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mikekuceramikekucera
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Fixes #108 (again). Run HeatMapUpdateTask in a separate thread to avoid
deadlock.
1 parent cb380c4 commit 24919d9

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

Lines changed: 87 additions & 221 deletions
Original file line numberDiff line numberDiff line change
@@ -43,22 +43,9 @@
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package org.baderlab.csplugins.enrichmentmap.actions;
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import java.util.HashMap;
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import java.util.List;
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import java.util.TreeMap;
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import javax.swing.ListSelectionModel;
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import javax.swing.table.TableModel;
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import org.baderlab.csplugins.enrichmentmap.EnrichmentMapManager;
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import org.baderlab.csplugins.enrichmentmap.autoannotate.AutoAnnotationManager;
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import org.baderlab.csplugins.enrichmentmap.autoannotate.AutoAnnotationParameters;
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import org.baderlab.csplugins.enrichmentmap.autoannotate.model.AnnotationSet;
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import org.baderlab.csplugins.enrichmentmap.autoannotate.model.Cluster;
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import org.baderlab.csplugins.enrichmentmap.autoannotate.task.Observer;
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import org.baderlab.csplugins.enrichmentmap.heatmap.HeatMapParameters;
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import org.baderlab.csplugins.enrichmentmap.heatmap.task.UpdateHeatMapTask;
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import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
@@ -75,228 +62,107 @@
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import org.cytoscape.model.events.RowsSetEvent;
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import org.cytoscape.model.events.RowsSetListener;
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import org.cytoscape.util.swing.FileUtil;
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import org.cytoscape.view.model.CyNetworkView;
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import org.cytoscape.work.SynchronousTaskManager;
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import org.cytoscape.work.TaskIterator;
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/**
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* Created by
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* User: risserlin
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* Date: Feb 2, 2009
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* Time: 1:25:36 PM
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* Created by User: risserlin Date: Feb 2, 2009 Time: 1:25:36 PM
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* <p>
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* Class listener for node and edge selections. For each enrichment map there is a separate instance of this
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* class specifying the enrichment map parameters, selected nodes, selected edges and heatmap panels
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* Class listener for node and edge selections. For each enrichment map there is
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* a separate instance of this class specifying the enrichment map parameters,
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* selected nodes, selected edges and heatmap panels
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*/
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public class EnrichmentMapActionListener implements RowsSetListener{
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private EnrichmentMap map;
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private HeatMapPanel edgeOverlapPanel;
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private HeatMapPanel nodeOverlapPanel;
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public class EnrichmentMapActionListener implements RowsSetListener {
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private List<CyNode> Nodes;
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private List<CyEdge> Edges;
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private CyApplicationManager applicationManager;
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private SynchronousTaskManager syncTaskManager;
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private final CytoPanel cytoPanelSouth;
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private FileUtil fileUtil;
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private StreamUtil streamUtil;
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private HeatMapPanel edgeOverlapPanel;
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private HeatMapPanel nodeOverlapPanel;
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private CyApplicationManager applicationManager;
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private SynchronousTaskManager syncTaskManager;
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private final CytoPanel cytoPanelSouth;
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private FileUtil fileUtil;
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private StreamUtil streamUtil;
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private boolean heatMapUpdating;
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/**
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* Constructor for network action listener.
