diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
index dddfce69fadb128914c23b94a85dc416f91090ea..0434c77729cc99cb1b5185841b66b217c6f7a4bf 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
@@ -83,7 +83,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
try {
if (query instanceof String) {
String name = (String) query;
- result = getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, name));
+ result = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, name));
} else {
throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
}
@@ -109,7 +109,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
}
- MiriamData miriamData = new MiriamData(md);
+ MiriamData miriamData = createMiriamData(md);
miriamData.setResource(miriamData.getResource().replaceAll("[\n\r]+", " "));
String annotation = getCacheValue(miriamData.getResource());
@@ -282,7 +282,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
this.setCache(null);
try {
- String annotations = getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+ String annotations = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
status.setStatus(ExternalServiceStatusType.OK);
if (annotations == null) {
@@ -302,7 +302,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
public void annotateElement(BioEntity element) throws AnnotatorException {
if (isAnnotatable(element)) {
try {
- String annotationString = getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, element.getName()));
+ String annotationString = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, element.getName()));
if (annotationString != null) {
if (element.getMiriamData().size() == 0) {
element.addMiriamData(rap.getMiriamData(annotationString));
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
index cbd483007aead40c0e940b701a590c339b08245d..cf4feb8ac6c20d943dbeade01661b2443f57efa7 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
@@ -66,7 +66,7 @@ public class BrendaAnnotator extends ElementAnnotator implements IExternalServic
this.setCache(null);
try {
- Collection<MiriamData> mds = uniprotToBrenda(new MiriamData(MiriamType.UNIPROT, "P12345"));
+ Collection<MiriamData> mds = uniprotToBrenda(createMiriamData(MiriamType.UNIPROT, "P12345"));
status.setStatus(ExternalServiceStatusType.OK);
List<String> ecs = new ArrayList<>();
@@ -148,7 +148,7 @@ public class BrendaAnnotator extends ElementAnnotator implements IExternalServic
Collection<MiriamData> result = new HashSet<MiriamData>();
Matcher m = uniprotECMatcher.matcher(pageContent);
while (m.find()) {
- result.add(new MiriamData(MiriamType.BRENDA, m.group(1)));
+ result.add(createMiriamData(MiriamType.BRENDA, m.group(1)));
}
return result;
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
index a0fa95d5159e28a81914173bdb5aeaba8e008c75..5426692ee0b5cf183706af080f019139fbd8dfcb 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
@@ -66,7 +66,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
this.setCache(null);
try {
- MiriamData md = uniprotToCazy(new MiriamData(MiriamType.UNIPROT, "Q9SG95"));
+ MiriamData md = uniprotToCazy(createMiriamData(MiriamType.UNIPROT, "Q9SG95"));
status.setStatus(ExternalServiceStatusType.OK);
if (md == null || !md.getResource().equalsIgnoreCase("GH5_7")) {
@@ -144,7 +144,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
Collection<MiriamData> result = new HashSet<MiriamData>();
Matcher m = cazyIdMatcher.matcher(pageContent);
if (m.find()) {
- result.add(new MiriamData(MiriamType.CAZY, m.group(1)));
+ result.add(createMiriamData(MiriamType.CAZY, m.group(1)));
}
return result;
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
index 99b71fdd1085e3955d2fd206b883390e3f8cd96a..224ea171fb2987b6d291766a083a9954650e342a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
@@ -91,10 +91,10 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
String name = (String) query;
if (name.startsWith(ID_PREFIX)) {
String id = name.substring(ID_PREFIX_LENGTH);
- result = chebiSerializer.objectToString(getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, id)));
+ result = chebiSerializer.objectToString(getChebiElementForChebiId(createMiriamData(MiriamType.CHEBI, id)));
} else if (name.startsWith(ONTOLOGY_PREFIX)) {
String id = name.substring(ONTOLOGY_PREFIX.length());
- result = miriamListToStringList(getOntologyChebiIdsForChebi(new MiriamData(MiriamType.CHEBI, id)));
