HeatMap was not thread safe. Fixes #267.

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/util/CoalesceTimerStore.java

@@ -0,0 +1,57 @@
+package org.baderlab.csplugins.enrichmentmap.util;
+
+import java.util.Map;
+import java.util.WeakHashMap;
+
+import javax.swing.Timer;
+
+public class CoalesceTimerStore<T> {
+
+	public static final int DEFAULT_DELAY = 120;
+	
+	// Note: I think this code can leak Timer objects. 
+	// Probably need to explicitly manage a ReferenceQueue.
+	
+	private final Map<T,Timer> store = new WeakHashMap<>();
+	private final int delay;
+	
+	public CoalesceTimerStore(int delay) {
+		this.delay = delay;
+	}
+	
+	public CoalesceTimerStore() {
+		this(DEFAULT_DELAY);
+	}
+	
+	/**
+	 * The Java standard library doesn't have a map with both concurrency and weak keys.
+	 * Also the default implementation of compute isn't atomic. Therefore we will synchronize explicitly.
+	 */
+	public synchronized void coalesce(T key, Runnable runnable) {
+		store.compute(key, (k,t) -> {
+			if(t == null) {
+				//System.out.println("start timer");
+				t = new Timer(0, evt -> {
+					//System.out.println("fire timer");
+					runnable.run();
+				});
+				t.setRepeats(false);
+				t.setCoalesce(true);
+			} else {
+				//System.out.println("reset timer");
+				t.stop();
+			}
+			
+			t.setInitialDelay(delay);
+			t.start();
+			return t;
+		});
+	}
+	
+	public synchronized void remove(T key) {
+		Timer timer = store.remove(key);
+		if(timer != null)
+			timer.stop();
+	}
+	
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/HeatMapMediator.java

@@ -16,6 +16,7 @@
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
 import org.baderlab.csplugins.enrichmentmap.model.Ranking;
 import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder;
+import org.baderlab.csplugins.enrichmentmap.util.CoalesceTimerStore;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.HeatMapParams.Compress;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.HeatMapParams.Operator;
 import org.cytoscape.application.CyApplicationManager;
@@ -56,6 +57,7 @@ public class HeatMapMediator implements RowsSetListener, SetCurrentNetworkViewLi
 	@Inject private CySwingApplication swingApplication;
 	@Inject private CyApplicationManager applicationManager;
 
+	private final CoalesceTimerStore<HeatMapMediator> selectionEventTimer = new CoalesceTimerStore<>(60);
 	private HeatMapParentPanel heatMapPanel = null;
 	private boolean onlyEdges;
 
@@ -89,15 +91,13 @@ private void bringToFront() {
 	public void handleEvent(RowsSetEvent e) {
 		if(heatMapPanel == null)
 			return;
-		// MKTODO If this has bad performance then add a reconciler timer delay.
-		// Cytoscape selection events can come in sets of 1-4 events.
 		if(e.containsColumn(CyNetwork.SELECTED)) {
 			CyNetworkView networkView = applicationManager.getCurrentNetworkView();
 			if(networkView != null) {
 				CyNetwork network = networkView.getModel();
 				// only handle event if it is a selected node
 				if(e.getSource() == network.getDefaultEdgeTable() || e.getSource() == network.getDefaultNodeTable()) {
-					updateHeatMap(networkView);
+					selectionEventTimer.coalesce(this, () -> updateHeatMap(networkView));
 				}
 			}
 		}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/HeatMapParentPanel.java

@@ -52,7 +52,11 @@ public void CreateContents() {
 		showEmptyView();
 	}
 
-	public void selectGenes(EnrichmentMap map, HeatMapParams params, List<RankingOption> moreRankOptions, Set<String> union, Set<String> intersection) {
+	public HeatMapMediator getMediator() {
+		return mediator;
+	}
+	
+	public synchronized void selectGenes(EnrichmentMap map, HeatMapParams params, List<RankingOption> moreRankOptions, Set<String> union, Set<String> intersection) {
 		if(mainPanel == null) {
 			removeAll();
 			mainPanel = mainPanelFactory.create(this);
@@ -61,11 +65,7 @@ public void selectGenes(EnrichmentMap map, HeatMapParams params, List<RankingOpt
 		mainPanel.reset(map, params, moreRankOptions, union, intersection);
 	}
 
-	public HeatMapMediator getMediator() {
-		return mediator;
-	}
-	
-	public void showEmptyView() {
+	public synchronized void showEmptyView() {
 		removeAll();
 		mainPanel = null;
 		add(new NullViewPanel(), BorderLayout.CENTER);