSite(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+
+ }
+
+ public String getDirection() {
+ return direction;
+ }
+
+ public void setDirection(String direction) {
+ this.direction = direction;
+ }
+
+ public Boolean getActive() {
+ return active;
+ }
+
+ public void setActive(Boolean active) {
+ this.active = active;
+ }
+
+ @Override
+ public String toString() {
+ return super.toString() + "," + getActive() + "," + getDirection();
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
index bc5e5dba08c7250e48850868b56e480021de61b1..d5aba762cb692d4f3db40571f07f0a586eca8ac5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
@@ -1,277 +1,302 @@
-package lcsb.mapviewer.model.user;
-
-/**
- * This enumerate defines all possible configuration parameter that are
- * configurable by the user.
- *
- * @author Piotr Gawron
- *
- */
-public enum ConfigurationElementType {
-
- /**
- * Email address used for sending email from the system.
- */
- EMAIL_ADDRESS("E-mail address", "your.account@domain.com", ConfigurationElementEditType.EMAIL, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
-
- /**
- * Login for the email account.
- */
- EMAIL_LOGIN("E-mail server login", "your@login", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
-
- /**
- * Password for the email account.
- */
- EMAIL_PASSWORD("E-mail server password", "email.secret.password", ConfigurationElementEditType.PASSWORD, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
-
- /**
- * Address of the IMAP server.
- */
- EMAIL_IMAP_SERVER("IMAP server", "your.imap.domain.com", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
-
- /**
- * Address of the SMTP server.
- */
- EMAIL_SMTP_SERVER("SMTP server", "your.smtp.domain.com", ConfigurationElementEditType.STRING, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
-
- /**
- * Port used for SMTP connection (sending e-mails).
- */
- EMAIL_SMTP_PORT("SMTP port", "25", ConfigurationElementEditType.INTEGER, true,
- ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
-
- /**
- * Default map that should be presented if no map is selected by user side.
- */
- DEFAULT_MAP("Default Project Id", "empty", ConfigurationElementEditType.STRING, false,
- ConfigurationElementTypeGroup.SERVER_CONFIGURATION), //
-
- /**
- * Logo presented in the system.
- */
- LOGO_IMG("Logo icon", "udl.png", ConfigurationElementEditType.URL, false,
- ConfigurationElementTypeGroup.LEGEND_AND_LOGO), //
-
- /**
- * Address connected to the logo.
- */
- LOGO_LINK("Logo link (after click)", "http://wwwen.uni.lu/", ConfigurationElementEditType.URL, false,
- ConfigurationElementTypeGroup.LEGEND_AND_LOGO), //
-
- /**
- * Maximum distance (in pixels) that is allowed during finding closest element
- * on the map.
- */
- SEARCH_DISTANCE("Max distance for clicking on element (px)", "10", ConfigurationElementEditType.DOUBLE, false,
- ConfigurationElementTypeGroup.POINT_AND_CLICK),
-
- /**
- * Email used for requesting an account (in client side).
- */
- REQUEST_ACCOUNT_EMAIL("Email used for requesting an account", "your.email@domain.com",
- ConfigurationElementEditType.EMAIL, false, ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
-
- /**
- * Max number of results in search box.
- */
- SEARCH_RESULT_NUMBER("Max number of results (this value indicates the max number of elements that will be returned from search - not the number of aggregated elements in the search box).", "100", ConfigurationElementEditType.INTEGER, false,
- ConfigurationElementTypeGroup.POINT_AND_CLICK),
-
- /**
- * Google Analytics tracking ID used for statistics. This tracking ID should
- * look like "UA-000000-01". More information about tracking ID can be found
- * <a href="https://support.google.com/analytics/answer/1032385?hl=en"> here
- * </a>.
- */
- GOOGLE_ANALYTICS_IDENTIFIER("Google Analytics tracking ID used for statistics", "",
- ConfigurationElementEditType.STRING, false, ConfigurationElementTypeGroup.SERVER_CONFIGURATION),
-
- /**
- * Description of the logo presented in the system.
- */
- LOGO_TEXT("Logo description", "University of Luxembourg", ConfigurationElementEditType.STRING, false,
- ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
-
- /**
- * Domain allowed to connect via x-frame technology.
- */
- X_FRAME_DOMAIN("Domain allowed to connect via x-frame technology", "", ConfigurationElementEditType.URL, false,
- ConfigurationElementTypeGroup.SERVER_CONFIGURATION),
-
- /**
- * Relative directory (in webapps folder) where big files will be stored.
- */
- BIG_FILE_STORAGE_DIR("Path to store big files", "minerva-big/", ConfigurationElementEditType.STRING, false,
- ConfigurationElementTypeGroup.SERVER_CONFIGURATION),
-
- /**
- * File where legend 1/4 is stored.
- */
- LEGEND_FILE_1("Legend 1 image file", "resources/images/legend_a.png", ConfigurationElementEditType.URL, false,
- ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
-
- /**
- * File where legend 2/4 is stored.
- */
- LEGEND_FILE_2("Legend 2 image file", "resources/images/legend_b.png", ConfigurationElementEditType.URL, false,
- ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
-
- /**
- * File where legend 3/4 is stored.
- */
- LEGEND_FILE_3("Legend 3 image file", "resources/images/legend_c.png", ConfigurationElementEditType.URL, false,
- ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
-
- /**
- * File where legend 4/4 is stored.
- */
- LEGEND_FILE_4("Legend 4 image file", "resources/images/legend_d.png", ConfigurationElementEditType.URL, false,
- ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
-
- /**
- * File where legend 4/4 is stored.
- */
- USER_MANUAL_FILE("User manual file", "resources/other/user_guide.pdf", ConfigurationElementEditType.URL, false,
- ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
-
- /**
- * Color used for negative overlay values.
- */
- MIN_COLOR_VAL("Overlay color for negative values", "FF0000", ConfigurationElementEditType.COLOR, false,
- ConfigurationElementTypeGroup.OVERLAYS),
-
- /**
- * Color used for positive overlay values.
- */
- MAX_COLOR_VAL("Overlay color for postive values", "0000FF", ConfigurationElementEditType.COLOR, false,
- ConfigurationElementTypeGroup.OVERLAYS),
-
- /**
- * Color used for undefined overlay values.
- */
- SIMPLE_COLOR_VAL("Overlay color when no values are defined", "00FF00", ConfigurationElementEditType.COLOR, false,
- ConfigurationElementTypeGroup.OVERLAYS),
-
- /**
- * Color used for 0 overlay value.
- */
- NEUTRAL_COLOR_VAL("Overlay color for value=0", "FFFFFF", ConfigurationElementEditType.COLOR, false,
- ConfigurationElementTypeGroup.OVERLAYS),
-
- /**
- * Opacity of data overlay objects in the frontend.
- */
- OVERLAY_OPACITY("Opacity used when drwaing data overlays (value between 0.0-1.0)", "0.8",
- ConfigurationElementEditType.DOUBLE, false, ConfigurationElementTypeGroup.OVERLAYS),
-
- /**
- * Default content of the email when requesting for an account in the system.
- */
- REQUEST_ACCOUNT_DEFAULT_CONTENT("Email content used for requesting an account",
- "Dear Disease map team,\nI would like to request an account in the system.\nKind regards",
- ConfigurationElementEditType.TEXT, false, ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
-
- DEFAULT_VIEW_PROJECT("Default user privilege for: " + PrivilegeType.VIEW_PROJECT.getCommonName(), "true",
- ConfigurationElementEditType.BOOLEAN, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
-
- DEFAULT_EDIT_COMMENTS_PROJECT("Default user privilege for: " + PrivilegeType.EDIT_COMMENTS_PROJECT.getCommonName(),
- "false", ConfigurationElementEditType.BOOLEAN, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
-
- DEFAULT_LAYOUT_MANAGEMENT("Default user privilege for: " + PrivilegeType.LAYOUT_MANAGEMENT.getCommonName(), "false",
- ConfigurationElementEditType.BOOLEAN, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
-
- SHOW_REACTION_TYPE("Show reaction type when browsing map", "true",
- ConfigurationElementEditType.BOOLEAN, false, ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
-
- GOOGLE_MAPS_API_KEY("By providing this Google Maps Platform API key I declare that I am aware that "
- + "I am a Customer of the Google Maps Platform and I agree to the terms of the <a href=\"https://cloud.google.com/maps-platform/terms/\" target='_blank'>license of Google Maps Platform</a>." +
- "In particular, I warrant that neither any of the maps nor publicly available data overlays "
- + "(\"General overlays\") on this MINERVA server contain Protected Health Information (as defined in and subject to HIPAA).",
- "", ConfigurationElementEditType.STRING, false, ConfigurationElementTypeGroup.SERVER_CONFIGURATION),
-
- /**
- * Terms of use.
- */
- TERMS_OF_USE("URL of platform Terms of Use file", "", ConfigurationElementEditType.URL, false, ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
-
- ;
-
- /**
- * Default value of the configuration parameter (it will be used only when value
- * doesn't exist in the DAO).
- */
- private String defaultValue = "";
-
- /**
- * Common name used for visualization (query user).
- */
- private String commonName = "";
-
- /**
- * How we want to edit specific parameter.
- */
- private ConfigurationElementEditType editType = null;
-
- private boolean serverSide = true;
- private ConfigurationElementTypeGroup group = null;
-
- /**
- * Default constructor.
- *
- * @param commonName
- * common name used for this parameter
- * @param editType
- * type defining how we want to edit this configuration parameter
- * @param defaultVal
- * default value assigned to this parameter
- */
- ConfigurationElementType(String commonName, String defaultVal, ConfigurationElementEditType editType,
- boolean serverSide, ConfigurationElementTypeGroup group) {
- this.defaultValue = defaultVal;
- this.commonName = commonName;
- this.editType = editType;
- this.serverSide = serverSide;
- this.group = group;
- }
-
- /**
- * @return the defaultValue
- * @see #defaultValue
- */
- public String getDefaultValue() {
- return defaultValue;
- }
-
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- * @return the editType
- * @see #editType
- */
- public ConfigurationElementEditType getEditType() {
- return editType;
- }
-
- /**
- * @return the serverSide
- * @see #serverSide
- */
- public boolean isServerSide() {
- return serverSide;
- }
-
- public ConfigurationElementTypeGroup getGroup() {
- return group;
- }
-}
+package lcsb.mapviewer.model.user;
+
+/**
+ * This enumerate defines all possible configuration parameter that are
+ * configurable by the user.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ConfigurationElementType {
+
+ /**
+ * Email address used for sending email from the system.
+ */
+ EMAIL_ADDRESS("E-mail address", "your.account@domain.com", ConfigurationElementEditType.EMAIL, true,
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+
+ /**
+ * Login for the email account.
+ */
+ EMAIL_LOGIN("E-mail server login", "your@login", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+
+ /**
+ * Password for the email account.
+ */
+ EMAIL_PASSWORD("E-mail server password", "email.secret.password", ConfigurationElementEditType.PASSWORD, true,
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+
+ /**
+ * Address of the IMAP server.
+ */
+ EMAIL_IMAP_SERVER("IMAP server", "your.imap.domain.com", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+
+ /**
+ * Address of the SMTP server.
+ */
+ EMAIL_SMTP_SERVER("SMTP server", "your.smtp.domain.com", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+
+ /**
+ * Port used for SMTP connection (sending e-mails).
+ */
+ EMAIL_SMTP_PORT("SMTP port", "25", ConfigurationElementEditType.INTEGER, true,
+ ConfigurationElementTypeGroup.EMAIL_NOTIFICATION), //
+
+ /**
+ * Default map that should be presented if no map is selected by user side.
+ */
+ DEFAULT_MAP("Default Project Id", "empty", ConfigurationElementEditType.STRING, false,
+ ConfigurationElementTypeGroup.SERVER_CONFIGURATION), //
+
+ /**
+ * Logo presented in the system.
+ */
+ LOGO_IMG("Logo icon", "udl.png", ConfigurationElementEditType.URL, false,
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO), //
+
+ /**
+ * Address connected to the logo.
+ */
+ LOGO_LINK("Logo link (after click)", "http://wwwen.uni.lu/", ConfigurationElementEditType.URL, false,
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO), //
+
+ /**
+ * Maximum distance (in pixels) that is allowed during finding closest element
+ * on the map.
+ */
+ SEARCH_DISTANCE("Max distance for clicking on element (px)", "10", ConfigurationElementEditType.DOUBLE, false,
+ ConfigurationElementTypeGroup.POINT_AND_CLICK),
+
+ /**
+ * Email used for requesting an account (in client side).
+ */
+ REQUEST_ACCOUNT_EMAIL("Email used for requesting an account", "your.email@domain.com",
+ ConfigurationElementEditType.EMAIL, false, ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
+
+ /**
+ * Max number of results in search box.
+ */
+ SEARCH_RESULT_NUMBER(
+ "Max number of results (this value indicates the max number of elements that will be returned from search - not the number of aggregated elements in the search box).",
+ "100", ConfigurationElementEditType.INTEGER, false, ConfigurationElementTypeGroup.POINT_AND_CLICK),
+
+ /**
+ * Google Analytics tracking ID used for statistics. This tracking ID should
+ * look like "UA-000000-01". More information about tracking ID can be found
+ * <a href="https://support.google.com/analytics/answer/1032385?hl=en"> here
+ * </a>.
+ */
+ GOOGLE_ANALYTICS_IDENTIFIER("Google Analytics tracking ID used for statistics", "",
+ ConfigurationElementEditType.STRING, false, ConfigurationElementTypeGroup.SERVER_CONFIGURATION),
+
+ /**
+ * Description of the logo presented in the system.
+ */
+ LOGO_TEXT("Logo description", "University of Luxembourg", ConfigurationElementEditType.STRING, false,
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
+
+ /**
+ * Domain allowed to connect via x-frame technology.
+ */
+ X_FRAME_DOMAIN("Domain allowed to connect via x-frame technology", "", ConfigurationElementEditType.URL, false,
+ ConfigurationElementTypeGroup.SERVER_CONFIGURATION),
+
+ /**
+ * Relative directory (in webapps folder) where big files will be stored.
+ */
+ BIG_FILE_STORAGE_DIR("Path to store big files", "minerva-big/", ConfigurationElementEditType.STRING, false,
+ ConfigurationElementTypeGroup.SERVER_CONFIGURATION),
+
+ /**
+ * File where legend 1/4 is stored.
+ */
+ LEGEND_FILE_1("Legend 1 image file", "resources/images/legend_a.png", ConfigurationElementEditType.URL, false,
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
+
+ /**
+ * File where legend 2/4 is stored.
+ */
+ LEGEND_FILE_2("Legend 2 image file", "resources/images/legend_b.png", ConfigurationElementEditType.URL, false,
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
+
+ /**
+ * File where legend 3/4 is stored.
+ */
+ LEGEND_FILE_3("Legend 3 image file", "resources/images/legend_c.png", ConfigurationElementEditType.URL, false,
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
+
+ /**
+ * File where legend 4/4 is stored.
+ */
+ LEGEND_FILE_4("Legend 4 image file", "resources/images/legend_d.png", ConfigurationElementEditType.URL, false,
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
+
+ /**
+ * File where legend 4/4 is stored.
+ */
+ USER_MANUAL_FILE("User manual file", "resources/other/user_guide.pdf", ConfigurationElementEditType.URL, false,
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
+
+ /**
+ * Color used for negative overlay values.
+ */
+ MIN_COLOR_VAL("Overlay color for negative values", "FF0000", ConfigurationElementEditType.COLOR, false,
+ ConfigurationElementTypeGroup.OVERLAYS),
+
+ /**
+ * Color used for positive overlay values.
+ */
+ MAX_COLOR_VAL("Overlay color for postive values", "0000FF", ConfigurationElementEditType.COLOR, false,
+ ConfigurationElementTypeGroup.OVERLAYS),
+
+ /**
+ * Color used for undefined overlay values.
+ */
+ SIMPLE_COLOR_VAL("Overlay color when no values are defined", "00FF00", ConfigurationElementEditType.COLOR, false,
+ ConfigurationElementTypeGroup.OVERLAYS),
+
+ /**
+ * Color used for 0 overlay value.
+ */
+ NEUTRAL_COLOR_VAL("Overlay color for value=0", "FFFFFF", ConfigurationElementEditType.COLOR, false,
+ ConfigurationElementTypeGroup.OVERLAYS),
+
+ /**
+ * Opacity of data overlay objects in the frontend.
+ */
+ OVERLAY_OPACITY("Opacity used when drwaing data overlays (value between 0.0-1.0)", "0.8",
+ ConfigurationElementEditType.DOUBLE, false, ConfigurationElementTypeGroup.OVERLAYS),
+
+ /**
+ * Default content of the email when requesting for an account in the system.
+ */
+ REQUEST_ACCOUNT_DEFAULT_CONTENT("Email content used for requesting an account",
+ "Dear Disease map team,\nI would like to request an account in the system.\nKind regards",
+ ConfigurationElementEditType.TEXT, false, ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
+
+ DEFAULT_VIEW_PROJECT("Default user privilege for: " + PrivilegeType.VIEW_PROJECT.getCommonName(), "true",
+ ConfigurationElementEditType.BOOLEAN, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
+
+ DEFAULT_EDIT_COMMENTS_PROJECT("Default user privilege for: " + PrivilegeType.EDIT_COMMENTS_PROJECT.getCommonName(),
+ "false", ConfigurationElementEditType.BOOLEAN, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
+
+ DEFAULT_LAYOUT_MANAGEMENT("Default user privilege for: " + PrivilegeType.LAYOUT_MANAGEMENT.getCommonName(), "false",
+ ConfigurationElementEditType.BOOLEAN, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
+
+ SHOW_REACTION_TYPE("Show reaction type when browsing map", "true", ConfigurationElementEditType.BOOLEAN, false,
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
+
+ GOOGLE_MAPS_API_KEY("By providing this Google Maps Platform API key I declare that I am aware that "
+ + "I am a Customer of the Google Maps Platform and I agree to the terms of the <a href=\"https://cloud.google.com/maps-platform/terms/\" target='_blank'>license of Google Maps Platform</a>."
+ + "In particular, I warrant that neither any of the maps nor publicly available data overlays "
+ + "(\"General overlays\") on this MINERVA server contain Protected Health Information (as defined in and subject to HIPAA).",
+ "", ConfigurationElementEditType.STRING, false, ConfigurationElementTypeGroup.SERVER_CONFIGURATION),
+
+ /**
+ * Terms of use.
+ */
+ TERMS_OF_USE("URL of platform Terms of Use file", "", ConfigurationElementEditType.URL, false,
+ ConfigurationElementTypeGroup.LEGEND_AND_LOGO),
+
+ LDAP_ADDRESS("LDAP address", "", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ LDAP_PORT("LDAP port", "389", ConfigurationElementEditType.INTEGER, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ LDAP_SSL("LDAP uses SSL", "false", ConfigurationElementEditType.BOOLEAN, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ LDAP_BIND_DN("LDAP bind DN", "", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ LDAP_PASSWORD("LDAP password", "", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ LDAP_BASE_DN("LDAP base DN", "", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ LDAP_OBJECT_CLASS("LDAP filter objectClass", "*", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ LDAP_FIRST_NAME_ATTRIBUTE("LDAP first name attribute", "givenName", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ LDAP_LAST_NAME_ATTRIBUTE("LDAP last name attribute", "sn", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+ LDAP_EMAIL_ATTRIBUTE("LDAP email attribute", "mail", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION),//
+ LDAP_FILTER("LDAP filter ", "(memberof=cn=minerva,cn=groups,cn=accounts,dc=uni,dc=lu)", ConfigurationElementEditType.STRING, true,
+ ConfigurationElementTypeGroup.LDAP_CONFIGURATION), //
+
+ ;
+
+ /**
+ * Default value of the configuration parameter (it will be used only when value
+ * doesn't exist in the DAO).
+ */
+ private String defaultValue = "";
+
+ /**
+ * Common name used for visualization (query user).
+ */
+ private String commonName = "";
+
+ /**
+ * How we want to edit specific parameter.
+ */
+ private ConfigurationElementEditType editType = null;
+
+ private boolean serverSide = true;
+ private ConfigurationElementTypeGroup group = null;
+
+ /**
+ * Default constructor.
+ *
+ * @param commonName
+ * common name used for this parameter
+ * @param editType
+ * type defining how we want to edit this configuration parameter
+ * @param defaultVal
+ * default value assigned to this parameter
+ */
+ ConfigurationElementType(String commonName, String defaultVal, ConfigurationElementEditType editType,
+ boolean serverSide, ConfigurationElementTypeGroup group) {
+ this.defaultValue = defaultVal;
+ this.commonName = commonName;
+ this.editType = editType;
+ this.serverSide = serverSide;
+ this.group = group;
+ }
+
+ /**
+ * @return the defaultValue
+ * @see #defaultValue
+ */
+ public String getDefaultValue() {
+ return defaultValue;
+ }
+
+ /**
+ * @return the commonName
+ * @see #commonName
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * @return the editType
+ * @see #editType
+ */
+ public ConfigurationElementEditType getEditType() {
+ return editType;
+ }
+
+ /**
+ * @return the serverSide
+ * @see #serverSide
+ */
+ public boolean isServerSide() {
+ return serverSide;
+ }
+
+ public ConfigurationElementTypeGroup getGroup() {
+ return group;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
index baa88ee2973d221024b8e8ed3780fa01c87745b3..6ca381ccc848f511f60eb71cef88e54ea648a14c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
@@ -7,6 +7,7 @@ public enum ConfigurationElementTypeGroup {
OVERLAYS("Overlays"), //
POINT_AND_CLICK("Point and click"), //
SERVER_CONFIGURATION("Server configuration"),//
+ LDAP_CONFIGURATION("LDAP configuration"),//
;
private String commonName;
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/User.java b/model/src/main/java/lcsb/mapviewer/model/user/User.java
index fdb5e080a10f840dda1a19bc7330acf051c72602..1add1fd25fd0f31d5ee946814b9f0b82b54f7c62 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/User.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/User.java
@@ -118,8 +118,13 @@ public class User implements Serializable {
*/
private boolean removed = false;
- @Column(name="terms_of_use_consent")
- private boolean termsOfUseConsent = false;
+ /**
+ * User is connected to LDAP directory.
+ */
+ private boolean connectedToLdap = false;
+
+ @Column(name = "terms_of_use_consent")
+ private boolean termsOfUseConsent = false;
/**
* Set of user privileges.
@@ -378,4 +383,12 @@ public class User implements Serializable {
this.termsOfUseConsent = termsOfUseConsent;
}
+ public boolean isConnectedToLdap() {
+ return connectedToLdap;
+ }
+
+ public void setConnectedToLdap(boolean connectedToLdap) {
+ this.connectedToLdap = connectedToLdap;
+ }
+
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
index 690e5c3e23d2e03934ca30e16ceeedd2feede7bd..c601f66be96c713282958e1b5413a23e8d66d9fa 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
@@ -4,14 +4,15 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import java.awt.geom.Point2D;
+
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
public class AntisenseRnaComparatorTest {
@@ -77,13 +78,12 @@ public class AntisenseRnaComparatorTest {
public AntisenseRna createAntisenseRna() {
AntisenseRna result = new AntisenseRna();
- AntisenseRnaRegion region1 = new AntisenseRnaRegion();
+ CodingRegion region1 = new CodingRegion();
result.addRegion(region1);
- region1.setIdAntisenseRnaRegion("a");
+ region1.setIdModificationResidue("a");
region1.setName("name");
- region1.setPos("1");
- region1.setSize("2");
- region1.setType(AntisenseRnaRegionType.CODING_REGION);
+ region1.setPosition(new Point2D.Double(0, 1));
+ region1.setWidth(2);
return result;
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
index a6c6ec3bfb23423caa372d4515fdf251d876711f..f52284cd4f8e1d5ba73d85d9854e48c779c6c85b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
@@ -1,93 +1,94 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-
-public class AntisenseRnaTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new AntisenseRna());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- AntisenseRna original = new AntisenseRna();
- original.addRegion(new AntisenseRnaRegion());
- AntisenseRna aRna = new AntisenseRna(original);
- assertNotNull(aRna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- AntisenseRna aRna = new AntisenseRna("id");
- assertNotNull(aRna.getStringType());
-
- List<AntisenseRnaRegion> regions = new ArrayList<>();
-
- aRna.setRegions(regions);
-
- assertEquals(regions, aRna.getRegions());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- AntisenseRna aRna = new AntisenseRna().copy();
- assertNotNull(aRna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- AntisenseRna element = Mockito.spy(AntisenseRna.class);
- element.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+public class AntisenseRnaTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new AntisenseRna());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ AntisenseRna original = new AntisenseRna();
+ original.addRegion(new CodingRegion());
+ AntisenseRna aRna = new AntisenseRna(original);
+ assertNotNull(aRna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ AntisenseRna aRna = new AntisenseRna("id");
+ assertNotNull(aRna.getStringType());
+
+ List<ModificationResidue> regions = new ArrayList<>();
+
+ aRna.setRegions(regions);
+
+ assertEquals(regions, aRna.getRegions());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ AntisenseRna aRna = new AntisenseRna().copy();
+ assertNotNull(aRna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ AntisenseRna element = Mockito.spy(AntisenseRna.class);
+ element.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
index 5d41302f56152bf90f730b765d50726423ca4301..95104c0be61d61a9a7db9307787413c0661fabc1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
@@ -1,110 +1,112 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-public class GeneComparatorTest {
-
- GeneComparator comparator = new GeneComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Gene gene1 = createGene();
- Gene gene2 = createGene();
-
- assertEquals(0, comparator.compare(gene1, gene1));
-
- assertEquals(0, comparator.compare(gene1, gene2));
- assertEquals(0, comparator.compare(gene2, gene1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Gene gene1 = createGene();
- Gene gene2 = createGene();
- gene1.getModificationResidues().get(0).setName("bla");
- assertTrue(comparator.compare(gene1, gene2) != 0);
- assertTrue(comparator.compare(gene2, gene1) != 0);
-
- gene1 = createGene();
- gene2 = createGene();
- gene1.getModificationResidues().clear();
- assertTrue(comparator.compare(gene1, gene2) != 0);
- assertTrue(comparator.compare(gene2, gene1) != 0);
-
- gene1 = createGene();
- gene2 = createGene();
- assertTrue(comparator.compare(null, gene2) != 0);
- assertTrue(comparator.compare(gene2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Gene gene = createGene();
- gene.setName("n");
- assertTrue(comparator.compare(gene, gene2) != 0);
-
- assertTrue(comparator.compare(gene, Mockito.mock(Gene.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Gene createGene() {
- Gene result = new Gene();
- result.setHypothetical(true);
-
- ModificationResidue residue = new ModificationResidue();
- result.addModificationResidue(residue);
-
- residue.setIdModificationResidue("a");
- residue.setName("name");
- residue.setAngle(1.0);
- residue.setSize(2.0);
- residue.setSide("23");
- residue.setState(ModificationState.ACETYLATED);
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- Gene object = Mockito.mock(Gene.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+public class GeneComparatorTest {
+
+ GeneComparator comparator = new GeneComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Gene gene1 = createGene();
+ Gene gene2 = createGene();
+
+ assertEquals(0, comparator.compare(gene1, gene1));
+
+ assertEquals(0, comparator.compare(gene1, gene2));
+ assertEquals(0, comparator.compare(gene2, gene1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Gene gene1 = createGene();
+ Gene gene2 = createGene();
+ gene1.getModificationResidues().get(0).setName("bla");
+ assertTrue(comparator.compare(gene1, gene2) != 0);
+ assertTrue(comparator.compare(gene2, gene1) != 0);
+
+ gene1 = createGene();
+ gene2 = createGene();
+ gene1.getModificationResidues().clear();
+ assertTrue(comparator.compare(gene1, gene2) != 0);
+ assertTrue(comparator.compare(gene2, gene1) != 0);
+
+ gene1 = createGene();
+ gene2 = createGene();
+ assertTrue(comparator.compare(null, gene2) != 0);
+ assertTrue(comparator.compare(gene2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Gene gene = createGene();
+ gene.setName("n");
+ assertTrue(comparator.compare(gene, gene2) != 0);
+
+ assertTrue(comparator.compare(gene, Mockito.mock(Gene.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Gene createGene() {
+ Gene result = new Gene();
+ result.setHypothetical(true);
+
+ AbstractSiteModification residue = new ModificationSite();
+ result.addModificationResidue(residue);
+
+ residue.setIdModificationResidue("a");
+ residue.setName("name");
+ residue.setPosition(new Point2D.Double(10, 20));
+ residue.setState(ModificationState.ACETYLATED);
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Gene object = Mockito.mock(Gene.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
index ec7c48dcd1948de83831f7f46b5f41332b7af6aa..5dd200337e5c9606ec99b7c20c0d4aca07f77c9d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
@@ -1,90 +1,91 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-public class GeneTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Gene());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- Gene original = new Gene();
- original.addModificationResidue(new ModificationResidue());
- Gene gene = new Gene(original);
- assertNotNull(gene);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- List<ModificationResidue> modificationResidues = new ArrayList<>();
- Gene gene = new Gene("id");
- assertNotNull(gene.getStringType());
- gene.setModificationResidues(modificationResidues);
- assertEquals(modificationResidues, gene.getModificationResidues());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Gene degraded = new Gene().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Gene gene = Mockito.spy(Gene.class);
- gene.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+
+public class GeneTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Gene());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Gene original = new Gene();
+ original.addModificationResidue(new ModificationSite());
+ Gene gene = new Gene(original);
+ assertNotNull(gene);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ List<ModificationResidue> modificationResidues = new ArrayList<>();
+ Gene gene = new Gene("id");
+ assertNotNull(gene.getStringType());
+ gene.setModificationResidues(modificationResidues);
+ assertEquals(modificationResidues, gene.getModificationResidues());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Gene degraded = new Gene().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Gene gene = Mockito.spy(Gene.class);
+ gene.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
index 177a924e8376767b092d0b42bcd0d659ce06b228..e07e6d0e81ea684b57e326e9463dc66c13aed0b5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
@@ -1,136 +1,138 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-public class ProteinComparatorTest {
-
- ProteinComparator comparator = new ProteinComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- GenericProtein protein1 = createProtein();
- GenericProtein protein2 = createProtein();
-
- assertEquals(0, comparator.compare(protein1, protein1));
-
- assertEquals(0, comparator.compare(protein1, protein2));
- assertEquals(0, comparator.compare(protein2, protein1));
-
- assertEquals(0, comparator.compare(null, null));
-
- assertEquals(0, comparator.compare(new TruncatedProtein(), new TruncatedProtein()));
- assertEquals(0, comparator.compare(new ReceptorProtein(), new ReceptorProtein()));
- assertEquals(0, comparator.compare(new IonChannelProtein(), new IonChannelProtein()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUnknownProteinImplementations() {
- try {
- Protein protein1 = Mockito.mock(Protein.class);
- assertEquals(0, comparator.compare(protein1, protein1));
-
- fail("Exception expected");
-
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- GenericProtein protein1 = createProtein();
- GenericProtein protein2 = createProtein();
- assertTrue(comparator.compare(null, protein2) != 0);
- assertTrue(comparator.compare(protein2, null) != 0);
-
- protein1.getModificationResidues().get(0).setName("bla");
- assertTrue(comparator.compare(protein1, protein2) != 0);
- assertTrue(comparator.compare(protein2, protein1) != 0);
-
- protein1 = createProtein();
- protein2 = createProtein();
- protein1.getModificationResidues().clear();
- assertTrue(comparator.compare(protein1, protein2) != 0);
- assertTrue(comparator.compare(protein2, protein1) != 0);
-
- protein1 = createProtein();
- protein2 = createProtein();
- assertTrue(comparator.compare(null, protein2) != 0);
- assertTrue(comparator.compare(protein2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- assertTrue(comparator.compare(protein2, new GenericProtein()) != 0);
-
- protein1 = createProtein();
- protein2 = createProtein();
- protein1.setName("a");
- assertTrue(comparator.compare(protein1, protein2) != 0);
- assertTrue(comparator.compare(protein2, protein1) != 0);
-
- protein1 = createProtein();
- protein2 = createProtein();
- protein1.setStructuralState("a");
- assertTrue(comparator.compare(protein1, protein2) != 0);
- assertTrue(comparator.compare(protein2, protein1) != 0);
-
- protein1 = createProtein();
- protein2 = createProtein();
- protein1.setHomodimer(1);
- assertTrue(comparator.compare(protein1, protein2) != 0);
- assertTrue(comparator.compare(protein2, protein1) != 0);
-
- assertTrue(comparator.compare(new GenericProtein(), new TruncatedProtein()) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public GenericProtein createProtein() {
- GenericProtein result = new GenericProtein();
- result.setHomodimer(12);
- result.setStructuralState("id1");
- result.setHypothetical(true);
-
- ModificationResidue residue = new ModificationResidue();
- result.addModificationResidue(residue);
-
- residue.setIdModificationResidue("a");
- residue.setName("name");
- residue.setAngle(1.0);
- residue.setSize(2.0);
- residue.setSide("23");
- residue.setState(ModificationState.DONT_CARE);
- return result;
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
+
+public class ProteinComparatorTest {
+ Logger logger= Logger.getLogger(ProteinComparatorTest.class);
+
+ ProteinComparator comparator = new ProteinComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ GenericProtein protein1 = createProtein();
+ GenericProtein protein2 = createProtein();
+
+ assertEquals(0, comparator.compare(protein1, protein1));
+
+ assertEquals(0, comparator.compare(protein1, protein2));
+ assertEquals(0, comparator.compare(protein2, protein1));
+
+ assertEquals(0, comparator.compare(null, null));
+
+ assertEquals(0, comparator.compare(new TruncatedProtein(), new TruncatedProtein()));
+ assertEquals(0, comparator.compare(new ReceptorProtein(), new ReceptorProtein()));
+ assertEquals(0, comparator.compare(new IonChannelProtein(), new IonChannelProtein()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUnknownProteinImplementations() {
+ try {
+ Protein protein1 = Mockito.mock(Protein.class);
+ assertEquals(0, comparator.compare(protein1, protein1));
+
+ fail("Exception expected");
+
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ GenericProtein protein1 = createProtein();
+ GenericProtein protein2 = createProtein();
+ assertTrue(comparator.compare(null, protein2) != 0);
+ assertTrue(comparator.compare(protein2, null) != 0);
+
+ protein1.getModificationResidues().get(0).setName("bla");
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+
+ protein1 = createProtein();
+ protein2 = createProtein();
+ protein1.getModificationResidues().clear();
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+
+ protein1 = createProtein();
+ protein2 = createProtein();
+ assertTrue(comparator.compare(null, protein2) != 0);
+ assertTrue(comparator.compare(protein2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ assertTrue(comparator.compare(protein2, new GenericProtein()) != 0);
+
+ protein1 = createProtein();
+ protein2 = createProtein();
+ protein1.setName("a");
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+
+ protein1 = createProtein();
+ protein2 = createProtein();
+ protein1.setStructuralState("a");
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+
+ protein1 = createProtein();
+ protein2 = createProtein();
+ protein1.setHomodimer(1);
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+
+ assertTrue(comparator.compare(new GenericProtein(), new TruncatedProtein()) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public GenericProtein createProtein() {
+ GenericProtein result = new GenericProtein();
+ result.setHomodimer(12);
+ result.setStructuralState("id1");
+ result.setHypothetical(true);
+
+ Residue residue = new Residue();
+ result.addModificationResidue(residue);
+
+ residue.setIdModificationResidue("a");
+ residue.setName("name");
+ residue.setPosition(new Point2D.Double(10, 20));
+ residue.setState(ModificationState.DONT_CARE);
+ return result;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
index 0a3a22c3db5bead5e7b859bc3383ec3b2a0dfd2d..6485005ac77f0f3eeab4762ca8ebaec10ad0096b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
@@ -1,105 +1,106 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-public class ProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new GenericProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- GenericProtein protein = new GenericProtein();
- protein.setStructuralState("srt");
- List<ModificationResidue> residues = new ArrayList<>();
- residues.add(new ModificationResidue());
-
- protein.setModificationResidues(residues);
- Protein protein2 = new GenericProtein(protein);
- assertNotNull(protein2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetStructuralState() {
- try {
- GenericProtein protein = new GenericProtein();
- protein.setStructuralState("str");
- protein.setStructuralState("str1");
-
- assertEquals("str1", protein.getStructuralState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- GenericProtein protein = new GenericProtein("id");
- assertNotNull(protein.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- GenericProtein protein = new GenericProtein().copy();
- assertNotNull(protein);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- GenericProtein mock = Mockito.spy(GenericProtein.class);
- mock.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.Residue;
+
+public class ProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new GenericProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ GenericProtein protein = new GenericProtein();
+ protein.setStructuralState("srt");
+ List<ModificationResidue> residues = new ArrayList<>();
+ residues.add(new Residue());
+
+ protein.setModificationResidues(residues);
+ Protein protein2 = new GenericProtein(protein);
+ assertNotNull(protein2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetStructuralState() {
+ try {
+ GenericProtein protein = new GenericProtein();
+ protein.setStructuralState("str");
+ protein.setStructuralState("str1");
+
+ assertEquals("str1", protein.getStructuralState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ GenericProtein protein = new GenericProtein("id");
+ assertNotNull(protein.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ GenericProtein protein = new GenericProtein().copy();
+ assertNotNull(protein);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ GenericProtein mock = Mockito.spy(GenericProtein.class);
+ mock.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
index 3ead55dee76b0c53b570b725795334aed2bfa48c..59ec62d18149ad8f01eefbaed3e55a38d7d679be 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
@@ -1,108 +1,108 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-
-public class RnaComparatorTest {
-
- RnaComparator comparator = new RnaComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Rna aRna1 = createRna();
- Rna aRna2 = createRna();
-
- assertEquals(0, comparator.compare(aRna1, aRna1));
-
- assertEquals(0, comparator.compare(aRna1, aRna2));
- assertEquals(0, comparator.compare(aRna2, aRna1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Rna aRna1 = createRna();
- Rna aRna2 = createRna();
- aRna1.getRegions().get(0).setState(ModificationState.ACETYLATED);
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createRna();
- aRna2 = createRna();
- aRna1.getRegions().clear();
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createRna();
- aRna2 = createRna();
- assertTrue(comparator.compare(null, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Rna rna = createRna();
- rna.setName("n");
- assertTrue(comparator.compare(rna, aRna2) != 0);
-
- assertTrue(comparator.compare(rna, Mockito.mock(Rna.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Rna createRna() {
- Rna result = new Rna();
- result.setHypothetical(true);
-
- RnaRegion region1 = new RnaRegion();
- result.addRegion(region1);
- region1.setIdRnaRegion("a");
- region1.setState(ModificationState.DONT_CARE);
- region1.setPos("1");
- region1.setSize("2");
- region1.setType("type");
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- Rna object = Mockito.mock(Rna.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+public class RnaComparatorTest {
+
+ RnaComparator comparator = new RnaComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Rna aRna1 = createRna();
+ Rna aRna2 = createRna();
+
+ assertEquals(0, comparator.compare(aRna1, aRna1));
+
+ assertEquals(0, comparator.compare(aRna1, aRna2));
+ assertEquals(0, comparator.compare(aRna2, aRna1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Rna aRna1 = createRna();
+ Rna aRna2 = createRna();
+ aRna1.getRegions().get(0).setName("X");
+ assertTrue(comparator.compare(aRna1, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, aRna1) != 0);
+
+ aRna1 = createRna();
+ aRna2 = createRna();
+ aRna1.getRegions().clear();
+ assertTrue(comparator.compare(aRna1, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, aRna1) != 0);
+
+ aRna1 = createRna();
+ aRna2 = createRna();
+ assertTrue(comparator.compare(null, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Rna rna = createRna();
+ rna.setName("n");
+ assertTrue(comparator.compare(rna, aRna2) != 0);
+
+ assertTrue(comparator.compare(rna, Mockito.mock(Rna.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Rna createRna() {
+ Rna result = new Rna();
+ result.setHypothetical(true);
+
+ CodingRegion region1 = new CodingRegion();
+ result.addRegion(region1);
+ region1.setIdModificationResidue("a");
+ region1.setPosition(new Point2D.Double(0, 10));
+ region1.setWidth(2.0);
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Rna object = Mockito.mock(Rna.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
index 6cde518d7d1b34b28ab957e6af989c077ffc3f52..948f46dcb1d15bb69d13a8cf2e4b2f08068e51e8 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
@@ -1,105 +1,106 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-
-public class RnaTest {
- Logger logger = Logger.getLogger(RnaTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Rna());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- Rna rna = new Rna("d");
- assertNotNull(rna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Rna rna = new Rna("d");
- rna.addRegion(new RnaRegion());
- Rna rna2 = new Rna(rna);
- assertEquals(rna.getRegions().size(), rna2.getRegions().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Rna rna = new Rna(new Rna());
- assertNotNull(rna.getStringType());
- List<RnaRegion> regions = new ArrayList<>();
-
- rna.setRegions(regions);
-
- assertEquals(regions, rna.getRegions());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Rna rna = new Rna().copy();
- assertNotNull(rna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Rna object = Mockito.spy(Rna.class);
- object.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+public class RnaTest {
+ Logger logger = Logger.getLogger(RnaTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Rna());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Rna rna = new Rna("d");
+ assertNotNull(rna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Rna rna = new Rna("d");
+ rna.addRegion(new CodingRegion());
+ Rna rna2 = new Rna(rna);
+ assertEquals(rna.getRegions().size(), rna2.getRegions().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Rna rna = new Rna(new Rna());
+ assertNotNull(rna.getStringType());
+ List<ModificationResidue> regions = new ArrayList<>();
+
+ rna.setRegions(regions);
+
+ assertEquals(regions, rna.getRegions());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Rna rna = new Rna().copy();
+ assertNotNull(rna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Rna object = Mockito.spy(Rna.class);
+ object.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
index 512ff1dab965e61c18b8a36b9adea44420f8d296..ccfe28648a77f1097d3fb50b297c674baf59fc4e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
@@ -5,12 +5,11 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AntisenseRnaRegionTest.class, //
- AntisenseRnaRegionTypeTest.class, //
+@SuiteClasses({ CodingRegionTest.class, //
ModificationStateTest.class, //
- ModificationResidueTest.class, //
+ ResidueTest.class, //
PositionToCompartmentTest.class, //
- RnaRegionTest.class,//
+ ProteinBindingDomainTest.class,//
StructureTest.class,//
UniprotRecordTest.class,//
})
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java
deleted file mode 100644
index 2821caabaf1b371a94d8804c4bcd47cb40167fa4..0000000000000000000000000000000000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java
+++ /dev/null
@@ -1,173 +0,0 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-
-public class AntisenseRnaRegionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new AntisenseRnaRegion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
- AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion(antisenseRna);
- assertNotNull(antisenseRna2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
- antisenseRna.setState(ModificationState.EMPTY);
- antisenseRna.setName("as");
- antisenseRna.setPos(3.0);
- AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion();
- antisenseRna2.update(antisenseRna);
- assertEquals(antisenseRna.getState(), antisenseRna2.getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidUpdate() {
- try {
- AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
- AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion();
- antisenseRna.setIdAntisenseRnaRegion("@1");
- antisenseRna2.setIdAntisenseRnaRegion("@");
- antisenseRna2.update(antisenseRna);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- AntisenseRnaRegion region = new AntisenseRnaRegion(new AntisenseRnaRegion());
- int id = 91;
- AntisenseRna species = new AntisenseRna("id");
- double pos = 4.6;
- double size = 5.3;
- AntisenseRnaRegionType type = AntisenseRnaRegionType.CODING_REGION;
- String name = "nam";
- String idAntisenseRnaRegion = "iddd";
-
- region.setId(id);
- region.setSpecies(species);
- region.setPos(pos);
- region.setSize(size);
- region.setType(type);
- region.setName(name);
- region.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
- region.setState(ModificationState.ACETYLATED);
-
- assertEquals(id, region.getId());
- assertEquals(species, region.getSpecies());
- assertEquals(pos, region.getPos(), Configuration.EPSILON);
- assertEquals(size, region.getSize(), Configuration.EPSILON);
- assertEquals(type, region.getType());
- assertEquals(name, region.getName());
- assertEquals(idAntisenseRnaRegion, region.getIdAntisenseRnaRegion());
-
- assertEquals(ModificationState.ACETYLATED, region.getState());
-
- try {
- region.setSize("text");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
-
- try {
- region.setPos("text");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
-
- region.setSize("1.0");
- region.setPos("1.0");
- assertEquals(1.0, region.getPos(), Configuration.EPSILON);
- assertEquals(1.0, region.getSize(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToString() {
- try {
- assertNotNull(new AntisenseRnaRegion().toString());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- AntisenseRnaRegion degraded = new AntisenseRnaRegion().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new AntisenseRnaRegion() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTypeTest.java
deleted file mode 100644
index c5a7537e0ebf47c63246848b760005b0bb93a7b0..0000000000000000000000000000000000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTypeTest.java
+++ /dev/null
@@ -1,53 +0,0 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class AntisenseRnaRegionTypeTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEnum() {
- try {
- for (AntisenseRnaRegionType type : AntisenseRnaRegionType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- AntisenseRnaRegionType.valueOf(type.name());
- assertNotNull(type.getName());
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEnumGetTypeByString() {
- try {
- assertNotNull(AntisenseRnaRegionType.getTypeByString("proteinBindingDomain"));
- assertNull(AntisenseRnaRegionType.getTypeByString("antisenseRnaDomainzz"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
-}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/CodingRegionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/CodingRegionTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..42287fa3fe2efa098a2260a751252904b9557c66
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/CodingRegionTest.java
@@ -0,0 +1,147 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+
+public class CodingRegionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CodingRegion());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CodingRegion antisenseRna = new CodingRegion();
+ CodingRegion antisenseRna2 = new CodingRegion(antisenseRna);
+ assertNotNull(antisenseRna2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ CodingRegion antisenseRna = new CodingRegion();
+ antisenseRna.setName("as");
+ antisenseRna.setPosition(new Point2D.Double(10, 0));
+ CodingRegion antisenseRna2 = new CodingRegion();
+ antisenseRna2.update(antisenseRna);
+ assertEquals(antisenseRna.getName(), antisenseRna2.getName());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidUpdate() {
+ try {
+ CodingRegion antisenseRna = new CodingRegion();
+ CodingRegion antisenseRna2 = new CodingRegion();
+ antisenseRna.setIdModificationResidue("@1");
+ antisenseRna2.setIdModificationResidue("@");
+ antisenseRna2.update(antisenseRna);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ CodingRegion region = new CodingRegion(new CodingRegion());
+ int id = 91;
+ AntisenseRna species = new AntisenseRna("id");
+ Point2D position = new Point2D.Double(10, 20);
+ double width = 5.3;
+ String name = "nam";
+ String idCodingRegion = "iddd";
+
+ region.setId(id);
+ region.setSpecies(species);
+ region.setPosition(position);
+ region.setWidth(width);
+ region.setName(name);
+ region.setIdModificationResidue(idCodingRegion);
+
+ assertEquals(id, region.getId());
+ assertEquals(species, region.getSpecies());
+ assertEquals(position.distance(region.getPosition()), 0, Configuration.EPSILON);
+ assertEquals(width, region.getWidth(), Configuration.EPSILON);
+ assertEquals(name, region.getName());
+ assertEquals(idCodingRegion, region.getIdModificationResidue());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToString() {
+ try {
+ assertNotNull(new CodingRegion().toString());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CodingRegion degraded = new CodingRegion().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Mockito.mock(CodingRegion.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationResidueTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationResidueTest.java
deleted file mode 100644
index 6b839c1379ca9b15929e1bf14355a74450f52961..0000000000000000000000000000000000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationResidueTest.java
+++ /dev/null
@@ -1,61 +0,0 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ModificationResidueTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- ModificationResidue mr = new ModificationResidue();
- Species species = new GenericProtein("id");
- int id = 94;
-
- mr.setSpecies(species);
- mr.setId(id);
-
- assertEquals(species, mr.getSpecies());
- assertEquals(id, mr.getId());
- }
-
- @Test
- public void testCopy() {
- ModificationResidue mr = new ModificationResidue().copy();
- assertNotNull(mr);
- }
-
- @Test
- public void testInvalidCopy() {
- ModificationResidue mr = Mockito.spy(ModificationResidue.class);
- try {
- mr.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- }
- }
-
-}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomainTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomainTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..1211018e2de52140c3f0979573c6e3b780a43ffb
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ProteinBindingDomainTest.java
@@ -0,0 +1,100 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.Rna;
+
+public class ProteinBindingDomainTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ProteinBindingDomain());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ ProteinBindingDomain region = new ProteinBindingDomain(new ProteinBindingDomain());
+ assertNotNull(region);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ ProteinBindingDomain region = new ProteinBindingDomain();
+ ProteinBindingDomain region2 = new ProteinBindingDomain();
+ region2.setName("asd");
+ region2.setPosition(new Point2D.Double(0, 10));
+ region.update(region2);
+ assertEquals(region2.getName(), region.getName());
+ assertTrue(region2.getPosition().distance(region.getPosition()) <= Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate2() {
+ try {
+ ProteinBindingDomain region = new ProteinBindingDomain();
+ region.setIdModificationResidue("1");
+ ProteinBindingDomain region2 = new ProteinBindingDomain();
+ region2.setIdModificationResidue("2");
+ region.update(region2);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ ProteinBindingDomain region = new ProteinBindingDomain();
+ double size = 2.5;
+ int id = 58;
+ Rna species = new Rna("id");
+ region.setWidth(size);
+ region.setSpecies(species);
+ region.setId(id);
+ assertEquals(id, region.getId());
+ assertEquals(size, region.getWidth(), Configuration.EPSILON);
+ assertEquals(species, region.getSpecies());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/ResidueTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ResidueTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..ff9289bb272fc7d157b285c995a4110b309b6218
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ResidueTest.java
@@ -0,0 +1,50 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ResidueTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ Residue mr = new Residue();
+ Species species = new GenericProtein("id");
+ int id = 94;
+
+ mr.setSpecies(species);
+ mr.setId(id);
+
+ assertEquals(species, mr.getSpecies());
+ assertEquals(id, mr.getId());
+ }
+
+ @Test
+ public void testCopy() {
+ Residue mr = new Residue().copy();
+ assertNotNull(mr);
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/RnaRegionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/RnaRegionTest.java
deleted file mode 100644
index 11e0edc346820fc24d8807caa425f8ed8d7e138e..0000000000000000000000000000000000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/RnaRegionTest.java
+++ /dev/null
@@ -1,133 +0,0 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.Rna;
-
-public class RnaRegionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new RnaRegion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- RnaRegion region = new RnaRegion(new RnaRegion());
- assertNotNull(region);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetSize() {
- try {
- RnaRegion region = new RnaRegion();
- try {
- region.setSize("as");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- region.setSize("0.0");
- assertEquals(0.0, region.getSize(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetPos() {
- try {
- RnaRegion region = new RnaRegion();
- try {
- region.setPos("as");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- region.setPos("1.0");
- assertEquals(1.0, region.getPos(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- RnaRegion region = new RnaRegion();
- RnaRegion region2 = new RnaRegion();
- region2.setState(ModificationState.ACETYLATED);
- region2.setName("asd");
- region2.setPos(2.2);
- region.update(region2);
- assertEquals(region2.getName(), region.getName());
- assertEquals(region2.getPos(), region.getPos());
- assertEquals(region2.getState(), region.getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate2() {
- try {
- RnaRegion region = new RnaRegion();
- region.setIdRnaRegion("1");
- RnaRegion region2 = new RnaRegion();
- region2.setIdRnaRegion("2");
- region.update(region2);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- RnaRegion region = new RnaRegion();
- double size = 2.5;
- int id = 58;
- Rna species = new Rna("id");
- region.setSize(size);
- region.setSpecies(species);
- region.setId(id);
- assertEquals(id, region.getId());
- assertEquals(size, region.getSize(), Configuration.EPSILON);
- assertEquals(species, region.getSpecies());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index fcd3f3e28dd180b3cacaa43ffa99ac353be42ed1..f2e88b01525577ae8be00329fa34db31aff8f33b 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -20,6 +20,7 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
@@ -58,7 +59,10 @@ import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.wikipathway.model.DataNode;
import lcsb.mapviewer.wikipathway.model.Edge;
@@ -82,1045 +86,1069 @@ import lcsb.mapviewer.wikipathway.utils.Geo;
*/
public class ModelContructor {
- /**
- * CellDesigner util class used for retrieving information about modifier
- * graphics.
