Copy model on subnetwork creation. Add OSGi-style events.

Author: mikekucera

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

@@ -25,6 +25,7 @@
 import org.cytoscape.model.CyNetworkTableManager;
 import org.cytoscape.model.CyTableFactory;
 import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
 import org.cytoscape.property.CyProperty;
 import org.cytoscape.service.util.CyServiceRegistrar;
 import org.cytoscape.session.CyNetworkNaming;
@@ -104,6 +105,7 @@ protected void configure() {
 		bindService(CyNetworkNaming.class);
 		bindService(CyApplicationConfiguration.class);
 		bindService(CyColorPaletteChooserFactory.class);
+		bindService(CyRootNetworkManager.class);
 
 		bindService(DialogTaskManager.class);
 		TypeLiteral<SynchronousTaskManager<?>> synchronousManager = new TypeLiteral<SynchronousTaskManager<?>>(){};

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

@@ -43,67 +43,118 @@
 
 package org.baderlab.csplugins.enrichmentmap.model;
 
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.Map;
 
+import org.baderlab.csplugins.enrichmentmap.model.event.AssociatedEnrichmentMapsChangedEvent;
+import org.baderlab.csplugins.enrichmentmap.model.event.EnrichmentMapAddedEvent;
+import org.baderlab.csplugins.enrichmentmap.model.io.ModelSerializer;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.HeatMapParams;
 import org.baderlab.csplugins.enrichmentmap.view.postanalysis.PADialogMediator;
+import org.cytoscape.event.CyEventHelper;
 import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkManager;
 import org.cytoscape.model.CyTable;
+import org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent;
+import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
 import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.events.NetworkViewAddedEvent;
+import org.cytoscape.view.model.events.NetworkViewAddedListener;
 
 import com.google.inject.Inject;
 import com.google.inject.Provider;
 import com.google.inject.Singleton;
 
 
 @Singleton
-public class EnrichmentMapManager {
+public class EnrichmentMapManager implements NetworkAboutToBeDestroyedListener, NetworkViewAddedListener {
 
 	private Map<Long, EnrichmentMap> enrichmentMaps = new LinkedHashMap<>();
 	private Map<Long, EnrichmentMap> associatedEnrichmentMaps = new LinkedHashMap<>();
 	private Map<Long, HeatMapParams> heatMapParams = new HashMap<>();
 	private Map<Long, HeatMapParams> heatMapParamsEdges = new HashMap<>();
 
 	@Inject private Provider<PADialogMediator> postAnalysisMediatorProvider;
+	
+	@Inject private CyEventHelper eventHelper;
+	@Inject private CyNetworkManager networkManager;
+	@Inject private CyRootNetworkManager rootNetworkManager;
+	
 
-	private final PropertyChangeSupport pcs = new PropertyChangeSupport(this);
+	/**
+	 * If the user creates a new network under the same network collection, we can just reuse the model.
+	 */
+	@Override
+	public void handleEvent(NetworkViewAddedEvent e) {
+		if(isEnrichmentMap(e.getNetworkView())) 
+			return;
+		
+		CyNetwork newNetwork = e.getNetworkView().getModel();
+		CyRootNetwork newNetworkRoot = rootNetworkManager.getRootNetwork(newNetwork);
+		
+		for(Long networkSuid : enrichmentMaps.keySet()) {
+			CyNetwork network = networkManager.getNetwork(networkSuid);
+			CyRootNetwork root = rootNetworkManager.getRootNetwork(network);
+			if(root == newNetworkRoot) {
+				System.out.println("Copying EnrichmentMap model");
+				// newly created network is under an enrichmentmap network
+				EnrichmentMap map = getEnrichmentMap(network.getSUID());
+				if(map != null) {
+					EnrichmentMap newMap = ModelSerializer.deepCopy(map);
+					newMap.setNetworkID(newNetwork.getSUID());
+					registerEnrichmentMap(newMap);
+				}
+				return;
+			}
+		}
+	}
+	
+	@Override
+	public void handleEvent(NetworkAboutToBeDestroyedEvent e) {
+		removeEnrichmentMap(e.getNetwork().getSUID());
+	}
+	
 
 	/**
 	 * Registers a newly created Network.
 	 */
 	public void registerEnrichmentMap(EnrichmentMap map) {
-		enrichmentMaps.put(map.getNetworkID(), map);
+		if(enrichmentMaps.containsKey(map.getNetworkID()))
+			return;
 