+ result = miriamListToStringList(getOntologyChebiIdsForChebi(createMiriamData(MiriamType.CHEBI, id)));
} else if (name.startsWith(NAME_PREFIX)) {
name = name.substring(NAME_PREFIX_LENGTH);
MiriamData md = getChebiForChebiName(name);
@@ -158,7 +158,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
String id = getCacheValue("name: " + name);
if (id != null) {
- return new MiriamData(MiriamType.CHEBI, id);
+ return createMiriamData(MiriamType.CHEBI, id);
}
try {
ChebiWebServiceClient client = getClient();
@@ -172,7 +172,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
String chebiName = entity.getChebiAsciiName();
if (chebiName.trim().equalsIgnoreCase(name)) {
setCacheValue("name: " + name, entity.getChebiId());
- return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
+ return createMiriamData(MiriamType.CHEBI, entity.getChebiId());
}
for (DataItem dataItem : entity.getFormulae()) {
String synonym = dataItem.getData();
@@ -265,7 +265,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
queue.add(md.getResource());
while (!queue.isEmpty()) {
String element = queue.poll();
- result.add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, element));
+ result.add(createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, element));
Entity entity = client.getCompleteEntity(element);
for (OntologyDataItem di : entity.getOntologyChildren()) {
if (!children.contains(di.getChebiId()) && "is a".equals(di.getType())) {
@@ -284,7 +284,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
Entity entity = client.getCompleteEntity(element);
for (OntologyDataItem di : entity.getOntologyParents()) {
if (!parents.contains(di.getChebiId()) && "is a".equals(di.getType())) {
- result.add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, di.getChebiId()));
+ result.add(createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, di.getChebiId()));
parents.add(di.getChebiId());
queue.add(di.getChebiId());
}
@@ -331,7 +331,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
String[] tmp = res.split(",");
List<MiriamData> result = new ArrayList<MiriamData>();
for (String string : tmp) {
- result.add(new MiriamData(MiriamType.CHEBI, string));
+ result.add(createMiriamData(MiriamType.CHEBI, string));
}
return result;
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index e71c85ce6a7d89f17e92b02a9e474e73102b7eca..98da3ebf29d5de24675d8d33d5500213349330f5 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -245,7 +245,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* annotation identifier
*/
protected void addHmdbMiriam(BioEntity element, String value) {
- element.addMiriamData(new MiriamData(MiriamType.HMDB, value));
+ element.addMiriamData(createMiriamData(MiriamType.HMDB, value));
}
/**
@@ -317,7 +317,7 @@ public abstract class ElementAnnotator extends CachableInterface {
if (!value.startsWith("CHEBI:")) {
value = "CHEBI:" + value;
}
- element.addMiriamData(new MiriamData(MiriamType.CHEBI, value));
+ element.addMiriamData(createMiriamData(MiriamType.CHEBI, value));
}
/**
@@ -349,7 +349,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* annotation identifier
*/
protected void addPubchemMiriam(BioEntity element, String value) {
- element.addMiriamData(new MiriamData(MiriamType.PUBCHEM, value));
+ element.addMiriamData(createMiriamData(MiriamType.PUBCHEM, value));
}
/**
@@ -361,7 +361,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* annotation identifier
*/
protected void addCogMiriam(BioEntity element, String value) {
- element.addMiriamData(new MiriamData(MiriamType.COG, value));
+ element.addMiriamData(createMiriamData(MiriamType.COG, value));
}
/**
@@ -391,7 +391,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* annotation identifier
*/
protected void addEcMiriam(BioEntity element, String value) {
- element.addMiriamData(new MiriamData(MiriamType.EC, value));
+ element.addMiriamData(createMiriamData(MiriamType.EC, value));
}
/**
@@ -407,13 +407,13 @@ public abstract class ElementAnnotator extends CachableInterface {
*/
protected void addKeggMiriam(BioEntity element, String value, String prefix) {
if (value.startsWith("C")) {
- MiriamData md = new MiriamData(MiriamType.KEGG_COMPOUND, value);
+ MiriamData md = createMiriamData(MiriamType.KEGG_COMPOUND, value);
element.addMiriamData(md);