- */
- private ModifierTypeUtils mtu = new ModifierTypeUtils();
-
- /**
- * Default color used by complexes.
- */
- private static final Color DEFAULT_COMPLEX_ALIAS_COLOR = new Color(102, 255, 255);
-
- /**
- * How much of central line is used by and operator that joins reactants.
- */
- private static final int AND_OPERATOR_CENTRAL_LINE_RATIO = 10;
-
- /**
- * How much of central line is used by split operator that split products.
- */
- private static final int SPLIT_OPERATOR_CENTRAL_LINE_RATIO = 10;
-
- /**
- * Epsilon used for double comparison.
- */
- private static final double EPSILON = 1e-6;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ModelContructor.class);
-
- /**
- * Parser used for extracting {@link MiriamData references} from GPML model.
- */
- private BiopaxParser biopaxParser = new BiopaxParser();
-
- /**
- * List of {@link Shape#shape shapes} that are not supported to be part of a
- * {@link Complex complex}.
- */
- private static final Set<String> INALID_COMPLEX_SHAPE_CHILDREN = new HashSet<>();
-
- static {
- INALID_COMPLEX_SHAPE_CHILDREN.add("Rectangle");
- INALID_COMPLEX_SHAPE_CHILDREN.add("Oval");
- INALID_COMPLEX_SHAPE_CHILDREN.add("RoundedRectangle");
- INALID_COMPLEX_SHAPE_CHILDREN.add("Golgi Apparatus");
- INALID_COMPLEX_SHAPE_CHILDREN.add("Brace");
- INALID_COMPLEX_SHAPE_CHILDREN.add("Sarcoplasmic Reticulum");
- INALID_COMPLEX_SHAPE_CHILDREN.add("Mitochondria");
- INALID_COMPLEX_SHAPE_CHILDREN.add("Endoplasmic Reticulum");
- INALID_COMPLEX_SHAPE_CHILDREN.add("Arc");
- INALID_COMPLEX_SHAPE_CHILDREN.add("Triangle");
- INALID_COMPLEX_SHAPE_CHILDREN.add("Hexagon");
- }
-
- /**
- * This function splits {@link PolylineData} into two parts. It also assumes
- * that last segment on the left part is equal to the length of the first
- * segment on the right side.
- *
- * @param pd
- * line to split
- * @return pair of lines into which parameter was split to
- */
- protected Pair<PolylineData, PolylineData> splitPolyline(PolylineData pd) {
- PolylineData p1 = new PolylineData();
- PolylineData p2 = new PolylineData();
- p1.setColor(pd.getColor());
- p2.setColor(pd.getColor());
-
- List<Line2D> lines = pd.getLines();
- double lenght = 0.0;
- for (Line2D line : lines) {
- lenght += Geo.lineLen(line);
- }
- if (lenght > Configuration.EPSILON) {
- double tmp = 0.0;
- boolean first = true;
- for (Line2D line : lines) {
- if (tmp + Geo.lineLen(line) > lenght / 2) {
- if (first) {
- double a = (lenght / 2 - tmp) / Geo.lineLen(line);
- double x = line.getX1() + a * (line.getX2() - line.getX1());
- double y = line.getY1() + a * (line.getY2() - line.getY1());
- p1.addPoint((Point2D) line.getP1().clone());
- p1.addPoint(new Point2D.Double(x, y));
- p2.addPoint(new Point2D.Double(x, y));
- first = false;
- }
- p2.addPoint((Point2D) line.getP2().clone());
- tmp += Geo.lineLen(line);
- } else {
- p1.addPoint((Point2D) line.getP1().clone());
- tmp += Geo.lineLen(line);
- }
- }
- } else { // we have line with empty length
- p1.addPoint((Point2D) pd.getBeginPoint().clone());
- p1.addPoint((Point2D) pd.getBeginPoint().clone());
- p2.addPoint((Point2D) pd.getBeginPoint().clone());
- p2.addPoint((Point2D) pd.getBeginPoint().clone());
- }
-
- // and now make sure that we have equal distances from left and right
- double leftDist = p1.getEndPoint().distance(p1.getPoints().get(p1.getPoints().size() - 2));
- double rightDist = p2.getEndPoint().distance(p2.getPoints().get(p2.getPoints().size() - 2));
- if (Math.abs(leftDist - rightDist) > Configuration.EPSILON) {
- if (leftDist > rightDist) {
- double ratio = rightDist / leftDist;
- double dx = p1.getPoints().get(p1.getPoints().size() - 1).getX() - p1.getPoints().get(p1.getPoints().size() - 2).getX();
- double dy = p1.getPoints().get(p1.getPoints().size() - 1).getY() - p1.getPoints().get(p1.getPoints().size() - 2).getY();
- double x = p1.getPoints().get(p1.getPoints().size() - 2).getX() + dx * ratio;
- double y = p1.getPoints().get(p1.getPoints().size() - 2).getY() + dy * ratio;
- Point2D newPoint = new Point2D.Double(x, y);
- p1.addPoint(p1.getPoints().size() - 1, newPoint);
- } else {
- double ratio = leftDist / rightDist;
- double dx = p2.getPoints().get(0).getX() - p2.getPoints().get(1).getX();
- double dy = p2.getPoints().get(0).getY() - p2.getPoints().get(1).getY();
- double x = p2.getPoints().get(1).getX() + dx * ratio;
- double y = p2.getPoints().get(1).getY() + dy * ratio;
- Point2D newPoint = new Point2D.Double(x, y);
- p2.addPoint(1, newPoint);
- }
- }
- return new Pair<PolylineData, PolylineData>(p1, p2);
- }
-
- /**
- * Support class to send less parameters in functions.
- *
- * @author Jan Badura
- */
- private final class Data {
- /**
- * Map between graphId and aliases created from gpml elements.
- */
- private Map<String, Element> id2alias;
-
- /**
- * Default layer.
- */
- private Layer layer;
-
- /**
- * Default constructor.
- */
- private Data() {
- id2alias = new HashMap<String, Element>();
- layer = new Layer();
- layer.setVisible(true);
- layer.setLayerId("1");
- layer.setName("defaultLayer");
- }
- }
-
- /**
- * This function creates Species from DataNode.
- *
- * @param dataNode
- * object from which species is created
- * @param data
- * ...
- * @return {@link Species} created from input {@link DataNode}
- */
- protected Species createAlias(DataNode dataNode, Data data) {
- Species res = null;
- String type = dataNode.getType();
- if (type == null || type.equals("")) {
- type = null;
- }
-
- if (type != null && type.equalsIgnoreCase("Metabolite")) {
- res = new SimpleMolecule(dataNode.getGraphId());
- } else if (type != null && type.equalsIgnoreCase("GeneProduct")) {
- res = new Gene(dataNode.getGraphId());
- } else if (type != null && type.equalsIgnoreCase("Pathway")) {
- res = new Phenotype(dataNode.getGraphId());
- } else if (type != null && type.equalsIgnoreCase("Rna")) {
- res = new Rna(dataNode.getGraphId());
- } else if (type != null && type.equalsIgnoreCase("Protein")) {
- res = new GenericProtein(dataNode.getGraphId());
- } else if (type != null && type.equalsIgnoreCase("Complex")) {
- res = new Complex(dataNode.getGraphId());
- } else if (type != null && type.equalsIgnoreCase("None")) {
- res = new Unknown(dataNode.getGraphId());
- } else {
- logger.warn("[" + dataNode.getGraphId() + "]\tUnknown species type: " + type + ". Using Unknown");
- res = new Unknown(dataNode.getGraphId());
- }
-
- res.addMiriamData(dataNode.getReferences());
- res.setName(dataNode.getName());
- return res;
- }
-
- /**
- * This function adds ComplexSpecies to model from graph. ComplexName is set
- * as groupId from .gpml
- *
- * @param model
- * to this model complexes will be added
- * @param graph
- * gpml data model
- * @param data
- * ...
- */
- protected void addComplexSpecies(Model model, Graph graph, Data data) {
- for (Group group : graph.getGroups()) {
- Complex alias = new Complex(group.getGraphId());
- alias.setName(group.getGraphId());
- if ("Complex".equalsIgnoreCase(group.getStyle())) {
- alias.setHypothetical(false);
- } else {
- alias.setHypothetical(true);
- }
-
- Rectangle2D rec = group.getRectangle();
- if (rec == null) {
- rec = new Rectangle2D.Double(0, 0, 0, 0);
- }
- alias.setX(rec.getX());
- alias.setY(rec.getY());
- alias.setWidth(rec.getWidth());
- alias.setHeight(rec.getHeight());
- alias.setColor(DEFAULT_COMPLEX_ALIAS_COLOR);
-
- data.id2alias.put(group.getGraphId(), alias);
- model.addElement(alias);
- }
- }
-
- /**
- * This function adds Species, TextLabels, Compartments and Shapes from graph.
- *
- * @param model
- * model to which species will be added
- * @param graph
- * gpml data model
- * @param data
- * ...
- */
- protected void addElement(Model model, Graph graph, Data data) {
- for (DataNode dataNode : graph.getDataNodes()) {
- Species species = createAlias(dataNode, data);
- species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), dataNode.getBiopaxReference()));
-
- Element alias = updateAlias(dataNode, species);
-
- data.id2alias.put(dataNode.getGraphId(), alias);
- model.addElement(alias);
- }
- for (Label label : graph.getLabels()) {
- if (label.isTreatAsNode()) {
- Species species = createSpecies(label);
- species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), label.getBiopaxReference()));
-
- Element alias = updateAlias(label, species);
-
- data.id2alias.put(label.getGraphId(), alias);
- model.addElement(alias);
- } else {
- LayerText text = createText(label);
- data.layer.addLayerText(text);
- }
- }
- for (Shape shape : graph.getShapes()) {
- if (shape.isTreatAsNode()) {
- Species species = createSpecies(shape);
- species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), shape.getBiopaxReference()));
-
- Element alias = updateAlias(shape, species);
-
- data.id2alias.put(shape.getGraphId(), alias);
- model.addElement(alias);
-
- } else {
- if (!shape.isCompartment()) {
- if (shape.getShape().equalsIgnoreCase("oval")) {
- LayerOval oval = createOval(shape);
- data.layer.addLayerOval(oval);
- } else {
- LayerRect rect = createRectangle(shape);
- data.layer.addLayerRect(rect);
- }
- } else {
- Compartment compartment = new Compartment(shape.getGraphId());
- Element cmpAl = updateAlias(shape, compartment);
- model.addElement(cmpAl);
- }
- }
- }
-
- for (State state : graph.getStates()) {
- // TODO this might not work
- Element species = data.id2alias.get(state.getGraphRef());
- if (state.getType() != null) {
- ModificationResidue mr = new ModificationResidue();
- mr.setIdModificationResidue(state.getGraphId());
- mr.setState(state.getType());
- Double angle = null;
- // CHECKSTYLE:OFF during to graphical transformation
- // right side of the element
- if (state.getRelX() >= 1.0 - Configuration.EPSILON) {
- angle = 0 + (state.getRelY() + 1.0) / 2;
- // bottom side of the element
- } else if (state.getRelY() >= 1.0 - Configuration.EPSILON) {
- angle = 1 + 1 - (state.getRelX() + 1.0) / 2;
- } else if (state.getRelX() <= -1.0 + Configuration.EPSILON) {
- // left side of the element
- angle = 2 + 1 - (state.getRelY() + 1.0) / 2;
- } else if (state.getRelY() <= -1.0 + Configuration.EPSILON) {
- // top side of the element
- angle = 3 + (state.getRelX() + 1.0) / 2;
- } else {
- logger.warn(state.getWarningPrefix() + "Unknown localisation on element for modification. RelX: " + state.getRelX() + ", RelY: " + state.getRelY());
- angle = 0.0;
- }
- angle /= 4.0;
- // CHECKSTYLE:ON
- mr.setAngle(angle);
-
- if (species instanceof Protein) {
- ((Protein) species).addModificationResidue(mr);
- } else if (species instanceof Gene) {
- ((Gene) species).addModificationResidue(mr);
- } else {
- logger.warn(state.getWarningPrefix() + "state for " + species.getClass().getSimpleName() + " is not supported.");
- }
- } else if (state.getStructuralState() != null) {
- if (species instanceof Protein) {
- Protein protein = ((Protein) species);
- if (protein.getStructuralState() == null) {
- protein.setStructuralState(state.getStructuralState());
- } else {
- logger.warn(state.getWarningPrefix() + " tries to override another state: " + protein.getStructuralState());
- }
- } else {
- logger.warn(state.getWarningPrefix() + "structural state for " + species.getClass().getSimpleName() + " is not supported.");
- }
- }
- }
- }
-
- /**
- * Creates {@link LayerRect} object from {@link Shape}.
- *
- * @param shape
- * source gpml object to be transformed
- * @return {@link LayerRect} obtained from {@link Shape} object
- */
- public LayerRect createRectangle(Shape shape) {
- LayerRect rect = new LayerRect();
- Rectangle2D rec = shape.getRectangle();
- rect.setX(rec.getX());
- rect.setY(rec.getY());
- rect.setHeight(rec.getHeight());
- rect.setWidth(rec.getWidth());
- rect.setColor(shape.getColor());
- return rect;
- }
-
- /**
- * Creates {@link LayerOval} object from {@link Shape}.
- *
- * @param shape
- * source gpml object to be transformed
- * @return {@link LayerOval} obtained from {@link Shape} object
- */
- public LayerOval createOval(Shape shape) {
- LayerOval oval = new LayerOval();
- Rectangle2D rec = shape.getRectangle();
- oval.setX(rec.getX());
- oval.setY(rec.getY());
- oval.setHeight(rec.getHeight());
- oval.setWidth(rec.getWidth());
- oval.setColor(shape.getColor());
- return oval;
- }
-
- /**
- * Creates {@link LayerText} from {@link Label}.
- *
- * @param label
- * object from which result will be created
- * @return {@link LayerText} from {@link Label}
- */
- public LayerText createText(Label label) {
- Rectangle2D rec = label.getRectangle();
-
- LayerText text = new LayerText();
- text.setX(rec.getX());
- text.setY(rec.getY());
- text.setHeight(rec.getHeight());
- text.setWidth(rec.getWidth());
- text.setColor(label.getColor());
- if (text.getColor().equals(Color.WHITE)) {
- text.setColor(Color.BLACK);
- }
- text.setNotes(label.getName());
- return text;
- }
-
- /**
- * Creates alias for {@link GraphicalPathwayElement}. Type of the alias is
- * defined by the parameter {@link Species}
- *
- * @param gpmlElement
- * object from which alias will be create
- * @param alias
- * specie for which alias will be created
- * @return {@link Species} created from input {@link Label}
- */
- public Element updateAlias(GraphicalPathwayElement gpmlElement, Element alias) {
- if (alias instanceof Compartment) {
- if (((Shape) gpmlElement).getShape().equalsIgnoreCase("oval")) {
- alias = new OvalCompartment((Compartment) alias);
- } else {
- alias = new SquareCompartment((Compartment) alias);
- }
- String name = ((Shape) gpmlElement).getTextLabel();
- if (name == null) {
- name = "";
- }
- alias.setName(name);
- }
-
- Rectangle2D rec = gpmlElement.getRectangle();
- alias.setX(rec.getX());
- alias.setY(rec.getY());
- alias.setWidth(rec.getWidth());
- alias.setHeight(rec.getHeight());
- alias.setColor(gpmlElement.getFillColor());
- return alias;
- }
-
- /**
- * Creates {@link Unknown species} from {@link Label}.
- *
- * @param label
- * original label from which output should be created
- * @return {@link Unknown} object created from input {@link Label}
- */
- private Species createSpecies(Label label) {
- logger.warn(label.getWarningPrefix() + " Label cannot be part of reaction. Tranforming to Unknown");
-
- Species res = new Unknown(label.getGraphId());
- res.setName(label.getName());
- return res;
- }
-
- /**
- * Creates {@link Unknown species} from {@link Shape}.
- *
- * @param shape
- * original label from which output should be created
- * @return {@link Unknown} object created from input {@link Label}
- */
- private Species createSpecies(Shape shape) {
- logger.warn(shape.getWarningPrefix() + " Shape can not be part of reaction. Tranforming to Unknown");
-
- Species res = new Unknown(shape.getGraphId());
- res.setName(shape.getName());
- return res;
- }
-
- /**
- * This function add Species to right Complexes.
- *
- * @param graph
- * gpml data model
- * @param data
- * ...
- * @throws UnknownChildClassException
- * thrown when complex contain invalid child
- */
- protected void putSpeciesIntoComplexes(Graph graph, Data data) throws UnknownChildClassException {
- for (Group group : graph.getGroups()) {
-
- Complex complexSpecies = (Complex) data.id2alias.get(group.getGraphId());
- for (PathwayElement pe : group.getNodes()) {
- Element species = data.id2alias.get(pe.getGraphId());
- if (species != null) {
- if (species instanceof Species) {
-
- Species speciesAlias = (Species) species;
- speciesAlias.setComplex(complexSpecies);
- complexSpecies.addSpecies(speciesAlias);
- }
- // we have label
- } else if (graph.getLabelByGraphId(pe.getGraphId()) != null) {
- Label label = graph.getLabelByGraphId(pe.getGraphId());
- // if complex has generic name then change it into label
- if (complexSpecies.getName().equals(group.getGraphId())) {
- complexSpecies.setName(label.getTextLabel());
- } else {
- // if there are more labels than one then merge labels
- complexSpecies.setName(complexSpecies.getName() + "\n" + label.getTextLabel());
- }
- } else if (graph.getShapeByGraphId(pe.getGraphId()) != null) {
- Shape shape = graph.getShapeByGraphId(pe.getGraphId());
- if (INALID_COMPLEX_SHAPE_CHILDREN.contains(shape.getShape())) {
- logger.warn(shape.getWarningPrefix() + shape.getShape() + " cannot be part of a complex. Skipping.");
- } else {
- throw new UnknownChildClassException(
- "Unknown class type with id \"" + pe.getGraphId() + "\": " + shape.getShape() + ". Group id: " + group.getGraphId());
- }
- } else {
- throw new UnknownChildClassException("Cannot find child with id: " + pe.getGraphId() + ". Group id: " + group.getGraphId());
- }
- }
- }
- }
-
- /**
- * This function creates {@link Reaction} from {@link Interaction} from graph.
- *
- * @param interaction
- * gpml interaction
- * @param graph
- * gpml data model
- * @param data
- * ...
- * @return reaction created from gpml {@link Interaction}
- */
- protected Reaction createReactionFromInteraction(Interaction interaction, Graph graph, Data data) {
- InteractionMapping mapping = InteractionMapping.getInteractionMapping(interaction.getType(), interaction.getLine().getType());
- if (mapping == null) {
- throw new InvalidArgumentException("Unknown interaction type: " + interaction.getType());
- }
- Reaction reaction = createReactionByType(mapping.getModelReactionType());
- reaction.setIdReaction(interaction.getGraphId());
- reaction.setReversible(mapping.isReversible());
-
- reaction.addMiriamData(interaction.getReferences());
- for (String ref : interaction.getBiopaxReferences()) {
- BiopaxPublication publication = graph.getBiopaxData().getPublicationByReference(ref);
- MiriamData md = biopaxParser.createMiriamData(publication);
- if (md != null) {
- reaction.addMiriamData(md);
- }
- }
-
- PolylineData pd = interaction.getLine();
-
- Pair<PolylineData, PolylineData> pair = splitPolyline(pd);
- PolylineData pdfirstpart = pair.getLeft();
- PolylineData pdsecondpart = pair.getRight();
-
- Reactant reactant = new Reactant();
- reactant.setElement(data.id2alias.get(interaction.getStart()));
- reactant.setLine(pdfirstpart);
- reaction.addReactant(reactant);
-
- Product product = new Product();
- product.setElement(data.id2alias.get(interaction.getEnd()));
- product.setLine(pdsecondpart);
- reaction.addProduct(product);
-
- for (Edge e : interaction.getReactants()) {
- Reactant reac = createReactantFromEdge(data, e);
- reaction.addReactant(reac);
- }
-
- for (Edge e : interaction.getProducts()) {
- Product pro = createProductFromEdge(data, e);
- reaction.addProduct(pro);
- }
-
- double centralLength = pdfirstpart.getPoints().get(pdfirstpart.getPoints().size() - 2).distance(pdfirstpart.getEndPoint()) * 2;
-
- if (reaction.getReactants().size() > 1) {
- PolylineData operatorLine = new PolylineData();
- operatorLine.setColor(pdfirstpart.getColor());
- operatorLine.addPoint((Point2D) pdfirstpart.getEndPoint().clone());
- operatorLine.addPoint((Point2D) pdfirstpart.getEndPoint().clone());
- pdfirstpart.trimEnd(centralLength / AND_OPERATOR_CENTRAL_LINE_RATIO);
- operatorLine.setStartPoint((Point2D) pdfirstpart.getEndPoint().clone());
- NodeOperator andOperator;
- // heterodimer association use association operator
- if (reaction instanceof HeterodimerAssociationReaction) {
- andOperator = new AssociationOperator();
- // all other reaction just force and operator between inputs
- } else {
- andOperator = new AndOperator();
- }
- andOperator.addInput(reactant);
- andOperator.setLine(operatorLine);
- for (int i = 1; i < reaction.getReactants().size(); i++) {
- Reactant r = reaction.getReactants().get(i);
- r.getLine().addPoint((Point2D) pdfirstpart.getEndPoint().clone());
- andOperator.addInput(r);
- }
- reaction.addNode(andOperator);
- }
-
- if (reaction.getProducts().size() > 1) {
- PolylineData operatorLine = new PolylineData();
- operatorLine.setColor(pdsecondpart.getColor());
-
- operatorLine.addPoint((Point2D) pdsecondpart.getBeginPoint().clone());
- pdsecondpart.trimBegin(centralLength / SPLIT_OPERATOR_CENTRAL_LINE_RATIO);
- operatorLine.addPoint((Point2D) pdsecondpart.getBeginPoint().clone());
- SplitOperator splitOperator = new SplitOperator();
- splitOperator.addOutput(product);
- splitOperator.setLine(operatorLine);
- for (int i = 1; i < reaction.getProducts().size(); i++) {
- Product r = reaction.getProducts().get(i);
- r.getLine().addPoint(0, (Point2D) pdsecondpart.getBeginPoint().clone());
- splitOperator.addOutput(r);
- }
- reaction.addNode(splitOperator);
- }
-
- for (Edge e : interaction.getModifiers()) {
- Modifier mod = createModifierFromEdge(data, e);
- reaction.addModifier(mod);
- }
- if (reaction instanceof TwoReactantReactionInterface && reaction.getReactants().size() < 2) {
- logger.warn("Reaction should contain at least 2 reactants. GraphId: " + interaction.getGraphId());
- reaction = new UnknownTransitionReaction(reaction);
- }
- if (reaction instanceof ReducedNotation
- && ((reaction.getReactants().size() > 1) || reaction.getProducts().size() > 1 || reaction.getModifiers().size() > 0)) {
- logger.warn("Reaction should contain only one reactant and one product. GraphId: " + interaction.getGraphId());
- reaction = new UnknownTransitionReaction(reaction);
- }
- ReactionLineData rld = ReactionLineData.getByReactionType(reaction.getClass());
- if (rld == null) {
- throw new InvalidArgumentException("Don't know how to process reaction type: " + reaction.getClass());
- }
- for (AbstractNode node : reaction.getNodes()) {
- if (!(node instanceof Modifier)) {
- node.getLine().setType(rld.getLineType());
- }
- }
- for (Product p : reaction.getProducts()) {
- p.getLine().getEndAtd().setArrowType(rld.getProductArrowType());
- if (rld.getProductLineTrim() > 0) {
- p.getLine().trimEnd(rld.getProductLineTrim());
- }
-
- }
- if (reaction.isReversible()) {
- for (Reactant r : reaction.getReactants()) {
- r.getLine().getBeginAtd().setArrowType(rld.getProductArrowType());
- if (rld.getProductLineTrim() > 0) {
- r.getLine().trimBegin(rld.getProductLineTrim());
- }
- }
- }
-
- ModifierTypeUtils mtu = new ModifierTypeUtils();
- for (Modifier m : reaction.getModifiers()) {
- m.getLine().setEndPoint(m.getLine().getPoints().get(m.getLine().getPoints().size() - 2));
- m.getLine().setEndPoint(mtu.getAnchorPointOnReactionRect(reaction, mtu.getTargetLineIndexByModifier(m)));
- }
-
- return reaction;
- }
-
- /**
- * Creates {@link Reactant} from gpml edge.
- *
- * @param data
- * ...
- * @param e
- * edge
- * @return {@link Reactant} from gpml edge
- */
- protected Reactant createReactantFromEdge(Data data, Edge e) {
- String id = null;
- if (data.id2alias.containsKey(e.getStart())) {
- id = e.getStart();
- } else if (data.id2alias.containsKey(e.getEnd())) {
- id = e.getEnd();
- }
- if (id == null) {
- throw new InvalidStateException("This reactant is invalid");
- }
-
- Reactant reac = new Reactant();
- reac.setElement(data.id2alias.get(id));
- reac.setLine(e.getLine());
-
- // if somebody drew the reaction in reverse order (starting from reaction
- // and going to the product) then reverse the order of points: order should
- // be from reactant to the product
- if (id.equals(e.getEnd())) {
- reac.setLine(reac.getLine().reverse());
- }
- return reac;
- }
-
- /**
- * Creates {@link Product} from gpml edge.
- *
- * @param data
- * ...
- * @param e
- * edge
- * @return {@link Product} from gpml edge
- */
- protected Product createProductFromEdge(Data data, Edge e) {
- String id = null;
- if (data.id2alias.containsKey(e.getStart())) {
- id = e.getStart();
- } else if (data.id2alias.containsKey(e.getEnd())) {
- id = e.getEnd();
- }
- if (id == null) {
- throw new InvalidStateException("This product is invalid");
- }
- Product pro = new Product();
- pro.setElement(data.id2alias.get(id));
- pro.setLine(e.getLine());
- // if somebody drew the reaction in reverse order (starting from reaction
- // and going to the product) then reverse the order of points: order should
- // be from reactant to the product
- if (id.equals(e.getStart())) {
- pro.setLine(pro.getLine().reverse());
- }
- return pro;
- }
-
- /**
- * Creates {@link Modifier} from gpml edge.
- *
- * @param data
- * ...
- * @param e
- * edge
- * @return {@link Modifier} from gpml edge
- */
- protected Modifier createModifierFromEdge(Data data, Edge e) {
- InteractionMapping modifierMapping = InteractionMapping.getInteractionMapping(e.getType(), e.getLine().getType());
- if (modifierMapping == null) {
- throw new InvalidArgumentException("Unknown interaction type: " + e.getType());
- }
-
- Class<? extends ReactionNode> modifierType = null;
- String id = null;
- if (data.id2alias.containsKey(e.getStart())) {
- modifierType = modifierMapping.getModelInputReactionNodeType();
- id = e.getStart();
- } else if (data.id2alias.containsKey(e.getEnd())) {
- modifierType = modifierMapping.getModelOutputReactionNodeType();
- id = e.getEnd();
- }
- if (id == null) {
- throw new InvalidStateException("This modifier is invalid");
- }
-
- Modifier mod = createModifierByType(modifierType, (Species) data.id2alias.get(id));
-
- ModifierType mt = mtu.getModifierTypeForClazz(mod.getClass());
-
- e.getLine().setEndAtd(mt.getAtd());
- e.getLine().setType(mt.getLineType());
- mod.setLine(e.getLine());
- return mod;
- }
-
- /**
- * Creates {@link Reaction} for a given class type.
- *
- * @param reactionType
- * type of reaction to create
- * @return new instance of the reactionType
- */
- private Reaction createReactionByType(Class<? extends Reaction> reactionType) {
- try {
- Reaction result = reactionType.getConstructor().newInstance();
- return result;
- } catch (Exception e) {
- throw new InvalidArgumentException("Cannot create reaction.", e);
- }
- }
-
- /**
- * Creates {@link Modifier} for a given class type.
- *
- * @param modifierType
- * type of modifier in reaction to create
- * @param alias
- * {@link Species alias } to which modifier is attached
- * @return new instance of the modifierType
- */
- private Modifier createModifierByType(Class<? extends ReactionNode> modifierType, Species alias) {
- try {
- Modifier result = (Modifier) modifierType.getConstructor(Element.class).newInstance(alias);
- return result;
- } catch (Exception e) {
- throw new InvalidArgumentException("Cannot create modifier.", e);
- }
- }
-
- /**
- * This function creates {@link Model} from {@link Graph}.
- *
- * @param graph
- * object with data obtained from gpml
- * @return {@link Model} object representing gpml
- * @throws ConverterException
- * exception thrown when conversion from graph couldn't be performed
- *
- */
- public Model getModel(Graph graph) throws ConverterException {
- try {
- Data data = new Data();
- Model model = new ModelFullIndexed(null);
- model.setWidth(graph.getBoardWidth());
- model.setHeight(graph.getBoardHeight());
-
- model.setIdModel("1");
- model.getLayers().add(data.layer);
-
- addComplexSpecies(model, graph, data);
- addElement(model, graph, data);
- putSpeciesIntoComplexes(graph, data);
-
- for (Interaction interaction : graph.getInteractions()) {
- Reaction reaction = createReactionFromInteraction(interaction, graph, data);
- model.addReaction(reaction);
- }
-
- removeEmptyComplexes(model);
-
- fixCompartmentAliases(model);
-
- StringBuilder tmp = new StringBuilder();
- for (String string : graph.getComments()) {
- tmp.append(string + "\n");
- }
- String notes = tmp.toString();
- boolean different = false;
- do {
- String newNotes = StringEscapeUtils.unescapeHtml4(notes);
- different = newNotes.compareTo(notes) != 0;
- notes = newNotes;
- } while (different);
- if (notes != null) {
- notes = StringEscapeUtils.unescapeHtml4(notes);
- }
- model.setNotes(notes);
- StringBuilder references = new StringBuilder("");
- for (String string : graph.getBiopaxReferences()) {
- references.append(string + ", ");
- }
- if (references.length() > 0) {
- logger.warn("[Biopax, " + references.toString() + "]\tModel annotations are not supported.");
- }
-
- assignNamesToComplexes(model);
- assignNamesToCompartments(model);
-
- data.layer.addLayerLines(createLines(graph));
-
- putAliasesIntoCompartments(model);
-
- return model;
- } catch (UnknownChildClassException e) {
- throw new ConverterException(e);
- }
- }
-
- /**
- * Method that put {@link Species aliases} that are not assigned into any
- * {@link Compartment} into a proper compartment.
- *
- * @param model
- * model where aliases will be modifed
- */
- private void putAliasesIntoCompartments(Model model) {
- for (Element alias : model.getElements()) {
- if (alias.getCompartment() == null) {
- if (alias instanceof Species) {
- Compartment selectedAlias = null;
- for (Compartment cAlias : model.getCompartments()) {
- if (cAlias.cross(alias)) {
- if (selectedAlias == null) {
- selectedAlias = cAlias;
- } else if (selectedAlias.getSize() > cAlias.getSize()) {
- selectedAlias = cAlias;
- }
- }
- }
- if (selectedAlias != null) {
- selectedAlias.addElement(alias);
- }
- }
- }
- }
- }
-
- /**
- * Removes empty complexes (with size 0) from model.
- *
- * @param model
- * model where operation is performed
- */
- private void removeEmptyComplexes(Model model) {
- Set<Element> aliasesInReaction = new HashSet<>();
- for (Reaction reaction : model.getReactions()) {
- for (ReactionNode node : reaction.getReactionNodes()) {
- aliasesInReaction.add(node.getElement());
- }
- }
- List<Element> toRemove = new ArrayList<>();
- ElementUtils eu = new ElementUtils();
- for (Element alias : model.getElements()) {
- if (alias instanceof Complex) {
- Complex cAlias = (Complex) alias;
- if (cAlias.getSize() <= EPSILON && cAlias.getAllChildren().size() == 0) {
- if (aliasesInReaction.contains(alias)) {
- logger.warn(eu.getElementTag(alias) + "Empty element is invalid, but it's a part of reaction.");
- } else {
- toRemove.add(alias);
- logger.warn(eu.getElementTag(alias) + "Empty element is invalid");
- }
- }
- }
- }
- for (Element alias : toRemove) {
- model.removeElement(alias);
- }
- }
-
- /**
- * Tries to find a name to assign to complexes if complexes don't contain
- * them.
- *
- * @param model
- * model where complexes are placed
- */
- private void assignNamesToComplexes(Model model) {
- for (Element alias : model.getElements()) {
- if (alias instanceof Complex) {
- if (alias.getName() == null || (alias.getName().isEmpty())) {
- for (Layer layer : model.getLayers()) {
- LayerText toRemove = null;
- for (LayerText lt : layer.getTexts()) {
- if (alias.contains(lt)) {
- alias.setName(lt.getNotes());
- toRemove = lt;
- break;
- }
- }
- if (toRemove != null) {
- layer.removeLayerText(toRemove);
- break;
- }
- }
- }
- }
- }
- }
-
- /**
- * Tries to find a name to assign to compartments if comparments don't contain
- * them.
- *
- * @param model
- * model where compartments are placed
- */
- private void assignNamesToCompartments(Model model) {
- for (Element alias : model.getElements()) {
- if (alias instanceof Compartment) {
- if (alias.getName() == null || alias.getName().isEmpty()) {
- for (Layer layer : model.getLayers()) {
- LayerText toRemove = null;
- for (LayerText lt : layer.getTexts()) {
- if (alias.contains(lt)) {
- alias.setName(lt.getNotes());
- toRemove = lt;
- break;
- }
- }
- if (toRemove != null) {
- layer.removeLayerText(toRemove);
- break;
- }
- }
- }
- }
- }
- }
-
- /**
- * Creates list of {@link LayerLine} in the model from gpml model.
- *
- * @param graph
- * gpml model
- * @return list of {@link LayerLine}
- */
- private Collection<PolylineData> createLines(Graph graph) {
- List<PolylineData> result = new ArrayList<PolylineData>();
- for (PolylineData pd : graph.getLines()) {
- result.add(pd);
- }
- return result;
- }
-
- /**
- * By default gpml doesn't offer information about compartments structure.
- * This function fixes assignments to compartment and compartment aliases.
- *
- * @param model
- * model where assignments are fixed.
- */
- private void fixCompartmentAliases(Model model) {
- List<Compartment> aliases = model.getCompartments();
- // clear all assignments
- for (Compartment compartmentAlias : aliases) {
- compartmentAlias.getElements().clear();
- }
-
- for (Element alias : model.getElements()) {
- // elements inside complexes shouldn't be considered
- if (alias instanceof Species) {
- if (((Species) alias).getComplex() != null) {
- continue;
- }
- }
- Compartment parentAlias = null;
- for (Compartment compartmentAlias : aliases) {
- if (compartmentAlias.contains(alias)) {
- if (parentAlias == null) {
- parentAlias = compartmentAlias;
- } else if (parentAlias.getSize() > compartmentAlias.getSize()) {
- parentAlias = compartmentAlias;
- }
- }
- }
- if (parentAlias != null) {
- parentAlias.addElement(alias);
- alias.setCompartment(parentAlias);
- }
- }
- }
+ /**
+ * CellDesigner util class used for retrieving information about modifier
+ * graphics.
+ */
+ private ModifierTypeUtils mtu = new ModifierTypeUtils();
+
+ /**
+ * Default color used by complexes.
+ */
+ private static final Color DEFAULT_COMPLEX_ALIAS_COLOR = new Color(102, 255, 255);
+
+ /**
+ * How much of central line is used by and operator that joins reactants.
+ */
+ private static final int AND_OPERATOR_CENTRAL_LINE_RATIO = 10;
+
+ /**
+ * How much of central line is used by split operator that split products.
+ */
+ private static final int SPLIT_OPERATOR_CENTRAL_LINE_RATIO = 10;
+
+ /**
+ * Epsilon used for double comparison.
+ */
+ private static final double EPSILON = 1e-6;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ModelContructor.class);
+
+ /**
+ * Parser used for extracting {@link MiriamData references} from GPML model.
+ */
+ private BiopaxParser biopaxParser = new BiopaxParser();
+
+ /**
+ * List of {@link Shape#shape shapes} that are not supported to be part of a
+ * {@link Complex complex}.
+ */
+ private static final Set<String> INALID_COMPLEX_SHAPE_CHILDREN = new HashSet<>();
+
+ static {
+ INALID_COMPLEX_SHAPE_CHILDREN.add("Rectangle");
+ INALID_COMPLEX_SHAPE_CHILDREN.add("Oval");
+ INALID_COMPLEX_SHAPE_CHILDREN.add("RoundedRectangle");
+ INALID_COMPLEX_SHAPE_CHILDREN.add("Golgi Apparatus");
+ INALID_COMPLEX_SHAPE_CHILDREN.add("Brace");
+ INALID_COMPLEX_SHAPE_CHILDREN.add("Sarcoplasmic Reticulum");
+ INALID_COMPLEX_SHAPE_CHILDREN.add("Mitochondria");
+ INALID_COMPLEX_SHAPE_CHILDREN.add("Endoplasmic Reticulum");
+ INALID_COMPLEX_SHAPE_CHILDREN.add("Arc");
+ INALID_COMPLEX_SHAPE_CHILDREN.add("Triangle");
+ INALID_COMPLEX_SHAPE_CHILDREN.add("Hexagon");
+ }
+
+ /**
+ * This function splits {@link PolylineData} into two parts. It also assumes
+ * that last segment on the left part is equal to the length of the first
+ * segment on the right side.
