code for generating semantic-zoom overlays with fixed levels

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;
-	}
-
 }

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/SemanticZoomLevelMatcher.java

+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;
+	}
+
+}

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) {