} else if (value.startsWith("R")) {
- MiriamData md = new MiriamData(MiriamType.KEGG_REACTION, value);
+ MiriamData md = createMiriamData(MiriamType.KEGG_REACTION, value);
element.addMiriamData(md);
} else if (value.startsWith("K")) {
- MiriamData md = new MiriamData(MiriamType.KEGG_ORTHOLOGY, value);
+ MiriamData md = createMiriamData(MiriamType.KEGG_ORTHOLOGY, value);
element.addMiriamData(md);
} else {
logger.warn(prefix + "Unknown Kegg identifier type (only Kegg compounds and reactions are supported): \"" + value + "\"");
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
index 07692f2bf2b14a16a8667aafc10c6b81f7897694..2a680742e77f56c5f5123641ff062218d5069168 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
@@ -110,7 +110,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
try {
GenericProtein proteinAlias = new GenericProtein("mock_id");
- proteinAlias.addMiriamData(new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764"));
+ proteinAlias.addMiriamData(createMiriamData(MiriamType.ENSEMBL, "ENSG00000157764"));
annotateElement(proteinAlias);
if (proteinAlias.getFullName() == null || proteinAlias.getFullName().isEmpty()) {
@@ -208,7 +208,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
if ("EntrezGene".equals(dbname)) {
String entrezId = super.getNodeAttr("primary_id", node);
if (entrezId != null && !entrezId.isEmpty()) {
- annotatedObject.addMiriamData(new MiriamData(MiriamType.ENTREZ, entrezId));
+ annotatedObject.addMiriamData(createMiriamData(MiriamType.ENTREZ, entrezId));
}
String symbol = super.getNodeAttr("display_id", node);
if (symbol != null) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
index 7b61647b9fdeb7cfae84b2bf6196f5e7b436fe53..1c1242bf11268adaa99847dd297ea6df888a904a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
@@ -86,10 +86,10 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
result = getWebPageContent(name);
} else if (name.startsWith(ENTREZ_DATA_PREFIX)) {
String id = name.replace(ENTREZ_DATA_PREFIX, "");
- result = entrezSerializer.objectToString(getEntrezForMiriamData(new MiriamData(MiriamType.ENTREZ, id), null));
+ result = entrezSerializer.objectToString(getEntrezForMiriamData(createMiriamData(MiriamType.ENTREZ, id), null));
} else if (name.startsWith(CACHE_HGNC_ID_PREFIX)) {
String id = name.replace(CACHE_HGNC_ID_PREFIX, "");
- MiriamData md = getHgncIdFromEntrez(new MiriamData(MiriamType.ENTREZ, id));
+ MiriamData md = getHgncIdFromEntrez(createMiriamData(MiriamType.ENTREZ, id));
if (md != null) {
result = md.getResource();
}
@@ -131,7 +131,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
try {
GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.ENTREZ, "9999"));
+ proteinAlias.addMiriamData(createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.ENTREZ, "9999"));
annotateElement(proteinAlias);
if (proteinAlias.getFullName() == null || proteinAlias.getFullName().equals("")) {
@@ -271,11 +271,11 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
if ("HGNC".equals(dbName)) {
if (dbId != null && !dbId.isEmpty()) {
dbId = dbId.replaceAll("HGNC:", "");
- result.addMiriamData(new MiriamData(MiriamType.HGNC, dbId));
+ result.addMiriamData(createMiriamData(MiriamType.HGNC, dbId));
}
} else if ("Ensembl".equals(dbName)) {
if (dbId != null && !dbId.isEmpty()) {
- result.addMiriamData(new MiriamData(MiriamType.ENSEMBL, dbId));
+ result.addMiriamData(createMiriamData(MiriamType.ENSEMBL, dbId));
}
}
@@ -359,7 +359,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
} else if (value.equals("null")) {
return null;
} else {
- return new MiriamData(MiriamType.HGNC, value);
+ return createMiriamData(MiriamType.HGNC, value);
}
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
index e4a7a7f4a1d3bcc2424bf920836d942e82385420..2c606da86135efcbf36ade48729b53ffeb6a67cc 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
@@ -69,7 +69,7 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
String name = (String) query;
if (name.startsWith(GO_TERM_CACHE_PREFIX)) {
String term = name.substring(GO_TERM_CACHE_PREFIX.length());
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, term);
+ MiriamData md = createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, term);
result = goSerializer.objectToString(getGoElement(md));
} else if (name.startsWith("http")) {
result = getWebPageContent(name);