+ *
+ * @param pd
+ * line to split
+ * @return pair of lines into which parameter was split to
+ */
+ protected Pair<PolylineData, PolylineData> splitPolyline(PolylineData pd) {
+ PolylineData p1 = new PolylineData();
+ PolylineData p2 = new PolylineData();
+ p1.setColor(pd.getColor());
+ p2.setColor(pd.getColor());
+
+ List<Line2D> lines = pd.getLines();
+ double lenght = 0.0;
+ for (Line2D line : lines) {
+ lenght += Geo.lineLen(line);
+ }
+ if (lenght > Configuration.EPSILON) {
+ double tmp = 0.0;
+ boolean first = true;
+ for (Line2D line : lines) {
+ if (tmp + Geo.lineLen(line) > lenght / 2) {
+ if (first) {
+ double a = (lenght / 2 - tmp) / Geo.lineLen(line);
+ double x = line.getX1() + a * (line.getX2() - line.getX1());
+ double y = line.getY1() + a * (line.getY2() - line.getY1());
+ p1.addPoint((Point2D) line.getP1().clone());
+ p1.addPoint(new Point2D.Double(x, y));
+ p2.addPoint(new Point2D.Double(x, y));
+ first = false;
+ }
+ p2.addPoint((Point2D) line.getP2().clone());
+ tmp += Geo.lineLen(line);
+ } else {
+ p1.addPoint((Point2D) line.getP1().clone());
+ tmp += Geo.lineLen(line);
+ }
+ }
+ } else { // we have line with empty length
+ p1.addPoint((Point2D) pd.getBeginPoint().clone());
+ p1.addPoint((Point2D) pd.getBeginPoint().clone());
+ p2.addPoint((Point2D) pd.getBeginPoint().clone());
+ p2.addPoint((Point2D) pd.getBeginPoint().clone());
+ }
+
+ // and now make sure that we have equal distances from left and right
+ double leftDist = p1.getEndPoint().distance(p1.getPoints().get(p1.getPoints().size() - 2));
+ double rightDist = p2.getEndPoint().distance(p2.getPoints().get(p2.getPoints().size() - 2));
+ if (Math.abs(leftDist - rightDist) > Configuration.EPSILON) {
+ if (leftDist > rightDist) {
+ double ratio = rightDist / leftDist;
+ double dx = p1.getPoints().get(p1.getPoints().size() - 1).getX()
+ - p1.getPoints().get(p1.getPoints().size() - 2).getX();
+ double dy = p1.getPoints().get(p1.getPoints().size() - 1).getY()
+ - p1.getPoints().get(p1.getPoints().size() - 2).getY();
+ double x = p1.getPoints().get(p1.getPoints().size() - 2).getX() + dx * ratio;
+ double y = p1.getPoints().get(p1.getPoints().size() - 2).getY() + dy * ratio;
+ Point2D newPoint = new Point2D.Double(x, y);
+ p1.addPoint(p1.getPoints().size() - 1, newPoint);
+ } else {
+ double ratio = leftDist / rightDist;
+ double dx = p2.getPoints().get(0).getX() - p2.getPoints().get(1).getX();
+ double dy = p2.getPoints().get(0).getY() - p2.getPoints().get(1).getY();
+ double x = p2.getPoints().get(1).getX() + dx * ratio;
+ double y = p2.getPoints().get(1).getY() + dy * ratio;
+ Point2D newPoint = new Point2D.Double(x, y);
+ p2.addPoint(1, newPoint);
+ }
+ }
+ return new Pair<PolylineData, PolylineData>(p1, p2);
+ }
+
+ /**
+ * Support class to send less parameters in functions.
+ *
+ * @author Jan Badura
+ */
+ private final class Data {
+ /**
+ * Map between graphId and aliases created from gpml elements.
+ */
+ private Map<String, Element> id2alias;
+
+ /**
+ * Default layer.
+ */
+ private Layer layer;
+
+ /**
+ * Default constructor.
+ */
+ private Data() {
+ id2alias = new HashMap<String, Element>();
+ layer = new Layer();
+ layer.setVisible(true);
+ layer.setLayerId("1");
+ layer.setName("defaultLayer");
+ }
+ }
+
+ /**
+ * This function creates Species from DataNode.
+ *
+ * @param dataNode
+ * object from which species is created
+ * @param data
+ * ...
+ * @return {@link Species} created from input {@link DataNode}
+ */
+ protected Species createAlias(DataNode dataNode, Data data) {
+ Species res = null;
+ String type = dataNode.getType();
+ if (type == null || type.equals("")) {
+ type = null;
+ }
+
+ if (type != null && type.equalsIgnoreCase("Metabolite")) {
+ res = new SimpleMolecule(dataNode.getGraphId());
+ } else if (type != null && type.equalsIgnoreCase("GeneProduct")) {
+ res = new Gene(dataNode.getGraphId());
+ } else if (type != null && type.equalsIgnoreCase("Pathway")) {
+ res = new Phenotype(dataNode.getGraphId());
+ } else if (type != null && type.equalsIgnoreCase("Rna")) {
+ res = new Rna(dataNode.getGraphId());
+ } else if (type != null && type.equalsIgnoreCase("Protein")) {
+ res = new GenericProtein(dataNode.getGraphId());
+ } else if (type != null && type.equalsIgnoreCase("Complex")) {
+ res = new Complex(dataNode.getGraphId());
+ } else if (type != null && type.equalsIgnoreCase("None")) {
+ res = new Unknown(dataNode.getGraphId());
+ } else {
+ logger.warn("[" + dataNode.getGraphId() + "]\tUnknown species type: " + type + ". Using Unknown");
+ res = new Unknown(dataNode.getGraphId());
+ }
+
+ res.addMiriamData(dataNode.getReferences());
+ res.setName(dataNode.getName());
+ return res;
+ }
+
+ /**
+ * This function adds ComplexSpecies to model from graph. ComplexName is set as
+ * groupId from .gpml
+ *
+ * @param model
+ * to this model complexes will be added
+ * @param graph
+ * gpml data model
+ * @param data
+ * ...
+ */
+ protected void addComplexSpecies(Model model, Graph graph, Data data) {
+ for (Group group : graph.getGroups()) {
+ Complex alias = new Complex(group.getGraphId());
+ alias.setName(group.getGraphId());
+ if ("Complex".equalsIgnoreCase(group.getStyle())) {
+ alias.setHypothetical(false);
+ } else {
+ alias.setHypothetical(true);
+ }
+
+ Rectangle2D rec = group.getRectangle();
+ if (rec == null) {
+ rec = new Rectangle2D.Double(0, 0, 0, 0);
+ }
+ alias.setX(rec.getX());
+ alias.setY(rec.getY());
+ alias.setWidth((int) rec.getWidth());
+ alias.setHeight((int) rec.getHeight());
+ alias.setColor(DEFAULT_COMPLEX_ALIAS_COLOR);
+
+ data.id2alias.put(group.getGraphId(), alias);
+ model.addElement(alias);
+ }
+ }
+
+ /**
+ * This function adds Species, TextLabels, Compartments and Shapes from graph.
+ *
+ * @param model
+ * model to which species will be added
+ * @param graph
+ * gpml data model
+ * @param data
+ * ...
+ */
+ protected void addElement(Model model, Graph graph, Data data) {
+ for (DataNode dataNode : graph.getDataNodes()) {
+ Species species = createAlias(dataNode, data);
+ species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), dataNode.getBiopaxReference()));
+
+ Element alias = updateAlias(dataNode, species);
+
+ data.id2alias.put(dataNode.getGraphId(), alias);
+ model.addElement(alias);
+ }
+ for (Label label : graph.getLabels()) {
+ if (label.isTreatAsNode()) {
+ Species species = createSpecies(label);
+ species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), label.getBiopaxReference()));
+
+ Element alias = updateAlias(label, species);
+
+ data.id2alias.put(label.getGraphId(), alias);
+ model.addElement(alias);
+ } else {
+ LayerText text = createText(label);
+ data.layer.addLayerText(text);
+ }
+ }
+ for (Shape shape : graph.getShapes()) {
+ if (shape.isTreatAsNode()) {
+ Species species = createSpecies(shape);
+ species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), shape.getBiopaxReference()));
+
+ Element alias = updateAlias(shape, species);
+
+ data.id2alias.put(shape.getGraphId(), alias);
+ model.addElement(alias);
+
+ } else {
+ if (!shape.isCompartment()) {
+ if (shape.getShape().equalsIgnoreCase("oval")) {
+ LayerOval oval = createOval(shape);
+ data.layer.addLayerOval(oval);
+ } else {
+ LayerRect rect = createRectangle(shape);
+ data.layer.addLayerRect(rect);
+ }
+ } else {
+ Compartment compartment = new Compartment(shape.getGraphId());
+ Element cmpAl = updateAlias(shape, compartment);
+ model.addElement(cmpAl);
+ }
+ }
+ }
+
+ for (State state : graph.getStates()) {
+ // TODO this might not work
+ Element species = data.id2alias.get(state.getGraphRef());
+ if (state.getType() != null) {
+ AbstractSiteModification mr = null;
+
+ if (species instanceof Protein) {
+ mr = new Residue();
+ ((Protein) species).addModificationResidue(mr);
+ } else if (species instanceof Gene) {
+ mr = new ModificationSite();
+ ((Gene) species).addModificationResidue(mr);
+ } else {
+ logger.warn(
+ state.getWarningPrefix() + "state for " + species.getClass().getSimpleName() + " is not supported.");
+ }
+ if (mr != null) {
+ mr.setIdModificationResidue(state.getGraphId());
+ mr.setState(state.getType());
+
+ Double x = state.getRelX() * species.getWidth() / 2 + species.getCenterX();
+ Double y = state.getRelY() * species.getHeight() / 2 + species.getCenterY();
+ mr.setPosition(new Point2D.Double(x, y));
+ adjustModificationCoordinates(species);
+ }
+ } else if (state.getStructuralState() != null) {
+ if (species instanceof Protein) {
+ Protein protein = ((Protein) species);
+ if (protein.getStructuralState() == null) {
+ protein.setStructuralState(state.getStructuralState());
+ } else {
+ logger.warn(state.getWarningPrefix() + " tries to override another state: " + protein.getStructuralState());
+ }
+ } else {
+ logger.warn(state.getWarningPrefix() + "structural state for " + species.getClass().getSimpleName()
+ + " is not supported.");
+ }
+ }
+ }
+ }
+
+ /**
+ * {@link ModificationResidue} in element might have slightly off coordinates
+ * (due to different symbol shapes). For that we need to align them to match our
+ * model.
+ *
+ * @param species
+ */
+ protected void adjustModificationCoordinates(Element species) {
+ if (species instanceof Protein) {
+ Protein protein = (Protein) species;
+ if (protein.getModificationResidues().size() > 0) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(species, true);
+ for (ModificationResidue mr : protein.getModificationResidues()) {
+ double angle = converter.getAngleForPoint(species, mr.getPosition());
+ mr.setPosition(converter.getResidueCoordinates(species, angle));
+ }
+ }
+ } else if (species instanceof Gene) {
+ Gene gene = (Gene) species;
+ if (gene.getModificationResidues().size() > 0) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(species, true);
+ for (ModificationResidue mr : gene.getModificationResidues()) {
+ double angle = converter.getAngleForPoint(species, mr.getPosition());
+ mr.setPosition(converter.getResidueCoordinates(species, angle));
+ }
+ }
+
+ }
+ }
+
+ /**
+ * Creates {@link LayerRect} object from {@link Shape}.
+ *
+ * @param shape
+ * source gpml object to be transformed
+ * @return {@link LayerRect} obtained from {@link Shape} object
+ */
+ public LayerRect createRectangle(Shape shape) {
+ LayerRect rect = new LayerRect();
+ Rectangle2D rec = shape.getRectangle();
+ rect.setX(rec.getX());
+ rect.setY(rec.getY());
+ rect.setHeight(rec.getHeight());
+ rect.setWidth(rec.getWidth());
+ rect.setColor(shape.getColor());
+ return rect;
+ }
+
+ /**
+ * Creates {@link LayerOval} object from {@link Shape}.
+ *
+ * @param shape
+ * source gpml object to be transformed
+ * @return {@link LayerOval} obtained from {@link Shape} object
+ */
+ public LayerOval createOval(Shape shape) {
+ LayerOval oval = new LayerOval();
+ Rectangle2D rec = shape.getRectangle();
+ oval.setX(rec.getX());
+ oval.setY(rec.getY());
+ oval.setHeight(rec.getHeight());
+ oval.setWidth(rec.getWidth());
+ oval.setColor(shape.getColor());
+ return oval;
+ }
+
+ /**
+ * Creates {@link LayerText} from {@link Label}.
+ *
+ * @param label
+ * object from which result will be created
+ * @return {@link LayerText} from {@link Label}
+ */
+ public LayerText createText(Label label) {
+ Rectangle2D rec = label.getRectangle();
+
+ LayerText text = new LayerText();
+ text.setX(rec.getX());
+ text.setY(rec.getY());
+ text.setHeight(rec.getHeight());
+ text.setWidth(rec.getWidth());
+ text.setColor(label.getColor());
+ if (text.getColor().equals(Color.WHITE)) {
+ text.setColor(Color.BLACK);
+ }
+ text.setNotes(label.getName());
+ return text;
+ }
+
+ /**
+ * Creates alias for {@link GraphicalPathwayElement}. Type of the alias is
+ * defined by the parameter {@link Species}
+ *
+ * @param gpmlElement
+ * object from which alias will be create
+ * @param alias
+ * specie for which alias will be created
+ * @return {@link Species} created from input {@link Label}
+ */
+ public Element updateAlias(GraphicalPathwayElement gpmlElement, Element alias) {
+ if (alias instanceof Compartment) {
+ if (((Shape) gpmlElement).getShape().equalsIgnoreCase("oval")) {
+ alias = new OvalCompartment((Compartment) alias);
+ } else {
+ alias = new SquareCompartment((Compartment) alias);
+ }
+ String name = ((Shape) gpmlElement).getTextLabel();
+ if (name == null) {
+ name = "";
+ }
+ alias.setName(name);
+ }
+
+ Rectangle2D rec = gpmlElement.getRectangle();
+ alias.setX(rec.getX());
+ alias.setY(rec.getY());
+ alias.setWidth((int) rec.getWidth());
+ alias.setHeight((int) rec.getHeight());
+ alias.setColor(gpmlElement.getFillColor());
+ return alias;
+ }
+
+ /**
+ * Creates {@link Unknown species} from {@link Label}.
+ *
+ * @param label
+ * original label from which output should be created
+ * @return {@link Unknown} object created from input {@link Label}
+ */
+ private Species createSpecies(Label label) {
+ logger.warn(label.getWarningPrefix() + " Label cannot be part of reaction. Tranforming to Unknown");
+
+ Species res = new Unknown(label.getGraphId());
+ res.setName(label.getName());
+ return res;
+ }
+
+ /**
+ * Creates {@link Unknown species} from {@link Shape}.
+ *
+ * @param shape
+ * original label from which output should be created
+ * @return {@link Unknown} object created from input {@link Label}
+ */
+ private Species createSpecies(Shape shape) {
+ logger.warn(shape.getWarningPrefix() + " Shape can not be part of reaction. Tranforming to Unknown");
+
+ Species res = new Unknown(shape.getGraphId());
+ res.setName(shape.getName());
+ return res;
+ }
+
+ /**
+ * This function add Species to right Complexes.
+ *
+ * @param graph
+ * gpml data model
+ * @param data
+ * ...
+ * @throws UnknownChildClassException
+ * thrown when complex contain invalid child
+ */
+ protected void putSpeciesIntoComplexes(Graph graph, Data data) throws UnknownChildClassException {
+ for (Group group : graph.getGroups()) {
+
+ Complex complexSpecies = (Complex) data.id2alias.get(group.getGraphId());
+ for (PathwayElement pe : group.getNodes()) {
+ Element species = data.id2alias.get(pe.getGraphId());
+ if (species != null) {
+ if (species instanceof Species) {
+
+ Species speciesAlias = (Species) species;
+ speciesAlias.setComplex(complexSpecies);
+ complexSpecies.addSpecies(speciesAlias);
+ }
+ // we have label
+ } else if (graph.getLabelByGraphId(pe.getGraphId()) != null) {
+ Label label = graph.getLabelByGraphId(pe.getGraphId());
+ // if complex has generic name then change it into label
+ if (complexSpecies.getName().equals(group.getGraphId())) {
+ complexSpecies.setName(label.getTextLabel());
+ } else {
+ // if there are more labels than one then merge labels
+ complexSpecies.setName(complexSpecies.getName() + "\n" + label.getTextLabel());
+ }
+ } else if (graph.getShapeByGraphId(pe.getGraphId()) != null) {
+ Shape shape = graph.getShapeByGraphId(pe.getGraphId());
+ if (INALID_COMPLEX_SHAPE_CHILDREN.contains(shape.getShape())) {
+ logger.warn(shape.getWarningPrefix() + shape.getShape() + " cannot be part of a complex. Skipping.");
+ } else {
+ throw new UnknownChildClassException("Unknown class type with id \"" + pe.getGraphId() + "\": "
+ + shape.getShape() + ". Group id: " + group.getGraphId());
+ }
+ } else {
+ throw new UnknownChildClassException(
+ "Cannot find child with id: " + pe.getGraphId() + ". Group id: " + group.getGraphId());
+ }
+ }
+ }
+ }
+
+ /**
+ * This function creates {@link Reaction} from {@link Interaction} from graph.
+ *
+ * @param interaction
+ * gpml interaction
+ * @param graph
+ * gpml data model
+ * @param data
+ * ...
+ * @return reaction created from gpml {@link Interaction}
+ */
+ protected Reaction createReactionFromInteraction(Interaction interaction, Graph graph, Data data) {
+ InteractionMapping mapping = InteractionMapping.getInteractionMapping(interaction.getType(),
+ interaction.getLine().getType());
+ if (mapping == null) {
+ throw new InvalidArgumentException("Unknown interaction type: " + interaction.getType());
+ }
+ Reaction reaction = createReactionByType(mapping.getModelReactionType());
+ reaction.setIdReaction(interaction.getGraphId());
+ reaction.setReversible(mapping.isReversible());
+
+ reaction.addMiriamData(interaction.getReferences());
+ for (String ref : interaction.getBiopaxReferences()) {
+ BiopaxPublication publication = graph.getBiopaxData().getPublicationByReference(ref);
+ MiriamData md = biopaxParser.createMiriamData(publication);
+ if (md != null) {
+ reaction.addMiriamData(md);
+ }
+ }
+
+ PolylineData pd = interaction.getLine();
+
+ Pair<PolylineData, PolylineData> pair = splitPolyline(pd);
+ PolylineData pdfirstpart = pair.getLeft();
+ PolylineData pdsecondpart = pair.getRight();
+
+ Reactant reactant = new Reactant();
+ reactant.setElement(data.id2alias.get(interaction.getStart()));
+ reactant.setLine(pdfirstpart);
+ reaction.addReactant(reactant);
+
+ Product product = new Product();
+ product.setElement(data.id2alias.get(interaction.getEnd()));
+ product.setLine(pdsecondpart);
+ reaction.addProduct(product);
+
+ for (Edge e : interaction.getReactants()) {
+ Reactant reac = createReactantFromEdge(data, e);
+ reaction.addReactant(reac);
+ }
+
+ for (Edge e : interaction.getProducts()) {
+ Product pro = createProductFromEdge(data, e);
+ reaction.addProduct(pro);
+ }
+
+ double centralLength = pdfirstpart.getPoints().get(pdfirstpart.getPoints().size() - 2)
+ .distance(pdfirstpart.getEndPoint()) * 2;
+
+ if (reaction.getReactants().size() > 1) {
+ PolylineData operatorLine = new PolylineData();
+ operatorLine.setColor(pdfirstpart.getColor());
+ operatorLine.addPoint((Point2D) pdfirstpart.getEndPoint().clone());
+ operatorLine.addPoint((Point2D) pdfirstpart.getEndPoint().clone());
+ pdfirstpart.trimEnd(centralLength / AND_OPERATOR_CENTRAL_LINE_RATIO);
+ operatorLine.setStartPoint((Point2D) pdfirstpart.getEndPoint().clone());
+ NodeOperator andOperator;
+ // heterodimer association use association operator
+ if (reaction instanceof HeterodimerAssociationReaction) {
+ andOperator = new AssociationOperator();
+ // all other reaction just force and operator between inputs
+ } else {
+ andOperator = new AndOperator();
+ }
+ andOperator.addInput(reactant);
+ andOperator.setLine(operatorLine);
+ for (int i = 1; i < reaction.getReactants().size(); i++) {
+ Reactant r = reaction.getReactants().get(i);
+ r.getLine().addPoint((Point2D) pdfirstpart.getEndPoint().clone());
+ andOperator.addInput(r);
+ }
+ reaction.addNode(andOperator);
+ }
+
+ if (reaction.getProducts().size() > 1) {
+ PolylineData operatorLine = new PolylineData();
+ operatorLine.setColor(pdsecondpart.getColor());
+
+ operatorLine.addPoint((Point2D) pdsecondpart.getBeginPoint().clone());
+ pdsecondpart.trimBegin(centralLength / SPLIT_OPERATOR_CENTRAL_LINE_RATIO);
+ operatorLine.addPoint((Point2D) pdsecondpart.getBeginPoint().clone());
+ SplitOperator splitOperator = new SplitOperator();
+ splitOperator.addOutput(product);
+ splitOperator.setLine(operatorLine);
+ for (int i = 1; i < reaction.getProducts().size(); i++) {
+ Product r = reaction.getProducts().get(i);
+ r.getLine().addPoint(0, (Point2D) pdsecondpart.getBeginPoint().clone());
+ splitOperator.addOutput(r);
+ }
+ reaction.addNode(splitOperator);
+ }
+
+ for (Edge e : interaction.getModifiers()) {
+ Modifier mod = createModifierFromEdge(data, e);
+ reaction.addModifier(mod);
+ }
+ if (reaction instanceof TwoReactantReactionInterface && reaction.getReactants().size() < 2) {
+ logger.warn("Reaction should contain at least 2 reactants. GraphId: " + interaction.getGraphId());
+ reaction = new UnknownTransitionReaction(reaction);
+ }
+ if (reaction instanceof ReducedNotation && ((reaction.getReactants().size() > 1)
+ || reaction.getProducts().size() > 1 || reaction.getModifiers().size() > 0)) {
+ logger.warn("Reaction should contain only one reactant and one product. GraphId: " + interaction.getGraphId());
+ reaction = new UnknownTransitionReaction(reaction);
+ }
+ ReactionLineData rld = ReactionLineData.getByReactionType(reaction.getClass());
+ if (rld == null) {
+ throw new InvalidArgumentException("Don't know how to process reaction type: " + reaction.getClass());
+ }
+ for (AbstractNode node : reaction.getNodes()) {
+ if (!(node instanceof Modifier)) {
+ node.getLine().setType(rld.getLineType());
+ }
+ }
+ for (Product p : reaction.getProducts()) {
+ p.getLine().getEndAtd().setArrowType(rld.getProductArrowType());
+ if (rld.getProductLineTrim() > 0) {
+ p.getLine().trimEnd(rld.getProductLineTrim());
+ }
+
+ }
+ if (reaction.isReversible()) {
+ for (Reactant r : reaction.getReactants()) {
+ r.getLine().getBeginAtd().setArrowType(rld.getProductArrowType());
+ if (rld.getProductLineTrim() > 0) {
+ r.getLine().trimBegin(rld.getProductLineTrim());
+ }
+ }
+ }
+
+ ModifierTypeUtils mtu = new ModifierTypeUtils();
+ for (Modifier m : reaction.getModifiers()) {
+ m.getLine().setEndPoint(m.getLine().getPoints().get(m.getLine().getPoints().size() - 2));
+ m.getLine().setEndPoint(mtu.getAnchorPointOnReactionRect(reaction, mtu.getTargetLineIndexByModifier(m)));
+ }
+
+ return reaction;
+ }
+
+ /**
+ * Creates {@link Reactant} from gpml edge.
+ *
+ * @param data
+ * ...
+ * @param e
+ * edge
+ * @return {@link Reactant} from gpml edge
+ */
+ protected Reactant createReactantFromEdge(Data data, Edge e) {
+ String id = null;
+ if (data.id2alias.containsKey(e.getStart())) {
+ id = e.getStart();
+ } else if (data.id2alias.containsKey(e.getEnd())) {
+ id = e.getEnd();
+ }
+ if (id == null) {
+ throw new InvalidStateException("This reactant is invalid");
+ }
+
+ Reactant reac = new Reactant();
+ reac.setElement(data.id2alias.get(id));
+ reac.setLine(e.getLine());
+
+ // if somebody drew the reaction in reverse order (starting from reaction
+ // and going to the product) then reverse the order of points: order should
+ // be from reactant to the product
+ if (id.equals(e.getEnd())) {
+ reac.setLine(reac.getLine().reverse());
+ }
+ return reac;
+ }
+
+ /**
+ * Creates {@link Product} from gpml edge.
+ *
+ * @param data
+ * ...
+ * @param e
+ * edge
+ * @return {@link Product} from gpml edge
+ */
+ protected Product createProductFromEdge(Data data, Edge e) {
+ String id = null;
+ if (data.id2alias.containsKey(e.getStart())) {
+ id = e.getStart();
+ } else if (data.id2alias.containsKey(e.getEnd())) {
+ id = e.getEnd();
+ }
+ if (id == null) {
+ throw new InvalidStateException("This product is invalid");
+ }
+ Product pro = new Product();
+ pro.setElement(data.id2alias.get(id));
+ pro.setLine(e.getLine());
+ // if somebody drew the reaction in reverse order (starting from reaction
+ // and going to the product) then reverse the order of points: order should
+ // be from reactant to the product
+ if (id.equals(e.getStart())) {
+ pro.setLine(pro.getLine().reverse());
+ }
+ return pro;
+ }
+
+ /**
+ * Creates {@link Modifier} from gpml edge.
+ *
+ * @param data
+ * ...
+ * @param e
+ * edge
+ * @return {@link Modifier} from gpml edge
+ */
+ protected Modifier createModifierFromEdge(Data data, Edge e) {
+ InteractionMapping modifierMapping = InteractionMapping.getInteractionMapping(e.getType(), e.getLine().getType());
+ if (modifierMapping == null) {
+ throw new InvalidArgumentException("Unknown interaction type: " + e.getType());
+ }
+
+ Class<? extends ReactionNode> modifierType = null;
+ String id = null;
+ if (data.id2alias.containsKey(e.getStart())) {
+ modifierType = modifierMapping.getModelInputReactionNodeType();
+ id = e.getStart();
+ } else if (data.id2alias.containsKey(e.getEnd())) {
+ modifierType = modifierMapping.getModelOutputReactionNodeType();
+ id = e.getEnd();
+ }
+ if (id == null) {
+ throw new InvalidStateException("This modifier is invalid");
+ }
+
+ Modifier mod = createModifierByType(modifierType, (Species) data.id2alias.get(id));
+
+ ModifierType mt = mtu.getModifierTypeForClazz(mod.getClass());
+
+ e.getLine().setEndAtd(mt.getAtd());
+ e.getLine().setType(mt.getLineType());
+ mod.setLine(e.getLine());
+ return mod;
+ }
+
+ /**
+ * Creates {@link Reaction} for a given class type.
+ *
+ * @param reactionType
+ * type of reaction to create
+ * @return new instance of the reactionType
+ */
+ private Reaction createReactionByType(Class<? extends Reaction> reactionType) {
+ try {
+ Reaction result = reactionType.getConstructor().newInstance();
+ return result;
+ } catch (Exception e) {
+ throw new InvalidArgumentException("Cannot create reaction.", e);
+ }
+ }
+
+ /**
+ * Creates {@link Modifier} for a given class type.
+ *
+ * @param modifierType
+ * type of modifier in reaction to create
+ * @param alias
+ * {@link Species alias } to which modifier is attached
+ * @return new instance of the modifierType
+ */
+ private Modifier createModifierByType(Class<? extends ReactionNode> modifierType, Species alias) {
+ try {
+ Modifier result = (Modifier) modifierType.getConstructor(Element.class).newInstance(alias);
+ return result;
+ } catch (Exception e) {
+ throw new InvalidArgumentException("Cannot create modifier.", e);
+ }
+ }
+
+ /**
+ * This function creates {@link Model} from {@link Graph}.
+ *
+ * @param graph
+ * object with data obtained from gpml
+ * @return {@link Model} object representing gpml
+ * @throws ConverterException
+ * exception thrown when conversion from graph couldn't be performed
+ *
+ */
+ public Model getModel(Graph graph) throws ConverterException {
+ try {
+ Data data = new Data();
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(graph.getBoardWidth());
+ model.setHeight(graph.getBoardHeight());
+
+ model.setIdModel("1");
+ model.getLayers().add(data.layer);
+
+ addComplexSpecies(model, graph, data);
+ addElement(model, graph, data);
+ putSpeciesIntoComplexes(graph, data);
+
+ for (Interaction interaction : graph.getInteractions()) {
+ Reaction reaction = createReactionFromInteraction(interaction, graph, data);
+ model.addReaction(reaction);
+ }
+
+ removeEmptyComplexes(model);
+
+ fixCompartmentAliases(model);
+
+ StringBuilder tmp = new StringBuilder();
+ for (String string : graph.getComments()) {
+ tmp.append(string + "\n");
+ }
+ String notes = tmp.toString();
+ boolean different = false;
+ do {
+ String newNotes = StringEscapeUtils.unescapeHtml4(notes);
+ different = newNotes.compareTo(notes) != 0;
+ notes = newNotes;
+ } while (different);
+ if (notes != null) {
+ notes = StringEscapeUtils.unescapeHtml4(notes);
+ }
+ model.setNotes(notes);
+ StringBuilder references = new StringBuilder("");
+ for (String string : graph.getBiopaxReferences()) {
+ references.append(string + ", ");
+ }
+ if (references.length() > 0) {
+ logger.warn("[Biopax, " + references.toString() + "]\tModel annotations are not supported.");
+ }
+
+ assignNamesToComplexes(model);
+ assignNamesToCompartments(model);
+
+ data.layer.addLayerLines(createLines(graph));
+
+ putAliasesIntoCompartments(model);
+
+ return model;
+ } catch (UnknownChildClassException e) {
+ throw new ConverterException(e);
+ }
+ }
+
+ /**
+ * Method that put {@link Species aliases} that are not assigned into any
+ * {@link Compartment} into a proper compartment.
+ *
+ * @param model
+ * model where aliases will be modifed
+ */
+ private void putAliasesIntoCompartments(Model model) {
+ for (Element alias : model.getElements()) {
+ if (alias.getCompartment() == null) {
+ if (alias instanceof Species) {
+ Compartment selectedAlias = null;
+ for (Compartment cAlias : model.getCompartments()) {
+ if (cAlias.cross(alias)) {
+ if (selectedAlias == null) {
+ selectedAlias = cAlias;
+ } else if (selectedAlias.getSize() > cAlias.getSize()) {
+ selectedAlias = cAlias;
+ }
+ }
+ }
+ if (selectedAlias != null) {
+ selectedAlias.addElement(alias);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Removes empty complexes (with size 0) from model.
+ *
+ * @param model
+ * model where operation is performed
+ */
+ private void removeEmptyComplexes(Model model) {
+ Set<Element> aliasesInReaction = new HashSet<>();
+ for (Reaction reaction : model.getReactions()) {
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ aliasesInReaction.add(node.getElement());
+ }
+ }
+ List<Element> toRemove = new ArrayList<>();
+ ElementUtils eu = new ElementUtils();
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Complex) {
+ Complex cAlias = (Complex) alias;
+ if (cAlias.getSize() <= EPSILON && cAlias.getAllChildren().size() == 0) {
+ if (aliasesInReaction.contains(alias)) {
+ logger.warn(eu.getElementTag(alias) + "Empty element is invalid, but it's a part of reaction.");
+ } else {
+ toRemove.add(alias);
+ logger.warn(eu.getElementTag(alias) + "Empty element is invalid");
+ }
+ }
+ }
+ }
+ for (Element alias : toRemove) {
+ model.removeElement(alias);
+ }
+ }
+
+ /**
+ * Tries to find a name to assign to complexes if complexes don't contain them.
+ *
+ * @param model
+ * model where complexes are placed
+ */
+ private void assignNamesToComplexes(Model model) {
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Complex) {
+ if (alias.getName() == null || (alias.getName().isEmpty())) {
+ for (Layer layer : model.getLayers()) {
+ LayerText toRemove = null;
+ for (LayerText lt : layer.getTexts()) {
+ if (alias.contains(lt)) {
+ alias.setName(lt.getNotes());
+ toRemove = lt;
+ break;
+ }
+ }
+ if (toRemove != null) {
+ layer.removeLayerText(toRemove);
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Tries to find a name to assign to compartments if comparments don't contain
+ * them.
+ *
+ * @param model
+ * model where compartments are placed
+ */
+ private void assignNamesToCompartments(Model model) {
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Compartment) {
+ if (alias.getName() == null || alias.getName().isEmpty()) {
+ for (Layer layer : model.getLayers()) {
+ LayerText toRemove = null;
+ for (LayerText lt : layer.getTexts()) {
+ if (alias.contains(lt)) {
+ alias.setName(lt.getNotes());
+ toRemove = lt;
+ break;
+ }
+ }
+ if (toRemove != null) {
+ layer.removeLayerText(toRemove);
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Creates list of {@link LayerLine} in the model from gpml model.
+ *
+ * @param graph
+ * gpml model
+ * @return list of {@link LayerLine}
+ */
+ private Collection<PolylineData> createLines(Graph graph) {
+ List<PolylineData> result = new ArrayList<PolylineData>();
+ for (PolylineData pd : graph.getLines()) {
+ result.add(pd);
+ }
+ return result;
+ }
+
+ /**
+ * By default gpml doesn't offer information about compartments structure. This
+ * function fixes assignments to compartment and compartment aliases.
+ *
+ * @param model
+ * model where assignments are fixed.
