diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
index eaa090e2966932c54e93380b2f1844dd52f5217c..83ea40c73472ad4b2659099afbe4484ef0b19abe 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
@@ -38,13 +38,15 @@ public abstract class BioEntityConverter<T extends BioEntity> {
* Default class logger.
*/
@SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(BioEntityConverter.class);
+ private final Logger logger = Logger.getLogger(BioEntityConverter.class);
+
+ private SemanticZoomLevelMatcher semanticZoomLevelMatcher = new SemanticZoomLevelMatcher();
/**
* Alpha value (0..255) used for visualizing overlay data that are normally
* visualized in javascript.
*/
- public static final int LAYOUT_ALPHA = 200;
+ public static final int LAYOUT_ALPHA = 200;
/**
* This function draw representation of the alias on the graphics object.
@@ -144,8 +146,8 @@ public abstract class BioEntityConverter<T extends BioEntity> {
}
/**
- * Checks if {@link BioEntity} is visible according to visualization
- * given in params.
+ * Checks if {@link BioEntity} is visible according to visualization given in
+ * params.
*
* @param bioEntity
* visibility of this object will be checked
@@ -155,7 +157,7 @@ public abstract class BioEntityConverter<T extends BioEntity> {
*/
protected boolean isVisible(BioEntity bioEntity, ConverterParams params) {
if (params.isSemanticZoomingOn()) {
- boolean result = matchLevel(params.getLevel(), bioEntity.getSemanticZoomLevelVisibility());
+ boolean result = semanticZoomLevelMatcher.matchLevel(params.getLevel(), bioEntity.getSemanticZoomLevelVisibility());
if (bioEntity instanceof Element) {
Compartment compartment = ((Element) bioEntity).getCompartment();
if (compartment != null) {
@@ -219,33 +221,4 @@ public abstract class BioEntityConverter<T extends BioEntity> {
return result;
}
- /**
- * Checks if level belongs to the range defined in
- * semanticZoomLevelVisibility.
- *
- * @param level
- * level to ve checked
- * @param semanticZoomLevelVisibility
- * range of levels to be checked
- * @return true if level is in the range
- */
- protected boolean matchLevel(int level, String semanticZoomLevelVisibility) {
- if (semanticZoomLevelVisibility == null || semanticZoomLevelVisibility.isEmpty()) {
- return true;
- }
- if (semanticZoomLevelVisibility.contains("{")) {
- String strLevels = semanticZoomLevelVisibility.replace("{", "").replace("}", "");
- String[] ranges = strLevels.split(",");
- for (String string : ranges) {
- if (Integer.valueOf(string).equals(level)) {
- return true;
- }
- }
- }
- if (Integer.valueOf(semanticZoomLevelVisibility) <= level) {
- return true;
- }
- return false;
- }
-
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/SemanticZoomLevelMatcher.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/SemanticZoomLevelMatcher.java
new file mode 100644
index 0000000000000000000000000000000000000000..195b6e4916344c1838861a851220c82bb323c6f6
--- /dev/null
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/SemanticZoomLevelMatcher.java
@@ -0,0 +1,34 @@
+package lcsb.mapviewer.converter.graphics.bioEntity;
+
+public class SemanticZoomLevelMatcher {
+
+ /**
+ * Checks if level belongs to the range defined in
+ * semanticZoomLevelVisibility.
+ *
+ * @param level
+ * level to ve checked
+ * @param semanticZoomLevelVisibility
+ * range of levels to be checked
+ * @return true if level is in the range
+ */
+ public boolean matchLevel(int level, String semanticZoomLevelVisibility) {
+ if (semanticZoomLevelVisibility == null || semanticZoomLevelVisibility.isEmpty()) {
+ return true;
+ }
+ if (semanticZoomLevelVisibility.contains("{")) {
+ String strLevels = semanticZoomLevelVisibility.replace("{", "").replace("}", "");
+ String[] ranges = strLevels.split(",");
+ for (String string : ranges) {
+ if (Integer.valueOf(string).equals(level)) {
+ return true;
+ }
+ }
+ }
+ if (Integer.valueOf(semanticZoomLevelVisibility) <= level) {
+ return true;
+ }
+ 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 272848fa2a2ec240be53102dc03b3324ae30c15b..0b95943a44f02eea6dfb63cf89cb3b317a73aeed 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -52,6 +52,7 @@ import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.converter.graphics.MapGenerator;
import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
+import lcsb.mapviewer.converter.graphics.bioEntity.SemanticZoomLevelMatcher;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
@@ -612,40 +613,64 @@ public class ProjectService implements IProjectService {
int counter = 0;
for (final Model model : models) {
for (int i = 0; i < model.getLayouts().size(); i++) {
- String directory = model.getLayouts().get(i).getDirectory();
Layout layout = model.getLayouts().get(i);
if (layout.getInputData() == null) {
-
- Model output = model;
- if (layout.isHierarchicalView()) {
- output = new CopyCommand(model).execute();
- }
- if (layout.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
- output = new CopyCommand(model).execute();
- new ClearColorModelCommand(output).execute();