@@ -174,7 +174,7 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
try {
Compartment compartmentAlias = new Compartment("some_id");
- compartmentAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0046902"));
+ compartmentAlias.addMiriamData(createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0046902"));
annotateElement(compartmentAlias);
if (compartmentAlias.getFullName() == null || compartmentAlias.getFullName().equals("")) {
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 b7cd593c8d99a78aeea7d1b947a28397df869160..b1b4678ce880f67b197bf5c410c774d597e00939 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
@@ -100,7 +100,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
try {
GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias
- .addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.HGNC_SYMBOL, "SNCA"));
+ .addMiriamData(createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.HGNC_SYMBOL, "SNCA"));
annotateElement(proteinAlias);
if (proteinAlias.getFullName() == null || proteinAlias.getFullName().equals("")) {
@@ -182,16 +182,16 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
// add hgnc id only when there was no hgnc_id in the element
String id = getNodeValue(node);
id = id.replaceAll("HGNC:", "");
- element.addMiriamData(new MiriamData(MiriamType.HGNC, id));
+ element.addMiriamData(createMiriamData(MiriamType.HGNC, id));
} else if (type.equals("ensembl_gene_id")) {
- element.addMiriamData(new MiriamData(MiriamType.ENSEMBL, getNodeValue(node)));
+ element.addMiriamData(createMiriamData(MiriamType.ENSEMBL, getNodeValue(node)));
} else if (type.equals("entrez_id")) {
- element.addMiriamData(new MiriamData(MiriamType.ENTREZ, getNodeValue(node)));
+ element.addMiriamData(createMiriamData(MiriamType.ENTREZ, getNodeValue(node)));
} else if (type.equals("symbol")) {
if (symbols.size() == 0) {
// add hgnc symbol annnotation only when there was no
// hgnc_symbol in the element
- element.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, getNodeValue(node)));
+ element.addMiriamData(createMiriamData(MiriamType.HGNC_SYMBOL, getNodeValue(node)));
}
setSymbol(element, getNodeValue(node), prefix);
} else if (type.equals("name")) {
@@ -204,7 +204,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
for (int j = 0; j < sublist.getLength(); j++) {
Node subnode = sublist.item(j);
if (subnode.getNodeType() == Node.ELEMENT_NODE) {
- element.addMiriamData(new MiriamData(MiriamType.REFSEQ, getNodeValue(subnode)));
+ element.addMiriamData(createMiriamData(MiriamType.REFSEQ, getNodeValue(subnode)));
}
}
} else if (type.equals("prev_symbol")) {
@@ -316,7 +316,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
Node uniprotNode = uniprotList.item(j);
if (uniprotNode.getNodeType() == Node.ELEMENT_NODE) {
if (uniprotNode.getNodeName().equals("str")) {
- result.add(new MiriamData(MiriamType.UNIPROT, uniprotNode.getTextContent()));
+ result.add(createMiriamData(MiriamType.UNIPROT, uniprotNode.getTextContent()));
}
}
}
@@ -332,7 +332,6 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
} catch (Exception e) {
throw new AnnotatorException(e);
}
-
}
/**
@@ -372,7 +371,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
if (node.getNodeName().equals("str")) {
String type = getNodeAttr("name", node);
if (type.equals("symbol")) {
- return new MiriamData(MiriamType.HGNC_SYMBOL, node.getTextContent());
+ return createMiriamData(MiriamType.HGNC_SYMBOL, node.getTextContent());
}
}
}
@@ -444,7 +443,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
String type = getNodeAttr("name", node);
if (type.equals("entrez_id")) {
String id = getNodeValue(node);
- return new MiriamData(MiriamType.ENTREZ, id);
+ return createMiriamData(MiriamType.ENTREZ, id);
}
}
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
index f2dca91d0de5a103bcddb2dc0897f576a77492ee..3c2c45af31db02c679e38cdfebe7354cf9460041 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
@@ -82,7 +82,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
this.setCache(null);
try {
- Collection<Structure> structures = uniProtToPdb(new MiriamData(MiriamType.UNIPROT, "P29373"));
+ Collection<Structure> structures = uniProtToPdb(createMiriamData(MiriamType.UNIPROT, "P29373"));
if (structures.size() > 0){
if (structures.iterator().next().getPdbId() != null) { //TODO - is this id?