+ */
+ private void fixCompartmentAliases(Model model) {
+ List<Compartment> aliases = model.getCompartments();
+ // clear all assignments
+ for (Compartment compartmentAlias : aliases) {
+ compartmentAlias.getElements().clear();
+ }
+
+ for (Element alias : model.getElements()) {
+ // elements inside complexes shouldn't be considered
+ if (alias instanceof Species) {
+ if (((Species) alias).getComplex() != null) {
+ continue;
+ }
+ }
+ Compartment parentAlias = null;
+ for (Compartment compartmentAlias : aliases) {
+ if (compartmentAlias.contains(alias)) {
+ if (parentAlias == null) {
+ parentAlias = compartmentAlias;
+ } else if (parentAlias.getSize() > compartmentAlias.getSize()) {
+ parentAlias = compartmentAlias;
+ }
+ }
+ }
+ if (parentAlias != null) {
+ parentAlias.addElement(alias);
+ alias.setCompartment(parentAlias);
+ }
+ }
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index 63d7d4c0cc8cb5b99e9ade47cf4025e4d11a4000..4a32fc7fb2b20eb25f0d94eead4982f921e54edd 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -30,662 +30,664 @@ import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
public class GPMLToModelTest extends WikipathwaysTestFunctions {
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(GPMLToModelTest.class);
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(GPMLToModelTest.class);
- private ModelComparator mc = new ModelComparator(1.0);
+ private ModelComparator mc = new ModelComparator(1.0);
- @Test
- public void DopamineTest() throws Exception {
- try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "Dopamine.gpml";
+ @Test
+ public void DopamineTest() throws Exception {
+ try {
+ String pathToFile = "testFiles/wikipathways/";
+ String fileName = "Dopamine.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(22, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(22, getWarnings().size());
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void WP1403_75220Test() throws Exception {
- try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP1403_75220.gpml";
+ @Test
+ public void WP1403_75220Test() throws Exception {
+ try {
+ String pathToFile = "testFiles/wikipathways/";
+ String fileName = "WP1403_75220.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(22, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(22, getWarnings().size());
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void WP528_76269Test() throws Exception {
- try {
+ @Test
+ public void WP528_76269Test() throws Exception {
+ try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP528_76269.gpml";
+ String pathToFile = "testFiles/wikipathways/";
+ String fileName = "WP528_76269.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(15, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(15, getWarnings().size());
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void WP550_73391Test() throws Exception {
- try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP550_73391.gpml";
+ @Test
+ public void WP550_73391Test() throws Exception {
+ try {
+ String pathToFile = "testFiles/wikipathways/";
+ String fileName = "WP550_73391.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(16, getWarnings().size());
+ assertEquals(16, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void WP197_69902Test() throws Exception {
- try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP197_69902.gpml";
+ @Test
+ public void WP197_69902Test() throws Exception {
+ try {
+ String pathToFile = "testFiles/wikipathways/";
+ String fileName = "WP197_69902.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(3, getWarnings().size());
+ assertEquals(3, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void WP179_70629Test() throws Exception {
- try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP179_70629.gpml";
+ @Test
+ public void WP179_70629Test() throws Exception {
+ try {
+ String pathToFile = "testFiles/wikipathways/";
+ String fileName = "WP179_70629.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(38, getWarnings().size());
+ assertEquals(38, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void WP306_71714Test() throws Exception {
- try {
+ @Test
+ public void WP306_71714Test() throws Exception {
+ try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP306_71714.gpml";
+ String pathToFile = "testFiles/wikipathways/";
+ String fileName = "WP306_71714.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(41, getWarnings().size());
+ assertEquals(41, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void WP481_72080Test() throws Exception {
- try {
+ @Test
+ public void WP481_72080Test() throws Exception {
+ try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP481_72080.gpml";
+ String pathToFile = "testFiles/wikipathways/";
+ String fileName = "WP481_72080.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(22, getWarnings().size());
+ assertEquals(22, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testTwoReactants() throws Exception {
- try {
+ @Test
+ public void testTwoReactants() throws Exception {
+ try {
- String pathToFile = "testFiles/small/";
- String fileName = "two_reactant.gpml";
+ String pathToFile = "testFiles/small/";
+ String fileName = "two_reactant.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(0, getWarnings().size());
+ assertEquals(0, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testTwoPubmeds() throws Exception {
- try {
+ @Test
+ public void testTwoPubmeds() throws Exception {
+ try {
- String pathToFile = "testFiles/small/reaction_with_two_pubmeds.gpml";
+ String pathToFile = "testFiles/small/reaction_with_two_pubmeds.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile);
- assertEquals(2, model1.getReactions().iterator().next().getMiriamData().size());
+ Model model1 = new GPMLToModel().getModel(pathToFile);
+ assertEquals(2, model1.getReactions().iterator().next().getMiriamData().size());
- assertEquals(0, getWarnings().size());
+ assertEquals(0, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testComment() throws Exception {
- try {
+ @Test
+ public void testComment() throws Exception {
+ try {
- String pathToFile = "testFiles/small/comment.gpml";
+ String pathToFile = "testFiles/small/comment.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile);
- assertTrue(model1.getNotes().contains("Metabolic Process"));
+ Model model1 = new GPMLToModel().getModel(pathToFile);
+ assertTrue(model1.getNotes().contains("Metabolic Process"));
- assertEquals(0, getWarnings().size());
+ assertEquals(0, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testGstp() throws Exception {
- try {
+ @Test
+ public void testGstp() throws Exception {
+ try {
- String pathToFile = "testFiles/wikipathways/gstp.gpml";
+ String pathToFile = "testFiles/wikipathways/gstp.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile);
+ Model model1 = new GPMLToModel().getModel(pathToFile);
- assertEquals(3, getWarnings().size());
+ assertEquals(3, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testMissingAliasesInCompartment() throws Exception {
- try {
+ @Test
+ public void testMissingAliasesInCompartment() throws Exception {
+ try {
- String pathToFile = "testFiles/small/missing_aliases_in_compartment.gpml";
+ String pathToFile = "testFiles/small/missing_aliases_in_compartment.gpml";
- Model model1 = new GPMLToModel().getModel(pathToFile);
+ Model model1 = new GPMLToModel().getModel(pathToFile);
- assertEquals(3, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModelLines() throws Exception {
- try {
-
- String fileName = "testFiles/small/model_with_line.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(0, getWarnings().size());
-
- assertEquals(1, model1.getLayers().iterator().next().getLines().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModelShapes() throws Exception {
- try {
- String fileName = "testFiles/small/shapes.gpml";
- new GPMLToModel().getModel(fileName);
-
- assertEquals(11, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHypotheticlaComplex() throws Exception {
- try {
- String fileName = "testFiles/complex/hypothetical_complex.gpml";
- Model model = new GPMLToModel().getModel(fileName);
- for (Complex species : model.getComplexList()) {
- assertTrue("Complex parsed from gpml should be hypothetical", species.isHypothetical());
- }
-
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNonHypotheticlaComplex() throws Exception {
- try {
- String fileName = "testFiles/complex/nonhypothetical_complex.gpml";
- Model model = new GPMLToModel().getModel(fileName);
- for (Complex species : model.getComplexList()) {
- assertFalse("Complex parsed from gpml should be hypothetical", species.isHypothetical());
- }
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexName() throws Exception {
- try {
- String fileName = "testFiles/complex/complex_with_name.gpml";
- Model model = new GPMLToModel().getModel(fileName);
- boolean nameFound = false;
- for (Complex species : model.getComplexList()) {
- if ("p70 S6 Kinases".equals(species.getName())) {
- nameFound = true;
- }
- }
- assertTrue("Complex parsed from gpml should have a valid name", nameFound);
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompartmentName() throws Exception {
- try {
- String fileName = "testFiles/compartment/compartment_name.gpml";
- Model model = new GPMLToModel().getModel(fileName);
- for (Compartment compartment : model.getCompartments()) {
- assertEquals("Compartment parsed from gpml should have a valid name", "Label", compartment.getName());
- }
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 30000)
- @Ignore
- public void test() throws Exception {
- try {
- String fileName = "D:/WP3408_81714.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().model(model1).width(model1.getWidth()).height(model1.getHeight());
- PngImageGenerator pig = new PngImageGenerator(params);
- pig.saveToFile("D:/tes1.png");
-
- Desktop.getDesktop().open(new File("D:/tes1.png"));
-
- params = new AbstractImageGenerator.Params().model(model2).width(model2.getWidth()).height(model2.getHeight());
- pig = new PngImageGenerator(params);
- pig.saveToFile("D:/tes2.png");
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexInCompartment() throws Exception {
- try {
- String fileName = "testFiles/compartment/complex_in_compartment.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- assertEquals(2, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionToComplex() throws Exception {
- try {
- String fileName = "testFiles/small/reaction_to_complex.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- assertEquals(54, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColorfullComplexReaction() throws Exception {
- try {
- String fileName = "testFiles/reactions/complex_color_reaction.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColorfullComplexReaction2() throws Exception {
- try {
- String fileName = "testFiles/reactions/complex_color_reaction2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProteinWithModification() throws Exception {
- try {
- String fileName = "testFiles/small/protein_with_modification.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(0, getWarnings().size());
-
- Gene protein = (Gene) model1.getElementByElementId("be3de");
- assertNotNull(protein);
- assertEquals(2, protein.getModificationResidues().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProteinWithModification2() throws Exception {
- try {
- String fileName = "testFiles/small/protein_with_modification_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(0, getWarnings().size());
-
- Gene protein = (Gene) model1.getElementByElementId("be3de");
- assertNotNull(protein);
- assertEquals(2, protein.getModificationResidues().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModifierPosition() throws Exception {
- try {
- String fileName = "testFiles/small/modifier_misaligned.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- double distance = reaction.getCenterPoint().distance(reaction.getModifiers().get(0).getLine().getEndPoint());
- assertTrue("Modifier is too far from center point: " + distance, distance < ReactionCellDesignerConverter.RECT_SIZE);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionToLabel() throws Exception {
- try {
- String fileName = "testFiles/small/reaction_to_label.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, getWarnings().size());
-
- assertEquals(1, model1.getReactions().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModifierAsLabel() throws Exception {
- try {
- String fileName = "testFiles/small/modifier_to_label.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
- assertEquals(3, model1.getReactions().iterator().next().getNodes().size());
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(3, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModelLines() throws Exception {
+ try {
+
+ String fileName = "testFiles/small/model_with_line.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(0, getWarnings().size());
+
+ assertEquals(1, model1.getLayers().iterator().next().getLines().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModelShapes() throws Exception {
+ try {
+ String fileName = "testFiles/small/shapes.gpml";
+ new GPMLToModel().getModel(fileName);
+
+ assertEquals(11, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHypotheticlaComplex() throws Exception {
+ try {
+ String fileName = "testFiles/complex/hypothetical_complex.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ for (Complex species : model.getComplexList()) {
+ assertTrue("Complex parsed from gpml should be hypothetical", species.isHypothetical());
+ }
+
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNonHypotheticlaComplex() throws Exception {
+ try {
+ String fileName = "testFiles/complex/nonhypothetical_complex.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ for (Complex species : model.getComplexList()) {
+ assertFalse("Complex parsed from gpml should be hypothetical", species.isHypothetical());
+ }
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexName() throws Exception {
+ try {
+ String fileName = "testFiles/complex/complex_with_name.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ boolean nameFound = false;
+ for (Complex species : model.getComplexList()) {
+ if ("p70 S6 Kinases".equals(species.getName())) {
+ nameFound = true;
+ }
+ }
+ assertTrue("Complex parsed from gpml should have a valid name", nameFound);
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompartmentName() throws Exception {
+ try {
+ String fileName = "testFiles/compartment/compartment_name.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+ for (Compartment compartment : model.getCompartments()) {
+ assertEquals("Compartment parsed from gpml should have a valid name", "Label", compartment.getName());
+ }
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 30000)
+ @Ignore
+ public void test() throws Exception {
+ try {
+ String fileName = "D:/WP3408_81714.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().model(model1).width(model1.getWidth())
+ .height(model1.getHeight());
+ PngImageGenerator pig = new PngImageGenerator(params);
+ pig.saveToFile("D:/tes1.png");
+
+ Desktop.getDesktop().open(new File("D:/tes1.png"));
+
+ params = new AbstractImageGenerator.Params().model(model2).width(model2.getWidth()).height(model2.getHeight());
+ pig = new PngImageGenerator(params);
+ pig.saveToFile("D:/tes2.png");
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexInCompartment() throws Exception {
+ try {
+ String fileName = "testFiles/compartment/complex_in_compartment.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ assertEquals(2, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionToComplex() throws Exception {
+ try {
+ String fileName = "testFiles/small/reaction_to_complex.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ assertEquals(54, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColorfullComplexReaction() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/complex_color_reaction.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColorfullComplexReaction2() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/complex_color_reaction2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProteinWithModification() throws Exception {
+ try {
+ String fileName = "testFiles/small/protein_with_modification.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(0, getWarnings().size());
+
+ Gene protein = (Gene) model1.getElementByElementId("be3de");
+ assertNotNull(protein);
+ assertEquals(2, protein.getModificationResidues().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProteinWithModification2() throws Exception {
+ try {
+ String fileName = "testFiles/small/protein_with_modification_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(0, getWarnings().size());
+
+ Gene protein = (Gene) model1.getElementByElementId("be3de");
+ assertNotNull(protein);
+ assertEquals(2, protein.getModificationResidues().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModifierPosition() throws Exception {
+ try {
+ String fileName = "testFiles/small/modifier_misaligned.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ double distance = reaction.getCenterPoint().distance(reaction.getModifiers().get(0).getLine().getEndPoint());
+ assertTrue("Modifier is too far from center point: " + distance,
+ distance < ReactionCellDesignerConverter.RECT_SIZE);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionToLabel() throws Exception {
+ try {
+ String fileName = "testFiles/small/reaction_to_label.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, getWarnings().size());
+
+ assertEquals(1, model1.getReactions().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModifierAsLabel() throws Exception {
+ try {
+ String fileName = "testFiles/small/modifier_to_label.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+ assertEquals(3, model1.getReactions().iterator().next().getNodes().size());
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void testModifierAdsLabel() throws Exception {
+ try {
+ String fileName = "testFiles/small/protein_with_state.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ Protein protein = (Protein) model1.getElementsByName("Protein").get(0);
+ assertEquals(0, protein.getModificationResidues().size());
+ assertEquals("GTP", protein.getStructuralState());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- @Test
- public void testModifierAdsLabel() throws Exception {
- try {
- String fileName = "testFiles/small/protein_with_state.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- Protein protein = (Protein) model1.getElementsByName("Protein").get(0);
- assertEquals(0, protein.getModificationResidues().size());
- assertEquals("GTP", protein.getStructuralState());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/persist/src/db/12.1.0~alpha.0/fix_db_20180705.sql b/persist/src/db/12.1.0~alpha.0/fix_db_20180705.sql
new file mode 100644
index 0000000000000000000000000000000000000000..d7bfbb3822d9b7af353d10b4e91556e39c903273
--- /dev/null
+++ b/persist/src/db/12.1.0~alpha.0/fix_db_20180705.sql
@@ -0,0 +1,7 @@
+-- coordinates for antisense rna changed into absolute x,y
+
+alter table antisense_rna_region_table add column position varchar(255);
+update antisense_rna_region_table set position=concat(element_table.x+(element_table.width*3/4*antisense_rna_region_table.pos),',',element_table.y) from element_table where element_table.iddb = antisense_rna_region_table.idspeciesdb and not pos is null;
+update antisense_rna_region_table set position=concat(element_table.x,',',element_table.y) from element_table where element_table.iddb = antisense_rna_region_table.idspeciesdb and pos is null;
+alter table antisense_rna_region_table drop column pos;
+
diff --git a/persist/src/db/12.1.0~alpha.0/fix_db_20180709.sql b/persist/src/db/12.1.0~alpha.0/fix_db_20180709.sql
new file mode 100644
index 0000000000000000000000000000000000000000..00778adbbc79f3ee1601e6f1605fdd700251dc31
--- /dev/null
+++ b/persist/src/db/12.1.0~alpha.0/fix_db_20180709.sql
@@ -0,0 +1,55 @@
+-- antisense rna uses string type
+
+alter table antisense_rna_region_table add column type_string varchar(255);
+update antisense_rna_region_table set type_string ='MODIFICATION_SITE' where type =0;
+update antisense_rna_region_table set type_string ='CODING_REGION' where type =1;
+update antisense_rna_region_table set type_string ='PROTEIN_BINDING_DOMAIN' where type =2;
+alter table antisense_rna_region_table drop column type;
+alter table antisense_rna_region_table rename COLUMN type_string to type;
+
+-- antisense region doesn't have state
+alter table antisense_rna_region_table drop column state;
+
+--size is changed to width for antisense rna region
+alter table antisense_rna_region_table add column width numeric(6,2);
+update antisense_rna_region_table set width=element_table.width*antisense_rna_region_table.size from element_table where element_table.iddb = antisense_rna_region_table.idspeciesdb and not size is null;
+alter table antisense_rna_region_table drop column size;
+
+-- unused CellDesigner 'side' parameter removed
+alter table modification_residue_table drop column side;
+
+-- unused CellDesigner 'size' parameter removed
+alter table modification_residue_table drop column size;
+
+-- changing modification residue angle into x,y coordinates
+update modification_residue_table set angle=0 where angle>=2*pi();
+alter table modification_residue_table add column position varchar(255);
+--GENE
+update modification_residue_table set position=concat(element_table.x+modification_residue_table.angle/(2*pi())*element_table.width,',',element_table.y) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='GENE_ALIAS';
+
+--GENERIC PROTEIN
+update modification_residue_table set position=concat(element_table.x+element_table.width,',',element_table.y+element_table.height/2-modification_residue_table.angle/(pi()/4)*element_table.height/2) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='GENERIC_PROTEIN_ALIAS' and angle<=pi()/4;
+update modification_residue_table set position=concat(element_table.x+element_table.width-(modification_residue_table.angle-pi()/4)/(pi()/2)*element_table.width,',',element_table.y) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='GENERIC_PROTEIN_ALIAS' and angle>pi()/4 and angle<=3*pi()/4;
+update modification_residue_table set position=concat(element_table.x,',',element_table.y+((modification_residue_table.angle-3*pi()/4)/(pi()/2)*element_table.height)) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='GENERIC_PROTEIN_ALIAS' and angle>3*pi()/4 and angle<=5*pi()/4;
+update modification_residue_table set position=concat(element_table.x+((modification_residue_table.angle-5*pi()/4)/(pi()/2)*element_table.width),',',element_table.y+element_table.height) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='GENERIC_PROTEIN_ALIAS' and angle>5*pi()/4 and angle<=7*pi()/4;
+update modification_residue_table set position=concat(element_table.x+element_table.width,',',element_table.y+element_table.height-((modification_residue_table.angle-7*pi()/4)/(pi()/2)*element_table.height)) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='GENERIC_PROTEIN_ALIAS' and angle>7*pi()/4;
+--ION CHANNEL (it's the same as in generic protein - bug in old version)
+update modification_residue_table set position=concat(element_table.x+element_table.width,',',element_table.y+element_table.height/2-modification_residue_table.angle/(pi()/4)*element_table.height/2) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='ION_CHANNEL_PROTEIN_ALIAS' and angle<=pi()/4;
+update modification_residue_table set position=concat(element_table.x+element_table.width-(modification_residue_table.angle-pi()/4)/(pi()/2)*element_table.width,',',element_table.y) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='ION_CHANNEL_PROTEIN_ALIAS' and angle>pi()/4 and angle<=3*pi()/4;
+update modification_residue_table set position=concat(element_table.x,',',element_table.y+((modification_residue_table.angle-3*pi()/4)/(pi()/2)*element_table.height)) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='ION_CHANNEL_PROTEIN_ALIAS' and angle>3*pi()/4 and angle<=5*pi()/4;
+update modification_residue_table set position=concat(element_table.x+((modification_residue_table.angle-5*pi()/4)/(pi()/2)*element_table.width),',',element_table.y+element_table.height) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='ION_CHANNEL_PROTEIN_ALIAS' and angle>5*pi()/4 and angle<=7*pi()/4;
+update modification_residue_table set position=concat(element_table.x+element_table.width,',',element_table.y+element_table.height-((modification_residue_table.angle-7*pi()/4)/(pi()/2)*element_table.height)) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='ION_CHANNEL_PROTEIN_ALIAS' and angle>7*pi()/4;
+--RECEPTOR PROTEIN
+update modification_residue_table set position=concat(element_table.x+element_table.width,',',element_table.y+(1-modification_residue_table.angle/(pi()/4))*2.0/5.0*element_table.height) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='RECEPTOR_PROTEIN_ALIAS' and angle<=pi()/4;
+update modification_residue_table set position=concat(element_table.x+element_table.width-(modification_residue_table.angle-pi()/4)/(pi()/4)*element_table.width/2,',',element_table.y+(modification_residue_table.angle-pi()/4)/(pi()/4)*1.0/5.0*element_table.height) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='RECEPTOR_PROTEIN_ALIAS' and angle>pi()/4 and angle<=2*pi()/4;
+update modification_residue_table set position=concat(element_table.x+element_table.width/2-(modification_residue_table.angle-pi()/2)/(pi()/4)*element_table.width/2,',',element_table.y+1.0/5.0*element_table.height-(modification_residue_table.angle-pi()/2)/(pi()/4)*1.0/5.0*element_table.height) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='RECEPTOR_PROTEIN_ALIAS' and angle>2*pi()/4 and angle<=3*pi()/4;
+update modification_residue_table set position=concat(element_table.x,',',element_table.y+((modification_residue_table.angle-3*pi()/4)/(pi()/2)*4.0/5.0*element_table.height)) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='RECEPTOR_PROTEIN_ALIAS' and angle>3*pi()/4 and angle<=5*pi()/4;
+update modification_residue_table set position=concat(element_table.x+(modification_residue_table.angle-5*pi()/4)/(pi()/4)*element_table.width/2,',',element_table.y+4.0/5.0*element_table.height+(modification_residue_table.angle-5*pi()/4)/(pi()/4)*1.0/5.0*element_table.height) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='RECEPTOR_PROTEIN_ALIAS' and angle>5*pi()/4 and angle<=6*pi()/4;
+update modification_residue_table set position=concat(element_table.x+element_table.width/2+(modification_residue_table.angle-6*pi()/4)/(pi()/4)*element_table.width/2,',',element_table.y+element_table.height-(modification_residue_table.angle-6*pi()/4)/(pi()/4)*1.0/5.0*element_table.height) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='RECEPTOR_PROTEIN_ALIAS' and angle>6*pi()/4 and angle<=7*pi()/4;
+update modification_residue_table set position=concat(element_table.x+element_table.width,',',element_table.y+4.0/5.0*element_table.height-(modification_residue_table.angle-7*pi()/4)/(pi()/4)*2.0/5.0*element_table.height) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='RECEPTOR_PROTEIN_ALIAS' and angle>7*pi()/4;
+--TRUNCATED PROTEIN ALIAS
+update modification_residue_table set position=concat(element_table.x+element_table.width,',',element_table.y+element_table.height/2-modification_residue_table.angle/(pi()/4)*element_table.height/2) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='TRUNCATED_PROTEIN_ALIAS' and angle<=pi()/4;
+update modification_residue_table set position=concat(element_table.x+element_table.width-(modification_residue_table.angle-pi()/4)/(pi()/2)*element_table.width,',',element_table.y) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='TRUNCATED_PROTEIN_ALIAS' and angle>pi()/4 and angle<=3*pi()/4;
+update modification_residue_table set position=concat(element_table.x,',',element_table.y+((modification_residue_table.angle-3*pi()/4)/(pi()/2)*element_table.height)) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='TRUNCATED_PROTEIN_ALIAS' and angle>3*pi()/4 and angle<=5*pi()/4;
+update modification_residue_table set position=concat(element_table.x+((modification_residue_table.angle-5*pi()/4)/(pi()/2)*4.0/5.0*element_table.width),',',element_table.y+element_table.height) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='TRUNCATED_PROTEIN_ALIAS' and angle>5*pi()/4 and angle<=7*pi()/4;
+update modification_residue_table set position=concat(element_table.x+4.0/5.0*element_table.width,',',element_table.y+element_table.height-((modification_residue_table.angle-7*pi()/4)/(pi()/2)*element_table.height)) from element_table where element_table.iddb = modification_residue_table.idspeciesdb and element_type_db='TRUNCATED_PROTEIN_ALIAS' and angle>7*pi()/4;
diff --git a/persist/src/db/12.1.0~alpha.0/fix_db_20180710.sql b/persist/src/db/12.1.0~alpha.0/fix_db_20180710.sql
new file mode 100644
index 0000000000000000000000000000000000000000..c391524b79276d2df05443cda3f190fafd25ae18
--- /dev/null
+++ b/persist/src/db/12.1.0~alpha.0/fix_db_20180710.sql
@@ -0,0 +1,27 @@
+-- state of modification_residue is mapped via string
+
+alter table modification_residue_table add column state_string varchar(255);
+update modification_residue_table set state_string='PHOSPHORYLATED' where state=0;
+update modification_residue_table set state_string='ACETYLATED' where state=1;
+update modification_residue_table set state_string='UBIQUITINATED' where state=2;
+update modification_residue_table set state_string='METHYLATED' where state=3;
+update modification_residue_table set state_string='HYDROXYLATED' where state=4;
+update modification_residue_table set state_string='MYRISTOYLATED' where state=5;
+update modification_residue_table set state_string='SULFATED' where state=6;
+update modification_residue_table set state_string='PRENYLATED' where state=7;
+update modification_residue_table set state_string='GLYCOSYLATED' where state=8;
+update modification_residue_table set state_string='PALMYTOYLATED' where state=9;
+update modification_residue_table set state_string='UNKNOWN' where state=10;
+update modification_residue_table set state_string='EMPTY' where state=11;
+update modification_residue_table set state_string='PROTONATED' where state=12;
+update modification_residue_table set state_string='DONT_CARE' where state=13;
+alter table modification_residue_table drop column state;
+alter table modification_residue_table rename column state_string to state;
+
+-- coordinates for rna region changed into absolute x,y
+
+alter table rna_region_table add column position varchar(255);
+update rna_region_table set position=concat(element_table.x+element_table.width/4 +(element_table.width*3/4*rna_region_table.pos),',',element_table.y) from element_table where element_table.iddb = rna_region_table.idspeciesdb and not pos is null;
+update rna_region_table set position=concat(element_table.x,',',element_table.y) from element_table where element_table.iddb = rna_region_table.idspeciesdb and pos is null;
+alter table rna_region_table drop column pos;
+
diff --git a/persist/src/db/12.1.0~alpha.0/fix_db_20180711.sql b/persist/src/db/12.1.0~alpha.0/fix_db_20180711.sql
new file mode 100644
index 0000000000000000000000000000000000000000..f6867729b929fa57ebb957f66fe64bd21f3b7cc7
--- /dev/null
+++ b/persist/src/db/12.1.0~alpha.0/fix_db_20180711.sql
@@ -0,0 +1,21 @@
+--size is changed to width for rna region
+alter table rna_region_table add column width numeric(6,2);
+update rna_region_table set width=element_table.width*rna_region_table.size from element_table where element_table.iddb = rna_region_table.idspeciesdb and not size is null;
+alter table rna_region_table drop column size;
+
+--modifications includes different type of modification (that will be resolved to different classes)
+alter table modification_residue_table add column modification_type varchar(255);
+update modification_residue_table set modification_type='MODIFICATION_SITE' from element_table where modification_residue_table.idspeciesdb=element_table.iddb and element_type_db='GENE_ALIAS';
+update modification_residue_table set modification_type='RESIDUE' from element_table where modification_residue_table.idspeciesdb=element_table.iddb and modification_type is null;
+
+-- move antisense rna regions into modification table
+alter table modification_residue_table add column width numeric(6,2);
+insert into modification_residue_table (idmodificationresidue, name, idspeciesdb, position, state, modification_type, width) select idantisensernaregion, name, idspeciesdb, position, null, type, width from antisense_rna_region_table;
+drop table antisense_rna_region_table;
+
+-- move rna regions into modification table
+insert into modification_residue_table (idmodificationresidue, name, idspeciesdb, position, state, modification_type, width) select idrnaregion, name, idspeciesdb, position, state, type, width from rna_region_table;
+update modification_residue_table set modification_type='MODIFICATION_SITE' where modification_type='Modification Site';
+update modification_residue_table set modification_type='PROTEIN_BINDING_DOMAIN' where modification_type='proteinBindingDomain';
+update modification_residue_table set modification_type='CODING_REGION' where modification_type='CodingRegion';
+drop table rna_region_table;
diff --git a/persist/src/db/12.1.0~alpha.0/fix_db_20180712.sql b/persist/src/db/12.1.0~alpha.0/fix_db_20180712.sql
new file mode 100644
index 0000000000000000000000000000000000000000..1383f8dffb33214795aaeaaf49f861afaafddfd5
--- /dev/null
+++ b/persist/src/db/12.1.0~alpha.0/fix_db_20180712.sql
@@ -0,0 +1,6 @@
+-- modification residue should have height
+alter table modification_residue_table add column height numeric(6,2);
+update modification_residue_table set height = 10.0;
+
+-- transcription site activity and direction
+alter table modification_residue_table add column direction varchar(255);
diff --git a/persist/src/db/12.1.0~alpha.0/fix_db_20180718.sql b/persist/src/db/12.1.0~alpha.0/fix_db_20180718.sql
new file mode 100644
index 0000000000000000000000000000000000000000..6872876ec79cbd77890de8f7bacdad58780af5eb
--- /dev/null
+++ b/persist/src/db/12.1.0~alpha.0/fix_db_20180718.sql
@@ -0,0 +1,2 @@
+-- user account can be connected to LDAP directory
+alter table user_table add column connectedtoldap boolean default false;
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/user/UserDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/user/UserDao.java
index 84af311b9bf9fdcf675954b54995d6a3e257e203..b40e97920c451c461c04ec04326a38f3d6fb2fc4 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/user/UserDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/user/UserDao.java
@@ -2,9 +2,6 @@ package lcsb.mapviewer.persist.dao.user;
import java.util.List;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.crypto.password.PasswordEncoder;
-
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.BaseDao;
@@ -16,102 +13,60 @@ import lcsb.mapviewer.persist.dao.BaseDao;
*/
public class UserDao extends BaseDao<User> {
- /**
- * Service that provides password encoding.
- */
- @Autowired
- private PasswordEncoder passwordEncoder;
-
- /**
- * Default constructor.
- */
- public UserDao() {
- super(User.class, "removed");
- }
-
- /**
- * Returns user with a given login and password.
- *
- * @param login
- * user login
- * @param password
- * - user password (plain text)
- * @return user for given login and password
- */
- public User getUserByLoginAndPassword(String login, String password) {
- if (password == null) {
- return getUserByLoginAndCryptedPassword(login, null);
- }
- return getUserByLoginAndCryptedPassword(login, passwordEncoder.encode(password));
- }
-
- /**
- * Returns user with a given login and password.
- *
- * @param login
- * user login
- * @param password
- * - user password (encrypted)
- * @return user for given login and password
- */
- public User getUserByLoginAndCryptedPassword(String login, String password) {
- List<?> list = getSession()
- .createQuery(" from User where login=:login and cryptedPassword =:passwd " + removableAndStatemant()).setParameter("login", login)
- .setParameter("passwd", password).list();
- if (list.size() == 0) {
- return null;
- } else {
- User user = (User) list.get(0);
- return user;
- }
- }
-
- /**
- * Returns user with a given login.
- *
- * @param login
- * user login
- * @return user for a given login
- */
- public User getUserByLogin(String login) {
- return getByParameter("login", login);
- }
+ /**
+ * Default constructor.
+ */
+ public UserDao() {
+ super(User.class, "removed");
+ }
- /**
- * Returns user with a given email.
- *
- * @param email
- * user email
- * @return user for a given email
- */
- public User getUserByEmail(String email) {
- return getByParameter("email", email);
- }
+ /**
+ * Returns user with a given login and password.
+ *
+ * @param login
+ * user login
+ * @param password
+ * - user password (encrypted)
+ * @return user for given login and password
+ */
+ public User getUserByLoginAndCryptedPassword(String login, String password) {
+ List<?> list = getSession()
+ .createQuery(" from User where login=:login and cryptedPassword =:passwd " + removableAndStatemant())
+ .setParameter("login", login).setParameter("passwd", password).list();
+ if (list.size() == 0) {
+ return null;
+ } else {
+ User user = (User) list.get(0);
+ return user;
+ }
+ }
- @Override
- public void delete(User object) {
- object.setRemoved(true);
- object.setLogin("[REMOVED]_" + object.getId() + "_" + object.getLogin());
- update(object);
- }
+ /**
+ * Returns user with a given login.
+ *
+ * @param login
+ * user login
+ * @return user for a given login
+ */
+ public User getUserByLogin(String login) {
+ return getByParameter("login", login);
+ }
- /**
- * Returns {@link User} for given "name surname" string.
- *
- * @param nameSurnameString
- * string identifing user with name and surname separated by single
- * space
- * @return {@link User} for given "name surname" string
- */
- public User getUserByNameSurname(String nameSurnameString) {
- List<?> list = getSession()
- .createQuery(" from " + this.getClazz().getSimpleName() + " where concat(name, ' ', surname) " + " = :param_val " + removableAndStatemant())
- .setParameter("param_val", nameSurnameString).list();
- if (list.size() == 0) {
- return null;
- } else {
- return (User) list.get(0);
- }
- }
+ /**
+ * Returns user with a given email.
+ *
+ * @param email
+ * user email
+ * @return user for a given email
+ */
+ public User getUserByEmail(String email) {
+ return getByParameter("email", email);
+ }
+ @Override
+ public void delete(User object) {
+ object.setRemoved(true);
+ object.setLogin("[REMOVED]_" + object.getId() + "_" + object.getLogin());
+ update(object);
+ }
}
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 94e3760435c033093c2fed4f762ceb4c0d5490b3..104c0fb09f89b0e439566319960bf65309fed9ef 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -176,9 +176,13 @@
<value>lcsb.mapviewer.model.map.species.TruncatedProtein</value>
<value>lcsb.mapviewer.model.map.species.Unknown</value>
- <value>lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion</value>
- <value>lcsb.mapviewer.model.map.species.field.ModificationResidue</value>
- <value>lcsb.mapviewer.model.map.species.field.RnaRegion</value>
+ <value>lcsb.mapviewer.model.map.species.field.BindingRegion</value>
+ <value>lcsb.mapviewer.model.map.species.field.CodingRegion</value>
+ <value>lcsb.mapviewer.model.map.species.field.ModificationSite</value>
+ <value>lcsb.mapviewer.model.map.species.field.ProteinBindingDomain</value>
+ <value>lcsb.mapviewer.model.map.species.field.RegulatoryRegion</value>
+ <value>lcsb.mapviewer.model.map.species.field.Residue</value>
+ <value>lcsb.mapviewer.model.map.species.field.TranscriptionSite</value>
<value>lcsb.mapviewer.model.map.species.field.UniprotRecord</value>
<value>lcsb.mapviewer.model.map.species.field.Structure</value>
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
index 03b6cad1942c420382e0e165f6ef8e59029c6a58..80cdbd417b4393348102b0e4826b9af81e0e1814 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
@@ -56,241 +56,241 @@ import lcsb.mapviewer.persist.dao.user.UserDao;
@Transactional(value = "txManager")
@Rollback(true)
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
- "/test-applicationContext.xml", //
- "/dataSource.xml" //
- })
+@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
+ "/test-applicationContext.xml", //
+ "/dataSource.xml" //
+})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class PersistTestFunctions {
- private Logger logger = Logger.getLogger(PersistTestFunctions.class);
-
- public double EPSILON = 1e-6;
-
- @Autowired
- protected LogDao logDao;
-
- @Autowired
- protected SearchHistoryDao searchHistoryDao;
-
- @Autowired
- private PasswordEncoder passwordEncoder;
-
- @Autowired
- protected ProjectDao projectDao;
-
- @Autowired
- protected CacheQueryDao cacheQueryDao;
-
- @Autowired
- protected PolylineDao polylineDao;
-
- @Autowired
- protected ModelDao modelDao;
-
- @Autowired
- protected UserDao userDao;
-
- @Autowired
- protected PrivilegeDao privilegeDao;
-
- @Autowired
- protected CommentDao commentDao;
-
- @Autowired
- protected DbUtils dbUtils;
-
- @Autowired
- protected ReactionDao reactionDao;
-
- @Autowired
- protected ElementDao aliasDao;
-
- protected User user;
-
- @Autowired
- protected CacheTypeDao cacheTypeDao;
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- /**
- * This method remove model with all connections from db (used only when the
- * db must be handled manually)
- *
- * @param id
- */
- protected void removeModelById(int id) {
- modelDao.delete(modelDao.getById(id));
- }
-
- protected void createUser() {
- user = new User();
- user.setName("John");
- user.setSurname("Doe");
- user.setEmail("john.doe@uni.lu");
- user.setLogin("john.doe");
- user.setCryptedPassword(passwordEncoder.encode("passwd"));
- userDao.add(user);
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public PrivilegeDao getPrivilegeDao() {
- return privilegeDao;
- }
-
- public void setPrivilegeDao(PrivilegeDao privilegeDao) {
- this.privilegeDao = privilegeDao;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
+ private Logger logger = Logger.getLogger(PersistTestFunctions.class);
+
+ public double EPSILON = 1e-6;
+
+ @Autowired
+ protected LogDao logDao;
+
+ @Autowired
+ protected SearchHistoryDao searchHistoryDao;
+
+ @Autowired
+ private PasswordEncoder passwordEncoder;
+
+ @Autowired
+ protected ProjectDao projectDao;
+
+ @Autowired
+ protected CacheQueryDao cacheQueryDao;
+
+ @Autowired
+ protected PolylineDao polylineDao;
+
+ @Autowired
+ protected ModelDao modelDao;
+
+ @Autowired
+ protected UserDao userDao;
+
+ @Autowired
+ protected PrivilegeDao privilegeDao;
+
+ @Autowired
+ protected CommentDao commentDao;
+
+ @Autowired
+ protected DbUtils dbUtils;
+
+ @Autowired
+ protected ReactionDao reactionDao;
+
+ @Autowired
+ protected ElementDao elementDao;
+
+ protected User user;
+
+ @Autowired
+ protected CacheTypeDao cacheTypeDao;
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ /**
+ * This method remove model with all connections from db (used only when the db
+ * must be handled manually)
+ *
+ * @param id
+ */
+ protected void removeModelById(int id) {
+ modelDao.delete(modelDao.getById(id));
+ }
+
+ protected void createUser() {
+ user = new User();
+ user.setName("John");
+ user.setSurname("Doe");
+ user.setEmail("john.doe@uni.lu");
+ user.setLogin("john.doe");
+ user.setCryptedPassword(passwordEncoder.encode("passwd"));
+ userDao.add(user);
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public PrivilegeDao getPrivilegeDao() {
+ return privilegeDao;
+ }
+
+ public void setPrivilegeDao(PrivilegeDao privilegeDao) {
+ this.privilegeDao = privilegeDao;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ URLConnection urlConn = url.openConnection();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ }
}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDaoTest.java
index e7bbd2c94aa9f69577d1c092ac2630fbf086291b..39aad751d664333c46ddc40602814da613db67fd 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDaoTest.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.persist.dao.cache;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.model.cache.BigFileEntry;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class BigFileEntryDaoTest extends PersistTestFunctions {
-
- @Autowired
- BigFileEntryDao bigFileEntryDao;
-
- @Autowired
- DbUtils dbUtils;
-
- boolean flush;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- flush = dbUtils.isAutoFlush();
- dbUtils.setAutoFlush(true);
- }
-
- @After
- public void tearDown() throws Exception {
- dbUtils.setAutoFlush(flush);
- }
-
- @Test
- public void testAdd() {
- try {
- BigFileEntry entry = new BigFileEntry();
- long count = bigFileEntryDao.getCount();
- bigFileEntryDao.add(entry);
- long count2 = bigFileEntryDao.getCount();
- bigFileEntryDao.delete(entry);
- long count3 = bigFileEntryDao.getCount();
-
- assertEquals(count + 1, count2);
- assertEquals(count2 - 1, count3);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetByUrl() {
- try {
- String url = "xxx.yyy";
- BigFileEntry entry = new BigFileEntry();
- entry.setUrl(url);
-
- BigFileEntry result = bigFileEntryDao.getByUrl(url);
- assertNull(result);
- bigFileEntryDao.add(entry);
-
- result = bigFileEntryDao.getByUrl(url);
- assertEquals(entry, result);
-
- bigFileEntryDao.delete(entry);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.cache;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.model.cache.BigFileEntry;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class BigFileEntryDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ BigFileEntryDao bigFileEntryDao;
+
+ @Autowired
+ DbUtils dbUtils;
+
+ boolean flush;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ flush = dbUtils.isAutoFlush();
+ dbUtils.setAutoFlush(true);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ dbUtils.setAutoFlush(flush);
+ }
+
+ @Test
+ public void testAdd() {
+ try {
+ BigFileEntry entry = new BigFileEntry();
+ long count = bigFileEntryDao.getCount();
+ bigFileEntryDao.add(entry);
+ long count2 = bigFileEntryDao.getCount();
+ bigFileEntryDao.delete(entry);
+ long count3 = bigFileEntryDao.getCount();
+
+ assertEquals(count + 1, count2);
+ assertEquals(count2 - 1, count3);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetByUrl() {
+ try {
+ String url = "xxx.yyy";
+ BigFileEntry entry = new BigFileEntry();
+ entry.setUrl(url);
+
+ BigFileEntry result = bigFileEntryDao.getByUrl(url);
+ assertNull(result);
+ bigFileEntryDao.add(entry);
+
+ result = bigFileEntryDao.getByUrl(url);
+ assertEquals(entry, result);
+
+ bigFileEntryDao.delete(entry);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
index b18a7cba2a305f7f2885bef08bdb49817ef45c37..e00f0b9d3a59dd54fd112a61054a5dc23879a434 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
@@ -1,185 +1,186 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import static org.junit.Assert.assertEquals;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class CommentDaoTest extends PersistTestFunctions {
- int identifierCounter = 1;
-
- private Project project;
- String projectId = "Some_id";
-
- @Before
- public void setUp() throws Exception {
- project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- }
-
- @After
- public void tearDown() throws Exception {
- projectDao.delete(project);
- }
-
- @Test
- public void testGetComments() {
- try {
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
-
- Comment comment = new Comment();
- comment.setDeleted(true);
- comment.setModel(model);
- commentDao.add(comment);
-
- Comment comment2 = new Comment();
- comment2.setPinned(true);
- comment2.setModel(model);
- commentDao.add(comment2);
-
- assertEquals(0, commentDao.getCommentByModel(model, true, true).size());
- assertEquals(1, commentDao.getCommentByModel(model, false, true).size());
- assertEquals(1, commentDao.getCommentByModel(model, null, true).size());
- assertEquals(1, commentDao.getCommentByModel(model, true, false).size());
- assertEquals(0, commentDao.getCommentByModel(model, false, false).size());
- assertEquals(1, commentDao.getCommentByModel(model, null, false).size());
- assertEquals(1, commentDao.getCommentByModel(model, true, null).size());
- assertEquals(1, commentDao.getCommentByModel(model, false, null).size());
- assertEquals(2, commentDao.getCommentByModel(model, null, null).size());
-
- assertEquals(0, commentDao.getCommentByModel(model.getModelData(), true, true).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), false, true).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), null, true).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), true, false).size());
- assertEquals(0, commentDao.getCommentByModel(model.getModelData(), false, false).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), null, false).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), true, null).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), false, null).size());
- assertEquals(2, commentDao.getCommentByModel(model.getModelData(), null, null).size());
-
- commentDao.delete(comment);
- commentDao.delete(comment2);
- modelDao.delete(model);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- GenericProtein alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
- model.addElement(alias);
- alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
- model.addElement(alias);
- alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
- model.addElement(alias);
- alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
- model.addElement(alias);
-
- alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addSpecies(alias);
- alias3.addSpecies(alias2);
- alias.setComplex(alias3);
- alias2.setComplex(alias3);
-
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
-
- Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
- model.addElement(cAlias);
- model.setWidth(2000);
- model.setHeight(2000);
-
- Layer layer = new Layer();
- model.addLayer(layer);
-
- LayerRect lr = new LayerRect();
- lr.setColor(Color.YELLOW);
- layer.addLayerRect(lr);
-
- Reaction reaction = new TransportReaction();
- reaction.addProduct(new Product(alias));
- reaction.addReactant(new Reactant(alias2));
- reaction.setIdReaction("re" + identifierCounter++);
- model.addReaction(reaction);
-
- alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
- model.addElement(alias);
-
- ModificationResidue mr = new ModificationResidue();
- mr.setName("mr");
- alias.addModificationResidue(mr);
-
- alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
- return model;
- }
-
- private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private GenericProtein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- GenericProtein alias = new GenericProtein(aliasId);
- alias.setName("SNCA");
- alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.Comment;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class CommentDaoTest extends PersistTestFunctions {
+ int identifierCounter = 1;
+
+ private Project project;
+ String projectId = "Some_id";
+
+ @Before
+ public void setUp() throws Exception {
+ project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ projectDao.delete(project);
+ }
+
+ @Test
+ public void testGetComments() {
+ try {
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+
+ Comment comment = new Comment();
+ comment.setDeleted(true);
+ comment.setModel(model);
+ commentDao.add(comment);
+
+ Comment comment2 = new Comment();
+ comment2.setPinned(true);
+ comment2.setModel(model);
+ commentDao.add(comment2);
+
+ assertEquals(0, commentDao.getCommentByModel(model, true, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model, false, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model, null, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model, true, false).size());
+ assertEquals(0, commentDao.getCommentByModel(model, false, false).size());
+ assertEquals(1, commentDao.getCommentByModel(model, null, false).size());
+ assertEquals(1, commentDao.getCommentByModel(model, true, null).size());
+ assertEquals(1, commentDao.getCommentByModel(model, false, null).size());
+ assertEquals(2, commentDao.getCommentByModel(model, null, null).size());
+
+ assertEquals(0, commentDao.getCommentByModel(model.getModelData(), true, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), false, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), null, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), true, false).size());
+ assertEquals(0, commentDao.getCommentByModel(model.getModelData(), false, false).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), null, false).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), true, null).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), false, null).size());
+ assertEquals(2, commentDao.getCommentByModel(model.getModelData(), null, null).size());
+
+ commentDao.delete(comment);
+ commentDao.delete(comment2);
+ modelDao.delete(model);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ GenericProtein alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
+ model.addElement(alias);
+ alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
+ model.addElement(alias);
+ alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
+ model.addElement(alias);
+ alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
+ model.addElement(alias);
+
+ alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
+ alias.setComplex(alias3);
+ alias2.setComplex(alias3);
+
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
+
+ Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
+ model.addElement(cAlias);
+ model.setWidth(2000);
+ model.setHeight(2000);
+
+ Layer layer = new Layer();
+ model.addLayer(layer);
+
+ LayerRect lr = new LayerRect();
+ lr.setColor(Color.YELLOW);
+ layer.addLayerRect(lr);
+
+ Reaction reaction = new TransportReaction();
+ reaction.addProduct(new Product(alias));
+ reaction.addReactant(new Reactant(alias2));
+ reaction.setIdReaction("re" + identifierCounter++);
+ model.addReaction(reaction);
+
+ alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
+ model.addElement(alias);
+
+ ModificationResidue mr = new Residue();
+ mr.setName("mr");
+ alias.addModificationResidue(mr);
+
+ alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
+ return model;
+ }
+
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private GenericProtein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ GenericProtein alias = new GenericProtein(aliasId);
+ alias.setName("SNCA");
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
index 8b67d43aa92791640ad6fe43c9f55f89f9545ae9..83572545fdaf861ba0299e25b96d7880550b44f6 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
@@ -1,230 +1,230 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import java.awt.Color;
-import java.nio.charset.StandardCharsets;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class LayoutDaoTest extends PersistTestFunctions {
-
- @Autowired
- private LayoutDao layoutDao;
-
- final static Logger logger = Logger.getLogger(LayoutDaoTest.class);
-
- int identifierCounter = 0;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * After adding layouts to model.
- *
- * @throws Exception
- */
- @Test
- public void testLayoutsWithData() throws Exception {
- try {
- Model model = createModel();
-
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
-
- Layout layout = new Layout();
- layout.setDirectory("tmp");
- layout.setTitle("temporary name");
-
- byte[] data = "test".getBytes();
- UploadedFileEntry fileEntry = new UploadedFileEntry();
- fileEntry.setFileContent(data);
-
- layout.setInputData(fileEntry);
- model.addLayout(layout);
- layoutDao.add(layout);
-
- layoutDao.evict(layout);
-
- layout = layoutDao.getById(layout.getId());
-
- assertEquals("test", new String(layout.getInputData().getFileContent(), StandardCharsets.UTF_8));
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding layouts to model.
- *
- * @throws Exception
- */
- @Test
- public void testLayoutsWithoutData() throws Exception {
- try {
- Model model = createModel();
- String tempName = "temporary name";
-
- createUser();
-
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
-
- assertEquals(0, layoutDao.getCountByUser(user));
- assertEquals(0, layoutDao.getLayoutsByModel(model).size());
- assertNull(layoutDao.getLayoutByName(model, tempName));
-
- Layout layout = new Layout();
- layout.setDirectory("tmp");
- layout.setTitle(tempName);
- layout.setCreator(user);
- model.addLayout(layout);
- layoutDao.add(layout);
-
- layoutDao.evict(layout);
-
- layout = layoutDao.getById(layout.getId());
-
- assertEquals(1, layoutDao.getLayoutsByModel(model).size());
- assertNotNull(layoutDao.getLayoutByName(model, tempName));
- assertEquals(1, layoutDao.getCountByUser(user));
-
- assertNull(layout.getInputData());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
-
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- Species alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
- model.addElement(alias);
- alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
- model.addElement(alias);
- alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
- model.addElement(alias);
- alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
- model.addElement(alias);
-
- alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addSpecies(alias);
- alias3.addSpecies(alias2);
- alias.setComplex(alias3);
- alias2.setComplex(alias3);
-
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
-
- Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
- model.addElement(cAlias);
- model.setWidth(2000);
- model.setHeight(2000);
-
- Layer layer = new Layer();
- model.addLayer(layer);
-
- LayerRect lr = new LayerRect();
- lr.setColor(Color.YELLOW);
- layer.addLayerRect(lr);
-
- Reaction reaction = new TransportReaction();
- reaction.addProduct(new Product(alias));
- reaction.addReactant(new Reactant(alias2));
- reaction.setIdReaction("re" + identifierCounter++);
- model.addReaction(reaction);
-
- Protein protein = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
- model.addElement(protein);
-
- ModificationResidue mr = new ModificationResidue();
- mr.setName("mr");
- protein.addModificationResidue(mr);
-
- protein.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
- return model;
- }
-
- private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Protein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- GenericProtein alias = new GenericProtein("s" + identifierCounter++);
- alias.setElementId(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import java.awt.Color;
+import java.nio.charset.StandardCharsets;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class LayoutDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ private LayoutDao layoutDao;
+
+ final static Logger logger = Logger.getLogger(LayoutDaoTest.class);
+
+ int identifierCounter = 0;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * After adding layouts to model.
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testLayoutsWithData() throws Exception {
+ try {
+ Model model = createModel();
+
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+
+ Layout layout = new Layout();
+ layout.setDirectory("tmp");
+ layout.setTitle("temporary name");
+
+ byte[] data = "test".getBytes();
+ UploadedFileEntry fileEntry = new UploadedFileEntry();
+ fileEntry.setFileContent(data);
+
+ layout.setInputData(fileEntry);
+ model.addLayout(layout);
+ layoutDao.add(layout);
+
+ layoutDao.evict(layout);
+
+ layout = layoutDao.getById(layout.getId());
+
+ assertEquals("test", new String(layout.getInputData().getFileContent(), StandardCharsets.UTF_8));
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding layouts to model.
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testLayoutsWithoutData() throws Exception {
+ try {
+ Model model = createModel();
+ String tempName = "temporary name";
+
+ createUser();
+
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+
+ assertEquals(0, layoutDao.getCountByUser(user));
+ assertEquals(0, layoutDao.getLayoutsByModel(model).size());
+ assertNull(layoutDao.getLayoutByName(model, tempName));
+
+ Layout layout = new Layout();
+ layout.setDirectory("tmp");
+ layout.setTitle(tempName);
+ layout.setCreator(user);
+ model.addLayout(layout);
+ layoutDao.add(layout);
+
+ layoutDao.evict(layout);
+
+ layout = layoutDao.getById(layout.getId());
+
+ assertEquals(1, layoutDao.getLayoutsByModel(model).size());
+ assertNotNull(layoutDao.getLayoutByName(model, tempName));
+ assertEquals(1, layoutDao.getCountByUser(user));
+
+ assertNull(layout.getInputData());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ Species alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
+ model.addElement(alias);
+ alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
+ model.addElement(alias);
+ alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
+ model.addElement(alias);
+ alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
+ model.addElement(alias);
+
+ alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
+ alias.setComplex(alias3);
+ alias2.setComplex(alias3);
+
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
+
+ Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
+ model.addElement(cAlias);
+ model.setWidth(2000);
+ model.setHeight(2000);
+
+ Layer layer = new Layer();
+ model.addLayer(layer);
+
+ LayerRect lr = new LayerRect();
+ lr.setColor(Color.YELLOW);
+ layer.addLayerRect(lr);
+
+ Reaction reaction = new TransportReaction();
+ reaction.addProduct(new Product(alias));
+ reaction.addReactant(new Reactant(alias2));
+ reaction.setIdReaction("re" + identifierCounter++);
+ model.addReaction(reaction);
+
+ Protein protein = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
+ model.addElement(protein);
+
+ Residue mr = new Residue();
+ mr.setName("mr");
+ protein.addModificationResidue(mr);
+
+ protein.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
+ return model;
+ }
+
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Protein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ GenericProtein alias = new GenericProtein("s" + identifierCounter++);
+ alias.setElementId(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
index 3a211e414adc17f9c450e630f7377714bac0ec4f..02bf55c42b3c0adef12ae00f1fb6a1cc8e479e70 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
@@ -1,465 +1,470 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class ModelDaoTest extends PersistTestFunctions {
- ModelComparator modelComparator = new ModelComparator();
-
- Logger logger = Logger.getLogger(ModelDaoTest.class);
- private Project project;
- String projectId = "Some_id";
- int identifierCounter = 0;
-
- @Before
- public void setUp() throws Exception {
- project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- }
-
- @After
- public void tearDown() throws Exception {
- projectDao.delete(project);
- }
-
- @Test
- public void testLoadFromDb() throws Exception {
- try {
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
-
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
- assertNotNull(model2);
- assertFalse(model2 == model);
-
- assertEquals(model.getElements().size(), model2.getElements().size());
- assertEquals(model.getLayers().size(), model2.getLayers().size());
- assertEquals(model.getReactions().size(), model2.getReactions().size());
-
- modelDao.delete(model2);
- model2 = modelDao.getById(model.getId());
- assertNull(model2);
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIndexesReload() throws Exception {
- try {
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
- Model fullModel = new ModelFullIndexed(model2);
- assertNotNull(model2);
-
- assertEquals(model.getElements().size(), model2.getElements().size());
- assertEquals(model.getLayers().size(), model2.getLayers().size());
- assertEquals(model.getReactions().size(), model2.getReactions().size());
-
- // check if we really performed a test
- boolean test = false;
-
- for (Element alias : model.getElements()) {
- assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
- test = true;
- }
- assertTrue(test);
-
- test = false;
- for (Element alias : model.getElements()) {
- if (alias instanceof Compartment) {
- assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
- test = true;
- }
- }
- assertTrue(test);
-
- model2.setHeight(32);
- modelDao.update(model2.getModel());
-
- modelDao.delete(model2);
- model2 = modelDao.getById(model.getId());
- assertNull(model2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionInModelAfterReload() throws Exception {
- try {
- Model model = createModel();
- Reaction reaction = model.getReactions().iterator().next();
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
-
- Reaction reaction2 = null;
- for (Reaction r : model2.getReactions()) {
- if (r.getIdReaction().equals(reaction.getIdReaction())) {
- reaction2 = r;
- }
- }
- assertNotNull(reaction2);
- assertFalse(reaction.equals(reaction2));
-
- assertEquals(reaction.getNodes().size(), reaction2.getNodes().size());
-
- modelDao.delete(model2);
- model2 = modelDao.getById(model.getId());
- assertNull(model2);
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionInWithKinetics() throws Exception {
- try {
- Model model = createModel();
- Reaction reaction = model.getReactions().iterator().next();
- SbmlKinetics kinetics = new SbmlKinetics();
- kinetics.addElement(reaction.getReactants().get(0).getElement());
- kinetics.addFunction(createFunction());
- model.addFunctions(kinetics.getFunctions());
- kinetics.addParameter(createParameter());
- model.addUnit(kinetics.getParameters().iterator().next().getUnits());
- reaction.setKinetics(kinetics);
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
-
- assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
-
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModelWithParameters() throws Exception {
- try {
- Model model = createModel();
- model.addParameter(createParameter());
- model.addUnit(model.getParameters().iterator().next().getUnits());
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
-
- assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
-
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private SbmlParameter createParameter() {
- SbmlParameter parameter = new SbmlParameter("param_id");
- parameter.setName("X");
- parameter.setValue(4.7);
- parameter.setUnits(createUnits());
- return parameter;
- }
-
- private SbmlUnit createUnits() {
- SbmlUnit unit = new SbmlUnit("unit_id");
- unit.setName("u name");
- unit.addUnitTypeFactor(new SbmlUnitTypeFactor(SbmlUnitType.AMPERE, 1, 2, 3));
- return unit;
- }
-
- private SbmlFunction createFunction() {
- SbmlFunction result = new SbmlFunction("fun_id");
- result.setDefinition("def(k1)");
- result.addArgument("k1");
- result.setName("fun name");
- return result;
- }
-
- @Test
- public void testGetLastModelForProjectName() throws Exception {
- try {
- ModelData model3 = modelDao.getLastModelForProjectIdentifier(projectId, false);
- assertNull(model3);
-
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
-
- ModelData newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
- assertNotNull(newModel);
- assertEquals(model.getId(), newModel.getId());
-
- Model model2 = createModel();
- project.addModel(model2);
- modelDao.add(model2);
-
- newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
- assertNotNull(newModel);
- assertEquals(model2.getId(), newModel.getId());
-
- modelDao.delete(model2);
- modelDao.delete(model);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding model to db, modification residues disappear from the model...