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*
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* @param params - enrichment map parameters associated with this actionlistener
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*/
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public EnrichmentMapActionListener(HeatMapPanel heatMapPanel_node,HeatMapPanel heatMapPanel_edge,
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CyApplicationManager applicationManager,CySwingApplication application,
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FileUtil fileUtil, StreamUtil streamUtil,SynchronousTaskManager syncTaskManager) {
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this.applicationManager = applicationManager;
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this.fileUtil = fileUtil;
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this.streamUtil = streamUtil;
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this.syncTaskManager = syncTaskManager;
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this.edgeOverlapPanel = heatMapPanel_edge;
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this.nodeOverlapPanel = heatMapPanel_node;
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heatMapUpdating = false;
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this.cytoPanelSouth = application.getCytoPanel(CytoPanelName.SOUTH);
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public EnrichmentMapActionListener(HeatMapPanel heatMapPanel_node, HeatMapPanel heatMapPanel_edge,
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CyApplicationManager applicationManager, CySwingApplication application, FileUtil fileUtil,
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StreamUtil streamUtil, SynchronousTaskManager syncTaskManager) {
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}
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this.applicationManager = applicationManager;
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this.fileUtil = fileUtil;
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this.streamUtil = streamUtil;
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this.syncTaskManager = syncTaskManager;
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this.edgeOverlapPanel = heatMapPanel_edge;
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this.nodeOverlapPanel = heatMapPanel_node;
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public boolean isHeatMapUpdating() {
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return heatMapUpdating;
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this.cytoPanelSouth = application.getCytoPanel(CytoPanelName.SOUTH);
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}
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/**
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* intialize the parameters needed for this instance of the action
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*/
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private boolean initialize(CyNetwork network){
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//get the static enrichment map manager.
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EnrichmentMapManager manager = EnrichmentMapManager.getInstance();
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this.map = manager.getMap(network.getSUID());
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if(map != null){
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if(map.getParams().isData() && map.getParams().getHmParams() == null){
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//create a heatmap parameters instance for this action listener
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HeatMapParameters hmParams = new HeatMapParameters(edgeOverlapPanel, nodeOverlapPanel);
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//If there are two distinct datasets intialize the theme and range for the heatmap coloring separately.
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if(map.getParams().isData2() && map.getDataset(EnrichmentMap.DATASET2).getExpressionSets() != null
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&& !map.getDataset(EnrichmentMap.DATASET1).getExpressionSets().getFilename().equalsIgnoreCase(map.getDataset(EnrichmentMap.DATASET2).getExpressionSets().getFilename()))
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hmParams.initColorGradients(this.map.getDataset(EnrichmentMap.DATASET1).getExpressionSets(),this.map.getDataset(EnrichmentMap.DATASET2).getExpressionSets());
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else
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hmParams.initColorGradients(this.map.getDataset(EnrichmentMap.DATASET1).getExpressionSets());
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//associate the newly created heatmap parameters with the current enrichment map paramters
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this.map.getParams().setHmParams(hmParams);
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}
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this.Nodes = this.map.getParams().getSelectedNodes();
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this.Edges = this.map.getParams().getSelectedEdges();
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return true;
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}
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return false;
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}
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/**
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* Handle network action. This method handles edge or node selection or unselections.
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*
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* @param event
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*/
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public void handleEvent(RowsSetEvent e) {
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//TODO: improve performance of calculating the Union of genesets (Nodes) and intersection of overlaps (Edges)
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// Meanwhile we have a flag to skip the updating of the Heatmap, which can be toggled by a check-mark in the EM-Menu
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heatMapUpdating = true;
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boolean override_revalidate_heatmap = EnrichmentMapManager.getInstance().isOverrideHeatmapRevalidation();
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//get the current network
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CyNetwork network = this.applicationManager.getCurrentNetwork();
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CyNetworkView view = this.applicationManager.getCurrentNetworkView();
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//only handle event if it is a selected node
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if(network != null && e != null && (e.getSource() == network.getDefaultEdgeTable() || e.getSource() == network.getDefaultNodeTable())){
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if(initialize(network)){
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//There is no flag to indicate that this is only an edge/node selection
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//After select get the nodes and the edges that were selected.
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if( ! override_revalidate_heatmap ) {
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//get the edges
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List<CyEdge> selectedEdges = CyTableUtil.getEdgesInState(network, CyNetwork.SELECTED, true);
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Edges.clear();
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Edges.addAll(selectedEdges);
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List<CyNode> selectedNodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
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Nodes.clear();
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Nodes.addAll(selectedNodes);
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//once we have amalgamated all the nodes and edges, launch a task to update the heatmap.