@@ -147,7 +147,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
//do not have the concept of hierarchy or complex data types)
Set<MiriamData> annotations = new HashSet<MiriamData>();
for (Structure s : structures) {
- annotations.add(new MiriamData(MiriamType.PDB, s.getPdbId()));
+ annotations.add(createMiriamData(MiriamType.PDB, s.getPdbId()));
}
bioEntity.addMiriamData(annotations);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
index 37a36f9a530e5d3a739aa6820ac8a205fe6a9b7d..af301fbee0bfac23db696d06ab66ec6837540c66 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
@@ -85,7 +85,7 @@ public class StitchAnnotator extends ElementAnnotator implements IExternalServic
return;
}
- object.addMiriamData(new MiriamData(MiriamType.STITCH, inchiKeyExtractMainLayer(inchiKey)));
+ object.addMiriamData(createMiriamData(MiriamType.STITCH, inchiKeyExtractMainLayer(inchiKey)));
} catch(ChebiSearchException exception) {
logger.warn("No ChEBI element retrieved fro ChEBI ID: " + mdChebi.getResource());
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
index 70e9d34d2a164a264bdaa385a1c8ff8e3a53be1b..dcb6ff9e54a36bd611f2b150f368f33a0c92e0e3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
@@ -95,7 +95,7 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
}
- return new MiriamData(MiriamType.STRING, uniprot.getResource());
+ return createMiriamData(MiriamType.STRING, uniprot.getResource());
}
@Override
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
index 332354bed41576191fcd66fc72d10f5f8e4eacf1..ca9c48cca44dc7d349ee22b5a7a29a1a15957227 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
@@ -68,7 +68,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
this.setCache(null);
try {
- MiriamData md = uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, "P37840"));
+ MiriamData md = uniProtToHgnc(createMiriamData(MiriamType.UNIPROT, "P37840"));
status.setStatus(ExternalServiceStatusType.OK);
if (md == null) {
@@ -109,7 +109,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
annotations.addAll(parseHgnc(pageContent));
annotations.addAll(parseEntrez(pageContent));
if (!uniprotFound) {
- annotations.add(new MiriamData(MiriamType.UNIPROT, uniprotId));
+ annotations.add(createMiriamData(MiriamType.UNIPROT, uniprotId));
}
object.addMiriamData(annotations);
} else {
@@ -149,7 +149,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
Collection<MiriamData> result = new HashSet<MiriamData>();
Matcher m = uniprotToEntrez.matcher(pageContent);
if (m.find()) {
- result.add(new MiriamData(MiriamType.ENTREZ, m.group(1)));
+ result.add(createMiriamData(MiriamType.ENTREZ, m.group(1)));
}
return result;
}
@@ -166,7 +166,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
Collection<MiriamData> result = new HashSet<MiriamData>();
Matcher m = uniprotToHgnc.matcher(pageContent);
if (m.find()) {
- result.add(new MiriamData(MiriamType.HGNC_SYMBOL, m.group(1)));
+ result.add(createMiriamData(MiriamType.HGNC_SYMBOL, m.group(1)));
}
return result;
}