- *
- * @throws Exception
- */
- @Test
- public void testModificationsInProteins() throws Exception {
- try {
- Model model = createModel();
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
- Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
-
- Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
- Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
-
- assertFalse(originalSpecies.equals(fromDbSpecies));
- assertEquals(originalSpecies.getModificationResidues().size(), fromDbSpecies.getModificationResidues().size());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding model to db, miriam annotations disappear...
- *
- * @throws Exception
- */
- @Test
- public void testMiriamInSpecies() throws Exception {
- try {
- Model model = createModel();
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
- Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
-
- Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
- Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
-
- assertFalse(originalSpecies.equals(fromDbSpecies));
- assertEquals(originalSpecies.getMiriamData().size(), fromDbSpecies.getMiriamData().size());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding layouts to model.
- *
- * @throws Exception
- */
- @Test
- public void testLayoutsInModel() throws Exception {
- try {
- Model model = createModel();
-
- Layout layout = new Layout();
- layout.setDirectory("tmp");
- layout.setTitle("temporary name");
- model.addLayout(layout);
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
- ModelData model2 = modelDao.getById(model.getId());
-
- assertEquals(1, model2.getLayouts().size());
- assertEquals("tmp", model2.getLayouts().get(0).getDirectory());
- assertEquals("temporary name", model2.getLayouts().get(0).getTitle());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- GenericProtein alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
- model.addElement(alias);
- alias = createSpecies(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
- model.addElement(alias);
- alias = createSpecies(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
- model.addElement(alias);
- alias = createSpecies(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
- model.addElement(alias);
-
- alias = createSpecies(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpecies(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplex(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addSpecies(alias);
- alias3.addSpecies(alias2);
- alias.setComplex(alias3);
- alias2.setComplex(alias3);
-
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
-
- Compartment cAlias = createCompartment(380.0, 416.0, 1893.0, 1866.0, "ca1");
- model.addElement(cAlias);
- model.setWidth(2000);
- model.setHeight(2000);
-
- Layer layer = new Layer();
- model.addLayer(layer);
-
- LayerRect lr = new LayerRect();
- lr.setColor(Color.YELLOW);
- layer.addLayerRect(lr);
-
- Reaction reaction = new TransportReaction();
- reaction.addProduct(new Product(alias));
- reaction.addReactant(new Reactant(alias2));
- reaction.setIdReaction("re" + identifierCounter++);
- model.addReaction(reaction);
-
- alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
- model.addElement(alias);
-
- ModificationResidue mr = new ModificationResidue();
- mr.setName("mr");
- alias.addModificationResidue(mr);
-
- alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
- return model;
- }
-
- private Compartment createCompartment(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private GenericProtein createSpecies(double x, double y, double width, double height, String aliasId) {
- GenericProtein alias = new GenericProtein(aliasId);
- alias.setName("SNCA");
- alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
- alias.setElementId(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Complex createComplex(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class ModelDaoTest extends PersistTestFunctions {
+ ModelComparator modelComparator = new ModelComparator();
+
+ Logger logger = Logger.getLogger(ModelDaoTest.class);
+ private Project project;
+ String projectId = "Some_id";
+ int identifierCounter = 0;
+
+ @Before
+ public void setUp() throws Exception {
+ project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ projectDao.delete(project);
+ }
+
+ @Test
+ public void testLoadFromDb() throws Exception {
+ try {
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+ assertNotNull(model2);
+ assertFalse(model2 == model);
+
+ assertEquals(model.getElements().size(), model2.getElements().size());
+ assertEquals(model.getLayers().size(), model2.getLayers().size());
+ assertEquals(model.getReactions().size(), model2.getReactions().size());
+
+ ModelComparator comparator = new ModelComparator();
+ assertEquals(0, comparator.compare(model, new ModelFullIndexed(model2)));
+
+ modelDao.delete(model2);
+ model2 = modelDao.getById(model.getId());
+ assertNull(model2);
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIndexesReload() throws Exception {
+ try {
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+ Model fullModel = new ModelFullIndexed(model2);
+ assertNotNull(model2);
+
+ assertEquals(model.getElements().size(), model2.getElements().size());
+ assertEquals(model.getLayers().size(), model2.getLayers().size());
+ assertEquals(model.getReactions().size(), model2.getReactions().size());
+
+ // check if we really performed a test
+ boolean test = false;
+
+ for (Element alias : model.getElements()) {
+ assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
+ test = true;
+ }
+ assertTrue(test);
+
+ test = false;
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Compartment) {
+ assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
+ test = true;
+ }
+ }
+ assertTrue(test);
+
+ model2.setHeight(32);
+ modelDao.update(model2.getModel());
+
+ modelDao.delete(model2);
+ model2 = modelDao.getById(model.getId());
+ assertNull(model2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionInModelAfterReload() throws Exception {
+ try {
+ Model model = createModel();
+ Reaction reaction = model.getReactions().iterator().next();
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ Reaction reaction2 = null;
+ for (Reaction r : model2.getReactions()) {
+ if (r.getIdReaction().equals(reaction.getIdReaction())) {
+ reaction2 = r;
+ }
+ }
+ assertNotNull(reaction2);
+ assertFalse(reaction.equals(reaction2));
+
+ assertEquals(reaction.getNodes().size(), reaction2.getNodes().size());
+
+ modelDao.delete(model2);
+ model2 = modelDao.getById(model.getId());
+ assertNull(model2);
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionInWithKinetics() throws Exception {
+ try {
+ Model model = createModel();
+ Reaction reaction = model.getReactions().iterator().next();
+ SbmlKinetics kinetics = new SbmlKinetics();
+ kinetics.addElement(reaction.getReactants().get(0).getElement());
+ kinetics.addFunction(createFunction());
+ model.addFunctions(kinetics.getFunctions());
+ kinetics.addParameter(createParameter());
+ model.addUnit(kinetics.getParameters().iterator().next().getUnits());
+ reaction.setKinetics(kinetics);
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
+
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModelWithParameters() throws Exception {
+ try {
+ Model model = createModel();
+ model.addParameter(createParameter());
+ model.addUnit(model.getParameters().iterator().next().getUnits());
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
+
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private SbmlParameter createParameter() {
+ SbmlParameter parameter = new SbmlParameter("param_id");
+ parameter.setName("X");
+ parameter.setValue(4.7);
+ parameter.setUnits(createUnits());
+ return parameter;
+ }
+
+ private SbmlUnit createUnits() {
+ SbmlUnit unit = new SbmlUnit("unit_id");
+ unit.setName("u name");
+ unit.addUnitTypeFactor(new SbmlUnitTypeFactor(SbmlUnitType.AMPERE, 1, 2, 3));
+ return unit;
+ }
+
+ private SbmlFunction createFunction() {
+ SbmlFunction result = new SbmlFunction("fun_id");
+ result.setDefinition("def(k1)");
+ result.addArgument("k1");
+ result.setName("fun name");
+ return result;
+ }
+
+ @Test
+ public void testGetLastModelForProjectName() throws Exception {
+ try {
+ ModelData model3 = modelDao.getLastModelForProjectIdentifier(projectId, false);
+ assertNull(model3);
+
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+
+ ModelData newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
+ assertNotNull(newModel);
+ assertEquals(model.getId(), newModel.getId());
+
+ Model model2 = createModel();
+ project.addModel(model2);
+ modelDao.add(model2);
+
+ newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
+ assertNotNull(newModel);
+ assertEquals(model2.getId(), newModel.getId());
+
+ modelDao.delete(model2);
+ modelDao.delete(model);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding model to db, modification residues disappear from the model...
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testModificationsInProteins() throws Exception {
+ try {
+ Model model = createModel();
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+ Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
+
+ Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
+ Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
+
+ assertFalse(originalSpecies.equals(fromDbSpecies));
+ assertEquals(originalSpecies.getModificationResidues().size(), fromDbSpecies.getModificationResidues().size());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding model to db, miriam annotations disappear...
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testMiriamInSpecies() throws Exception {
+ try {
+ Model model = createModel();
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+ Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
+
+ Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
+ Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
+
+ assertFalse(originalSpecies.equals(fromDbSpecies));
+ assertEquals(originalSpecies.getMiriamData().size(), fromDbSpecies.getMiriamData().size());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding layouts to model.
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testLayoutsInModel() throws Exception {
+ try {
+ Model model = createModel();
+
+ Layout layout = new Layout();
+ layout.setDirectory("tmp");
+ layout.setTitle("temporary name");
+ model.addLayout(layout);
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(1, model2.getLayouts().size());
+ assertEquals("tmp", model2.getLayouts().get(0).getDirectory());
+ assertEquals("temporary name", model2.getLayouts().get(0).getTitle());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ GenericProtein alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
+ model.addElement(alias);
+ alias = createSpecies(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
+ model.addElement(alias);
+ alias = createSpecies(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
+ model.addElement(alias);
+ alias = createSpecies(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
+ model.addElement(alias);
+
+ alias = createSpecies(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpecies(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplex(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
+ alias.setComplex(alias3);
+ alias2.setComplex(alias3);
+
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
+
+ Compartment cAlias = createCompartment(380.0, 416.0, 1893.0, 1866.0, "ca1");
+ model.addElement(cAlias);
+ model.setWidth(2000);
+ model.setHeight(2000);
+
+ Layer layer = new Layer();
+ model.addLayer(layer);
+
+ LayerRect lr = new LayerRect();
+ lr.setColor(Color.YELLOW);
+ layer.addLayerRect(lr);
+
+ Reaction reaction = new TransportReaction();
+ reaction.addProduct(new Product(alias));
+ reaction.addReactant(new Reactant(alias2));
+ reaction.setIdReaction("re" + identifierCounter++);
+ model.addReaction(reaction);
+
+ alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
+ model.addElement(alias);
+
+ Residue mr = new Residue();
+ mr.setName("mr");
+ mr.setPosition(new Point2D.Double(10, 20));
+ alias.addModificationResidue(mr);
+
+ alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
+ return model;
+ }
+
+ private Compartment createCompartment(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private GenericProtein createSpecies(double x, double y, double width, double height, String aliasId) {
+ GenericProtein alias = new GenericProtein(aliasId);
+ alias.setName("SNCA");
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
+ alias.setElementId(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Complex createComplex(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java
index 3bab7806b996767c2978bb1438fbff6ecd9b17a8..2d02a5e4e6ae6f125b019a2cb3e9a3235e777da0 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java
@@ -1,146 +1,146 @@
-package lcsb.mapviewer.persist.dao.map.layout.alias;
-
-import static org.junit.Assert.assertEquals;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.SearchIndex;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class AliasDaoTest extends PersistTestFunctions {
- Logger logger = Logger.getLogger(AliasDaoTest.class);
-
- private Project project;
- String projectId = "Some_id";
-
- int identifierCounter = 0;
-
- @Before
- public void setUp() throws Exception {
- project = projectDao.getProjectByProjectId(projectId);
- if (project!=null) {
- projectDao.delete(project);
- }
- project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- }
-
- @After
- public void tearDown() throws Exception {
- projectDao.delete(project);
- }
-
- @Test
- public void anotherSaveDaoTest() throws Exception {
- try {
- Model model = createModel();
- project.addModel(model);
-
- Species alias = (Species) model.getElementByElementId("sa2");
-
- alias.getSearchIndexes().add(new SearchIndex("blabla"));
-
- modelDao.add(model);
-
- Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
-
- Species alias2 = (Species) aliasDao.getById(model2.getElementByElementId("sa2").getId());
-
- assertEquals(1, alias2.getSearchIndexes().size());
-
- modelDao.delete(model);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
- model.addElement(createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
- model.addElement(createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
- model.addElement(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
- model.addElement(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
-
- Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addSpecies(alias);
- alias3.addSpecies(alias2);
- alias.setComplex(alias3);
- alias2.setComplex(alias3);
-
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
-
- model.addElement(createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1"));
- model.setWidth(2000);
- model.setHeight(2000);
- return model;
- }
-
- private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Species createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- SimpleMolecule alias = new SimpleMolecule(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- @Test
- public void saveAliasWithSubmodelTest() throws Exception {
- try {
- long count = modelDao.getCount();
- Model model = createModel();
- Model model1 = createModel();
- Element alias = model.getElementByElementId("sa2");
- ElementSubmodelConnection submodel = new ElementSubmodelConnection(model1, SubmodelType.UNKNOWN);
- alias.setSubmodel(submodel);
- project.addModel(model);
-
- projectDao.add(project);
- projectDao.flush();
-
- long count2 = modelDao.getCount();
- assertEquals(count + 2, count2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.layout.alias;
+
+import static org.junit.Assert.assertEquals;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class AliasDaoTest extends PersistTestFunctions {
+ Logger logger = Logger.getLogger(AliasDaoTest.class);
+
+ private Project project;
+ String projectId = "Some_id";
+
+ int identifierCounter = 0;
+
+ @Before
+ public void setUp() throws Exception {
+ project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ projectDao.delete(project);
+ }
+
+ @Test
+ public void anotherSaveDaoTest() throws Exception {
+ try {
+ Model model = createModel();
+ project.addModel(model);
+
+ Species alias = (Species) model.getElementByElementId("sa2");
+
+ alias.getSearchIndexes().add(new SearchIndex("blabla"));
+
+ modelDao.add(model);
+
+ Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
+
+ Species alias2 = (Species) elementDao.getById(model2.getElementByElementId("sa2").getId());
+
+ assertEquals(1, alias2.getSearchIndexes().size());
+
+ modelDao.delete(model);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+ model.addElement(createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
+ model.addElement(createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
+ model.addElement(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
+ model.addElement(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
+
+ Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
+ alias.setComplex(alias3);
+ alias2.setComplex(alias3);
+
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
+
+ model.addElement(createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1"));
+ model.setWidth(2000);
+ model.setHeight(2000);
+ return model;
+ }
+
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Species createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ SimpleMolecule alias = new SimpleMolecule(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ @Test
+ public void saveAliasWithSubmodelTest() throws Exception {
+ try {
+ long count = modelDao.getCount();
+ Model model = createModel();
+ Model model1 = createModel();
+ Element alias = model.getElementByElementId("sa2");
+ ElementSubmodelConnection submodel = new ElementSubmodelConnection(model1, SubmodelType.UNKNOWN);
+ alias.setSubmodel(submodel);
+ project.addModel(model);
+
+ projectDao.add(project);
+ projectDao.flush();
+
+ long count2 = modelDao.getCount();
+ assertEquals(count + 2, count2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
index 1aefeefe0383b3e6b860bbe77ab348f73461bc50..abab8f1ff18ba61d06e5297769f517dd076474b0 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
@@ -1,311 +1,301 @@
-package lcsb.mapviewer.persist.dao.map.layout.alias;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Chemical;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class AliasDaoTest2 extends PersistTestFunctions {
- static Logger logger = Logger.getLogger(AliasDaoTest.class);
-
- private Integer testChargeVal = 1;
- private String testIdAlias = "a";
- private Double testInitialAmount = 2.0;
- private Double testInitialConcentration = 3.0;
- private String testName = "d";
- private String testNotes = "e";
- private Boolean testOnlySubstanceunits = true;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAdd() throws Exception {
- try {
-
- GenericProtein sp = new GenericProtein(testIdAlias);
- sp.setCharge(testChargeVal);
- sp.setInitialAmount(testInitialAmount);
- sp.setInitialConcentration(testInitialConcentration);
- sp.setName(testName);
- sp.setNotes(testNotes);
- sp.setOnlySubstanceUnits(testOnlySubstanceunits);
-
- Compartment parent = new Compartment("comp id");
- sp.setCompartment(parent);
-
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.UNKNOWN, "c");
- sp.addMiriamData(md);
-
- aliasDao.add(sp);
-
- Species sp2 = (Species) aliasDao.getById(sp.getId());
- assertNotNull(sp2);
- assertEquals(sp.getCharge(), sp2.getCharge());
- assertEquals(sp.getElementId(), sp2.getElementId());
- assertEquals(sp.getInitialAmount(), sp2.getInitialAmount());
- assertEquals(sp.getInitialConcentration(), sp2.getInitialConcentration());
- assertEquals(sp.getName(), sp2.getName());
- assertEquals(sp.getNotes(), sp2.getNotes());
- assertEquals(sp.hasOnlySubstanceUnits(), sp2.hasOnlySubstanceUnits());
-
- Compartment parent2 = sp2.getCompartment();
- assertNotNull(parent2);
- assertEquals("comp id", parent2.getElementId());
-
- assertNotNull(sp2.getMiriamData());
-
- MiriamData md2 = sp2.getMiriamData().iterator().next();
- assertNotNull(md2);
- assertEquals(md.getDataType(), md2.getDataType());
- assertEquals(md.getRelationType(), md2.getRelationType());
- assertEquals(md.getResource(), md2.getResource());
-
- aliasDao.delete(sp);
- sp2 = (Species) aliasDao.getById(sp.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProtein() throws Exception {
- try {
-
- Protein protein = new GenericProtein(testIdAlias);
- ModificationResidue mr = new ModificationResidue();
- mr.setAngle(2.0);
- mr.setName("name");
- mr.setSide("side");
- mr.setSize(3.0);
- mr.setState(ModificationState.GLYCOSYLATED);
- protein.addModificationResidue(mr);
-
- aliasDao.add(protein);
-
- Protein sp2 = (Protein) aliasDao.getById(protein.getId());
- assertNotNull(sp2);
- assertEquals(protein.getElementId(), sp2.getElementId());
-
- assertNotNull(sp2.getModificationResidues());
- assertEquals(1, sp2.getModificationResidues().size());
-
- assertEquals(sp2.getModificationResidues().get(0).getAngle(), mr.getAngle());
- assertEquals(sp2.getModificationResidues().get(0).getIdModificationResidue(), mr.getIdModificationResidue());
- assertEquals(sp2.getModificationResidues().get(0).getName(), mr.getName());
- assertEquals(sp2.getModificationResidues().get(0).getSide(), mr.getSide());
- assertEquals(sp2.getModificationResidues().get(0).getSize(), mr.getSize());
- assertEquals(sp2.getModificationResidues().get(0).getState(), mr.getState());
-
- aliasDao.delete(sp2);
- sp2 = (Protein) aliasDao.getById(protein.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRna() throws Exception {
- try {
-
- Rna sp = new Rna(testIdAlias);
- RnaRegion mr = new RnaRegion();
- mr.setName("name");
- mr.setSize(3.0);
- mr.setState(ModificationState.DONT_CARE);
- sp.addRegion(mr);
-
- aliasDao.add(sp);
- aliasDao.evict(sp);
-
- Rna sp2 = (Rna) aliasDao.getById(sp.getId());
- assertNotNull(sp2);
- assertEquals(sp.getElementId(), sp2.getElementId());
-
- assertNotNull(sp2.getRegions());
- assertEquals(1, sp2.getRegions().size());
-
- assertEquals(sp2.getRegions().get(0).getId(), mr.getId());
- assertEquals(sp2.getRegions().get(0).getName(), mr.getName());
- assertEquals(sp2.getRegions().get(0).getSize(), mr.getSize(), EPSILON);
- assertEquals(sp2.getRegions().get(0).getState(), mr.getState());
-
- aliasDao.delete(sp2);
- sp2 = (Rna) aliasDao.getById(sp.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAntisenseRna() throws Exception {
- try {
-
- AntisenseRna sp = new AntisenseRna(testIdAlias);
- AntisenseRnaRegion mr = new AntisenseRnaRegion();
- mr.setName("name");
- mr.setSize(3.0);
- mr.setType(AntisenseRnaRegionType.MODIFICATION_SITE);
- mr.setState(ModificationState.UNKNOWN);
- sp.addRegion(mr);
-
- aliasDao.add(sp);
- aliasDao.evict(sp);
-
- AntisenseRna sp2 = (AntisenseRna) aliasDao.getById(sp.getId());
- assertNotNull(sp2);
- assertEquals(sp.getElementId(), sp2.getElementId());
-
- assertNotNull(sp2.getRegions());
- assertEquals(1, sp2.getRegions().size());
-
- assertEquals(sp2.getRegions().get(0).getIdAntisenseRnaRegion(), mr.getIdAntisenseRnaRegion());
- assertEquals(sp2.getRegions().get(0).getName(), mr.getName());
- assertEquals(sp2.getRegions().get(0).getSize(), mr.getSize(), EPSILON);
- assertEquals(sp2.getRegions().get(0).getState(), mr.getState());
- assertEquals(sp2.getRegions().get(0).getType(), mr.getType());
-
- aliasDao.delete(sp2);
- sp2 = (AntisenseRna) aliasDao.getById(sp.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSynonymsInAlias() throws Exception {
- try {
- Protein protein = new GenericProtein(testIdAlias);
- protein.addSynonym("Synonym");
- protein.addSynonym("Synonym A");
- protein.addSynonym("A");
-
- protein.addFormerSymbol("Sym");
- protein.addFormerSymbol("Sym A");
- protein.addFormerSymbol("DD");
-
- aliasDao.add(protein);
- aliasDao.flush();
-
- aliasDao.evict(protein);
- Protein sp2 = (Protein) aliasDao.getById(protein.getId());
-
- assertNotNull(sp2.getSynonyms());
- assertEquals(protein.getSynonyms().size(), sp2.getSynonyms().size());
-
- for (int i = 0; i < protein.getSynonyms().size(); i++) {
- assertEquals(protein.getSynonyms().get(i), sp2.getSynonyms().get(i));
- }
-
- assertNotNull(sp2.getFormerSymbols());
- assertEquals(protein.getFormerSymbols().size(), sp2.getFormerSymbols().size());
-
- for (int i = 0; i < protein.getFormerSymbols().size(); i++) {
- assertEquals(protein.getFormerSymbols().get(i), sp2.getFormerSymbols().get(i));
- }
-
- aliasDao.delete(sp2);
- sp2 = (Protein) aliasDao.getById(protein.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChemicals() throws Exception {
- try {
- Chemical ion = new Ion(testIdAlias);
- ion.setInChI("come inchi");
- ion.setInChIKey("keyyy");
- ion.setSmiles("smile");
-
- aliasDao.add(ion);
- aliasDao.flush();
-
- aliasDao.evict(ion);
- Ion sp2 = (Ion) aliasDao.getById(ion.getId());
-
- assertNotNull(sp2.getSynonyms());
- assertEquals(ion.getSynonyms().size(), sp2.getSynonyms().size());
-
- assertEquals(ion.getSmiles(), sp2.getSmiles());
- assertEquals(ion.getInChIKey(), sp2.getInChIKey());
- assertEquals(ion.getInChI(), sp2.getInChI());
-
- aliasDao.delete(sp2);
- sp2 = (Ion) aliasDao.getById(ion.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPhenotype() throws Exception {
- try {
- Phenotype phenotype = new Phenotype(testIdAlias);
-
- aliasDao.add(phenotype);
- aliasDao.flush();
-
- aliasDao.evict(phenotype);
- Phenotype sp2 = (Phenotype) aliasDao.getById(phenotype.getId());
-
- assertNotNull(sp2.getSynonyms());
- assertEquals(phenotype.getSynonyms().size(), phenotype.getSynonyms().size());
-
- aliasDao.delete(sp2);
- sp2 = (Phenotype) aliasDao.getById(phenotype.getId());
- assertNull(sp2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.persist.dao.map.layout.alias;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Chemical;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class AliasDaoTest2 extends PersistTestFunctions {
+ static Logger logger = Logger.getLogger(AliasDaoTest.class);
+
+ private Integer testChargeVal = 1;
+ private String testIdAlias = "a";
+ private Double testInitialAmount = 2.0;
+ private Double testInitialConcentration = 3.0;
+ private String testName = "d";
+ private String testNotes = "e";
+ private Boolean testOnlySubstanceunits = true;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAdd() throws Exception {
+ try {
+
+ GenericProtein sp = new GenericProtein(testIdAlias);
+ sp.setCharge(testChargeVal);
+ sp.setInitialAmount(testInitialAmount);
+ sp.setInitialConcentration(testInitialConcentration);
+ sp.setName(testName);
+ sp.setNotes(testNotes);
+ sp.setOnlySubstanceUnits(testOnlySubstanceunits);
+
+ Compartment parent = new Compartment("comp id");
+ sp.setCompartment(parent);
+
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.UNKNOWN, "c");
+ sp.addMiriamData(md);
+
+ elementDao.add(sp);
+
+ Species sp2 = (Species) elementDao.getById(sp.getId());
+ assertNotNull(sp2);
+ assertEquals(sp.getCharge(), sp2.getCharge());
+ assertEquals(sp.getElementId(), sp2.getElementId());
+ assertEquals(sp.getInitialAmount(), sp2.getInitialAmount());
+ assertEquals(sp.getInitialConcentration(), sp2.getInitialConcentration());
+ assertEquals(sp.getName(), sp2.getName());
+ assertEquals(sp.getNotes(), sp2.getNotes());
+ assertEquals(sp.hasOnlySubstanceUnits(), sp2.hasOnlySubstanceUnits());
+
+ Compartment parent2 = sp2.getCompartment();
+ assertNotNull(parent2);
+ assertEquals("comp id", parent2.getElementId());
+
+ assertNotNull(sp2.getMiriamData());
+
+ MiriamData md2 = sp2.getMiriamData().iterator().next();
+ assertNotNull(md2);
+ assertEquals(md.getDataType(), md2.getDataType());
+ assertEquals(md.getRelationType(), md2.getRelationType());
+ assertEquals(md.getResource(), md2.getResource());
+
+ elementDao.delete(sp);
+ sp2 = (Species) elementDao.getById(sp.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProtein() throws Exception {
+ try {
+
+ Protein protein = new GenericProtein(testIdAlias);
+ Residue mr = new Residue();
+ mr.setPosition(new Point2D.Double(10, 20));
+ mr.setName("name");
+ mr.setState(ModificationState.GLYCOSYLATED);
+ protein.addModificationResidue(mr);
+
+ elementDao.add(protein);
+
+ Protein sp2 = (Protein) elementDao.getById(protein.getId());
+ assertNotNull(sp2);
+ assertEquals(protein.getElementId(), sp2.getElementId());
+
+ assertNotNull(sp2.getModificationResidues());
+ assertEquals(1, sp2.getModificationResidues().size());
+
+ Residue copy = (Residue) sp2.getModificationResidues().get(0);
+ assertEquals(copy.getPosition(), mr.getPosition());
+ assertEquals(copy.getIdModificationResidue(), mr.getIdModificationResidue());
+ assertEquals(copy.getName(), mr.getName());
+ assertEquals(copy.getState(), mr.getState());
+
+ elementDao.delete(sp2);
+ sp2 = (Protein) elementDao.getById(protein.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRna() throws Exception {
+ try {
+
+ Rna sp = new Rna(testIdAlias);
+ ModificationSite mr = new ModificationSite();
+ mr.setName("name");
+ mr.setState(ModificationState.DONT_CARE);
+ sp.addRegion(mr);
+
+ elementDao.add(sp);
+ elementDao.evict(sp);
+
+ Rna sp2 = (Rna) elementDao.getById(sp.getId());
+ assertNotNull(sp2);
+ assertEquals(sp.getElementId(), sp2.getElementId());
+
+ assertNotNull(sp2.getRegions());
+ assertEquals(1, sp2.getRegions().size());
+
+ ModificationSite copy = (ModificationSite) sp2.getRegions().get(0);
+ assertEquals(copy.getId(), mr.getId());
+ assertEquals(copy.getName(), mr.getName());
+ assertEquals(copy.getState(), mr.getState());
+
+ elementDao.delete(sp2);
+ sp2 = (Rna) elementDao.getById(sp.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAntisenseRna() throws Exception {
+ try {
+
+ AntisenseRna sp = new AntisenseRna(testIdAlias);
+ ModificationSite mr = new ModificationSite();
+ mr.setName("name");
+ sp.addRegion(mr);
+
+ elementDao.add(sp);
+ elementDao.evict(sp);
+
+ AntisenseRna sp2 = (AntisenseRna) elementDao.getById(sp.getId());
+ assertNotNull(sp2);
+ assertEquals(sp.getElementId(), sp2.getElementId());
+
+ assertNotNull(sp2.getRegions());
+ assertEquals(1, sp2.getRegions().size());
+
+ assertEquals(sp2.getRegions().get(0).getIdModificationResidue(), mr.getIdModificationResidue());
+ assertEquals(sp2.getRegions().get(0).getName(), mr.getName());
+
+ elementDao.delete(sp2);
+ sp2 = (AntisenseRna) elementDao.getById(sp.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSynonymsInAlias() throws Exception {
+ try {
+ Protein protein = new GenericProtein(testIdAlias);
+ protein.addSynonym("Synonym");
+ protein.addSynonym("Synonym A");
+ protein.addSynonym("A");
+
+ protein.addFormerSymbol("Sym");
+ protein.addFormerSymbol("Sym A");
+ protein.addFormerSymbol("DD");
+
+ elementDao.add(protein);
+ elementDao.flush();
+
+ elementDao.evict(protein);
+ Protein sp2 = (Protein) elementDao.getById(protein.getId());
+
+ assertNotNull(sp2.getSynonyms());
+ assertEquals(protein.getSynonyms().size(), sp2.getSynonyms().size());
+
+ for (int i = 0; i < protein.getSynonyms().size(); i++) {
+ assertEquals(protein.getSynonyms().get(i), sp2.getSynonyms().get(i));
+ }
+
+ assertNotNull(sp2.getFormerSymbols());
+ assertEquals(protein.getFormerSymbols().size(), sp2.getFormerSymbols().size());
+
+ for (int i = 0; i < protein.getFormerSymbols().size(); i++) {
+ assertEquals(protein.getFormerSymbols().get(i), sp2.getFormerSymbols().get(i));
+ }
+
+ elementDao.delete(sp2);
+ sp2 = (Protein) elementDao.getById(protein.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChemicals() throws Exception {
+ try {
+ Chemical ion = new Ion(testIdAlias);
+ ion.setInChI("come inchi");
+ ion.setInChIKey("keyyy");
+ ion.setSmiles("smile");
+
+ elementDao.add(ion);
+ elementDao.flush();
+
+ elementDao.evict(ion);
+ Ion sp2 = (Ion) elementDao.getById(ion.getId());
+
+ assertNotNull(sp2.getSynonyms());
+ assertEquals(ion.getSynonyms().size(), sp2.getSynonyms().size());
+
+ assertEquals(ion.getSmiles(), sp2.getSmiles());
+ assertEquals(ion.getInChIKey(), sp2.getInChIKey());
+ assertEquals(ion.getInChI(), sp2.getInChI());
+
+ elementDao.delete(sp2);
+ sp2 = (Ion) elementDao.getById(ion.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPhenotype() throws Exception {
+ try {
+ Phenotype phenotype = new Phenotype(testIdAlias);
+
+ elementDao.add(phenotype);
+ elementDao.flush();
+
+ elementDao.evict(phenotype);
+ Phenotype sp2 = (Phenotype) elementDao.getById(phenotype.getId());
+
+ assertNotNull(sp2.getSynonyms());
+ assertEquals(phenotype.getSynonyms().size(), phenotype.getSynonyms().size());
+
+ elementDao.delete(sp2);
+ sp2 = (Phenotype) elementDao.getById(phenotype.getId());
+ assertNull(sp2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
index 02c33a2fc3ba37e16ada8225dd09f7ed302b1507..44bb7dcec7e4cc03078389b86f2b6fcf2e4c5373 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
@@ -1,88 +1,88 @@
-package lcsb.mapviewer.persist.dao.map.layout.alias;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.test.annotation.Rollback;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-@Rollback(true)
-public class AntisenseRnaTest extends PersistTestFunctions {
- Logger logger = Logger.getLogger(AntisenseRnaTest.class);
-
- int identifierCounter = 0;
- String projectId = "Some_id";
-
- @Before
- public void setUp() throws Exception {
- Project project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAntisenseRnaRegionInDb() throws Exception {
- try {
- Project project = new Project();
- project.setProjectId(projectId);
-
- Model model = createModel();
-
- project.addModel(model);
- projectDao.add(project);
- projectDao.evict(project);
-
- Project project2 = projectDao.getProjectByProjectId(projectId);
- assertNotNull(project2);
- assertFalse(project2.equals(project));
- assertEquals(project.getId(), project2.getId());
-
- Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
-
- Element sp = model.getElements().iterator().next();
- AntisenseRna ar = (AntisenseRna) sp;
-
- Element sp2 = model2.getElements().iterator().next();
- AntisenseRna ar2 = (AntisenseRna) sp2;
-
- projectDao.delete(project2);
-
- assertEquals(ar.getRegions().size(), ar2.getRegions().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- AntisenseRna alias = new AntisenseRna("As");
- alias.addRegion(new AntisenseRnaRegion());
- alias.setX(1);
- alias.setY(2);
- alias.setWidth(10);
- alias.setHeight(20);
- model.addElement(alias);
-
- return model;
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.layout.alias;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.test.annotation.Rollback;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+@Rollback(true)
+public class AntisenseRnaTest extends PersistTestFunctions {
+ Logger logger = Logger.getLogger(AntisenseRnaTest.class);
+
+ int identifierCounter = 0;
+ String projectId = "Some_id";
+
+ @Before
+ public void setUp() throws Exception {
+ Project project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAntisenseRnaRegionInDb() throws Exception {
+ try {
+ Project project = new Project();
+ project.setProjectId(projectId);
+
+ Model model = createModel();
+
+ project.addModel(model);
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ Project project2 = projectDao.getProjectByProjectId(projectId);
+ assertNotNull(project2);
+ assertFalse(project2.equals(project));
+ assertEquals(project.getId(), project2.getId());
+
+ Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
+
+ Element sp = model.getElements().iterator().next();
+ AntisenseRna ar = (AntisenseRna) sp;
+
+ Element sp2 = model2.getElements().iterator().next();
+ AntisenseRna ar2 = (AntisenseRna) sp2;
+
+ projectDao.delete(project2);
+
+ assertEquals(ar.getRegions().size(), ar2.getRegions().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ AntisenseRna alias = new AntisenseRna("As");
+ alias.addRegion(new CodingRegion());
+ alias.setX(1);
+ alias.setY(2);
+ alias.setWidth(10);
+ alias.setHeight(20);
+ model.addElement(alias);
+
+ return model;
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
index 04da77ac6f445aa3dea8f1755afa915499f53e8e..4eea1e67a969bfceb63b199381fe79e7d95e4464 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
@@ -1,87 +1,87 @@
-package lcsb.mapviewer.persist.dao.map.layout.alias;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class RnaTest extends PersistTestFunctions {
- Logger logger = Logger.getLogger(RnaTest.class);
-
- int identifierCounter = 0;
-
- String projectId = "Some_id";
-
- @Before
- public void setUp() throws Exception {
- Project project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testRnaRegionInDb() throws Exception {
- try {
- Project project = new Project();
- project.setProjectId(projectId);
-
- Model model = createModel();
-
- project.addModel(model);
- projectDao.add(project);
- projectDao.evict(project);
-
- Project project2 = projectDao.getProjectByProjectId(projectId);
- assertNotNull(project2);
- assertFalse(project2.equals(project));
- assertEquals(project.getId(), project2.getId());
-
- Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
-
- Element sp = model.getElements().iterator().next();
- Rna ar = (Rna) sp;
-
- Element sp2 = model2.getElements().iterator().next();
- Rna ar2 = (Rna) sp2;
-
- projectDao.delete(project2);
-
- assertEquals(ar.getRegions().size(), ar2.getRegions().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- Rna alias = new Rna("As");
- alias.addRegion(new RnaRegion());
- alias.setX(1);
- alias.setY(2);
- alias.setWidth(10);
- alias.setHeight(20);
- model.addElement(alias);
-
- return model;
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.layout.alias;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class RnaTest extends PersistTestFunctions {
+ Logger logger = Logger.getLogger(RnaTest.class);
+
+ int identifierCounter = 0;
+
+ String projectId = "Some_id";
+
+ @Before
+ public void setUp() throws Exception {
+ Project project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testRnaRegionInDb() throws Exception {
+ try {
+ Project project = new Project();
+ project.setProjectId(projectId);
+
+ Model model = createModel();
+
+ project.addModel(model);
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ Project project2 = projectDao.getProjectByProjectId(projectId);
+ assertNotNull(project2);
+ assertFalse(project2.equals(project));
+ assertEquals(project.getId(), project2.getId());
+
+ Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
+
+ Element sp = model.getElements().iterator().next();
+ Rna ar = (Rna) sp;
+
+ Element sp2 = model2.getElements().iterator().next();
+ Rna ar2 = (Rna) sp2;
+
+ projectDao.delete(project2);
+
+ assertEquals(ar.getRegions().size(), ar2.getRegions().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ Rna alias = new Rna("As");
+ alias.addRegion(new CodingRegion());
+ alias.setX(1);
+ alias.setY(2);
+ alias.setWidth(10);
+ alias.setHeight(20);
+ model.addElement(alias);
+
+ return model;
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
index 0192989f6d3471a9bd30b06f1a97ed4c8332223e..aad6f041c4ff8015282de4d5152c84becfa82f44 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
@@ -122,49 +122,6 @@ public class UserDaoTest extends PersistTestFunctions {
}
}
- @Test
- public void testGetUserByLoginAndPassword() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(passwordEncoder.encode(testPasswd));
- user.setLogin(testLogin);
- userDao.add(user);
- User user2 = userDao.getUserByLoginAndPassword(testLogin, testPasswd);
- assertNotNull(user2);
- assertEquals(user2.getId(), user.getId());
- assertEquals(user2.getLogin(), user.getLogin());
- assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
- userDao.delete(user);
- // after we remove it we shouldn't be able to get it
- User user3 = userDao.getUserByLoginAndPassword(testLogin, testPasswd);
- assertNull(user3);
-
- // after we remove it we shouldn't be able to get the removed and modified
- // object
- User user4 = userDao.getUserByLoginAndPassword(user2.getLogin(), testPasswd);
- assertNull(user4);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUserByLoginAndEmptyPassword() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(passwordEncoder.encode(testPasswd));
- user.setLogin(testLogin);
- userDao.add(user);
- User user2 = userDao.getUserByLoginAndPassword(testLogin, null);
- assertNull(user2);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testGetUserByLogin() throws Exception {
try {
@@ -208,27 +165,6 @@ public class UserDaoTest extends PersistTestFunctions {
}
}
- @Test
- public void testGetUserByNameSurname() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(passwordEncoder.encode(testPasswd));
- user.setLogin(testLogin);
- user.setEmail(testEmail);
- user.setName(testName);
- user.setSurname(testSurname);
- userDao.add(user);
- User user2 = userDao.getUserByNameSurname(testName + " " + testSurname);
- assertNotNull(user2);
- user2 = userDao.getUserByNameSurname(testName + " " + testSurname);
- assertNull(user2);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testGetAll() throws Exception {
try {
diff --git a/pom.xml b/pom.xml
index be583c05b21d751798a01048bf847c29d2a6e06f..d5d32a9cadb483204b206b47cce6112ac4f49447 100644
--- a/pom.xml
+++ b/pom.xml
@@ -82,6 +82,8 @@
<cglib.version>2.2.2</cglib.version>
+
+ <unboundid-ldapsdk.version>4.0.6</unboundid-ldapsdk.version>
<mockito.version>1.10.19</mockito.version>
</properties>
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
index 67b4a370f098d4b3c23627b47751a9a158c6386a..cbcb47bcad6476b71d847b34013efab9a2cf3f3e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
@@ -1,16 +1,21 @@
package lcsb.mapviewer.api.genomics;
+import java.io.IOException;
+import java.util.List;
import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
+import org.springframework.util.MultiValueMap;
import org.springframework.web.bind.annotation.CookieValue;
import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
import javassist.tools.rmi.ObjectNotFoundException;
+import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Configuration;
@@ -32,4 +37,88 @@ public class ReferenceGenomeController extends BaseController {
) throws SecurityException, QueryException, ObjectNotFoundException {
return referenceGenomeController.getReferenceGenome(token, organism, type, version);
}
+
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}:getAvailableRemoteUrls", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getRemoteUrls(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism, //
+ @PathVariable(value = "type") String type, //
+ @PathVariable(value = "version") String version//
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getRemoteUrls(token, organism, type, version);
+ }
+
+ @RequestMapping(value = "/genomics/taxonomies/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getGenomeTaxonomies(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomeTaxonomies(token);
+ }
+
+ @RequestMapping(value = "/genomics/", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addGenome(//
+ @RequestBody MultiValueMap<String, Object> formData, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ return referenceGenomeController.addReferenceGenome(formData, token);
+ }
+
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getGenomeTaxonomyTypes(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomeTypes(token, organism);
+ }
+
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getGenomeVersion(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism, //
+ @PathVariable(value = "type") String type //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomeVersions(token, organism, type);
+ }
+
+ @RequestMapping(value = "/genomics/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getDownloaded(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomes(token);
+ }
+
+ @RequestMapping(value = "/genomics/{genomeId}/", method = { RequestMethod.DELETE }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> removeGenome(//
+ @PathVariable(value = "genomeId") String genomeId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException {
+ return referenceGenomeController.removeGenome(genomeId, token);
+ }
+
+ @RequestMapping(value = "/genomics/{genomeId}/geneMapping/{mappingId}/", method = { RequestMethod.DELETE }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> removeGeneMapping(//
+ @PathVariable(value = "genomeId") String genomeId, //
+ @PathVariable(value = "mappingId") String mappingId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException, lcsb.mapviewer.api.ObjectNotFoundException {
+ return referenceGenomeController.removeGeneMapping(genomeId,mappingId, token);
+ }
+
+ @RequestMapping(value = "/genomics/{genomeId}/geneMapping/", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addGeneMapping(//
+ @PathVariable(value = "genomeId") String genomeId, //
+ @RequestBody MultiValueMap<String, Object> formData, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ return referenceGenomeController.addGeneMapping(formData, genomeId, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
index 9c1f782af4c1debc383b2bc0aeeb405a29e93959..b47cf24709cfd7ac17eb4937aa75b761904fca9f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
@@ -1,16 +1,23 @@
package lcsb.mapviewer.api.genomics;
import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.URISyntaxException;
import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.TreeMap;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
+import org.springframework.util.MultiValueMap;
import lcsb.mapviewer.annotation.cache.BigFileCache;
+import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.api.QueryException;
@@ -19,6 +26,7 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ReferenceGenome;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
@@ -62,16 +70,42 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
}
}
+ public List<Map<String, Object>> getRemoteUrls(String token, String organismId, String type, String version)
+ throws SecurityException, QueryException, ObjectNotFoundException {
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ try {
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ String url = referenceGenomeService.getUrlForGenomeVersion(genomeType, organism, version);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+ if (url != null) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("url", url);
+ result.add(row);
+ }
+ return result;
+ } catch (IllegalArgumentException e) {
+ throw new QueryException("Cannot find type: " + type);
+ }
+ }
+
private Map<String, Object> genomeToMap(ReferenceGenome genome) {
Map<String, Object> result = new TreeMap<>();
result.put("organism", super.createAnnotation(genome.getOrganism()));
result.put("version", genome.getVersion());
+ result.put("type", genome.getType());
result.put("downloadProgress", genome.getDownloadProgress());
result.put("sourceUrl", genome.getSourceUrl());
result.put("localUrl", getLocalUrl(genome.getSourceUrl()));
+ result.put("idObject", genome.getId());
result.put("geneMapping", geneMappingToMaps(genome.getGeneMapping()));
- return null;
+ return result;
}
private String getLocalUrl(String sourceUrl) {
@@ -99,7 +133,153 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
result.put("localUrl", getLocalUrl(mapping.getSourceUrl()));
result.put("sourceUrl", mapping.getSourceUrl());
result.put("name", mapping.getName());
+ result.put("idObject", mapping.getId());
return result;
}
+ public List<Map<String, Object>> getReferenceGenomeTaxonomies(String token) throws QueryException {
+ try {
+ Set<MiriamData> organisms = new HashSet<>();
+ for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
+ organisms.addAll(referenceGenomeService.getOrganismsByReferenceGenomeType(type));
+ }
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (MiriamData miriamData : organisms) {
+ result.add(createAnnotation(miriamData));
+ }
+ return result;
+ } catch (ReferenceGenomeConnectorException e) {
+ throw new QueryException("Problem with obtaining organism list", e);
+ }
+ }
+
+ public List<Map<String, Object>> getReferenceGenomeTypes(String token, String organismId) throws QueryException {
+ try {
+ Set<MiriamData> organisms = new HashSet<>();
+ for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
+ organisms.addAll(referenceGenomeService.getOrganismsByReferenceGenomeType(type));
+ }
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (MiriamData miriamData : organisms) {
+ if (miriamData.getResource().equals(organismId)) {
+ Map<String, Object> entry = new HashMap<>();
+ entry.put("type", ReferenceGenomeType.UCSC.toString());
+ result.add(entry);
+ }
+ }
+ return result;
+ } catch (ReferenceGenomeConnectorException e) {
+ throw new QueryException("Problem with obtaining organism list", e);
+ }
+ }
+
+ public List<Map<String, Object>> getReferenceGenomeVersions(String token, String organismId, String type)
+ throws QueryException {
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ List<String> versions;
+ try {
+ versions = referenceGenomeService.getAvailableGenomeVersions(genomeType, organism);
+ } catch (ReferenceGenomeConnectorException e) {
+ throw new QueryException("Problem with obtaining version list", e);
+ }
+
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (String string : versions) {
+ Map<String, Object> entry = new HashMap<>();
+ entry.put("version", string);
+ result.add(entry);
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getReferenceGenomes(String token)
+ throws SecurityException, QueryException, ObjectNotFoundException {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ReferenceGenome genome : referenceGenomeService.getDownloadedGenomes()) {
+ result.add(genomeToMap(genome));
+ }
+ return result;
+ }
+
+ public Map<String, Object> removeGenome(String genomeId, String token) throws SecurityException, IOException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(Integer.parseInt(genomeId), token);
+ referenceGenomeService.removeGenome(genome);
+ return okStatus();
+ }
+
+ public Map<String, Object> addReferenceGenome(MultiValueMap<String, Object> formData, String token)
+ throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+
+ String organismId = getFirstValue(formData.get("organismId"));
+ String type = getFirstValue(formData.get("type"));
+ String version = getFirstValue(formData.get("version"));
+ String url = getFirstValue(formData.get("sourceUrl"));
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ try {
+ referenceGenomeService.addReferenceGenome(genomeType, organism, version, url);
+ return okStatus();
+ } catch (URISyntaxException e) {
+ throw new QueryException("Problem wih given uri", e);
+ }
+ }
+
+ public Map<String, Object> addGeneMapping(MultiValueMap<String, Object> formData, String genomeId, String token)
+ throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+
+ int id = Integer.parseInt(genomeId);
+ try {
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(id, token);
+ String name = getFirstValue(formData.get("name"));
+ String url = getFirstValue(formData.get("url"));
+ referenceGenomeService.addReferenceGenomeGeneMapping(genome, name, url);
+ return okStatus();
+ } catch (URISyntaxException e) {
+ throw new QueryException("Problem wih given uri", e);
+ }
+ }
+
+ public Map<String, Object> removeGeneMapping(String genomeId, String mappingId, String token)
+ throws SecurityException, IOException, ObjectNotFoundException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(Integer.parseInt(genomeId), token);
+ if (genome == null) {
+ throw new ObjectNotFoundException("Genome doesn't exist");
+ }
+ int id = Integer.parseInt(mappingId);
+ ReferenceGenomeGeneMapping geneMapping = null;
+ for (ReferenceGenomeGeneMapping mapping : genome.getGeneMapping()) {
+ if (mapping.getId() == id) {
+ geneMapping = mapping;
+ }
+ }
+ if (geneMapping == null) {
+ throw new ObjectNotFoundException("Gene mapping doesn't exist");
+ }
+ referenceGenomeService.removeReferenceGenomeGeneMapping(geneMapping);
+ return okStatus();
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index f34f2cbe61f28de4981c333b9405a4e0847fde11..785e3def809ca0460680c859f2f966e91fbdb0b9 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -39,15 +39,12 @@ public class DrugRestImpl extends BaseRestImpl {
@Autowired
private IDrugService drugService;
- @Autowired
- private IModelService modelService;
-
@Autowired
private IUserService userService;
public List<Map<String, Object>> getDrugsByQuery(String token, String projectId, String columns, String query)
throws SecurityException, QueryException {
- Model model = modelService.getLastModelByProjectId(projectId, token);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -87,23 +84,6 @@ public class DrugRestImpl extends BaseRestImpl {
this.userService = userService;
}
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
private Map<String, Object> prepareDrug(Drug drug, Set<String> columnsSet, List<Model> models) {
Map<String, Object> result = new TreeMap<>();
for (String string : columnsSet) {
@@ -171,7 +151,7 @@ public class DrugRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getDrugsByTarget(String token, String projectId, String targetType, String targetId,
String columns) throws SecurityException, QueryException {
- Model model = modelService.getLastModelByProjectId(projectId, token);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index 5aac8ca42447821d037d06e2573fef3d6ed764c9..d2f3739d5417c2ec12897b5c1e5e299a34f6e148 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -12,16 +12,27 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ElementModification;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.model.map.species.field.Structure;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
import lcsb.mapviewer.model.map.species.field.UniprotRecord;
import lcsb.mapviewer.services.SecurityException;
@@ -213,12 +224,16 @@ public class ElementsRestImpl extends BaseRestImpl {
structuralState = protein.getStructuralState();
} else if (element instanceof Rna) {
Rna rna = ((Rna) element);
- modifications = getModifications(((Rna) element).getRegions());
+ modifications = getModifications(rna.getRegions());
structuralState = rna.getState();
} else if (element instanceof AntisenseRna) {
AntisenseRna antisenseRna = ((AntisenseRna) element);
- modifications = getModifications(((AntisenseRna) element).getRegions());
+ modifications = getModifications(antisenseRna.getRegions());
structuralState = antisenseRna.getState();
+ } else if (element instanceof Gene) {
+ Gene gene = ((Gene) element);
+ modifications = getModifications(gene.getModificationResidues());
+ structuralState = gene.getState();
}
if (element instanceof Species) {
structures = getStructures(((Species) element).getUniprots());
@@ -230,16 +245,42 @@ public class ElementsRestImpl extends BaseRestImpl {
return result;
}
- private List<Map<String, Object>> getModifications(List<? extends ElementModification> elements) {
+ private List<Map<String, Object>> getModifications(List<? extends ModificationResidue> elements) {
List<Map<String, Object>> result = new ArrayList<>();
- for (ElementModification region : elements) {
- if (region.getState() != null) {
- Map<String, Object> row = new TreeMap<>();
- row.put("name", region.getName());
- String state = region.getState().name();
- row.put("state", state);
- result.add(row);
+ for (ModificationResidue region : elements) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("name", region.getName());
+ row.put("modificationId", region.getIdModificationResidue());
+ if (region instanceof AbstractSiteModification) {
+ AbstractSiteModification siteModification = ((AbstractSiteModification) region);
+ if (siteModification.getState() != null) {
+ row.put("state", siteModification.getState().name());
+ }
+ }
+ String type = null;
+ if (region instanceof Residue) {
+ type = ModificationType.RESIDUE.name();
+ } else if (region instanceof BindingRegion) {
+ type = ModificationType.BINDING_REGION.name();
+ } else if (region instanceof CodingRegion) {
+ type = ModificationType.CODING_REGION.name();
+ } else if (region instanceof ProteinBindingDomain) {
+ type = ModificationType.PROTEIN_BINDING_DOMAIN.name();
+ } else if (region instanceof RegulatoryRegion) {
+ type = ModificationType.REGULATORY_REGION.name();
+ } else if (region instanceof TranscriptionSite) {
+ if (((TranscriptionSite) region).getDirection().equals("LEFT")) {
+ type = ModificationType.TRANSCRIPTION_SITE_LEFT.name();
+ } else {
+ type = ModificationType.TRANSCRIPTION_SITE_RIGHT.name();
+ }
+ } else if (region instanceof ModificationSite) {
+ type = ModificationType.MODIFICATION_SITE.name();
+ } else {
+ throw new InvalidArgumentException("Unknown class: " + region.getClass());
}
+ row.put("type", type);
+ result.add(row);
}
return result;
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
index de838df959d2569ba49fe26d57fc0f12c666c7fd..4753bfa1e50f66992d8eec1b52614698b46c57b4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
@@ -1,609 +1,628 @@
-package lcsb.mapviewer.api.users;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-import org.springframework.util.MultiValueMap;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.user.BasicPrivilege;
-import lcsb.mapviewer.model.user.ConfigurationOption;
-import lcsb.mapviewer.model.user.ObjectPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.model.user.UserAnnotationSchema;
-import lcsb.mapviewer.model.user.UserAnnotatorsParam;
-import lcsb.mapviewer.model.user.UserClassAnnotators;
-import lcsb.mapviewer.model.user.UserClassRequiredAnnotations;
-import lcsb.mapviewer.model.user.UserClassValidAnnotations;
-import lcsb.mapviewer.model.user.UserGuiPreference;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-
-@Transactional(value = "txManager")
-public class UserRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(UserRestImpl.class);
-
- @Autowired
- private ILayoutService layoutService;
-
- @Autowired
- private IConfigurationService configurationService;
-
- public Map<String, Object> getUser(String token, String login, String columns)
- throws SecurityException, ObjectNotFoundException {
- User ownUserData = getUserService().getUserByToken(token);
-
- Set<String> columnSet = createUserColumnSet(columns);
-
- boolean isAdmin = getUserService().userHasPrivilege(ownUserData, PrivilegeType.USER_MANAGEMENT);
-
- if (ownUserData.getLogin().equals(login) || isAdmin) {
- User user = getUserService().getUserByLogin(login);
- if (user == null) {
- throw new ObjectNotFoundException("User doesn't exist");
- }
- return prepareUse(user, columnSet, isAdmin);
- } else {
- throw new SecurityException("You cannot access data of the user with given id");
- }
- }
-
- private Set<String> createUserColumnSet(String columns) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("id");
- columnsSet.add("login");
- columnsSet.add("name");
- columnsSet.add("surname");
- columnsSet.add("email");
- columnsSet.add("minColor");
- columnsSet.add("maxColor");
- columnsSet.add("neutralColor");
- columnsSet.add("simpleColor");
- columnsSet.add("removed");
- columnsSet.add("privileges");
- columnsSet.add("termsOfUseConsent");
- } else {
- for (String str : columns.split(",")) {
- columnsSet.add(str);
- }
- }
- return columnsSet;
- }
-
- private Map<String, Object> prepareUse(User user, Set<String> columnsSet, boolean admin) {
- Map<String, Object> result = new TreeMap<>();
- for (String string : columnsSet) {
- String column = string.toLowerCase();
- Object value = null;
- if (column.equals("id") || column.equals("idobject")) {
- value = user.getId();
- } else if (column.equals("name")) {
- value = user.getName();
- } else if (column.equals("surname")) {
- value = user.getSurname();
- } else if (column.equals("login")) {
- value = user.getLogin();
- } else if (column.equals("email")) {
- value = user.getEmail();
- } else if (column.equals("mincolor")) {
- value = user.getMinColor();
- } else if (column.equals("maxcolor")) {
- value = user.getMaxColor();
- } else if (column.equals("neutralcolor")) {
- value = user.getNeutralColor();
- } else if (column.equals("simplecolor")) {
- value = user.getSimpleColor();
- } else if (column.equals("removed")) {
- value = user.isRemoved();
- } else if (column.equals("termsofuseconsent")) {
- value = user.isTermsOfUseConsent();
- } else if (column.equals("privileges") && admin) {
- value = preparePrivileges(user);
- } else if (column.equals("preferences")) {
- value = preparePreferences(user);
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- private Map<String, Object> preparePreferences(User user) {
- Map<String, Object> result = new TreeMap<>();
- UserAnnotationSchema schema = getProjectService().prepareUserAnnotationSchema(user);
- result.put("project-upload", prepareProjectUploadPreferences(schema));
- result.put("element-annotators", prepareElementAnnotators(schema.getClassAnnotators()));
- result.put("element-required-annotations", prepareRequiredAnnotations(schema.getClassRequiredAnnotators()));
- result.put("element-valid-annotations", prepareValidAnnotations(schema.getClassValidAnnotators()));
- result.put("annotators-parameters", prepareAnnotatorsParams(schema.getAnnotatorsParams()));
- result.put("gui-preferences", prepareGuiPreferences(schema.getGuiPreferences()));
- return result;
- }
-
- Map<String, Object> prepareGuiPreferences(Set<UserGuiPreference> guiPreferences) {
- Map<String, Object> result = new TreeMap<>();
- for (UserGuiPreference userGuiPreference : guiPreferences) {
- result.put(userGuiPreference.getKey(), userGuiPreference.getValue());
- }
- return result;
- }
-
- /**
- * Prepares annotator parameters in the form of a map having annotators class
- * names as keys and map of name:value pairs of given annotator as values.
