Use ImmutableSet for GeneSet when deserializing to save memory.

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java

@@ -4,6 +4,7 @@
 
 import org.baderlab.csplugins.enrichmentmap.ApplicationModule.Headless;
 import org.baderlab.csplugins.enrichmentmap.actions.OpenEnrichmentMapAction;
+import org.baderlab.csplugins.enrichmentmap.actions.ShowEnrichmentMapDialogAction;
 import org.baderlab.csplugins.enrichmentmap.commands.BuildEnrichmentMapTuneableTaskFactory;
 import org.baderlab.csplugins.enrichmentmap.commands.EnrichmentMapGSEACommandHandlerTaskFactory;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
@@ -106,6 +107,10 @@ public void shutDown() {
 				// Close the legend panel
 				LegendPanelMediator legendPanelMediator = injector.getInstance(LegendPanelMediator.class);
 				legendPanelMediator.hideDialog();
+				
+				// Dispose the creation dialog, or else lots of memory leaks.
+				ShowEnrichmentMapDialogAction dialogAction = injector.getInstance(ShowEnrichmentMapDialogAction.class);
+				dialogAction.dispose();
 			}
 		} finally {
 			super.shutDown();

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/actions/ShowEnrichmentMapDialogAction.java

@@ -3,19 +3,22 @@
 import java.awt.event.ActionEvent;
 
 import javax.swing.AbstractAction;
+import javax.swing.JFrame;
 
 import org.baderlab.csplugins.enrichmentmap.view.creation.CreationDialogParameters;
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialog;
-import org.cytoscape.application.swing.CySwingApplication;
+import org.baderlab.csplugins.enrichmentmap.view.util.SwingUtil;
 
 import com.google.inject.Inject;
 import com.google.inject.Provider;
+import com.google.inject.Singleton;
 
 @SuppressWarnings("serial")
+@Singleton
 public class ShowEnrichmentMapDialogAction extends AbstractAction {
 
 	@Inject private Provider<CreationDialogParameters> dialogParametersProvider;
-	@Inject private CySwingApplication application;
+	@Inject private Provider<JFrame> jframeProvider;
 
 	private CardDialog masterMapDialog;
 
@@ -27,9 +30,17 @@ public ShowEnrichmentMapDialogAction() {
 	public void actionPerformed(ActionEvent e) {
 		if (masterMapDialog == null) {
 			CreationDialogParameters params = dialogParametersProvider.get();
-			masterMapDialog = new CardDialog(application.getJFrame(), params);
+			masterMapDialog = new CardDialog(jframeProvider.get(), params);
 		}
-		
 		masterMapDialog.open();
 	}
+	
+	
+	public void dispose() {
+		if(masterMapDialog != null) {
+			SwingUtil.invokeOnEDTAndWait(() -> {
+				masterMapDialog.dispose();
+			});
+		}
+	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/GeneSet.java

@@ -53,13 +53,14 @@ public class GeneSet {
 
 	private final String name;
 	private final String description;
-	private final Set<Integer> genes;
+	// ImmutableSet uses less memory than a HashSet, also this forces GSON to deserialize using ImmutableSet.
+	private final ImmutableSet<Integer> genes;
 	private final Optional<String> source;
 
 	public GeneSet(String name, String description, Set<Integer> genes) {
 		this.name = name;
 		this.description = description;
-		this.genes = genes;
+		this.genes = ImmutableSet.copyOf(genes);
 
 		String[] name_tokens = name.split("%");
 		if(name_tokens.length > 1)

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/SetOfGeneSets.java

@@ -13,10 +13,15 @@ public class SetOfGeneSets {
 	//name of results (ie. Dataset1 or name specified by user)
 	private String name;
 
-	//the set of genesets
-	// Hash Key = name of gene set
-	// Hash Value = Gene set
-	private Map<String, GeneSet> geneSets;
+	/** 
+	 * The set of genesets
+	 * Hash Key = name of gene set
+	 * Hash Value = Gene set
+	 * 
+	 * Note: Must declare the type as HashMap because it forces GSON to deserialize using 
+	 * an actual HashMap, otherwise it wants to use a LinkedTreeMap which uses much more memory.
+	 */
+	private HashMap<String, GeneSet> geneSets;
 
 	//filename
 	private String filename;
@@ -48,7 +53,7 @@ public SetOfGeneSets(String ds, HashMap<String, String> props) {
 	 * the genes found in the expression file.
 	 */
 	public void filterGeneSets(Set<Integer> datasetGenes) {
-		Map<String, GeneSet> filteredGenesets = new HashMap<>();
+		HashMap<String, GeneSet> filteredGenesets = new HashMap<>();
 
 		//iterate through each geneset and filter each one
 		for (String geneSetName : geneSets.keySet()) {

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/io/ModelSerializer.java

@@ -15,8 +15,10 @@
 
 import com.google.common.collect.BiMap;
 import com.google.common.collect.HashBiMap;
+import com.google.common.collect.ImmutableSet;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
+import com.google.gson.JsonArray;
 import com.google.gson.JsonDeserializationContext;
 import com.google.gson.JsonDeserializer;
 import com.google.gson.JsonElement;
@@ -25,6 +27,7 @@
 import com.google.gson.JsonPrimitive;
 import com.google.gson.JsonSerializationContext;
 import com.google.gson.JsonSerializer;
+import com.google.gson.reflect.TypeToken;
 
 public class ModelSerializer {
 
@@ -44,10 +47,13 @@ public static String serialize(EnrichmentMap map) {
 
 
 	public static EnrichmentMap deserialize(String json) {
+		Type immutableIntSetType = new TypeToken<ImmutableSet<Integer>>() {}.getType();
+		
 		Gson gson = new GsonBuilder()
 				.registerTypeAdapter(BiMap.class, new BiMapAdapter())
 				.registerTypeHierarchyAdapter(Path.class, new PathAdapter())
 				.registerTypeAdapter(EnrichmentResult.class, new EnrichmentResultAdapter())
+				.registerTypeAdapter(immutableIntSetType, new ImmutableIntSetAdapter())
 				.create();
 
 		try {
@@ -76,6 +82,19 @@ public BiMap<Integer,String> deserialize(JsonElement json, Type type, JsonDeseri
         }
 	}
 
+	private static class ImmutableIntSetAdapter implements JsonDeserializer<ImmutableSet<Integer>> {
+	    @Override
+	    public ImmutableSet<Integer> deserialize(JsonElement json, Type type, JsonDeserializationContext context) {
+	    	ImmutableSet.Builder<Integer> builder = ImmutableSet.builder();
+	    	JsonArray array = (JsonArray) json;
+	    	for(JsonElement element : array) {
+	    		int gene = element.getAsInt();
+	    		builder.add(gene);
+	    	}
+	    	return builder.build();
+	    }
+	}
+	
 	private static class PathAdapter implements JsonDeserializer<Path>, JsonSerializer<Path> {
 	    @Override
 	    public Path deserialize(JsonElement jsonElement, Type type, JsonDeserializationContext context) {

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/util/CardDialog.java

@@ -54,6 +54,11 @@ public void open() {
 		dialog.setVisible(true);
 	}
 
+	public void dispose() {
+		dialog.setVisible(false);
+		dialog.dispose();
+	}
+	
 	public boolean isVisible() {
 		return dialog != null && dialog.isVisible();
 	}