+		enrichmentMaps.put(map.getNetworkID(), map);
 		for (Long id : map.getAssociatedNetworkIDs())
 			associatedEnrichmentMaps.put(id, map);
+		
+		// This event is reentrant (fires on the same thread that called registerEnrichmentMap). But that is safe 
+		// because the only listeners are inside this App so we can control what code is actually being run here.
+		eventHelper.fireEvent(new EnrichmentMapAddedEvent(this, map));
 	}
 
+	
 	public Map<Long, EnrichmentMap> getAllEnrichmentMaps() {
 		return new LinkedHashMap<>(enrichmentMaps);
 	}
 
+	
 	public EnrichmentMap getEnrichmentMap(Long networkId) {
 		EnrichmentMap map = enrichmentMaps.get(networkId);
-		
 		return map != null ? map : associatedEnrichmentMaps.get(networkId);
 	}
 
+	
 	public EnrichmentMap removeEnrichmentMap(Long networkId) {
 		EnrichmentMap map = enrichmentMaps.remove(networkId);
-		
 		if (map != null)
 			postAnalysisMediatorProvider.get().removeEnrichmentMap(map);
 
 		// Update our internal genemania map and fire an event if it changed
-		Map<Long, EnrichmentMap> oldValue = getAssociatedEnrichmentMaps();
-		
-		if (associatedEnrichmentMaps.remove(networkId) != null)
-			pcs.firePropertyChange("associatedEnrichmentMaps", oldValue, getAssociatedEnrichmentMaps());
-		
+		if (associatedEnrichmentMaps.remove(networkId) != null) {
+			eventHelper.fireEvent(new AssociatedEnrichmentMapsChangedEvent(this, map, getAssociatedEnrichmentMaps()));
+		}
 		return map;
 	}
 
@@ -127,10 +178,9 @@ public void addAssociatedAppAttributes(CyNetwork network, EnrichmentMap map, Ass
 		Columns.EM_ASSOCIATED_APP.set(table.getRow(network.getSUID()), app.name());
 
 		// Update our internal map and fire an event if it changed
-		Map<Long, EnrichmentMap> oldValue = getAssociatedEnrichmentMaps();
-		
-		if (associatedEnrichmentMaps.put(network.getSUID(), map) == null)
-			pcs.firePropertyChange("associatedEnrichmentMaps", oldValue, getAssociatedEnrichmentMaps());
+		if (associatedEnrichmentMaps.put(network.getSUID(), map) == null) {
+			eventHelper.fireEvent(new AssociatedEnrichmentMapsChangedEvent(this, map, getAssociatedEnrichmentMaps()));
+		}
 	}
 
 	public boolean isAssociatedEnrichmentMap(Long networkId) {
@@ -160,27 +210,9 @@ public HeatMapParams getHeatMapParams(Long networkId, boolean edges) {
 	}
 
 	public void reset() {
-		for (PropertyChangeListener listener : pcs.getPropertyChangeListeners())
-			pcs.removePropertyChangeListener(listener);
-		
 		enrichmentMaps.clear();
 		associatedEnrichmentMaps.clear();
 		heatMapParams.clear();
 	}
-	
-	public void addPropertyChangeListener(PropertyChangeListener listener) {
-		pcs.addPropertyChangeListener(listener);
-	}
-
-	public void removePropertyChangeListener(PropertyChangeListener listener) {
-		pcs.removePropertyChangeListener(listener);
-	}
 
-	public void addPropertyChangeListener(String propertyName, PropertyChangeListener listener) {
-		pcs.addPropertyChangeListener(propertyName, listener);
-	}
-
-	public void removePropertyChangeListener(String propertyName, PropertyChangeListener listener) {
-		pcs.removePropertyChangeListener(propertyName, listener);
-	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/event/AssociatedEnrichmentMapsChangedEvent.java

@@ -0,0 +1,27 @@
+package org.baderlab.csplugins.enrichmentmap.model.event;
+
+import java.util.Map;
+
+import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
+import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
+import org.cytoscape.event.AbstractCyEvent;
+
+public class AssociatedEnrichmentMapsChangedEvent extends AbstractCyEvent<EnrichmentMapManager> {
+
+	private final EnrichmentMap map;
+	private final Map<Long,EnrichmentMap> associatedMaps;
+	
+	public AssociatedEnrichmentMapsChangedEvent(EnrichmentMapManager source, EnrichmentMap map, Map<Long,EnrichmentMap> associatedMaps) {
+		super(source, AssociatedEnrichmentMapsChangedListener.class);
+		this.map = map;
+		this.associatedMaps = associatedMaps;
+	}
+	
+	public EnrichmentMap getEnrichmentMap() {
+		return map;
+	}
+	
+	public Map<Long,EnrichmentMap> getAssociatedMaps() {
+		return associatedMaps;
+	}
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/event/AssociatedEnrichmentMapsChangedListener.java