- *
- * @param annotatorsParams
- * @return
- */
- private Map<String, Object> prepareAnnotatorsParams(List<UserAnnotatorsParam> annotatorsParams) {
- Map<String, Object> result = new TreeMap<>();
- for (UserAnnotatorsParam param : annotatorsParams) {
- String className = param.getAnnotatorClassName().getName();
- Map<String, String> annotatorParams = (Map<String, String>) result.get(className);
- if (annotatorParams == null) {
- annotatorParams = new TreeMap<>();
- result.put(className, annotatorParams);
- }
- annotatorParams.put(param.getParamName(), param.getParamValue());
- }
- return result;
- }
-
- private Map<String, Object> prepareValidAnnotations(List<UserClassValidAnnotations> classValidAnnotators) {
- Map<String, Object> result = new TreeMap<>();
- for (UserClassValidAnnotations userClassAnnotators : classValidAnnotators) {
- result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getValidMiriamTypes()));
- }
- return result;
- }
-
- private void updateValidAnnotations(UserAnnotationSchema schema, Map<String, Object> data) {
- for (String key : data.keySet()) {
- UserClassValidAnnotations annotator = null;
- for (UserClassValidAnnotations userClassAnnotators : schema.getClassValidAnnotators()) {
- if (userClassAnnotators.getClassName().equals(key)) {
- annotator = userClassAnnotators;
- }
- }
- if (annotator == null) {
- annotator = new UserClassValidAnnotations();
- annotator.setClassName(key);
- schema.addClassValidAnnotations(annotator);
- }
- annotator.getValidMiriamTypes().clear();
- for (Object row : (List<?>) data.get(key)) {
- annotator.getValidMiriamTypes().add(MiriamType.valueOf((String) row));
- }
- }
- }
-
- private void updateAnnotatorsParams(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
- for (String annotatorClassname : data.keySet()) {
- Map<String, Object> nameValueS = (Map<String, Object>) data.get(annotatorClassname);
- for (String name : nameValueS.keySet()) {
- String value = (String) nameValueS.get(name);
- try {
- UserAnnotatorsParam param = new UserAnnotatorsParam(Class.forName(annotatorClassname), name, value);
- schema.addAnnotatorParam(param);
- } catch (ClassNotFoundException e) {
- throw new QueryException("Unknown annotator class name: " + annotatorClassname);
- }
- }
- }
- }
-
- private void updateGuiPreferences(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
- for (String key : data.keySet()) {
- Object object = data.get(key);
- String value = "";
- if (object instanceof Integer) {
- value = object + "";
- } else if (object instanceof String) {
- value = (String) data.get(key);
- } else {
- throw new InvalidArgumentException("Invalid value class: " + value);
- }
- schema.setGuiPreference(key, value);
- }
- }
-
- private Map<String, Object> prepareRequiredAnnotations(List<UserClassRequiredAnnotations> classRequiredAnnotators) {
- Map<String, Object> result = new TreeMap<>();
- for (UserClassRequiredAnnotations requiredAnnotations : classRequiredAnnotators) {
- Map<String, Object> row = new TreeMap<>();
- row.put("require-at-least-one", requiredAnnotations.getRequireAtLeastOneAnnotation());
- List<String> miriamTypes = new ArrayList<>();
-
- for (MiriamType mt : requiredAnnotations.getRequiredMiriamTypes()) {
- miriamTypes.add(mt.name());
- }
- row.put("annotation-list", miriamTypes);
- result.put(requiredAnnotations.getClassName(), row);
- }
- return result;
- }
-
- private void updateRequiredAnnotations(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
- for (String key : data.keySet()) {
- UserClassRequiredAnnotations annotator = null;
- for (UserClassRequiredAnnotations userClassAnnotators : schema.getClassRequiredAnnotators()) {
- if (userClassAnnotators.getClassName().equals(key)) {
- annotator = userClassAnnotators;
- }
- }
- if (annotator == null) {
- annotator = new UserClassRequiredAnnotations();
- annotator.setClassName(key);
- schema.addClassRequiredAnnotations(annotator);
- }
- updateAnnotator(annotator, (Map<String, Object>) data.get(key));
- }
- }
-
- private void updateAnnotator(UserClassRequiredAnnotations annotator, Map<String, Object> data) throws QueryException {
- for (String key : data.keySet()) {
- if (key.equals("require-at-least-one")) {
- annotator.setRequireAtLeastOneAnnotation((Boolean) data.get("require-at-least-one"));
- } else if (key.equals("annotation-list")) {
- annotator.getRequiredMiriamTypes().clear();
- for (Object row : (List<?>) data.get(key)) {
- annotator.getRequiredMiriamTypes().add(MiriamType.valueOf((String) row));
- }
- } else {
- throw new QueryException("Unknown field: " + key);
- }
- }
-
- }
-
- private Map<String, Object> prepareElementAnnotators(List<UserClassAnnotators> classAnnotators) {
- Map<String, Object> result = new TreeMap<>();
- for (UserClassAnnotators userClassAnnotators : classAnnotators) {
- result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getAnnotators()));
- }
- return result;
- }
-
- private void updateElementAnnotators(UserAnnotationSchema schema, Map<String, Object> data) {
- for (String key : data.keySet()) {
- UserClassAnnotators annotator = null;
- for (UserClassAnnotators userClassAnnotators : schema.getClassAnnotators()) {
- if (userClassAnnotators.getClassName().equals(key)) {
- annotator = userClassAnnotators;
- }
- }
- if (annotator == null) {
- annotator = new UserClassAnnotators();
- annotator.setClassName(key);
- schema.addClassAnnotator(annotator);
- }
- annotator.getAnnotators().clear();
- annotator.getAnnotators().addAll((List<String>) data.get(key));
- }
- }
-
- private Map<String, Object> prepareProjectUploadPreferences(UserAnnotationSchema schema) {
- Map<String, Object> result = new TreeMap<>();
- result.put("validate-miriam", schema.getValidateMiriamTypes());
- result.put("annotate-model", schema.getAnnotateModel());
- result.put("cache-data", schema.getCacheData());
- result.put("auto-resize", schema.getAutoResizeMap());
- result.put("semantic-zooming", schema.getSemanticZooming());
- result.put("sbgn", schema.getSbgnFormat());
- return result;
- }
-
- private List<Map<String, Object>> preparePrivileges(User user) {
- List<Map<String, Object>> result = new ArrayList<>();
- Set<PrivilegeType> definedDefaultProjectPrivilegeTypes = new HashSet<>();
- List<BasicPrivilege> privileges = new ArrayList<>();
- privileges.addAll(user.getPrivileges());
- privileges.sort(BasicPrivilege.ID_COMPARATOR);
- for (BasicPrivilege privilege : privileges) {
- if (privilege instanceof ObjectPrivilege) {
- if (Project.class.equals(privilege.getType().getPrivilegeObjectType())
- && ((ObjectPrivilege) privilege).getIdObject() == null) {
- definedDefaultProjectPrivilegeTypes.add(privilege.getType());
- }
- result.add(prepareObjectPrivilege((ObjectPrivilege) privilege));
- } else {
- result.add(prepareBasicPrivilege(privilege));
- }
- }
- for (PrivilegeType privilegeType : PrivilegeType.values()) {
- if (Project.class.equals(privilegeType.getPrivilegeObjectType())
- && !definedDefaultProjectPrivilegeTypes.contains(privilegeType)) {
- result.add(prepareDefaultObjectPrivilege(privilegeType));
- }
- }
- Map<String, Object> customLayouts = new TreeMap<>();
- customLayouts.put("type", "CUSTOM_LAYOUTS_AVAILABLE");
- customLayouts.put("value", layoutService.getAvailableCustomLayoutsNumber(user));
- result.add(customLayouts);
- return result;
- }
-
- private Map<String, Object> prepareDefaultObjectPrivilege(PrivilegeType privilegeType) {
- Map<String, Object> result = new TreeMap<>();
- result.put("type", privilegeType);
- ConfigurationOption value = configurationService.getValue(privilegeType);
- if (value == null) {
- result.put("value", 0);
- } else if (value.getValue().equalsIgnoreCase("true")) {
- result.put("value", 1);
- } else if (value.getValue().equalsIgnoreCase("false")) {
- result.put("value", 0);
- } else {
- result.put("value", value.getValue());
- }
- result.put("objectId", null);
- return result;
- }
-
- private Map<String, Object> prepareObjectPrivilege(ObjectPrivilege privilege) {
- Map<String, Object> result = new TreeMap<>();
- result.put("type", privilege.getType());
- result.put("value", privilege.getLevel());
- result.put("objectId", privilege.getIdObject());
- return result;
- }
-
- private Map<String, Object> prepareBasicPrivilege(BasicPrivilege privilege) {
- Map<String, Object> result = new TreeMap<>();
- if (privilege.getClass().equals(BasicPrivilege.class)) {
- result.put("type", privilege.getType());
- result.put("value", privilege.getLevel());
- return result;
- } else {
- throw new InvalidArgumentException("Don't know how to handle class: " + privilege.getClass());
- }
- }
-
- /**
- * @return the layoutService
- * @see #layoutService
- */
- public ILayoutService getLayoutService() {
- return layoutService;
- }
-
- /**
- * @param layoutService
- * the layoutService to set
- * @see #layoutService
- */
- public void setLayoutService(ILayoutService layoutService) {
- this.layoutService = layoutService;
- }
-
- public List<Map<String, Object>> getUsers(String token, String columns) throws SecurityException {
- User ownUserData = getUserService().getUserByToken(token);
- boolean isAdmin = getUserService().userHasPrivilege(ownUserData, PrivilegeType.USER_MANAGEMENT);
-
- Set<String> columnSet = createUserColumnSet(columns);
-
- List<Map<String, Object>> result = new ArrayList<>();
- List<User> users = getUserService().getUsers(token);
- users.sort(User.LOGIN_COMPARATOR);
- for (User user : users) {
- result.add(prepareUse(user, columnSet, isAdmin));
- }
- return result;
- }
-
- public Map<String, Object> updatePrivileges(String token, String login, Map<String, Object> privilegesData)
- throws SecurityException, QueryException {
- if (privilegesData == null) {
- throw new QueryException("Privileges not defined");
- }
- try {
- User modifiedUser = getUserService().getUserByLogin(login);
-
- for (String key : privilegesData.keySet()) {
- Object value = privilegesData.get(key);
-
- PrivilegeType type = PrivilegeType.valueOf(key);
-
- if (type.getPrivilegeClassType().equals(BasicPrivilege.class)) {
- getUserService().setUserPrivilege(modifiedUser, type, value, token);
- } else if (type.getPrivilegeClassType().equals(ObjectPrivilege.class)) {
- if (value instanceof Map) {
- Map<?, ?> objects = (Map<?, ?>) value;
- for (Object objectId : objects.keySet()) {
- Integer objectIdAsInteger = null;
- if (!objectId.equals("null")) {
- objectIdAsInteger = Integer.valueOf((String) objectId);
- }
- getUserService().setUserPrivilege(modifiedUser, type, objects.get(objectId), objectIdAsInteger, token);
- }
- } else {
- throw new QueryException("Invalid value for privilege: " + key);
- }
- } else {
- throw new QueryException("Unknown privilege type: " + key);
- }
-
- }
- return getUser(token, login, "");
- } catch (IllegalArgumentException e) {
- throw new QueryException("Invalid input", e);
- }
- }
-
- public Map<String, Object> updatePreferences(String token, String login, Map<String, Object> preferencesData)
- throws SecurityException, QueryException {
- if (preferencesData == null) {
- throw new QueryException("Preferences not defined");
- }
- try {
- User modifiedUser = getUserService().getUserByLogin(login);
- if (modifiedUser == null) {
- throw new ObjectNotFoundException("User doesn't exist");
- }
-
- UserAnnotationSchema schema = getProjectService().prepareUserAnnotationSchema(modifiedUser);
-
- for (String key : preferencesData.keySet()) {
- Map<String, Object> value = (Map<String, Object>) preferencesData.get(key);
-
- if (key.equals("project-upload")) {
- updateUploadPreferences(schema, value);
- } else if (key.equals("element-annotators")) {
- updateElementAnnotators(schema, value);
- } else if (key.equals("element-required-annotations")) {
- updateRequiredAnnotations(schema, value);
- } else if (key.equals("element-valid-annotations")) {
- updateValidAnnotations(schema, value);
- } else if (key.equals("annotators-parameters")) {
- updateAnnotatorsParams(schema, value);
- } else if (key.equals("gui-preferences")) {
- updateGuiPreferences(schema, value);
- } else {
- throw new QueryException("Unknown preferences field: " + key);
- }
- }
- modifiedUser.setAnnotationSchema(schema);
- getUserService().updateUser(modifiedUser, token);
- return getUser(token, login, "preferences");
- } catch (IllegalArgumentException e) {
- throw new QueryException("Invalid input", e);
- }
- }
-
- private void updateUploadPreferences(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
- for (String key : data.keySet()) {
- Boolean value = (Boolean) data.get(key);
- if (value != null) {
- if (key.equals("validate-miriam")) {
- schema.setValidateMiriamTypes(value);
- } else if (key.equals("annotate-model")) {
- schema.setAnnotateModel(value);
- } else if (key.equals("cache-data")) {
- schema.setCacheData(value);
- } else if (key.equals("auto-resize")) {
- schema.setAutoResizeMap(value);
- } else if (key.equals("semantic-zooming")) {
- schema.setSemanticZooming(value);
- } else if (key.equals("sbgn")) {
- schema.setSbgnFormat(value);
- } else {
- throw new QueryException("Unknown upload preference field: " + key);
- }
- }
- }
-
- }
-
- public Map<String, Object> updateUser(String token, String login, Map<String, Object> userData)
- throws QueryException, SecurityException {
- if (userData == null) {
- throw new QueryException("user field cannot be undefined");
- }
- User user = getUserService().getUserByLogin(login);
- if (user == null) {
- throw new ObjectNotFoundException("user doesn't exist");
- }
- boolean isAdmin = getUserService().userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT);
- if (!isAdmin && !login.equalsIgnoreCase(getUserService().getUserByToken(token).getLogin())) {
- throw new SecurityException("Access denied");
- }
- for (String key : userData.keySet()) {
- Object value = userData.get(key);
- String stringValue = null;
- if (value instanceof String) {
- stringValue = (String) value;
- }
- if (key.equalsIgnoreCase("name")) {
- user.setName(stringValue);
- } else if (key.equalsIgnoreCase("surname")) {
- user.setSurname(stringValue);
- } else if (key.equalsIgnoreCase("email")) {
- user.setEmail(stringValue);
- } else if (key.equalsIgnoreCase("termsofuseconsent")) {
- user.setTermsOfUseConsent((Boolean) value);
- } else if (key.equalsIgnoreCase("password")) {
- if (stringValue != null && !stringValue.trim().isEmpty()) {
- user.setCryptedPassword(getUserService().encodePassword(stringValue));
- }
- } else if (key.equalsIgnoreCase("login")) {
- if (!user.getLogin().equals((String) value)) {
- throw new QueryException("login cannot be modified");
- }
- } else {
- throw new QueryException("Unknown parameter: " + key);
- }
- }
- getUserService().updateUser(user);
- return getUser(token, login, "");
- }
-
- public Map<String, Object> addProject(String token, String login, MultiValueMap<String, Object> userData)
- throws QueryException, SecurityException {
- if (!getUserService().userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
- throw new SecurityException("Access denied");
- }
-
- User user = getUserService().getUserByLogin(login);
- if (user != null) {
- throw new QueryException("user exists");
- }
- user = new User();
- user.setLogin(login);
- for (String key : userData.keySet()) {
- String stringValue = getFirstValue((List<Object>) userData.get(key));
- if (key.equalsIgnoreCase("name")) {
- user.setName(stringValue);
- } else if (key.equalsIgnoreCase("surname")) {
- user.setSurname(stringValue);
- } else if (key.equalsIgnoreCase("email")) {
- user.setEmail(stringValue);
- } else if (key.equalsIgnoreCase("password")) {
- if (stringValue != null && !stringValue.trim().isEmpty()) {
- user.setCryptedPassword(getUserService().encodePassword(stringValue));
- }
- } else if (key.equalsIgnoreCase("login")) {
- if (!user.getLogin().equals(stringValue)) {
- throw new QueryException("login must match url");
- }
- } else {
- throw new QueryException("Unknown parameter: " + key);
- }
- }
- getUserService().addUser(user);
- return getUser(token, login, "");
- }
-
- public Map<String, Object> removeUser(String token, String login) throws SecurityException, QueryException {
- User user = getUserService().getUserByLogin(login);
- if (!getUserService().userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
- throw new SecurityException("Access denied");
- }
- if (user == null) {
- throw new QueryException("user doesn't exists");
- }
- getUserService().deleteUser(user);
- return okStatus();
- }
-
-}
+package lcsb.mapviewer.api.users;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.util.MultiValueMap;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.user.BasicPrivilege;
+import lcsb.mapviewer.model.user.ConfigurationOption;
+import lcsb.mapviewer.model.user.ObjectPrivilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.model.user.UserAnnotatorsParam;
+import lcsb.mapviewer.model.user.UserClassAnnotators;
+import lcsb.mapviewer.model.user.UserClassRequiredAnnotations;
+import lcsb.mapviewer.model.user.UserClassValidAnnotations;
+import lcsb.mapviewer.model.user.UserGuiPreference;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.ILayoutService;
+
+@Transactional(value = "txManager")
+public class UserRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(UserRestImpl.class);
+
+ @Autowired
+ private ILayoutService layoutService;
+
+ @Autowired
+ private IConfigurationService configurationService;
+
+ public Map<String, Object> getUser(String token, String login, String columns)
+ throws SecurityException, ObjectNotFoundException {
+ User ownUserData = getUserService().getUserByToken(token);
+
+ Set<String> columnSet = createUserColumnSet(columns);
+
+ boolean isAdmin = getUserService().userHasPrivilege(ownUserData, PrivilegeType.USER_MANAGEMENT);
+
+ if (ownUserData.getLogin().equals(login) || isAdmin) {
+ User user = getUserService().getUserByLogin(login);
+ if (user == null) {
+ throw new ObjectNotFoundException("User doesn't exist");
+ }
+ Boolean ldapAvailable = false;
+ if (columnSet.contains("ldapAccountAvailable")) {
+ List<User> userList = new ArrayList<>();
+ userList.add(ownUserData);
+ ldapAvailable = getUserService().ldapAccountExistsForLogin(userList).get(login);
+ }
+ return prepareUse(user, columnSet, isAdmin, ldapAvailable);
+ } else {
+ throw new SecurityException("You cannot access data of the user with given id");
+ }
+ }
+
+ private Set<String> createUserColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("id");
+ columnsSet.add("login");
+ columnsSet.add("name");
+ columnsSet.add("surname");
+ columnsSet.add("email");
+ columnsSet.add("minColor");
+ columnsSet.add("maxColor");
+ columnsSet.add("neutralColor");
+ columnsSet.add("simpleColor");
+ columnsSet.add("removed");
+ columnsSet.add("privileges");
+ columnsSet.add("termsOfUseConsent");
+ columnsSet.add("connectedToLdap");
+ columnsSet.add("ldapAccountAvailable");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ private Map<String, Object> prepareUse(User user, Set<String> columnsSet, boolean admin, Boolean ldapAvailable) {
+ Map<String, Object> result = new TreeMap<>();
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idobject")) {
+ value = user.getId();
+ } else if (column.equals("name")) {
+ value = user.getName();
+ } else if (column.equals("surname")) {
+ value = user.getSurname();
+ } else if (column.equals("login")) {
+ value = user.getLogin();
+ } else if (column.equals("email")) {
+ value = user.getEmail();
+ } else if (column.equals("mincolor")) {
+ value = user.getMinColor();
+ } else if (column.equals("maxcolor")) {
+ value = user.getMaxColor();
+ } else if (column.equals("neutralcolor")) {
+ value = user.getNeutralColor();
+ } else if (column.equals("simplecolor")) {
+ value = user.getSimpleColor();
+ } else if (column.equals("removed")) {
+ value = user.isRemoved();
+ } else if (column.equals("termsofuseconsent")) {
+ value = user.isTermsOfUseConsent();
+ } else if (column.equals("connectedtoldap") && admin) {
+ value = user.isConnectedToLdap();
+ } else if (column.equals("ldapaccountavailable") && admin) {
+ if (ldapAvailable == null) {
+ ldapAvailable = false;
+ }
+ value = ldapAvailable;
+ } else if (column.equals("privileges") && admin) {
+ value = preparePrivileges(user);
+ } else if (column.equals("preferences")) {
+ value = preparePreferences(user);
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private Map<String, Object> preparePreferences(User user) {
+ Map<String, Object> result = new TreeMap<>();
+ UserAnnotationSchema schema = getProjectService().prepareUserAnnotationSchema(user);
+ result.put("project-upload", prepareProjectUploadPreferences(schema));
+ result.put("element-annotators", prepareElementAnnotators(schema.getClassAnnotators()));
+ result.put("element-required-annotations", prepareRequiredAnnotations(schema.getClassRequiredAnnotators()));
+ result.put("element-valid-annotations", prepareValidAnnotations(schema.getClassValidAnnotators()));
+ result.put("annotators-parameters", prepareAnnotatorsParams(schema.getAnnotatorsParams()));
+ result.put("gui-preferences", prepareGuiPreferences(schema.getGuiPreferences()));
+ return result;
+ }
+
+ Map<String, Object> prepareGuiPreferences(Set<UserGuiPreference> guiPreferences) {
+ Map<String, Object> result = new TreeMap<>();
+ for (UserGuiPreference userGuiPreference : guiPreferences) {
+ result.put(userGuiPreference.getKey(), userGuiPreference.getValue());
+ }
+ return result;
+ }
+
+ /**
+ * Prepares annotator parameters in the form of a map having annotators class
+ * names as keys and map of name:value pairs of given annotator as values.
