Refs #209: Fixes bug where no edges are selected when they are compound.

Author: chrtannus

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/SelectNodesEdgesTask.java

@@ -2,12 +2,16 @@
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
 import org.baderlab.csplugins.enrichmentmap.model.AbstractDataSet;
+import org.baderlab.csplugins.enrichmentmap.model.EMSignatureDataSet;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyIdentifiable;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyRow;
@@ -28,17 +32,20 @@ public class SelectNodesEdgesTask extends AbstractTask {
 
 	private final CyNetworkView networkView;
 	private final Set<AbstractDataSet> dataSets;
+	private final boolean distinctEdges;
 
 	@Inject private CyEventHelper eventHelper;
 
 	public interface Factory {
-		SelectNodesEdgesTask create(CyNetworkView networkView, Set<AbstractDataSet> dataSets);
+		SelectNodesEdgesTask create(CyNetworkView networkView, Set<AbstractDataSet> dataSets, boolean distinctEdges);
 	}
 
 	@Inject
-	public SelectNodesEdgesTask(@Assisted CyNetworkView networkView, @Assisted Set<AbstractDataSet> dataSets) {
+	public SelectNodesEdgesTask(@Assisted CyNetworkView networkView, @Assisted Set<AbstractDataSet> dataSets,
+			@Assisted boolean distinctEdges) {
 		this.networkView = networkView;
 		this.dataSets = dataSets;
+		this.distinctEdges = distinctEdges;
 	}
 
 	@Override
@@ -47,8 +54,24 @@ public void run(TaskMonitor tm) {
 		tm.setStatusMessage("Getting Nodes and Edges from Data Sets...");
 		tm.setProgress(0.0);
 
-		Set<Long> dataSetNodes = EnrichmentMap.getNodesUnion(dataSets);
-		Set<Long> dataSetEdges = EnrichmentMap.getEdgesUnion(dataSets);
+		final Set<Long> dataSetNodes = EnrichmentMap.getNodesUnion(dataSets);
+		final Set<Long> dataSetEdges;
+		
+		if (distinctEdges) {
+			dataSetEdges = EnrichmentMap.getEdgesUnion(dataSets);
+		} else {
+			dataSetEdges = new HashSet<>();
+			
+			for (CyEdge e : networkView.getModel().getEdgeList()) {
+				if (dataSetNodes.contains(e.getSource().getSUID()) && dataSetNodes.contains(e.getTarget().getSUID()))
+					dataSetEdges.add(e.getSUID());
+			}
+			
+			for (AbstractDataSet ds : dataSets) {
+				if (ds instanceof EMSignatureDataSet)
+					dataSetEdges.addAll(EnrichmentMap.getEdgesUnion(Collections.singleton(ds)));
+			}
+		}
 
 		if (!cancelled) {
 			tm.setStatusMessage("Selecting Edges...");

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/control/ControlPanelMediator.java

@@ -485,8 +485,11 @@ private void maybeShowContextMenu(final MouseEvent e) {
 					final JPopupMenu contextMenu = new JPopupMenu();
 					{
 						JMenuItem mi = new JMenuItem("Select nodes and edges from selected data sets");
-						mi.addActionListener(evt -> selectNodesEdges(viewPanel.getNetworkView(),
-								viewPanel.getDataSetSelector().getSelectedItems()));
+						mi.addActionListener(evt -> selectNodesEdges(
+								viewPanel.getNetworkView(),
+								viewPanel.getDataSetSelector().getSelectedItems(),
+								map.getParams().getCreateDistinctEdges()
+						));
 						contextMenu.add(mi);
 					}
 					contextMenu.addSeparator();
@@ -819,8 +822,8 @@ private void showContextMenu(final JPopupMenu contextMenu, final MouseEvent e) {
 		});
 	}
 
-	private void selectNodesEdges(CyNetworkView netView, Set<AbstractDataSet> dataSets) {
-		SelectNodesEdgesTask task = selectNodesEdgesTaskFactory.create(netView, dataSets);
+	private void selectNodesEdges(CyNetworkView netView, Set<AbstractDataSet> dataSets, boolean distinctEdges) {
+		SelectNodesEdgesTask task = selectNodesEdgesTaskFactory.create(netView, dataSets, distinctEdges);
 		dialogTaskManager.execute(new TaskIterator(task));
 	}
 
@@ -928,8 +931,8 @@ private Set<CyEdge> getFilteredInEdges(Set<AbstractDataSet> selectedDataSets) {
 
 			Set<CyEdge> filteredInEdges = new HashSet<>();
 			CyNetwork net = netView.getModel();
-			
 			boolean distinct = params.getCreateDistinctEdges();
+			
 			if (distinct) {
 				for (CyEdge e : net.getEdgeList()) {
 					if (dataSetEdges.contains(e.getSUID()))