@@ -0,0 +1,9 @@
+package org.baderlab.csplugins.enrichmentmap.model.event;
+
+import org.cytoscape.event.CyListener;
+
+public interface AssociatedEnrichmentMapsChangedListener extends CyListener {
+	
+	public void handleEvent(AssociatedEnrichmentMapsChangedEvent e);
+	
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/event/EnrichmentMapAboutToBeRemovedEvent.java

@@ -0,0 +1,26 @@
+package org.baderlab.csplugins.enrichmentmap.model.event;
+
+import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
+import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
+import org.cytoscape.event.AbstractCyEvent;
+import org.cytoscape.view.model.CyNetworkView;
+
+public class EnrichmentMapAboutToBeRemovedEvent extends AbstractCyEvent<EnrichmentMapManager> {
+
+	private final EnrichmentMap map;
+	private final CyNetworkView networkView;
+	
+	public EnrichmentMapAboutToBeRemovedEvent(EnrichmentMapManager source, EnrichmentMap map, CyNetworkView networkView) {
+		super(source, EnrichmentMapAboutToBeRemovedListener.class);
+		this.map = map;
+		this.networkView = networkView;
+	}
+	
+	public EnrichmentMap getEnrichmentMap() {
+		return map;
+	}
+	
+	public CyNetworkView getNetworkView() {
+		return networkView;
+	}
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/event/EnrichmentMapAboutToBeRemovedListener.java

@@ -0,0 +1,9 @@
+package org.baderlab.csplugins.enrichmentmap.model.event;
+
+import org.cytoscape.event.CyListener;
+
+public interface EnrichmentMapAboutToBeRemovedListener extends CyListener {
+
+	public void handleEvent(EnrichmentMapAboutToBeRemovedEvent e);
+	
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/event/EnrichmentMapAddedEvent.java

@@ -0,0 +1,20 @@
+package org.baderlab.csplugins.enrichmentmap.model.event;
+
+import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
+import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
+import org.cytoscape.event.AbstractCyEvent;
+
+
+public class EnrichmentMapAddedEvent extends AbstractCyEvent<EnrichmentMapManager> {
+
+	private final EnrichmentMap map;
+	
+	public EnrichmentMapAddedEvent(EnrichmentMapManager source, EnrichmentMap map) {
+		super(source, EnrichmentMapAddedListener.class);
+		this.map = map;
+	}
+	
+	public EnrichmentMap getEnrichmentMap() {
+		return map;
+	}
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/event/EnrichmentMapAddedListener.java

@@ -0,0 +1,9 @@
+package org.baderlab.csplugins.enrichmentmap.model.event;
+
+import org.cytoscape.event.CyListener;
+
+public interface EnrichmentMapAddedListener extends CyListener {
+	
+	public void handleEvent(EnrichmentMapAddedEvent e);
+
+}

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

@@ -34,10 +34,16 @@ public class ModelSerializer {
 
 	private static final Logger logger = LoggerFactory.getLogger(ModelSerializer.class);
 
+	
+	public static EnrichmentMap deepCopy(EnrichmentMap map) {
+		// This could be done with less memory probably.
+		return deserialize(serialize(map));
+	}
+	
 	public static String serialize(EnrichmentMap map) {
 		return serialize(map, false);
 	}
-
+	
 	public static String serialize(EnrichmentMap map, boolean pretty) {
 		// When saving to the session file DO NOT enable pretty printing, the Cytoscape
 		// CSV parser is very slow for multi-line text

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/style/EMStyleBuilder.java

@@ -543,12 +543,11 @@ private void setNodeColors(VisualStyle vs, EMStyleOptions options) {
 			for (EMSignatureDataSet sds : signatureDataSets) {
 				for (Long suid : sds.getNodeSuids()) {
 					CyNode node = net.getNode(suid);
-					
 					if (node != null) {
 						View<CyNode> nv = netView.getNodeView(node);
-						
-						if (nv != null)
+						if (nv != null) {
 							nv.setLockedValue(NODE_FILL_COLOR, Colors.SIG_NODE_COLOR);
+						}
 					}
 				}
 			}