+ *
+ * @param annotatorsParams
+ * @return
+ */
+ private Map<String, Object> prepareAnnotatorsParams(List<UserAnnotatorsParam> annotatorsParams) {
+ Map<String, Object> result = new TreeMap<>();
+ for (UserAnnotatorsParam param : annotatorsParams) {
+ String className = param.getAnnotatorClassName().getName();
+ Map<String, String> annotatorParams = (Map<String, String>) result.get(className);
+ if (annotatorParams == null) {
+ annotatorParams = new TreeMap<>();
+ result.put(className, annotatorParams);
+ }
+ annotatorParams.put(param.getParamName(), param.getParamValue());
+ }
+ return result;
+ }
+
+ private Map<String, Object> prepareValidAnnotations(List<UserClassValidAnnotations> classValidAnnotators) {
+ Map<String, Object> result = new TreeMap<>();
+ for (UserClassValidAnnotations userClassAnnotators : classValidAnnotators) {
+ result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getValidMiriamTypes()));
+ }
+ return result;
+ }
+
+ private void updateValidAnnotations(UserAnnotationSchema schema, Map<String, Object> data) {
+ for (String key : data.keySet()) {
+ UserClassValidAnnotations annotator = null;
+ for (UserClassValidAnnotations userClassAnnotators : schema.getClassValidAnnotators()) {
+ if (userClassAnnotators.getClassName().equals(key)) {
+ annotator = userClassAnnotators;
+ }
+ }
+ if (annotator == null) {
+ annotator = new UserClassValidAnnotations();
+ annotator.setClassName(key);
+ schema.addClassValidAnnotations(annotator);
+ }
+ annotator.getValidMiriamTypes().clear();
+ for (Object row : (List<?>) data.get(key)) {
+ annotator.getValidMiriamTypes().add(MiriamType.valueOf((String) row));
+ }
+ }
+ }
+
+ private void updateAnnotatorsParams(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
+ for (String annotatorClassname : data.keySet()) {
+ Map<String, Object> nameValueS = (Map<String, Object>) data.get(annotatorClassname);
+ for (String name : nameValueS.keySet()) {
+ String value = (String) nameValueS.get(name);
+ try {
+ UserAnnotatorsParam param = new UserAnnotatorsParam(Class.forName(annotatorClassname), name, value);
+ schema.addAnnotatorParam(param);
+ } catch (ClassNotFoundException e) {
+ throw new QueryException("Unknown annotator class name: " + annotatorClassname);
+ }
+ }
+ }
+ }
+
+ private void updateGuiPreferences(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
+ for (String key : data.keySet()) {
+ Object object = data.get(key);
+ String value = "";
+ if (object instanceof Integer) {
+ value = object + "";
+ } else if (object instanceof String) {
+ value = (String) data.get(key);
+ } else {
+ throw new InvalidArgumentException("Invalid value class: " + value);
+ }
+ schema.setGuiPreference(key, value);
+ }
+ }
+
+ private Map<String, Object> prepareRequiredAnnotations(List<UserClassRequiredAnnotations> classRequiredAnnotators) {
+ Map<String, Object> result = new TreeMap<>();
+ for (UserClassRequiredAnnotations requiredAnnotations : classRequiredAnnotators) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("require-at-least-one", requiredAnnotations.getRequireAtLeastOneAnnotation());
+ List<String> miriamTypes = new ArrayList<>();
+
+ for (MiriamType mt : requiredAnnotations.getRequiredMiriamTypes()) {
+ miriamTypes.add(mt.name());
+ }
+ row.put("annotation-list", miriamTypes);
+ result.put(requiredAnnotations.getClassName(), row);
+ }
+ return result;
+ }
+
+ private void updateRequiredAnnotations(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
+ for (String key : data.keySet()) {
+ UserClassRequiredAnnotations annotator = null;
+ for (UserClassRequiredAnnotations userClassAnnotators : schema.getClassRequiredAnnotators()) {
+ if (userClassAnnotators.getClassName().equals(key)) {
+ annotator = userClassAnnotators;
+ }
+ }
+ if (annotator == null) {
+ annotator = new UserClassRequiredAnnotations();
+ annotator.setClassName(key);
+ schema.addClassRequiredAnnotations(annotator);
+ }
+ updateAnnotator(annotator, (Map<String, Object>) data.get(key));
+ }
+ }
+
+ private void updateAnnotator(UserClassRequiredAnnotations annotator, Map<String, Object> data) throws QueryException {
+ for (String key : data.keySet()) {
+ if (key.equals("require-at-least-one")) {
+ annotator.setRequireAtLeastOneAnnotation((Boolean) data.get("require-at-least-one"));
+ } else if (key.equals("annotation-list")) {
+ annotator.getRequiredMiriamTypes().clear();
+ for (Object row : (List<?>) data.get(key)) {
+ annotator.getRequiredMiriamTypes().add(MiriamType.valueOf((String) row));
+ }
+ } else {
+ throw new QueryException("Unknown field: " + key);
+ }
+ }
+
+ }
+
+ private Map<String, Object> prepareElementAnnotators(List<UserClassAnnotators> classAnnotators) {
+ Map<String, Object> result = new TreeMap<>();
+ for (UserClassAnnotators userClassAnnotators : classAnnotators) {
+ result.put(userClassAnnotators.getClassName(), new ArrayList<>(userClassAnnotators.getAnnotators()));
+ }
+ return result;
+ }
+
+ private void updateElementAnnotators(UserAnnotationSchema schema, Map<String, Object> data) {
+ for (String key : data.keySet()) {
+ UserClassAnnotators annotator = null;
+ for (UserClassAnnotators userClassAnnotators : schema.getClassAnnotators()) {
+ if (userClassAnnotators.getClassName().equals(key)) {
+ annotator = userClassAnnotators;
+ }
+ }
+ if (annotator == null) {
+ annotator = new UserClassAnnotators();
+ annotator.setClassName(key);
+ schema.addClassAnnotator(annotator);
+ }
+ annotator.getAnnotators().clear();
+ annotator.getAnnotators().addAll((List<String>) data.get(key));
+ }
+ }
+
+ private Map<String, Object> prepareProjectUploadPreferences(UserAnnotationSchema schema) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("validate-miriam", schema.getValidateMiriamTypes());
+ result.put("annotate-model", schema.getAnnotateModel());
+ result.put("cache-data", schema.getCacheData());
+ result.put("auto-resize", schema.getAutoResizeMap());
+ result.put("semantic-zooming", schema.getSemanticZooming());
+ result.put("sbgn", schema.getSbgnFormat());
+ return result;
+ }
+
+ private List<Map<String, Object>> preparePrivileges(User user) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ Set<PrivilegeType> definedDefaultProjectPrivilegeTypes = new HashSet<>();
+ List<BasicPrivilege> privileges = new ArrayList<>();
+ privileges.addAll(user.getPrivileges());
+ privileges.sort(BasicPrivilege.ID_COMPARATOR);
+ for (BasicPrivilege privilege : privileges) {
+ if (privilege instanceof ObjectPrivilege) {
+ if (Project.class.equals(privilege.getType().getPrivilegeObjectType())
+ && ((ObjectPrivilege) privilege).getIdObject() == null) {
+ definedDefaultProjectPrivilegeTypes.add(privilege.getType());
+ }
+ result.add(prepareObjectPrivilege((ObjectPrivilege) privilege));
+ } else {
+ result.add(prepareBasicPrivilege(privilege));
+ }
+ }
+ for (PrivilegeType privilegeType : PrivilegeType.values()) {
+ if (Project.class.equals(privilegeType.getPrivilegeObjectType())
+ && !definedDefaultProjectPrivilegeTypes.contains(privilegeType)) {
+ result.add(prepareDefaultObjectPrivilege(privilegeType));
+ }
+ }
+ Map<String, Object> customLayouts = new TreeMap<>();
+ customLayouts.put("type", "CUSTOM_LAYOUTS_AVAILABLE");
+ customLayouts.put("value", layoutService.getAvailableCustomLayoutsNumber(user));
+ result.add(customLayouts);
+ return result;
+ }
+
+ private Map<String, Object> prepareDefaultObjectPrivilege(PrivilegeType privilegeType) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("type", privilegeType);
+ ConfigurationOption value = configurationService.getValue(privilegeType);
+ if (value == null) {
+ result.put("value", 0);
+ } else if (value.getValue().equalsIgnoreCase("true")) {
+ result.put("value", 1);
+ } else if (value.getValue().equalsIgnoreCase("false")) {
+ result.put("value", 0);
+ } else {
+ result.put("value", value.getValue());
+ }
+ result.put("objectId", null);
+ return result;
+ }
+
+ private Map<String, Object> prepareObjectPrivilege(ObjectPrivilege privilege) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("type", privilege.getType());
+ result.put("value", privilege.getLevel());
+ result.put("objectId", privilege.getIdObject());
+ return result;
+ }
+
+ private Map<String, Object> prepareBasicPrivilege(BasicPrivilege privilege) {
+ Map<String, Object> result = new TreeMap<>();
+ if (privilege.getClass().equals(BasicPrivilege.class)) {
+ result.put("type", privilege.getType());
+ result.put("value", privilege.getLevel());
+ return result;
+ } else {
+ throw new InvalidArgumentException("Don't know how to handle class: " + privilege.getClass());
+ }
+ }
+
+ /**
+ * @return the layoutService
+ * @see #layoutService
+ */
+ public ILayoutService getLayoutService() {
+ return layoutService;
+ }
+
+ /**
+ * @param layoutService
+ * the layoutService to set
+ * @see #layoutService
+ */
+ public void setLayoutService(ILayoutService layoutService) {
+ this.layoutService = layoutService;
+ }
+
+ public List<Map<String, Object>> getUsers(String token, String columns) throws SecurityException {
+ User ownUserData = getUserService().getUserByToken(token);
+ boolean isAdmin = getUserService().userHasPrivilege(ownUserData, PrivilegeType.USER_MANAGEMENT);
+
+ Set<String> columnSet = createUserColumnSet(columns);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+ List<User> users = getUserService().getUsers(token);
+ users.sort(User.LOGIN_COMPARATOR);
+ Map<String, Boolean> ldapAvailability = getUserService().ldapAccountExistsForLogin(users);
+
+ for (User user : users) {
+ result.add(prepareUse(user, columnSet, isAdmin, ldapAvailability.get(user.getLogin())));
+ }
+ return result;
+ }
+
+ public Map<String, Object> updatePrivileges(String token, String login, Map<String, Object> privilegesData)
+ throws SecurityException, QueryException {
+ if (privilegesData == null) {
+ throw new QueryException("Privileges not defined");
+ }
+ try {
+ User modifiedUser = getUserService().getUserByLogin(login);
+
+ for (String key : privilegesData.keySet()) {
+ Object value = privilegesData.get(key);
+
+ PrivilegeType type = PrivilegeType.valueOf(key);
+
+ if (type.getPrivilegeClassType().equals(BasicPrivilege.class)) {
+ getUserService().setUserPrivilege(modifiedUser, type, value, token);
+ } else if (type.getPrivilegeClassType().equals(ObjectPrivilege.class)) {
+ if (value instanceof Map) {
+ Map<?, ?> objects = (Map<?, ?>) value;
+ for (Object objectId : objects.keySet()) {
+ Integer objectIdAsInteger = null;
+ if (!objectId.equals("null")) {
+ objectIdAsInteger = Integer.valueOf((String) objectId);
+ }
+ getUserService().setUserPrivilege(modifiedUser, type, objects.get(objectId), objectIdAsInteger, token);
+ }
+ } else {
+ throw new QueryException("Invalid value for privilege: " + key);
+ }
+ } else {
+ throw new QueryException("Unknown privilege type: " + key);
+ }
+
+ }
+ return getUser(token, login, "");
+ } catch (IllegalArgumentException e) {
+ throw new QueryException("Invalid input", e);
+ }
+ }
+
+ public Map<String, Object> updatePreferences(String token, String login, Map<String, Object> preferencesData)
+ throws SecurityException, QueryException {
+ if (preferencesData == null) {
+ throw new QueryException("Preferences not defined");
+ }
+ try {
+ User modifiedUser = getUserService().getUserByLogin(login);
+ if (modifiedUser == null) {
+ throw new ObjectNotFoundException("User doesn't exist");
+ }
+
+ UserAnnotationSchema schema = getProjectService().prepareUserAnnotationSchema(modifiedUser);
+
+ for (String key : preferencesData.keySet()) {
+ Map<String, Object> value = (Map<String, Object>) preferencesData.get(key);
+
+ if (key.equals("project-upload")) {
+ updateUploadPreferences(schema, value);
+ } else if (key.equals("element-annotators")) {
+ updateElementAnnotators(schema, value);
+ } else if (key.equals("element-required-annotations")) {
+ updateRequiredAnnotations(schema, value);
+ } else if (key.equals("element-valid-annotations")) {
+ updateValidAnnotations(schema, value);
+ } else if (key.equals("annotators-parameters")) {
+ updateAnnotatorsParams(schema, value);
+ } else if (key.equals("gui-preferences")) {
+ updateGuiPreferences(schema, value);
+ } else {
+ throw new QueryException("Unknown preferences field: " + key);
+ }
+ }
+ modifiedUser.setAnnotationSchema(schema);
+ getUserService().updateUser(modifiedUser, token);
+ return getUser(token, login, "preferences");
+ } catch (IllegalArgumentException e) {
+ throw new QueryException("Invalid input", e);
+ }
+ }
+
+ private void updateUploadPreferences(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
+ for (String key : data.keySet()) {
+ Boolean value = (Boolean) data.get(key);
+ if (value != null) {
+ if (key.equals("validate-miriam")) {
+ schema.setValidateMiriamTypes(value);
+ } else if (key.equals("annotate-model")) {
+ schema.setAnnotateModel(value);
+ } else if (key.equals("cache-data")) {
+ schema.setCacheData(value);
+ } else if (key.equals("auto-resize")) {
+ schema.setAutoResizeMap(value);
+ } else if (key.equals("semantic-zooming")) {
+ schema.setSemanticZooming(value);
+ } else if (key.equals("sbgn")) {
+ schema.setSbgnFormat(value);
+ } else {
+ throw new QueryException("Unknown upload preference field: " + key);
+ }
+ }
+ }
+
+ }
+
+ public Map<String, Object> updateUser(String token, String login, Map<String, Object> userData)
+ throws QueryException, SecurityException {
+ if (userData == null) {
+ throw new QueryException("user field cannot be undefined");
+ }
+ User user = getUserService().getUserByLogin(login);
+ if (user == null) {
+ throw new ObjectNotFoundException("user doesn't exist");
+ }
+ boolean isAdmin = getUserService().userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT);
+ if (!isAdmin && !login.equalsIgnoreCase(getUserService().getUserByToken(token).getLogin())) {
+ throw new SecurityException("Access denied");
+ }
+ for (String key : userData.keySet()) {
+ Object value = userData.get(key);
+ String stringValue = null;
+ if (value instanceof String) {
+ stringValue = (String) value;
+ }
+ if (key.equalsIgnoreCase("name")) {
+ user.setName(stringValue);
+ } else if (key.equalsIgnoreCase("surname")) {
+ user.setSurname(stringValue);
+ } else if (key.equalsIgnoreCase("email")) {
+ user.setEmail(stringValue);
+ } else if (key.equalsIgnoreCase("termsofuseconsent")) {
+ user.setTermsOfUseConsent((Boolean) value);
+ } else if (key.equalsIgnoreCase("connectedtoldap")) {
+ user.setConnectedToLdap((Boolean) value);
+ } else if (key.equalsIgnoreCase("password")) {
+ if (stringValue != null && !stringValue.trim().isEmpty()) {
+ user.setCryptedPassword(getUserService().encodePassword(stringValue));
+ }
+ } else if (key.equalsIgnoreCase("login")) {
+ if (!user.getLogin().equals((String) value)) {
+ throw new QueryException("login cannot be modified");
+ }
+ } else {
+ throw new QueryException("Unknown parameter: " + key);
+ }
+ }
+ getUserService().updateUser(user);
+ return getUser(token, login, "");
+ }
+
+ public Map<String, Object> addProject(String token, String login, MultiValueMap<String, Object> userData)
+ throws QueryException, SecurityException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
+ throw new SecurityException("Access denied");
+ }
+
+ User user = getUserService().getUserByLogin(login);
+ if (user != null) {
+ throw new QueryException("user exists");
+ }
+ user = new User();
+ user.setLogin(login);
+ for (String key : userData.keySet()) {
+ String stringValue = getFirstValue((List<Object>) userData.get(key));
+ if (key.equalsIgnoreCase("name")) {
+ user.setName(stringValue);
+ } else if (key.equalsIgnoreCase("surname")) {
+ user.setSurname(stringValue);
+ } else if (key.equalsIgnoreCase("email")) {
+ user.setEmail(stringValue);
+ } else if (key.equalsIgnoreCase("password")) {
+ if (stringValue != null && !stringValue.trim().isEmpty()) {
+ user.setCryptedPassword(getUserService().encodePassword(stringValue));
+ }
+ } else if (key.equalsIgnoreCase("login")) {
+ if (!user.getLogin().equals(stringValue)) {
+ throw new QueryException("login must match url");
+ }
+ } else {
+ throw new QueryException("Unknown parameter: " + key);
+ }
+ }
+ getUserService().addUser(user);
+ return getUser(token, login, "");
+ }
+
+ public Map<String, Object> removeUser(String token, String login) throws SecurityException, QueryException {
+ User user = getUserService().getUserByLogin(login);
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
+ throw new SecurityException("Access denied");
+ }
+ if (user == null) {
+ throw new QueryException("user doesn't exists");
+ }
+ getUserService().deleteUser(user);
+ return okStatus();
+ }
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
index 4d9929a940e2786a6e3e77ab936d070cacc055e1..35e85fa7db3d56036ca1bc37cea10ccde548ced3 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
@@ -1,8 +1,12 @@
package lcsb.mapviewer.api.genomics;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import java.util.List;
+import java.util.Map;
+
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.AfterClass;
@@ -58,4 +62,65 @@ public class ReferenceGenomeControllerTest extends RestTestFunctions {
}
}
+ @Test
+ public void testGetReferenceGenomeTaxonomies() throws Exception {
+ try {
+ List<Map<String, Object>> result = referenceGenomeRestImpl.getReferenceGenomeTaxonomies(token);
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetReferenceGenomeTypes() throws Exception {
+ try {
+ List<Map<String, Object>> result = referenceGenomeRestImpl.getReferenceGenomeTypes(token,"9606");
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetReferenceGenomeVersions() throws Exception {
+ try {
+ List<Map<String, Object>> result = referenceGenomeRestImpl.getReferenceGenomeVersions(token,"9606","UCSC");
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetRemoteUrls() throws Exception {
+ try {
+ List<Map<String, Object>> result = referenceGenomeRestImpl.getRemoteUrls(adminToken, "9606", "UCSC", "hg18");
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAllDowloadedReferenceGenomes() throws Exception {
+ try {
+ List<?> result = referenceGenomeRestImpl.getReferenceGenomes(token);
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
index 5608bc531c31ad1ef4998628f6440d62ffbd7b43..f93f3239832b58f798d2afd4e98f697c384cacf4 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
@@ -25,58 +25,61 @@ import lcsb.mapviewer.services.search.DbSearchCriteria;
import lcsb.mapviewer.services.search.chemical.IChemicalService;
public class ChemicalRestImplTest extends RestTestFunctions {
- Logger logger = Logger.getLogger(ChemicalRestImplTest.class);
+ Logger logger = Logger.getLogger(ChemicalRestImplTest.class);
- @Autowired
+ @Autowired
- private ChemicalRestImpl _drugRestImpl;
-
- @Autowired
- private IChemicalService chemicalService;
+ private ChemicalRestImpl _drugRestImpl;
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @Autowired
+ private IChemicalService chemicalService;
- @Before
- public void setUp() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @Test
- public void testPrepareChemical() throws Exception {
- try {
- Chemical chemical = new Chemical();
- chemical.setChemicalId(new MiriamData(MiriamType.MESH_2012, "D010300"));
- Map<String, Object> result = _drugRestImpl.prepareChemical(chemical, _drugRestImpl.createChemicalColumnSet(""), new ArrayList<>());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testPrepareChemical() throws Exception {
+ try {
+ Chemical chemical = new Chemical();
+ chemical.setChemicalId(new MiriamData(MiriamType.MESH_2012, "D010300"));
+ Map<String, Object> result = _drugRestImpl.prepareChemical(chemical, _drugRestImpl.createChemicalColumnSet(""),
+ new ArrayList<>());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
}
+ }
- @Test
- public void testPrepareChemicalWithProblematicMesh() throws Exception {
- try {
- Chemical chemical = chemicalService.getByName("Tetrachlorodibenzodioxin", new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
- Map<String, Object> result = _drugRestImpl.prepareChemical(chemical, _drugRestImpl.createChemicalColumnSet(""), new ArrayList<>());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ @Test
+ public void testPrepareChemicalWithProblematicMesh() throws Exception {
+ try {
+ Chemical chemical = chemicalService.getByName("Tetrachlorodibenzodioxin",
+ new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
+ Map<String, Object> result = _drugRestImpl.prepareChemical(chemical, _drugRestImpl.createChemicalColumnSet(""),
+ new ArrayList<>());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
}
+ }
- protected ChemicalRestImpl createMockChemicalRest(String string) throws Exception {
- Model model = super.getModelForFile(string, true);
- IModelService mockModelService = Mockito.mock(IModelService.class);
- Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
- _drugRestImpl.setModelService(mockModelService);
- return _drugRestImpl;
- }
+ protected ChemicalRestImpl createMockChemicalRest(String string) throws Exception {
+ Model model = super.getModelForFile(string, true);
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _drugRestImpl.setModelService(mockModelService);
+ return _drugRestImpl;
+ }
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index a5a06edbcebc117f303da8876033620b17043439..24b414c4f298d61a854932c6f9e9af93bee71ca3 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -27,10 +27,9 @@ import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.services.interfaces.IModelService;
public class ElementRestImplTest extends RestTestFunctions {
@@ -115,7 +114,7 @@ public class ElementRestImplTest extends RestTestFunctions {
try {
String state = "asd";
GenericProtein protein = new GenericProtein("s1");
- ModificationResidue mr = new ModificationResidue();
+ Residue mr = new Residue();
mr.setState(ModificationState.ACETYLATED);
mr.setName("S250");
protein.addModificationResidue(mr);
@@ -137,7 +136,7 @@ public class ElementRestImplTest extends RestTestFunctions {
try {
String state = "asd";
Rna rna = new Rna("s1");
- RnaRegion mr = new RnaRegion();
+ ModificationSite mr = new ModificationSite();
mr.setState(ModificationState.ACETYLATED);
mr.setName("S250");
rna.addRegion(mr);
@@ -159,12 +158,12 @@ public class ElementRestImplTest extends RestTestFunctions {
try {
String state = "asd";
AntisenseRna antisenseRna = new AntisenseRna("s1");
- AntisenseRnaRegion mr = new AntisenseRnaRegion();
- mr.setState(ModificationState.ACETYLATED);
+ ModificationSite mr = new ModificationSite();
mr.setName("S250");
antisenseRna.addRegion(mr);
antisenseRna.setState(state);
Map<String, Object> result = _elementsRestImpl.getOthersForElement(antisenseRna);
+ logger.debug(result);
assertNotNull(result.get("modifications"));
assertEquals(state, result.get("structuralState"));
List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
diff --git a/service/pom.xml b/service/pom.xml
index 683846f0af0938281b311caf2ece1656b55c0516..f80ec93ad194b0539355a3b82708891388aabd25 100644
--- a/service/pom.xml
+++ b/service/pom.xml
@@ -118,6 +118,13 @@
<version>3.12</version>
</dependency>
+ <!-- https://mvnrepository.com/artifact/com.unboundid/unboundid-ldapsdk -->
+ <dependency>
+ <groupId>com.unboundid</groupId>
+ <artifactId>unboundid-ldapsdk</artifactId>
+ <version>${unboundid-ldapsdk.version}</version>
+ </dependency>
+
<!-- mockito used for testing -->
<dependency>
<groupId>org.mockito</groupId>
diff --git a/service/src/main/java/lcsb/mapviewer/services/UserDTO.java b/service/src/main/java/lcsb/mapviewer/services/UserDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..d84f9836e4a3719b44bd37c95b75faeb2465ada4
--- /dev/null
+++ b/service/src/main/java/lcsb/mapviewer/services/UserDTO.java
@@ -0,0 +1,49 @@
+package lcsb.mapviewer.services;
+
+public class UserDTO {
+ private String login;
+ private String firstName;
+ private String lastName;
+ private String email;
+ private String bindDn;
+
+ public String getLogin() {
+ return login;
+ }
+
+ public void setLogin(String login) {
+ this.login = login;
+ }
+
+ public String getFirstName() {
+ return firstName;
+ }
+
+ public void setFirstName(String firstName) {
+ this.firstName = firstName;
+ }
+
+ public String getLastName() {
+ return lastName;
+ }
+
+ public void setLastName(String lastName) {
+ this.lastName = lastName;
+ }
+
+ public String getEmail() {
+ return email;
+ }
+
+ public void setEmail(String email) {
+ this.email = email;
+ }
+
+ public String getBindDn() {
+ return bindDn;
+ }
+
+ public void setBindDn(String bindDn) {
+ this.bindDn = bindDn;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LdapService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LdapService.java
new file mode 100644
index 0000000000000000000000000000000000000000..8e40c11e36f30899f3a7fcadc16fd2f6742d3d15
--- /dev/null
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LdapService.java
@@ -0,0 +1,240 @@
+package lcsb.mapviewer.services.impl;
+
+import java.security.GeneralSecurityException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import com.unboundid.ldap.sdk.Attribute;
+import com.unboundid.ldap.sdk.BindResult;
+import com.unboundid.ldap.sdk.Filter;
+import com.unboundid.ldap.sdk.LDAPConnection;
+import com.unboundid.ldap.sdk.LDAPException;
+import com.unboundid.ldap.sdk.ResultCode;
+import com.unboundid.ldap.sdk.SearchResult;
+import com.unboundid.ldap.sdk.SearchResultEntry;
+import com.unboundid.ldap.sdk.SearchScope;
+import com.unboundid.ldap.sdk.SimpleBindRequest;
+import com.unboundid.util.ssl.SSLUtil;
+import com.unboundid.util.ssl.TrustAllTrustManager;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.services.UserDTO;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.ILdapService;
+
+@Transactional(value = "txManager")
+public class LdapService implements ILdapService {
+ Logger logger = Logger.getLogger(LdapService.class);
+
+ @Autowired
+ private IConfigurationService configurationService;
+
+ protected LDAPConnection getConnection() throws LDAPException {
+ String address = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_ADDRESS);
+ if (address == null || address.trim().isEmpty()) {
+ return null;
+ }
+ boolean ssl = "true"
+ .equalsIgnoreCase(configurationService.getConfigurationValue(ConfigurationElementType.LDAP_SSL));
+
+ String portString = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_PORT);
+ if (portString == null || address.trim().isEmpty()) {
+ if (ssl) {
+ portString = "636";
+ } else {
+ portString = "389";
+ }
+ }
+ int port = Integer.parseInt(portString);
+ LDAPConnection connection;
+ if (ssl) {
+ SSLUtil sslUtil = new SSLUtil(new TrustAllTrustManager());
+ try {
+ connection = new LDAPConnection(sslUtil.createSSLSocketFactory());
+ } catch (GeneralSecurityException e) {
+ throw new InvalidStateException(e);
+ }
+ } else {
+ connection = new LDAPConnection();
+ }
+ connection.connect(address, port);
+
+ String bindDn = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_BIND_DN);
+ String password = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_PASSWORD);
+
+ if (bindDn == null || bindDn.trim().isEmpty()) {
+ connection.bind(new SimpleBindRequest());
+ } else {
+ connection.bind(bindDn, password);
+ }
+
+ return connection;
+ }
+
+ @Override
+ public boolean login(String login, String password) throws LDAPException {
+ if (!isValidConfiguration()) {
+ logger.warn("Invalid LDAP configuration");
+ return false;
+ }
+ LDAPConnection connection = getConnection();
+ UserDTO user = getUserByLogin(login);
+ if (user != null) {
+ try {
+ BindResult result = connection.bind(user.getBindDn(), password);
+ return result.getResultCode().equals(ResultCode.SUCCESS);
+ } catch (Exception e) {
+ return false;
+ }
+ }
+
+ return false;
+ }
+
+ @Override
+ public List<String> getUsernames() throws LDAPException {
+ if (!isValidConfiguration()) {
+ logger.warn("Invalid LDAP configuration");
+ return new ArrayList<>();
+ }
+ List<String> result = new ArrayList<>();
+ LDAPConnection connection = getConnection();
+
+ Filter f2 = createObjectClassFilter();
+ Filter f3 = createAttributeFilter();
+
+ Filter filter = Filter.createANDFilter(f2, f3);
+
+ String baseDn = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_BASE_DN);
+ SearchResult searchResult = connection.search(baseDn, SearchScope.SUB, filter);
+
+ for (SearchResultEntry entry : searchResult.getSearchEntries()) {
+ Attribute uid = entry.getAttribute("uid");
+ if (uid != null) {
+ result.add(uid.getValue());
+ } else {
+ logger.warn("Invalid ldap entry: " + entry);
+ }
+ }
+ connection.close();
+
+ return result;
+ }
+
+ @Override
+ public UserDTO getUserByLogin(String login) throws LDAPException {
+ if (!isValidConfiguration()) {
+ logger.warn("Invalid LDAP configuration");
+ return null;
+ }
+ LDAPConnection connection = getConnection();
+ try {
+ String baseDn = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_BASE_DN);
+ String firstNameAttribute = configurationService
+ .getConfigurationValue(ConfigurationElementType.LDAP_FIRST_NAME_ATTRIBUTE);
+ String lastNameAttribute = configurationService
+ .getConfigurationValue(ConfigurationElementType.LDAP_LAST_NAME_ATTRIBUTE);
+ String emailAttribute = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_EMAIL_ATTRIBUTE);
+
+ Filter f1 = createLoginFilter(login);
+ Filter f2 = createObjectClassFilter();
+ Filter f3 = createAttributeFilter();
+
+ Filter filter = Filter.createANDFilter(f1, f2, f3);
+ SearchResult searchResult = connection.search(baseDn, SearchScope.SUB, filter);
+
+ for (SearchResultEntry entry : searchResult.getSearchEntries()) {
+ UserDTO result = new UserDTO();
+ result.setBindDn(entry.getDN());
+
+ Attribute uidAttribute = entry.getAttribute("uid");
+ if (uidAttribute != null) {
+ result.setLogin(uidAttribute.getValue());
+ } else {
+ logger.warn("Invalid ldap entry: " + entry);
+ }
+ if (!firstNameAttribute.trim().isEmpty()) {
+ Attribute firstName = entry.getAttribute(firstNameAttribute);
+ if (firstName != null) {
+ result.setFirstName(firstName.getValue());
+ }
+ }
+
+ if (!lastNameAttribute.trim().isEmpty()) {
+ Attribute lastName = entry.getAttribute(lastNameAttribute);
+ if (lastName != null) {
+ result.setLastName(lastName.getValue());
+ }
+ }
+
+ if (!emailAttribute.trim().isEmpty()) {
+ Attribute emailName = entry.getAttribute(emailAttribute);
+ if (emailName != null) {
+ result.setEmail(emailName.getValue());
+ }
+ }
+
+ return result;
+ }
+ return null;
+ } finally {
+ connection.close();
+ }
+ }
+
+ private Filter createObjectClassFilter() throws LDAPException {
+ String objectClass = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_OBJECT_CLASS);
+
+ if (objectClass == null || objectClass.trim().isEmpty() || objectClass .equals( "*")) {
+ return Filter.create("objectClass=*");
+ }
+
+ return Filter.createEqualityFilter("objectClass", objectClass);
+ }
+
+ private Filter createAttributeFilter() throws LDAPException {
+ String ldapStringFilter = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_FILTER);
+
+ if (ldapStringFilter == null || ldapStringFilter.trim().isEmpty()) {
+ return Filter.create("");
+ }
+
+ return Filter.create(ldapStringFilter);
+ }
+
+ private Filter createLoginFilter(String login) {
+ return Filter.createEqualityFilter("uid", login);
+ }
+
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ @Override
+ public boolean isValidConfiguration() {
+ try {
+ String baseDn = configurationService.getConfigurationValue(ConfigurationElementType.LDAP_BASE_DN);
+ if (baseDn == null || baseDn.trim().isEmpty()) {
+ return false;
+ }
+ LDAPConnection connection = getConnection();
+ if (connection != null) {
+ connection.close();
+ return true;
+ }
+ return false;
+ } catch (Exception e) {
+ logger.error(e, e);
+ return false;
+ }
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index b79e0ef37258f9217ede64927ce122ad8b7148a5..fe26c10cbfc2658004f24ad926a9648b971eaadc 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -5,7 +5,6 @@ import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Calendar;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
@@ -60,7 +59,6 @@ import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectStatus;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.graphics.MapCanvasType;
import lcsb.mapviewer.model.log.LogType;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
@@ -477,20 +475,7 @@ public class ProjectService implements IProjectService {
for (User user : userDao.getAll()) {
if (!processedUser.contains(user)) {
processedUser.add(user);
- for (PrivilegeType type : PrivilegeType.values()) {
- if (Project.class.equals(type.getPrivilegeObjectType())) {
- int level = userService.getUserPrivilegeLevel(user, type, (Integer) null);
- if (level < 0) {
- if (configurationService.getValue(type).getValue().equalsIgnoreCase("true")) {
- level = 1;
- } else {
- level = 0;
- }
- }
- ObjectPrivilege privilege = new ObjectPrivilege(project, level, type, user);
- userService.setUserPrivilege(user, privilege);
- }
- }
+ userService.createDefaultProjectPrivilegesForUser(project, user);
}
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
index b3bc006549d1391246bc18d19aead5a5caeea55e..b7c1d54c7cf902a28928bacde42af146d56458ae 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
@@ -143,4 +143,9 @@ public class ReferenceGenomeService implements IReferenceGenomeService {
return null;
}
+ @Override
+ public ReferenceGenome getReferenceGenomeById(int id, String authenticationToken) {
+ return referenceGenomeDao.getById(id);
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
index 6eb486fdb5f1d404cb20b66d9fb9dded3d08ff1f..cfabf12b2a20ca1501772c3313a73557b6f643cd 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
@@ -1,530 +1,602 @@
-package lcsb.mapviewer.services.impl;
-
-import java.awt.Color;
-import java.math.BigInteger;
-import java.security.SecureRandom;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Random;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.core.authority.AuthorityUtils;
-import org.springframework.security.core.session.SessionInformation;
-import org.springframework.security.core.session.SessionRegistry;
-import org.springframework.security.crypto.password.PasswordEncoder;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.ObjectUtils;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.geometry.ColorParser;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.log.LogType;
-import lcsb.mapviewer.model.user.BasicPrivilege;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.ObjectPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
-import lcsb.mapviewer.persist.dao.user.UserDao;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.ILogService;
-import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
-import lcsb.mapviewer.services.interfaces.IUserService;
-
-/**
- * Implementation of the service that manages users.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class UserService implements IUserService {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(UserService.class);
-
- /**
- * Data access object for users.
- */
- @Autowired
- private UserDao userDao;
-
- /**
- * Data access object for projects.
- */
- @Autowired
- private ProjectDao projectDao;
-
- /**
- * Data access object for privileges.
- */
- @Autowired
- private PrivilegeDao privilegeDao;
-
- @Autowired
- private SessionRegistry sessionRegistry;
-
- /**
- * Service that provides password encoding.
- */
- @Autowired
- private PasswordEncoder passwordEncoder;
-
- /**
- * Service used for logging.
- */
- @Autowired
- private ILogService logService;
-
- /**
- * Service used for accessing configuration parameters.
- */
- @Autowired
- private IConfigurationService configurationService;
-
- @Override
- public String login(String login, String password) {
- Random random = new SecureRandom();
- String id = new BigInteger(130, random).toString(32);
- return this.login(login, password, id);
- }
-
- @Override
- public boolean userHasPrivilege(User user, PrivilegeType type) {
- return getUserPrivilegeLevel(user, type) > 0;
- }
-
- @Override
- public boolean userHasPrivilege(User user, PrivilegeType type, Object object) {
- return getUserPrivilegeLevel(user, type, object) > 0;
- }
-
- @Override
- public void setUserPrivilege(User user, BasicPrivilege privilege) {
- updateUserPrivilegesWithoutDbModification(user, privilege);
- updateUser(user);
- userDao.flush();
- }
-
- private void updateUserPrivilegesWithoutDbModification(User user, BasicPrivilege privilege) {
- BasicPrivilege oldPrivilege = null;
- for (BasicPrivilege privilegeIter : user.getPrivileges()) {
- if (privilegeIter.equalsPrivilege(privilege)) {
- oldPrivilege = privilegeIter;
- }
- }
- if (oldPrivilege != null) {
- privilege.setUser(null);
- oldPrivilege.setLevel(privilege.getLevel());
- } else {
- privilege.setUser(user);
- user.getPrivileges().add(privilege);
- }
- }
-
- @Override
- public void addUser(User user) {
- userDao.add(user);
- LogParams params = new LogParams().description("User " + user.getLogin() + " created.").type(LogType.USER_CREATED)
- .object(user);
- logService.log(params);
- }
-
- @Override
- public void updateUser(User user) {
- userDao.update(user);
- }
-
- @Override
- public void deleteUser(User user) {
- userDao.delete(user);
- LogParams params = new LogParams().description("User " + user.getLogin() + " removed.").type(LogType.USER_CREATED)
- .object(user);
- logService.log(params);
- }
-
- @Override
- public User getUserById(int id) {
- User result = userDao.getById(id);
- if (result != null) {
- userDao.refresh(result);
- }
- return result;
- }
-
- @Override
- public User getUserByLogin(String login) {
- User result = userDao.getUserByLogin(login);
- if (result != null) {
- userDao.refresh(result);
- }
- return result;
- }
-
- @Override
- public void dropPrivilegesForObjectType(PrivilegeType type, int id) {
- IntegerComparator integerComparator = new IntegerComparator();
- // this will be slow when number of user will increase (we fetch all
- // users and drop privileges one by one)
- List<User> users = userDao.getAll();
- for (User user : users) {
- List<BasicPrivilege> toRemove = new ArrayList<BasicPrivilege>();
- for (BasicPrivilege privilege : user.getPrivileges()) {
- if (privilege.getType().equals(type) && privilege instanceof ObjectPrivilege
- && integerComparator.compare(((ObjectPrivilege) privilege).getIdObject(), id) == 0) {
- toRemove.add(privilege);
- }
- }
- if (toRemove.size() > 0) {
- user.getPrivileges().removeAll(toRemove);
- userDao.update(user);
- }
- }
- }
-
- @Override
- public int getUserPrivilegeLevel(User user, PrivilegeType type) {
- if (type.getPrivilegeClassType() != BasicPrivilege.class) {
- throw new InvalidArgumentException("This privilege requires additional information");
- }
- for (BasicPrivilege privilege : user.getPrivileges()) {
- if (privilege.getType().equals(type)) {
- return privilege.getLevel();
- }
- }
- return 0;
- }
-
- @Override
- public int getUserPrivilegeLevel(User user, PrivilegeType type, Object object) {
- Integer id = null;
- if (object != null) {
- try {
- id = ObjectUtils.getIdOfObject(object);
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw new InvalidArgumentException("Internal server error. Problem with accessing id of the parameter object");
- }
- if (!type.getPrivilegeObjectType().isAssignableFrom(object.getClass())) {
- throw new InvalidArgumentException("This privilege accept only " + type.getPrivilegeObjectType()
- + " objects parameter, but " + object.getClass() + " class found.");
- }
- }
- return getUserPrivilegeLevel(user, type, id);
- }
-
- private int getUserPrivilegeLevel(User user, PrivilegeType type, Integer id) {
- if (type.getPrivilegeClassType() != ObjectPrivilege.class) {
- throw new InvalidArgumentException("This privilege doesn't accept object parameter");
- }
- if (user == null) {
- throw new InvalidArgumentException("User cannot be null");
- }
-
- // refresh user from db
- if (user.getId() != null) {
- user = userDao.getById(user.getId());
- }
- IntegerComparator integerComparator = new IntegerComparator();
- for (BasicPrivilege privilege : user.getPrivileges()) {
- if (privilege.getClass() == ObjectPrivilege.class) {
- ObjectPrivilege oPrivilege = (ObjectPrivilege) privilege;
- if (oPrivilege.getType().equals(type) && integerComparator.compare(oPrivilege.getIdObject(), id) == 0) {
- return privilege.getLevel();
- }
- }
- }
- return -1;
- }
-
- @Override
- public void setUserPrivilege(User user, PrivilegeType type, Integer value) {
- BasicPrivilege privilege = new BasicPrivilege(value, type, user);
-
- BasicPrivilege oldPrivilege = null;
- for (BasicPrivilege privilegeIter : user.getPrivileges()) {
- if (privilegeIter.getType().equals(type)) {
- oldPrivilege = privilegeIter;
- }
- }
- if (oldPrivilege != null) {
- user.getPrivileges().remove(oldPrivilege);
- oldPrivilege.setUser(null);
- }
- user.getPrivileges().add(privilege);
- updateUser(user);
- userDao.flush();
-
- }
-
- /**
- * @return the userDao
- * @see #userDao
- */
- public UserDao getUserDao() {
- return userDao;
- }
-
- /**
- * @param userDao
- * the userDao to set
- * @see #userDao
- */
- public void setUserDao(UserDao userDao) {
- this.userDao = userDao;
- }
-
- /**
- * @return the projectDao
- * @see #projectDao
- */
- public ProjectDao getProjectDao() {
- return projectDao;
- }
-
- /**
- * @param projectDao
- * the projectDao to set
- * @see #projectDao
- */
- public void setProjectDao(ProjectDao projectDao) {
- this.projectDao = projectDao;
- }
-
- /**
- * @return the privilegeDao
- * @see #privilegeDao
- */
- public PrivilegeDao getPrivilegeDao() {
- return privilegeDao;
- }
-
- /**
- * @param privilegeDao
- * the privilegeDao to set
- * @see #privilegeDao
- */
- public void setPrivilegeDao(PrivilegeDao privilegeDao) {
- this.privilegeDao = privilegeDao;
- }
-
- /**
- * @return the passwordEncoder
- * @see #passwordEncoder
- */
- public PasswordEncoder getPasswordEncoder() {
- return passwordEncoder;
- }
-
- /**
- * @param passwordEncoder
- * the passwordEncoder to set
- * @see #passwordEncoder
- */
- public void setPasswordEncoder(PasswordEncoder passwordEncoder) {
- this.passwordEncoder = passwordEncoder;
- }
-
- /**
- * @param password
- * input password
- * @return encoded password
- */
- @Override
- public String encodePassword(String password) {
- return passwordEncoder.encode(password);
- }
-
- @Override
- public User getUserByNameSurname(String nameSurnameString) {
- return userDao.getUserByNameSurname(nameSurnameString);
- }
-
- @Override
- public ColorExtractor getColorExtractorForUser(User loggedUser) {
- Color colorMin = null;
- Color colorMax = null;
- Color colorSimple = null;
- if (loggedUser != null) {
- User dbUser = getUserById(loggedUser.getId());
- if (dbUser != null) {
- colorMin = dbUser.getMinColor();
- colorMax = dbUser.getMaxColor();
- colorSimple = dbUser.getSimpleColor();
- }
- }
- ColorParser parser = new ColorParser();
-
- if (colorMin == null) {
- colorMin = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.MIN_COLOR_VAL));
- }
- if (colorMax == null) {
- colorMax = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.MAX_COLOR_VAL));
- }
- if (colorSimple == null) {
- colorSimple = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.SIMPLE_COLOR_VAL));
- }
- return new ColorExtractor(colorMin, colorMax, colorSimple);
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- @Override
- public User getUserByToken(String token) throws SecurityException {
- if (!isSessionExpired(token)) {
- String login = ((org.springframework.security.core.userdetails.User) (sessionRegistry.getSessionInformation(token)
- .getPrincipal())).getUsername();
- return userDao.getUserByLogin(login);
- } else {
- throw new SecurityException("Invalid token");
- }
- }
-
- private boolean isSessionExpired(String token) {
- SessionInformation sessionData = sessionRegistry.getSessionInformation(token);
- if (sessionData == null) {
- logger.debug("No session data for token id: " + token);
- return true;
- }
- return sessionData.isExpired();
- }
-
- @Override
- public boolean userHasPrivilege(String token, PrivilegeType type, Object object) throws SecurityException {
- return userHasPrivilege(getUserByToken(token), type, object);
- }
-
- @Override
- public void logout(String tokenString) {
- if (!isSessionExpired(tokenString)) {
- sessionRegistry.removeSessionInformation(tokenString);
- }
- }
-
- @Override
- public User getUserById(String creatorId, String authenticationToken) throws SecurityException {
- User user = getUserByToken(authenticationToken);
- Integer id = Integer.parseInt(creatorId);
- if (user.getId().equals(id)) {
- return user;
- } else if (userHasPrivilege(authenticationToken, PrivilegeType.USER_MANAGEMENT)) {
- return getUserById(id);
- } else {
- throw new SecurityException("You cannot access data of other users");
- }
- }
-
- @Override
- public List<User> getUsers(String token) throws SecurityException {
- if (userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
- return userDao.getAll();
- } else {
- throw new SecurityException("You have no access to users data");
- }
- }
-
- @Override
- public void setUserPrivilege(User user, PrivilegeType type, Object value, String token) throws SecurityException {
- if (!userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
- throw new SecurityException("You cannot modify user privileges");
- }
- if (value instanceof Integer) {
- setUserPrivilege(user, type, (Integer) value);
- } else if (value instanceof Boolean) {
- if ((Boolean) value) {
- setUserPrivilege(user, type, 1);
- } else {
- setUserPrivilege(user, type, 0);
- }
- } else {
- throw new InvalidArgumentException("Invalid privilege value: " + value);
- }
- }
-
- @Override
- public void setUserPrivilege(User user, PrivilegeType type, Object value, Integer objectId, String token)
- throws SecurityException {
- boolean canModify = userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT);
- if (!canModify) {
- if (type.getPrivilegeObjectType().isAssignableFrom(Project.class)) {
- canModify = getUserPrivilegeLevel(getUserByToken(token), type, objectId) > 0;
- }
- }
- if (!canModify) {
- throw new SecurityException("You cannot modify user privileges");
- }
- Project projectIdWrapper = new Project();
- if (objectId == null) {
- projectIdWrapper = null;
- } else {
- projectIdWrapper.setId(objectId);
- }
- if (value instanceof Integer) {
- setUserPrivilege(user, new ObjectPrivilege(projectIdWrapper, (Integer) value, type, user));
- } else if (value instanceof Boolean) {
- if ((Boolean) value) {
- setUserPrivilege(user, new ObjectPrivilege(projectIdWrapper, 1, type, user));
- } else {
- setUserPrivilege(user, new ObjectPrivilege(projectIdWrapper, 0, type, user));
- }
- } else {
- throw new InvalidArgumentException("Invalid privilege value: " + value);
- }
-
- }
-
- @Override
- public void updateUser(User modifiedUser, String token) throws SecurityException {
- User user = getUserByToken(token);
- if (user.getLogin().equals(modifiedUser.getLogin()) || userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
- updateUser(modifiedUser);
- } else {
- throw new SecurityException("You cannot modify user");
- }
-
- }
-
- @Override
- public boolean userHasPrivilege(String token, PrivilegeType type) throws SecurityException {
- return userHasPrivilege(getUserByToken(token), type);
- }
-
- @Override
- public String login(String login, String password, String token) {
- User user = userDao.getUserByLoginAndPassword(login, password);
- if (user == null && Configuration.ANONYMOUS_LOGIN.equals(login) && "".equals(password)) {
- user = getUserByLogin(Configuration.ANONYMOUS_LOGIN);
- }
- if (user != null) {
- sessionRegistry.registerNewSession(token, new org.springframework.security.core.userdetails.User(login,
- passwordEncoder.encode(password), AuthorityUtils.commaSeparatedStringToAuthorityList("")));
- return token;
- } else {
- return null;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import java.awt.Color;
+import java.math.BigInteger;
+import java.security.SecureRandom;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.core.authority.AuthorityUtils;
+import org.springframework.security.core.session.SessionInformation;
+import org.springframework.security.core.session.SessionRegistry;
+import org.springframework.security.crypto.password.PasswordEncoder;
+import org.springframework.transaction.annotation.Transactional;
+
+import com.unboundid.ldap.sdk.LDAPException;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.ObjectUtils;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.log.LogType;
+import lcsb.mapviewer.model.user.BasicPrivilege;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.ObjectPrivilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
+import lcsb.mapviewer.persist.dao.user.UserDao;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.UserDTO;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.ILdapService;
+import lcsb.mapviewer.services.interfaces.ILogService;
+import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
+import lcsb.mapviewer.services.interfaces.IUserService;
+
+/**
+ * Implementation of the service that manages users.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class UserService implements IUserService {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(UserService.class);
+
+ /**
+ * Data access object for users.
+ */
+ @Autowired
+ private UserDao userDao;
+
+ /**
+ * Data access object for privileges.
+ */
+ @Autowired
+ private PrivilegeDao privilegeDao;
+
+ @Autowired
+ private SessionRegistry sessionRegistry;
+
+ /**
+ * Service that provides password encoding.
+ */
+ @Autowired
+ private PasswordEncoder passwordEncoder;
+
+ /**
+ * Service used for logging.
+ */
+ @Autowired
+ private ILogService logService;
+
+ @Autowired
+ private ILdapService ldapService;
+
+ @Autowired
+ private ProjectDao projectDao;
+
+ /**
+ * Service used for accessing configuration parameters.