- }
-
final double imgCounter = counter;
final double finalSize = size;
- MapGeneratorParams imgParams = generator.new MapGeneratorParams()
- .model(output).directory(directory).sbgn(params.isSbgnFormat()).nested(layout.isHierarchicalView()).updater(new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(
- originalModel.getProject(), ProjectStatus.GENERATING_IMAGES,
- IProgressUpdater.MAX_PROGRESS * imgCounter / finalSize + progress / finalSize, params);
- }
- });
- if (layout.getTitle().contains(BuildInLayout.SEMANTIC.getTitle())) {
- imgParams.semanticZoom(params.isSemanticZoom());
- }
- generator.generateMapImages(imgParams);
+ IProgressUpdater updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(
+ originalModel.getProject(), ProjectStatus.GENERATING_IMAGES, IProgressUpdater.MAX_PROGRESS * imgCounter / finalSize + progress / finalSize,
+ params);
+ }
+ };
+
+ generateImagesForBuiltInOverlay(params, model, layout, updater);
}
counter++;
}
}
}
+ private void generateImagesForBuiltInOverlay(final CreateProjectParams params, final Model model, Layout layout, IProgressUpdater updater)
+ throws CommandExecutionException, IOException, DrawingException {
+ String directory = layout.getDirectory();
+ Model output = model;
+ if (layout.isHierarchicalView()) {
+ output = new CopyCommand(model).execute();
+ }
+ if (layout.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
+ output = new CopyCommand(model).execute();
+ new ClearColorModelCommand(output).execute();
+ }
+
+ MapGeneratorParams imgParams = generator.new MapGeneratorParams()
+ .directory(directory).sbgn(params.isSbgnFormat()).nested(layout.isHierarchicalView()).updater(updater);
+ if (layout.getTitle().contains(BuildInLayout.SEMANTIC.getTitle())) {
+ imgParams.semanticZoom(params.isSemanticZoom());
+ if (Character.isDigit(layout.getTitle().charAt(layout.getTitle().length() - 1))) {
+ output = prepareSemanticZoomModel(model, layout.getTitle().replaceAll("[^0-9.]", ""));
+ }
+ }
+ imgParams.model(output);
+ generator.generateMapImages(imgParams);
+ }
+
+ private Model prepareSemanticZoomModel(final Model model, String levelStr) {
+ SemanticZoomLevelMatcher matcher = new SemanticZoomLevelMatcher();
+ int level = Integer.valueOf(levelStr);
+ Model output = new CopyCommand(model).execute();
+ for (BioEntity bioEntity : output.getAnnotatedObjects()) {
+ if (matcher.matchLevel(level, bioEntity.getSemanticZoomLevelVisibility())) {
+ bioEntity.setSemanticZoomLevelVisibility(null);
+ } else {
+ bioEntity.setSemanticZoomLevelVisibility(Integer.MAX_VALUE + "");
+ }
+ }
+ return output;
+ }
+
/**
* Creates project. Loads model from the input and run PostLoadModification.
*
@@ -702,7 +727,6 @@ public class ProjectService implements IProjectService {
model.setZoomLevels(generator.computeZoomLevels(model));
model.setTileSize(MapGenerator.TILE_SIZE);
- Map<BuildInLayout, Layout> topLayoutsByType = new HashMap<>();
List<BuildInLayout> buildInLayouts = new ArrayList<>();
if (params.isNetworkLayoutAsDefault()) {
buildInLayouts.add(BuildInLayout.NORMAL);
@@ -728,29 +752,26 @@ public class ProjectService implements IProjectService {
Collections.reverse(buildInLayouts);
for (BuildInLayout buildInLayout : buildInLayouts) {
- Layout layout = new Layout(buildInLayout.getTitle(), params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + model.getId() + "/", true);
- layout.setStatus(LayoutStatus.NA);
- layout.setProgress(0.0);
- layout.setHierarchicalView(buildInLayout.isNested());
- model.addLayout(0, layout);
- topLayoutsByType.put(buildInLayout, layout);
- }
-
- int submodelId = 1;
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- for (BuildInLayout buildInLayout : buildInLayouts) {
+ Layout topLayout = new Layout(buildInLayout.getTitle(), params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + model.getId() + "/", true);
+ topLayout.setStatus(LayoutStatus.NA);
+ topLayout.setProgress(0.0);
+ topLayout.setHierarchicalView(buildInLayout.isNested());
+ model.addLayout(0, topLayout);
+ int submodelId = 1;
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
Layout layout = new Layout(buildInLayout.getTitle(), params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + submodelId + "/", true);
layout.setStatus(LayoutStatus.NA);
layout.setProgress(0.0);
layout.setHierarchicalView(buildInLayout.isNested());
- layout.setParentLayout(topLayoutsByType.get(buildInLayout));
+ layout.setParentLayout(topLayout);
connection.getSubmodel().addLayout(0, layout);
- }
- submodelId++;
+ submodelId++;
- connection.getSubmodel().setZoomLevels(generator.computeZoomLevels(connection.getSubmodel().getModel()));
- connection.getSubmodel().setTileSize(MapGenerator.TILE_SIZE);
+ connection.getSubmodel().setZoomLevels(generator.computeZoomLevels(connection.getSubmodel().getModel()));
+ connection.getSubmodel().setTileSize(MapGenerator.TILE_SIZE);
+ }
}
+
if (params.isUpdateAnnotations()) {
Map<Class<?>, List<ElementAnnotator>> annotators = null;
if (params.getAnnotatorsMap() != null) {