+ */
+ @Autowired
+ private IConfigurationService configurationService;
+
+ @Override
+ public String login(String login, String password) {
+ Random random = new SecureRandom();
+ String id = new BigInteger(130, random).toString(32);
+ return this.login(login, password, id);
+ }
+
+ @Override
+ public boolean userHasPrivilege(User user, PrivilegeType type) {
+ return getUserPrivilegeLevel(user, type) > 0;
+ }
+
+ @Override
+ public boolean userHasPrivilege(User user, PrivilegeType type, Object object) {
+ return getUserPrivilegeLevel(user, type, object) > 0;
+ }
+
+ @Override
+ public void setUserPrivilege(User user, BasicPrivilege privilege) {
+ updateUserPrivilegesWithoutDbModification(user, privilege);
+ updateUser(user);
+ userDao.flush();
+ }
+
+ private void updateUserPrivilegesWithoutDbModification(User user, BasicPrivilege privilege) {
+ BasicPrivilege oldPrivilege = null;
+ for (BasicPrivilege privilegeIter : user.getPrivileges()) {
+ if (privilegeIter.equalsPrivilege(privilege)) {
+ oldPrivilege = privilegeIter;
+ }
+ }
+ if (oldPrivilege != null) {
+ privilege.setUser(null);
+ oldPrivilege.setLevel(privilege.getLevel());
+ } else {
+ privilege.setUser(user);
+ user.getPrivileges().add(privilege);
+ }
+ }
+
+ @Override
+ public void addUser(User user) {
+ userDao.add(user);
+ LogParams params = new LogParams().description("User " + user.getLogin() + " created.").type(LogType.USER_CREATED)
+ .object(user);
+ logService.log(params);
+ }
+
+ @Override
+ public void updateUser(User user) {
+ userDao.update(user);
+ }
+
+ @Override
+ public void deleteUser(User user) {
+ userDao.delete(user);
+ LogParams params = new LogParams().description("User " + user.getLogin() + " removed.").type(LogType.USER_CREATED)
+ .object(user);
+ logService.log(params);
+ }
+
+ @Override
+ public User getUserByLogin(String login) {
+ User result = userDao.getUserByLogin(login);
+ if (result != null) {
+ userDao.refresh(result);
+ }
+ return result;
+ }
+
+ @Override
+ public void dropPrivilegesForObjectType(PrivilegeType type, int id) {
+ IntegerComparator integerComparator = new IntegerComparator();
+ // this will be slow when number of user will increase (we fetch all
+ // users and drop privileges one by one)
+ List<User> users = userDao.getAll();
+ for (User user : users) {
+ List<BasicPrivilege> toRemove = new ArrayList<>();
+ for (BasicPrivilege privilege : user.getPrivileges()) {
+ if (privilege.getType().equals(type) && privilege instanceof ObjectPrivilege
+ && integerComparator.compare(((ObjectPrivilege) privilege).getIdObject(), id) == 0) {
+ toRemove.add(privilege);
+ }
+ }
+ if (toRemove.size() > 0) {
+ user.getPrivileges().removeAll(toRemove);
+ userDao.update(user);
+ }
+ }
+ }
+
+ @Override
+ public int getUserPrivilegeLevel(User user, PrivilegeType type) {
+ if (type.getPrivilegeClassType() != BasicPrivilege.class) {
+ throw new InvalidArgumentException("This privilege requires additional information");
+ }
+ for (BasicPrivilege privilege : user.getPrivileges()) {
+ if (privilege.getType().equals(type)) {
+ return privilege.getLevel();
+ }
+ }
+ return 0;
+ }
+
+ @Override
+ public int getUserPrivilegeLevel(User user, PrivilegeType type, Object object) {
+ Integer id = null;
+ if (object != null) {
+ try {
+ id = ObjectUtils.getIdOfObject(object);
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw new InvalidArgumentException("Internal server error. Problem with accessing id of the parameter object");
+ }
+ if (!type.getPrivilegeObjectType().isAssignableFrom(object.getClass())) {
+ throw new InvalidArgumentException("This privilege accept only " + type.getPrivilegeObjectType()
+ + " objects parameter, but " + object.getClass() + " class found.");
+ }
+ }
+ return getUserPrivilegeLevel(user, type, id);
+ }
+
+ private int getUserPrivilegeLevel(User user, PrivilegeType type, Integer id) {
+ if (type.getPrivilegeClassType() != ObjectPrivilege.class) {
+ throw new InvalidArgumentException("This privilege doesn't accept object parameter");
+ }
+ if (user == null) {
+ throw new InvalidArgumentException("User cannot be null");
+ }
+
+ // refresh user from db
+ if (user.getId() != null) {
+ user = userDao.getById(user.getId());
+ }
+ IntegerComparator integerComparator = new IntegerComparator();
+ for (BasicPrivilege privilege : user.getPrivileges()) {
+ if (privilege.getClass() == ObjectPrivilege.class) {
+ ObjectPrivilege oPrivilege = (ObjectPrivilege) privilege;
+ if (oPrivilege.getType().equals(type) && integerComparator.compare(oPrivilege.getIdObject(), id) == 0) {
+ return privilege.getLevel();
+ }
+ }
+ }
+ return -1;
+ }
+
+ @Override
+ public void setUserPrivilege(User user, PrivilegeType type, Integer value) {
+ BasicPrivilege privilege = new BasicPrivilege(value, type, user);
+
+ BasicPrivilege oldPrivilege = null;
+ for (BasicPrivilege privilegeIter : user.getPrivileges()) {
+ if (privilegeIter.getType().equals(type)) {
+ oldPrivilege = privilegeIter;
+ }
+ }
+ if (oldPrivilege != null) {
+ user.getPrivileges().remove(oldPrivilege);
+ oldPrivilege.setUser(null);
+ }
+ user.getPrivileges().add(privilege);
+ updateUser(user);
+ userDao.flush();
+
+ }
+
+ /**
+ * @return the userDao
+ * @see #userDao
+ */
+ public UserDao getUserDao() {
+ return userDao;
+ }
+
+ /**
+ * @param userDao
+ * the userDao to set
+ * @see #userDao
+ */
+ public void setUserDao(UserDao userDao) {
+ this.userDao = userDao;
+ }
+
+ /**
+ * @return the privilegeDao
+ * @see #privilegeDao
+ */
+ public PrivilegeDao getPrivilegeDao() {
+ return privilegeDao;
+ }
+
+ /**
+ * @param privilegeDao
+ * the privilegeDao to set
+ * @see #privilegeDao
+ */
+ public void setPrivilegeDao(PrivilegeDao privilegeDao) {
+ this.privilegeDao = privilegeDao;
+ }
+
+ /**
+ * @return the passwordEncoder
+ * @see #passwordEncoder
+ */
+ public PasswordEncoder getPasswordEncoder() {
+ return passwordEncoder;
+ }
+
+ /**
+ * @param passwordEncoder
+ * the passwordEncoder to set
+ * @see #passwordEncoder
+ */
+ public void setPasswordEncoder(PasswordEncoder passwordEncoder) {
+ this.passwordEncoder = passwordEncoder;
+ }
+
+ /**
+ * @param password
+ * input password
+ * @return encoded password
+ */
+ @Override
+ public String encodePassword(String password) {
+ return passwordEncoder.encode(password);
+ }
+
+ @Override
+ public ColorExtractor getColorExtractorForUser(User loggedUser) {
+ Color colorMin = null;
+ Color colorMax = null;
+ Color colorSimple = null;
+ if (loggedUser != null) {
+ User dbUser = getUserByLogin(loggedUser.getLogin());
+ if (dbUser != null) {
+ colorMin = dbUser.getMinColor();
+ colorMax = dbUser.getMaxColor();
+ colorSimple = dbUser.getSimpleColor();
+ }
+ }
+ ColorParser parser = new ColorParser();
+
+ if (colorMin == null) {
+ colorMin = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.MIN_COLOR_VAL));
+ }
+ if (colorMax == null) {
+ colorMax = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.MAX_COLOR_VAL));
+ }
+ if (colorSimple == null) {
+ colorSimple = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.SIMPLE_COLOR_VAL));
+ }
+ return new ColorExtractor(colorMin, colorMax, colorSimple);
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ @Override
+ public User getUserByToken(String token) throws SecurityException {
+ if (!isSessionExpired(token)) {
+ String login = ((org.springframework.security.core.userdetails.User) (sessionRegistry.getSessionInformation(token)
+ .getPrincipal())).getUsername();
+ return userDao.getUserByLogin(login);
+ } else {
+ throw new SecurityException("Invalid token");
+ }
+ }
+
+ private boolean isSessionExpired(String token) {
+ SessionInformation sessionData = sessionRegistry.getSessionInformation(token);
+ if (sessionData == null) {
+ logger.debug("No session data for token id: " + token);
+ return true;
+ }
+ return sessionData.isExpired();
+ }
+
+ @Override
+ public boolean userHasPrivilege(String token, PrivilegeType type, Object object) throws SecurityException {
+ return userHasPrivilege(getUserByToken(token), type, object);
+ }
+
+ @Override
+ public void logout(String tokenString) {
+ if (!isSessionExpired(tokenString)) {
+ sessionRegistry.removeSessionInformation(tokenString);
+ }
+ }
+
+ @Override
+ public List<User> getUsers(String token) throws SecurityException {
+ if (userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
+ return userDao.getAll();
+ } else {
+ throw new SecurityException("You have no access to users data");
+ }
+ }
+
+ @Override
+ public void setUserPrivilege(User user, PrivilegeType type, Object value, String token) throws SecurityException {
+ if (!userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
+ throw new SecurityException("You cannot modify user privileges");
+ }
+ if (value instanceof Integer) {
+ setUserPrivilege(user, type, (Integer) value);
+ } else if (value instanceof Boolean) {
+ if ((Boolean) value) {
+ setUserPrivilege(user, type, 1);
+ } else {
+ setUserPrivilege(user, type, 0);
+ }
+ } else {
+ throw new InvalidArgumentException("Invalid privilege value: " + value);
+ }
+ }
+
+ @Override
+ public void setUserPrivilege(User user, PrivilegeType type, Object value, Integer objectId, String token)
+ throws SecurityException {
+ boolean canModify = userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT);
+ if (!canModify) {
+ if (type.getPrivilegeObjectType().isAssignableFrom(Project.class)) {
+ canModify = getUserPrivilegeLevel(getUserByToken(token), type, objectId) > 0;
+ }
+ }
+ if (!canModify) {
+ throw new SecurityException("You cannot modify user privileges");
+ }
+ Project projectIdWrapper = new Project();
+ if (objectId == null) {
+ projectIdWrapper = null;
+ } else {
+ projectIdWrapper.setId(objectId);
+ }
+ if (value instanceof Integer) {
+ setUserPrivilege(user, new ObjectPrivilege(projectIdWrapper, (Integer) value, type, user));
+ } else if (value instanceof Boolean) {
+ if ((Boolean) value) {
+ setUserPrivilege(user, new ObjectPrivilege(projectIdWrapper, 1, type, user));
+ } else {
+ setUserPrivilege(user, new ObjectPrivilege(projectIdWrapper, 0, type, user));
+ }
+ } else {
+ throw new InvalidArgumentException("Invalid privilege value: " + value);
+ }
+
+ }
+
+ @Override
+ public void updateUser(User modifiedUser, String token) throws SecurityException {
+ User user = getUserByToken(token);
+ if (user.getLogin().equals(modifiedUser.getLogin()) || userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
+ updateUser(modifiedUser);
+ } else {
+ throw new SecurityException("You cannot modify user");
+ }
+
+ }
+
+ @Override
+ public boolean userHasPrivilege(String token, PrivilegeType type) throws SecurityException {
+ return userHasPrivilege(getUserByToken(token), type);
+ }
+
+ @Override
+ public String login(String login, String password, String token) {
+ User user = userDao.getUserByLogin(login);
+ if (user == null) {
+ user = createUserFromLdap(login, password);
+ } else if (!user.isConnectedToLdap()) {
+ String cryptedPassword;
+ if (password != null) {
+ cryptedPassword = passwordEncoder.encode(password);
+ } else {
+ cryptedPassword = "";
+ }
+ user = userDao.getUserByLoginAndCryptedPassword(login, cryptedPassword);
+ } else {
+ if (!authenticateOverLdap(login, password)) {
+ user = null;
+ }
+ }
+
+ if (user == null && Configuration.ANONYMOUS_LOGIN.equals(login) && "".equals(password)) {
+ user = getUserByLogin(Configuration.ANONYMOUS_LOGIN);
+ }
+ if (user != null) {
+ sessionRegistry.registerNewSession(token, new org.springframework.security.core.userdetails.User(login,
+ passwordEncoder.encode(password), AuthorityUtils.commaSeparatedStringToAuthorityList("")));
+ return token;
+ } else {
+ return null;
+ }
+ }
+
+ private boolean authenticateOverLdap(String login, String password) {
+ if (!ldapService.isValidConfiguration()) {
+ return false;
+ }
+ try {
+ return ldapService.login(login, password);
+ } catch (LDAPException e) {
+ logger.warn("Problem with accessing LDAP directory", e);
+ return false;
+ }
+ }
+
+ private User createUserFromLdap(String login, String password) {
+ if (login == null || password == null) {
+ return null;
+ }
+ if (!ldapService.isValidConfiguration()) {
+ return null;
+ }
+ try {
+ User user = null;
+ boolean authenticatedOverLdap = ldapService.login(login, password);
+ if (authenticatedOverLdap) {
+ UserDTO ldapUserData = ldapService.getUserByLogin(login);
+ user = new User();
+ user.setLogin(login);
+ user.setCryptedPassword(passwordEncoder.encode(password));
+ user.setName(ldapUserData.getFirstName());
+ user.setSurname(ldapUserData.getLastName());
+ user.setEmail(ldapUserData.getEmail());
+ user.setConnectedToLdap(true);
+ addUser(user);
+ for (Project project : projectDao.getAll()) {
+ createDefaultProjectPrivilegesForUser(project, user);
+ }
+ }
+ return user;
+ } catch (LDAPException e) {
+ logger.warn("Problem with accessing LDAP directory", e);
+ return null;
+ }
+ }
+
+ @Override
+ public ILdapService getLdapService() {
+ return ldapService;
+ }
+
+ @Override
+ public void setLdapService(ILdapService ldapService) {
+ this.ldapService = ldapService;
+ }
+
+ @Override
+ public void createDefaultProjectPrivilegesForUser(Project project, User user) {
+ for (PrivilegeType type : PrivilegeType.values()) {
+ if (Project.class.equals(type.getPrivilegeObjectType())) {
+ int level = getUserPrivilegeLevel(user, type, (Integer) null);
+ if (level < 0) {
+ if (configurationService.getValue(type).getValue().equalsIgnoreCase("true")) {
+ level = 1;
+ } else {
+ level = 0;
+ }
+ }
+ ObjectPrivilege privilege = new ObjectPrivilege(project, level, type, user);
+ setUserPrivilege(user, privilege);
+ }
+ }
+ }
+
+ @Override
+ public Map<String, Boolean> ldapAccountExistsForLogin(Collection<User> logins) {
+ Map<String, Boolean> result = new HashMap<>();
+ for (User user : logins) {
+ result.put(user.getLogin(), false);
+ }
+
+ if (ldapService.isValidConfiguration()) {
+ try {
+ List<String> ldapUserNames = getLdapService().getUsernames();
+ for (String string : ldapUserNames) {
+ if (result.keySet().contains(string)) {
+ result.put(string, true);
+ }
+ }
+ } catch (LDAPException e) {
+ logger.error("Problem with accessing LDAP directory", e);
+ }
+ }
+ return result;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILdapService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILdapService.java
new file mode 100644
index 0000000000000000000000000000000000000000..8a56e5c37b2a3c3f68729b9a84c3406fb128d392
--- /dev/null
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILdapService.java
@@ -0,0 +1,61 @@
+package lcsb.mapviewer.services.interfaces;
+
+import java.util.List;
+
+import com.unboundid.ldap.sdk.LDAPException;
+
+import lcsb.mapviewer.model.user.ConfigurationElementTypeGroup;
+import lcsb.mapviewer.services.UserDTO;
+
+/**
+ * Connection service to LDAP server.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ILdapService {
+
+ /**
+ * Checks if login and password match
+ *
+ * @param login
+ * user login
+ * @param password
+ * password
+ * @return true if user login/password match
+ * @throws LDAPException
+ * thrown when there is problem with LDAP connection
+ */
+ boolean login(String login, String password) throws LDAPException;
+
+ /**
+ * Returns list of user names available in the LDAP server.
+ *
+ * @return list of user names
+ * @throws LDAPException
+ * thrown when there is problem with LDAP connection
+ */
+ List<String> getUsernames() throws LDAPException;
+
+ /**
+ * Returns user data information from LDAP for given login.
+ *
+ * @param login
+ * user for which we obtain data
+ * @return user data information from LDAP for given login or null if such user
+ * doesn't exist
+ * @throws LDAPException
+ * thrown when there is problem with LDAP connection
+ */
+ UserDTO getUserByLogin(String login) throws LDAPException;
+
+ /**
+ * Checks if LDAP configuration
+ * ({@link ConfigurationElementTypeGroup#LDAP_CONFIGURATION}) is valid.
+ *
+ * @return true if LDAP configuration
+ * ({@link ConfigurationElementTypeGroup#LDAP_CONFIGURATION}) is valid
+ */
+ boolean isValidConfiguration();
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
index 419116d1d747c16de154f38042f66797e009bf53..71af2fae75eedd66a5a6b5648d7d85eb0b1f0d73 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
@@ -11,7 +11,7 @@ import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
/**
- * Service used to maintain referemce genome data.
+ * Service used to maintain reference genome data.
*
* @author Piotr Gawron
*
@@ -24,7 +24,7 @@ public interface IReferenceGenomeService {
* @param type
* {@link ReferenceGenomeType type} of reference genome
* @param organism
- * organism for which renference genome is added
+ * organism for which reference genome is added
* @param version
* version of the reference genome
* @param customUrl
@@ -35,7 +35,7 @@ public interface IReferenceGenomeService {
* thrown when url is invalid
* @throws ReferenceGenomeConnectorException
* thrown when reference genome already exists or there is problem
- * wirh adding genome
+ * with adding genome
*/
void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
@@ -49,7 +49,7 @@ public interface IReferenceGenomeService {
* @return list of available organisms
* @throws ReferenceGenomeConnectorException
* thrown when there is a problem with accessing information about
- * reference genoems
+ * reference genomes
*/
List<MiriamData> getOrganismsByReferenceGenomeType(ReferenceGenomeType type) throws ReferenceGenomeConnectorException;
@@ -64,7 +64,7 @@ public interface IReferenceGenomeService {
* @return list of available organisms
* @throws ReferenceGenomeConnectorException
* thrown when there is a problem with accessing information about
- * reference genoems
+ * reference genomes
*/
List<String> getAvailableGenomeVersions(ReferenceGenomeType type, MiriamData organism)
throws ReferenceGenomeConnectorException;
@@ -83,9 +83,9 @@ public interface IReferenceGenomeService {
String getUrlForGenomeVersion(ReferenceGenomeType type, MiriamData organism, String version);
/**
- * Returns list of all downladed reference genomes.
+ * Returns list of all downloaded reference genomes.
*
- * @return list of all downladed reference genomes
+ * @return list of all downloaded reference genomes
*/
List<ReferenceGenome> getDownloadedGenomes();
@@ -100,7 +100,7 @@ public interface IReferenceGenomeService {
void removeGenome(ReferenceGenome genome) throws IOException;
/**
- * Adds gene mapping to refernce genome.
+ * Adds gene mapping to reference genome.
*
* @param referenceGenome
* reference genome where we add mapping
@@ -113,7 +113,7 @@ public interface IReferenceGenomeService {
* @throws URISyntaxException
* thrown when url is invalid
* @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with manipulatinf information about
+ * thrown when there is a problem with manipulating information about
* reference genome
*/
void addReferenceGenomeGeneMapping(ReferenceGenome referenceGenome, String name, String url)
@@ -142,4 +142,6 @@ public interface IReferenceGenomeService {
*/
ReferenceGenome getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType, String version,
String authenticationToken);
+
+ ReferenceGenome getReferenceGenomeById(int id, String authenticationToken);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
index d11ffec752a33098732d22d9c279e1c51a085784..66bc88d3128ee4385f9d4241d364cba99cfa16e0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
@@ -1,201 +1,189 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.util.List;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.model.user.BasicPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.SecurityException;
-
-/**
- * Service that manages users.
- *
- * @author Piotr Gawron
- *
- */
-public interface IUserService {
- /**
- * Check if its possible to login using given login and password.
- *
- * @param login
- * user login
- * @param password
- * plan password
- * @return {@link String} containing session id if credentials are valid,
- * <code>null</code> otherwise
- */
- String login(String login, String password);
-
- /**
- * Returns user by login.
- *
- * @param login
- * user login
- * @return user if the login is valid, <code>null</code> otherwise
- */
- User getUserByLogin(String login);
-
- /**
- * Checks if user has a given privilege.
- *
- * @param user
- * user for which the check is performed
- * @param type
- * type of the privilege
- * @return <code>true</code> if user has privilege, <code>false</code> otherwise
- */
- boolean userHasPrivilege(User user, PrivilegeType type);
-
- /**
- * Returns level of the user privilege.
- *
- * @param user
- * user for which the check is performed
- * @param type
- * type of the privilege
- * @return level of the privilege
- */
- int getUserPrivilegeLevel(User user, PrivilegeType type);
-
- /**
- * Checks if user has a given privilege on the object.
- *
- * @param user
- * user for which the check is performed
- * @param type
- * type of the privilege
- * @param object
- * object of the privilege
- * @return <code>true</code> if user has privilege, <code>false</code> otherwise
- */
- boolean userHasPrivilege(User user, PrivilegeType type, Object object);
-
- /**
- * Returns level of the user privilege.
- *
- * @param object
- * object of the privilege
- * @param user
- * user for which the check is performed
- * @param type
- * type of the privilege
- * @return level of the privilege
- */
- int getUserPrivilegeLevel(User user, PrivilegeType type, Object object);
-
- /**
- * Sets the user privilege.
- *
- * @param user
- * user for whom the privilege should be granted/dropped
- * @param privilege
- * user privilege
- */
- void setUserPrivilege(User user, BasicPrivilege privilege);
-
- /**
- * Adds user to the system.
- *
- * @param user
- * user to be added
- */
- void addUser(User user);
-
- /**
- * Updates user in the system.
- *
- * @param user
- * user to be updated
- */
- void updateUser(User user);
-
- /**
- * Removes user from the system.
- *
- * @param user
- * user to be removed
- */
- void deleteUser(User user);
-
- /**
- * Returns user by the database identifier.
- *
- * @param id
- * database identifier
- * @return user for the given identifier, null if user doesn't exist
- *
- */
- User getUserById(int id);
-
- /**
- * Drops privileges for every user on the given object and type.
- *
- * @param type
- * type of privilege that should be dropped
- * @param objectId
- * identifier of the object to which privileges should be dropped
- */
- void dropPrivilegesForObjectType(PrivilegeType type, int objectId);
-
- /**
- * Adds privilege to the user.
- *
- * @param user
- * user to which privilege should be added
- * @param type
- * type of the privilege
- */
- void setUserPrivilege(User user, PrivilegeType type, Integer value);
-
- /**
- * @param password
- * input password
- * @return encoded password
- */
- String encodePassword(String password);
-
- /**
- * Returns {@link User} for given "name surname" string.
- *
- * @param nameSurnameString
- * string identifying user with name and surname separated by single
- * space
- * @return {@link User} for given "name surname" string
- */
- User getUserByNameSurname(String nameSurnameString);
-
- /**
- * Returns {@link ColorExtractor} that transform overlay values into colors for
- * given user.
- *
- * @param user
- * {@link User} for which {@link ColorExtractor} will be obtained
- * @return {@link ColorExtractor} that transform overlay values into colors for
- * given user
- */
- ColorExtractor getColorExtractorForUser(User user);
-
- User getUserByToken(String token) throws SecurityException;
-
- boolean userHasPrivilege(String token, PrivilegeType type, Object object) throws SecurityException;
-
- void logout(String tokenString) throws SecurityException;
-
- boolean userHasPrivilege(String token, PrivilegeType addMap) throws SecurityException;
-
- User getUserById(String creatorId, String token) throws SecurityException;
-
- List<User> getUsers(String token) throws SecurityException;
-
- void setUserPrivilege(User modifiedUser, PrivilegeType type, Object privilegeToSet, String authenticationToken)
- throws SecurityException;
-
- void setUserPrivilege(User modifiedUser, PrivilegeType type, Object privilegeToSet, Integer objectId,
- String authenticationToken) throws SecurityException;
-
- void updateUser(User modifiedUser, String authenticationToken) throws SecurityException;
-
- String login(String login, String password, String id);
-
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.user.BasicPrivilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.SecurityException;
+
+/**
+ * Service that manages users.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IUserService {
+ /**
+ * Check if its possible to login using given login and password.
+ *
+ * @param login
+ * user login
+ * @param password
+ * plan password
+ * @return {@link String} containing session id if credentials are valid,
+ * <code>null</code> otherwise
+ */
+ String login(String login, String password);
+
+ /**
+ * Returns user by login.
+ *
+ * @param login
+ * user login
+ * @return user if the login is valid, <code>null</code> otherwise
+ */
+ User getUserByLogin(String login);
+
+ /**
+ * Checks if user has a given privilege.
+ *
+ * @param user
+ * user for which the check is performed
+ * @param type
+ * type of the privilege
+ * @return <code>true</code> if user has privilege, <code>false</code> otherwise
+ */
+ boolean userHasPrivilege(User user, PrivilegeType type);
+
+ /**
+ * Returns level of the user privilege.
+ *
+ * @param user
+ * user for which the check is performed
+ * @param type
+ * type of the privilege
+ * @return level of the privilege
+ */
+ int getUserPrivilegeLevel(User user, PrivilegeType type);
+
+ /**
+ * Checks if user has a given privilege on the object.
+ *
+ * @param user
+ * user for which the check is performed
+ * @param type
+ * type of the privilege
+ * @param object
+ * object of the privilege
+ * @return <code>true</code> if user has privilege, <code>false</code> otherwise
+ */
+ boolean userHasPrivilege(User user, PrivilegeType type, Object object);
+
+ /**
+ * Returns level of the user privilege.
+ *
+ * @param object
+ * object of the privilege
+ * @param user
+ * user for which the check is performed
+ * @param type
+ * type of the privilege
+ * @return level of the privilege
+ */
+ int getUserPrivilegeLevel(User user, PrivilegeType type, Object object);
+
+ /**
+ * Sets the user privilege.
+ *
+ * @param user
+ * user for whom the privilege should be granted/dropped
+ * @param privilege
+ * user privilege
+ */
+ void setUserPrivilege(User user, BasicPrivilege privilege);
+
+ /**
+ * Adds user to the system.
+ *
+ * @param user
+ * user to be added
+ */
+ void addUser(User user);
+
+ /**
+ * Updates user in the system.
+ *
+ * @param user
+ * user to be updated
+ */
+ void updateUser(User user);
+
+ /**
+ * Removes user from the system.
+ *
+ * @param user
+ * user to be removed
+ */
+ void deleteUser(User user);
+
+ /**
+ * Drops privileges for every user on the given object and type.
+ *
+ * @param type
+ * type of privilege that should be dropped
+ * @param objectId
+ * identifier of the object to which privileges should be dropped
+ */
+ void dropPrivilegesForObjectType(PrivilegeType type, int objectId);
+
+ /**
+ * Adds privilege to the user.
+ *
+ * @param user
+ * user to which privilege should be added
+ * @param type
+ * type of the privilege
+ */
+ void setUserPrivilege(User user, PrivilegeType type, Integer value);
+
+ /**
+ * @param password
+ * input password
+ * @return encoded password
+ */
+ String encodePassword(String password);
+
+ /**
+ * Returns {@link ColorExtractor} that transform overlay values into colors for
+ * given user.
+ *
+ * @param user
+ * {@link User} for which {@link ColorExtractor} will be obtained
+ * @return {@link ColorExtractor} that transform overlay values into colors for
+ * given user
+ */
+ ColorExtractor getColorExtractorForUser(User user);
+
+ User getUserByToken(String token) throws SecurityException;
+
+ boolean userHasPrivilege(String token, PrivilegeType type, Object object) throws SecurityException;
+
+ void logout(String tokenString) throws SecurityException;
+
+ boolean userHasPrivilege(String token, PrivilegeType addMap) throws SecurityException;
+
+ List<User> getUsers(String token) throws SecurityException;
+
+ void setUserPrivilege(User modifiedUser, PrivilegeType type, Object privilegeToSet, String authenticationToken)
+ throws SecurityException;
+
+ void setUserPrivilege(User modifiedUser, PrivilegeType type, Object privilegeToSet, Integer objectId,
+ String authenticationToken) throws SecurityException;
+
+ void updateUser(User modifiedUser, String authenticationToken) throws SecurityException;
+
+ String login(String login, String password, String id);
+
+ ILdapService getLdapService();
+
+ void setLdapService(ILdapService ldapService);
+
+ void createDefaultProjectPrivilegesForUser(Project project, User user);
+
+ Map<String, Boolean> ldapAccountExistsForLogin(Collection<User> logins);
+}
diff --git a/service/src/main/resources/applicationContext-service.xml b/service/src/main/resources/applicationContext-service.xml
index 1cbe2873d141f3332a21faec68675b62e05613c0..961c5a7b037e3da2064d1f974c6e52805b6d93d4 100644
--- a/service/src/main/resources/applicationContext-service.xml
+++ b/service/src/main/resources/applicationContext-service.xml
@@ -23,6 +23,8 @@
<bean id="LayoutService" class="lcsb.mapviewer.services.impl.LayoutService"/>
+ <bean id="LdapService" class="lcsb.mapviewer.services.impl.LdapService"/>
+
<bean id="LogService" class="lcsb.mapviewer.services.impl.LogService"/>
<bean id="MiriamService" class="lcsb.mapviewer.services.impl.MiriamService"/>
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java b/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
index f08941eeb3d935f91970189f8a742698756cf173..3a5bb0badde51ea8b6998a5c597b4151bfa4340f 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
@@ -6,13 +6,14 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ CommentServiceTest.class, //
- ConfigurationServiceTest.class, //
- ExternalServicesServiceTest.class, //
- LayoutServiceTest.class, //
- Md5PasswordEncoderTest.class, //
- ProjectServiceTest.class, //
- SearchServiceTest.class, //
- UserServiceTest.class,//
+ ConfigurationServiceTest.class, //
+ ExternalServicesServiceTest.class, //
+ LayoutServiceTest.class, //
+ LdapServiceTest.class, //
+ Md5PasswordEncoderTest.class, //
+ ProjectServiceTest.class, //
+ SearchServiceTest.class, //
+ UserServiceTest.class,//
})
public class AllImplServiceTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LdapServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LdapServiceTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..6e9446bb0c0107298cdfa8a6314f4555efa3aec8
--- /dev/null
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LdapServiceTest.java
@@ -0,0 +1,136 @@
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+import org.springframework.test.annotation.Rollback;
+
+import com.unboundid.ldap.listener.InMemoryDirectoryServer;
+import com.unboundid.ldap.listener.InMemoryDirectoryServerConfig;
+import com.unboundid.ldap.sdk.LDAPConnection;
+
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.UserDTO;
+
+@Rollback(true)
+public class LdapServiceTest extends ServiceTestFunctions {
+ static Logger logger = Logger.getLogger(LdapServiceTest.class);
+
+ LdapService ldapService;
+
+ @Before
+ public void setUp() throws Exception {
+ try {
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_BASE_DN, "dc=uni,dc=lu");
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_OBJECT_CLASS, "person");
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_FILTER, "memberof=cn=gitlab,cn=groups,cn=accounts,dc=uni,dc=lu");
+
+ ldapService = Mockito.spy(LdapService.class);
+ ldapService.setConfigurationService(configurationService);
+ Mockito.when(ldapService.getConnection()).thenAnswer(new Answer<LDAPConnection>() {
+
+ @Override
+ public LDAPConnection answer(InvocationOnMock invocation) throws Throwable {
+ // Create the configuration to use for the server.
+ InMemoryDirectoryServerConfig config = new InMemoryDirectoryServerConfig("dc=uni,dc=lu");
+ config.addAdditionalBindCredentials("uid=piotr.gawron,cn=users,cn=accounts,dc=uni,dc=lu", "test_passwd");
+ config.setSchema(null);
+
+ // Create the directory server instance, populate it with data from the
+ // "test-data.ldif" file, and start listening for client connections.
+ InMemoryDirectoryServer ds = new InMemoryDirectoryServer(config);
+ ds.importFromLDIF(true, "testFiles/ldap/testdata.ldif");
+ ds.startListening();
+ return ds.getConnection();
+ }
+ });
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testIsValidConfiguration() throws Exception {
+ try {
+ assertTrue(ldapService.isValidConfiguration());
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_BASE_DN, "");
+ assertFalse(ldapService.isValidConfiguration());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLogin() throws Exception {
+ try {
+ assertTrue(ldapService.login("piotr.gawron", "test_passwd"));
+ assertFalse(ldapService.login("piotr.gawron", "invalid_password"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUsernames() throws Exception {
+ try {
+ List<String> list = ldapService.getUsernames();
+ assertEquals(2, list.size());
+ assertTrue(list.contains("piotr.gawron"));
+ assertFalse(list.contains("john.doe"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUsernamesWithFiltering() throws Exception {
+ try {
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_FILTER,
+ "(memberof=cn=owncloud,cn=groups,cn=accounts,dc=uni,dc=lu)");
+
+ List<String> list = ldapService.getUsernames();
+ assertEquals(1, list.size());
+ assertTrue(list.contains("piotr.gawron"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUserByLogin() throws Exception {
+ try {
+ UserDTO user = ldapService.getUserByLogin("piotr.gawron");
+ assertEquals("Piotr", user.getFirstName());
+ assertEquals("Gawron", user.getLastName());
+ assertEquals("piotr.gawron", user.getLogin());
+ assertEquals("piotr.gawron@uni.lu", user.getEmail());
+ assertNotNull(user.getBindDn());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java
index 57ae4d75f0bd5a9f408471a92fcbf6d7449051f8..227edfbc2fb5efc5e3a3b3ba3c30b149b8cb1152 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java
@@ -11,14 +11,24 @@ import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
import org.springframework.test.annotation.Rollback;
+import com.unboundid.ldap.listener.InMemoryDirectoryServer;
+import com.unboundid.ldap.listener.InMemoryDirectoryServerConfig;
+import com.unboundid.ldap.sdk.LDAPConnection;
+import com.unboundid.ldap.sdk.LDAPException;
+
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.user.BasicPrivilege;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
import lcsb.mapviewer.model.user.ObjectPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.interfaces.ILdapService;
@Rollback(true)
public class UserServiceTest extends ServiceTestFunctions {
@@ -46,6 +56,59 @@ public class UserServiceTest extends ServiceTestFunctions {
}
}
+ @Test
+ public void testLoginFromLdap() throws Exception {
+ ILdapService originalLdapService = userService.getLdapService();
+ try {
+ String login = "john.doe.test";
+ String passwd = "test_passwd";
+
+ assertNull(userService.getUserByLogin(login));
+
+ LdapService ldapService = createMockLdapService("testFiles/ldap/john-doe-test-example.ldif", login, passwd);
+
+ userService.setLdapService(ldapService);
+ assertNull(userService.login(login, "incorrect password"));
+ assertNotNull("User from LDAP wasn't authenticated", userService.login(login, passwd));
+
+ User user = userService.getUserByLogin(login);
+ assertNotNull("After authentication from LDAP user is not present in the system", user);
+ assertTrue(user.isConnectedToLdap());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ userService.setLdapService(originalLdapService);
+ }
+ }
+
+ private LdapService createMockLdapService(String filename, String login, String passwd) throws LDAPException {
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_BASE_DN, "dc=uni,dc=lu");
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_OBJECT_CLASS, "person");
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_FILTER, "memberof=cn=gitlab,cn=groups,cn=accounts,dc=uni,dc=lu");
+
+ LdapService ldapService = Mockito.spy(LdapService.class);
+ ldapService.setConfigurationService(configurationService);
+ Mockito.when(ldapService.getConnection()).thenAnswer(new Answer<LDAPConnection>() {
+
+ @Override
+ public LDAPConnection answer(InvocationOnMock invocation) throws Throwable {
+ // Create the configuration to use for the server.
+ InMemoryDirectoryServerConfig config = new InMemoryDirectoryServerConfig("dc=uni,dc=lu");
+ config.addAdditionalBindCredentials("uid=" + login + ",cn=users,cn=accounts,dc=uni,dc=lu", passwd);
+ config.setSchema(null);
+
+ // Create the directory server instance, populate it with data from the
+ // "test-data.ldif" file, and start listening for client connections.
+ InMemoryDirectoryServer ds = new InMemoryDirectoryServer(config);
+ ds.importFromLDIF(true, filename);
+ ds.startListening();
+ return ds.getConnection();
+ }
+ });
+ return ldapService;
+ }
+
@Test
public void testLoginWithNull() {
try {
@@ -149,10 +212,10 @@ public class UserServiceTest extends ServiceTestFunctions {
long logCount2 = logDao.getCount();
assertEquals("Log entry is missing for add user event", logCount + 1, logCount2);
userDao.evict(user2);
- User user3 = userService.getUserById(user2.getId());
+ User user3 = userService.getUserByLogin(user2.getLogin());
assertNotNull(user3);
userService.deleteUser(user3);
- user3 = userService.getUserById(user2.getId());
+ user3 = userService.getUserByLogin(user2.getLogin());
assertNull(user3);
long logCount3 = logDao.getCount();
diff --git a/service/testFiles/ldap/john-doe-test-example.ldif b/service/testFiles/ldap/john-doe-test-example.ldif
new file mode 100644
index 0000000000000000000000000000000000000000..4d89df27e370421ae78cf33fa0a4d891c9a954d2
--- /dev/null
+++ b/service/testFiles/ldap/john-doe-test-example.ldif
@@ -0,0 +1,92 @@
+version: 1
+
+dn: dc=uni,dc=lu
+objectClass: top
+objectClass: domain
+dc: uni
+
+dn: cn=accounts,dc=uni,dc=lu
+objectClass: extensibleObject
+cn: accounts
+
+dn: cn=users,cn=accounts,dc=uni,dc=lu
+objectClass: extensibleObject
+cn: users
+
+dn: uid=john.doe.test,cn=users,cn=accounts,dc=uni,dc=lu
+objectClass: mepOriginEntry
+objectClass: ipaSshGroupOfPubKeys
+objectClass: posixaccount
+objectClass: inetuser
+objectClass: krbprincipalaux
+objectClass: krbticketpolicyaux
+objectClass: organizationalperson
+objectClass: inetorgperson
+objectClass: ipasshuser
+objectClass: top
+objectClass: person
+objectClass: ipaobject
+cn: John Doe
+gidNumber: 369550501
+homeDirectory: /home/john.doe.test
+ipaUniqueID: adf723e6-20e4-11e5-8907-001a4ae51219
+sn: Doe
+uid: john.doe.test
+uidNumber: 369550501
+displayName: John Doe
+gecos: John Doe
+givenName: John
+initials: JD
+krbLastPwdChange: 20180608111630Z
+krbPasswordExpiration: 20190223111630Z
+krbPrincipalName: john.doe.test@UNI.LU
+loginShell: /bin/bash
+mail: john.doe.test@uni.lu
+memberOf: cn=lcsb,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: ipaUniqueID=d7549fa2-03a2-11e5-95f9-00163e0a4f7b,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=eff7677e-03a2-11e5-add5-00163e0a4f7b,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: ipaUniqueID=f10ec0f6-7ef6-11e5-957b-001a4ae5121e,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=2cf9b59e-7ef7-11e5-89c0-001a4ae5121e,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: ipaUniqueID=eeb5f68e-9775-11e5-81fb-00163e0a4f7b,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=176f7fb4-9776-11e5-a097-00163e0a4f7b,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: ipaUniqueID=7dda82ae-99e1-11e5-834b-001a4ae5121e,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=a44d842c-99e1-11e5-9c2f-001a4ae5121e,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: cn=webdav-public-minerva,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: ipaUniqueID=1d1f58b8-a247-11e5-ac5d-00163e0a4f7b,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=41f879a8-a247-11e5-9d34-00163e0a4f7b,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: ipaUniqueID=33e9e6a2-c8d1-11e5-b578-001a4ae5121e,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=572fea30-c8d1-11e5-b770-001a4ae5121e,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: cn=lcsb-biocore,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=gitlab,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=xwiki,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=owncloud,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=xwiki-biocore,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=webdav-public-biocore,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=grafana-biocore-gitlab-viewers,cn=groups,cn=accounts,dc=uni,dc=
+ lu
+memberOf: cn=grafana-biocore-icinga-viewers,cn=groups,cn=accounts,dc=uni,dc=
+ lu
+memberOf: ipaUniqueID=634b5286-3781-11e6-93c5-001a4ae5121e,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=7fe6a210-3781-11e6-b515-001a4ae5121e,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: cn=ncer-pd-ada,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=r3lab-docker,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: ipaUniqueID=390a3ce0-854b-11e6-85c3-001a4ae5127c,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=6d558608-854b-11e6-9aa7-001a4ae5127c,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+telephoneNumber: +3524666445526
+
diff --git a/service/testFiles/ldap/testdata.ldif b/service/testFiles/ldap/testdata.ldif
new file mode 100644
index 0000000000000000000000000000000000000000..b319630ec5a05a1e92daaa053d93344fed84c9e1
--- /dev/null
+++ b/service/testFiles/ldap/testdata.ldif
@@ -0,0 +1,128 @@
+version: 1
+
+dn: dc=uni,dc=lu
+objectClass: top
+objectClass: domain
+dc: uni
+
+dn: cn=accounts,dc=uni,dc=lu
+objectClass: extensibleObject
+cn: accounts
+
+dn: cn=users,cn=accounts,dc=uni,dc=lu
+objectClass: extensibleObject
+cn: users
+
+dn: uid=piotr.gawron,cn=users,cn=accounts,dc=uni,dc=lu
+objectClass: mepOriginEntry
+objectClass: ipaSshGroupOfPubKeys
+objectClass: posixaccount
+objectClass: inetuser
+objectClass: krbprincipalaux
+objectClass: krbticketpolicyaux
+objectClass: organizationalperson
+objectClass: inetorgperson
+objectClass: ipasshuser
+objectClass: top
+objectClass: person
+objectClass: ipaobject
+cn: Piotr Gawron
+gidNumber: 369550501
+homeDirectory: /home/piotr.gawron
+ipaUniqueID: adf723e6-20e4-11e5-8907-001a4ae51219
+sn: Gawron
+uid: piotr.gawron
+uidNumber: 369550501
+displayName: Piotr Gawron
+gecos: Piotr Gawron
+givenName: Piotr
+initials: PG
+krbLastPwdChange: 20180608111630Z
+krbPasswordExpiration: 20190223111630Z
+krbPrincipalName: piotr.gawron@UNI.LU
+loginShell: /bin/bash
+mail: piotr.gawron@uni.lu
+memberOf: cn=lcsb,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: ipaUniqueID=d7549fa2-03a2-11e5-95f9-00163e0a4f7b,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=eff7677e-03a2-11e5-add5-00163e0a4f7b,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: ipaUniqueID=f10ec0f6-7ef6-11e5-957b-001a4ae5121e,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=2cf9b59e-7ef7-11e5-89c0-001a4ae5121e,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: ipaUniqueID=eeb5f68e-9775-11e5-81fb-00163e0a4f7b,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=176f7fb4-9776-11e5-a097-00163e0a4f7b,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: ipaUniqueID=7dda82ae-99e1-11e5-834b-001a4ae5121e,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=a44d842c-99e1-11e5-9c2f-001a4ae5121e,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: cn=webdav-public-minerva,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: ipaUniqueID=1d1f58b8-a247-11e5-ac5d-00163e0a4f7b,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=41f879a8-a247-11e5-9d34-00163e0a4f7b,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: ipaUniqueID=33e9e6a2-c8d1-11e5-b578-001a4ae5121e,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=572fea30-c8d1-11e5-b770-001a4ae5121e,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: cn=lcsb-biocore,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=gitlab,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=xwiki,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=owncloud,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=xwiki-biocore,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=webdav-public-biocore,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=grafana-biocore-gitlab-viewers,cn=groups,cn=accounts,dc=uni,dc=
+ lu
+memberOf: cn=grafana-biocore-icinga-viewers,cn=groups,cn=accounts,dc=uni,dc=
+ lu
+memberOf: ipaUniqueID=634b5286-3781-11e6-93c5-001a4ae5121e,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=7fe6a210-3781-11e6-b515-001a4ae5121e,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+memberOf: cn=ncer-pd-ada,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=r3lab-docker,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: ipaUniqueID=390a3ce0-854b-11e6-85c3-001a4ae5127c,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=6d558608-854b-11e6-9aa7-001a4ae5127c,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
+telephoneNumber: +3524666445526
+
+dn: uid=piotr.atyjaszyk,cn=users,cn=accounts,dc=uni,dc=lu
+objectClass: mepOriginEntry
+objectClass: ipaSshGroupOfPubKeys
+objectClass: posixaccount
+objectClass: inetuser
+objectClass: krbprincipalaux
+objectClass: krbticketpolicyaux
+objectClass: organizationalperson
+objectClass: inetorgperson
+objectClass: ipasshuser
+objectClass: top
+objectClass: person
+objectClass: ipaobject
+cn: Piotr Matyjaszyk
+gidNumber: 369513507
+homeDirectory: /home/piotr.atyjaszyk
+ipaUniqueID: ab674608-854a-11e6-8b8d-001a4ae5127c
+sn: Matyjaszyk
+uid: piotr.atyjaszyk
+uidNumber: 369513507
+displayName: Piotr Matyjaszyk
+gecos: Piotr Matyjaszyk
+givenName: Piotr
+initials: PM
+krbLastPwdChange: 20161003204712Z
+krbPasswordExpiration: 20170531204712Z
+krbPrincipalName: piotr.atyjaszyk@UNI.LU
+loginShell: /bin/bash
+mail: piotrmk1@gmail.com
+manager: uid=piotr.gawron,cn=users,cn=accounts,dc=uni,dc=lu
+memberOf: cn=gitlab,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: cn=external,cn=groups,cn=accounts,dc=uni,dc=lu
+memberOf: ipaUniqueID=929b4e02-854b-11e6-b870-001a4ae5127c,cn=hbac,dc=uni,dc
+ =lu
+memberOf: ipaUniqueID=bf23444e-a1bf-11e6-bf86-001a4ae5121e,cn=sudorules,cn=s
+ udo,dc=uni,dc=lu
diff --git a/web/src/main/java/lcsb/mapviewer/security/CustomAuthenticationProvider.java b/web/src/main/java/lcsb/mapviewer/security/CustomAuthenticationProvider.java
new file mode 100644
index 0000000000000000000000000000000000000000..6346901dd29fd3454054a33fcea9902e5435bcd8
--- /dev/null
+++ b/web/src/main/java/lcsb/mapviewer/security/CustomAuthenticationProvider.java
@@ -0,0 +1,53 @@
+package lcsb.mapviewer.security;
+
+import java.util.ArrayList;
+
+import org.apache.log4j.Logger;
+import org.springframework.security.authentication.AuthenticationProvider;
+import org.springframework.security.authentication.BadCredentialsException;
+import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
+import org.springframework.security.core.Authentication;
+import org.springframework.security.core.AuthenticationException;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.services.interfaces.IUserService;
+
+@Transactional(readOnly = false)
+public class CustomAuthenticationProvider implements AuthenticationProvider {
+ Logger logger = Logger.getLogger(CustomAuthenticationProvider.class);
+
+ private IUserService userService;
+
+ @Override
+ public Authentication authenticate(Authentication authentication) throws AuthenticationException {
+ // login
+ String name = authentication.getName();
+
+ // password
+ String password = null;
+ if (authentication.getCredentials() != null) {
+ password = authentication.getCredentials().toString();
+ }
+
+ // Your custom authentication logic here
+ if (userService.login(name, password) != null) {
+ Authentication auth = new UsernamePasswordAuthenticationToken(name, password, new ArrayList<>());
+ return auth;
+ }
+ throw new BadCredentialsException("Invalid credentials");
+ }
+
+ @Override
+ public boolean supports(Class<?> authentication) {
+ return authentication.equals(UsernamePasswordAuthenticationToken.class);
+ }
+
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/security/MvSecurityServiceImpl.java b/web/src/main/java/lcsb/mapviewer/security/MvSecurityServiceImpl.java
deleted file mode 100644
index 109a881dfa63c9e7796ecd1a5bd0365ee76834f7..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/security/MvSecurityServiceImpl.java
+++ /dev/null
@@ -1,72 +0,0 @@
-package lcsb.mapviewer.security;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.core.authority.AuthorityUtils;
-import org.springframework.security.core.userdetails.User;
-import org.springframework.security.core.userdetails.UserDetails;
-import org.springframework.security.core.userdetails.UserDetailsService;
-import org.springframework.security.core.userdetails.UsernameNotFoundException;
-import org.springframework.security.crypto.password.PasswordEncoder;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.interfaces.IUserService;
-
-/**
- * Spring implementation of class accessing user details.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(readOnly = false)
-public class MvSecurityServiceImpl implements UserDetailsService {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(MvSecurityServiceImpl.class);
-
- /**
- * Service used for accessing user data.
- */
- @Autowired
- private IUserService userService;
-
- @Autowired
- private PasswordEncoder passwordEncoder;
-
- @Override
- public UserDetails loadUserByUsername(String login) {
- if (login == null || login.trim().isEmpty() || login.equals(Configuration.ANONYMOUS_LOGIN)) {
- return new User(login, passwordEncoder.encode(""), AuthorityUtils.commaSeparatedStringToAuthorityList(""));
- }
-
- lcsb.mapviewer.model.user.User user = userService.getUserByLogin(login);
- if (user == null) {
- throw new UsernameNotFoundException("Invalid username or password.");
- }
- StringBuilder credentials = new StringBuilder();
-
- return new User(user.getLogin(), user.getCryptedPassword(),
- AuthorityUtils.commaSeparatedStringToAuthorityList(credentials.toString()));
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
-}
diff --git a/web/src/main/webapp/WEB-INF/security-context.xml b/web/src/main/webapp/WEB-INF/security-context.xml
index 41c1b8c8345460bcd9bdaa0ae1320bfb3f61de05..783c154e311a0d08767859e8dcbfe5c707d8f3a1 100644
--- a/web/src/main/webapp/WEB-INF/security-context.xml
+++ b/web/src/main/webapp/WEB-INF/security-context.xml
@@ -72,10 +72,6 @@
<constructor-arg value="/login.xhtml"></constructor-arg>
</bean>
- <bean id="userDetailsService" class="lcsb.mapviewer.security.MvSecurityServiceImpl">
- <property name="userService" ref="UserService" />
- </bean>
-
<bean id="sas" class="org.springframework.security.web.authentication.session.CompositeSessionAuthenticationStrategy">
<constructor-arg>
<list>
@@ -98,9 +94,8 @@
<bean id="httpSessionSecurityContextRepository" class="org.springframework.security.web.context.HttpSessionSecurityContextRepository"/>
- <bean id="authenticationProvider" class="org.springframework.security.authentication.dao.DaoAuthenticationProvider">
- <property name="userDetailsService" ref="userDetailsService" />
- <property name="passwordEncoder" ref="PasswordEncoder" />
+ <bean id="authenticationProvider" class="lcsb.mapviewer.security.CustomAuthenticationProvider">
+ <property name="userService" ref="UserService" />
</bean>
<security:authentication-manager alias="authenticationManager">