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UpdateHeatMapTask updateHeatmap = new UpdateHeatMapTask(map, Nodes, Edges, edgeOverlapPanel, nodeOverlapPanel, cytoPanelSouth,applicationManager);
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Observer observer = new Observer();
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syncTaskManager.execute(new TaskIterator(updateHeatmap), observer);
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while (!observer.isFinished()) {
202-
try {
203-
Thread.sleep(1);
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} catch (InterruptedException e1) {
205-
e1.printStackTrace();
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}
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}
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//if the network has been autoannotated we need to make sure the clusters have been selected
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//also only handle the node selection events (not edges)
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//TODO:need a cleaner way to find out if the currentView has an annotation
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if(AutoAnnotationManager.getInstance().getAnnotationPanel()!=null && !AutoAnnotationManager.getInstance().isClusterTableUpdating()
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&& e.getSource() == network.getDefaultNodeTable()){
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//go through all the clusters for this network to see if any of the cluster have all of their nodes selected
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HashMap<CyNetworkView, AutoAnnotationParameters> annotations = AutoAnnotationManager.getInstance().getNetworkViewToAutoAnnotationParameters();
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if(annotations.containsKey(view)){
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AnnotationSet currentAnnotation = annotations.get(view).getSelectedAnnotationSet();
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TableModel clusterTableModel = currentAnnotation.getClusterTable().getModel();
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ListSelectionModel clusterListSelectionModel = currentAnnotation.getClusterTable().getSelectionModel();
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//if there are clusters to add or to remove only do it once we have gone through all the clusters - to avoid race conditions.
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clusterListSelectionModel.setValueIsAdjusting(true);
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TreeMap<Integer, Cluster> clusters = currentAnnotation.getClusterMap();
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//go through each cluster - figure out which ones need to be selected and
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//which ones need to deselected
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//If any nodes in a cluster are no longer selected then deselect cluster
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//If all nodes in a cluster are selected then select cluster (in table and annotation)
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for(Cluster cluster:clusters.values()){
232-
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boolean select = true;
234-
boolean unselectCluster = false;
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for (CyNode node : cluster.getNodes()) {
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//if any of the nodes that belong to this cluster are not in the selected set
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//And the cluster is current marked as selected
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//then unselect the cluster
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if (!selectedNodes.contains(node) && cluster.isSelected()) {
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unselectCluster = true;
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break;
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}
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//if any of the nodes that belong to this cluster are not in the selected set
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//then do not select this cluster.
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if (!selectedNodes.contains(node)) {
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select = false;
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break;
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}
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}
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//one last check, if the cluster is already selected and all its nodes are
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//already selected then this is not a new selection event
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if(select == true && cluster.isSelected())
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select = false;
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//Cluster has been selected
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//if all nodes in a cluster are selected
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//update the cluster table
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if (select) {
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//set flag to tell listener that it shouldn't reselect the nodes as the user manually selected them.
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currentAnnotation.setManualSelection(true);
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for (int rowIndex = 0; rowIndex < clusterTableModel.getRowCount(); rowIndex++) {
263-
if (cluster.equals(clusterTableModel.getValueAt(rowIndex, 0))) {
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clusterListSelectionModel.addSelectionInterval(rowIndex, rowIndex);
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//AutoAnnotationManager.getInstance().flushPayloadEvents();
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break;
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}
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}
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}
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//Cluster has been unselected
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//update the cluster table
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if(unselectCluster){
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//set flag to tell listener that it shouldn't reselect the nodes as the user manually selected them.
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currentAnnotation.setManualSelection(true);
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for (int rowIndex = 0; rowIndex < clusterTableModel.getRowCount(); rowIndex++) {
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if (cluster.equals(clusterTableModel.getValueAt(rowIndex, 0))) {
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clusterListSelectionModel.removeSelectionInterval(rowIndex, rowIndex);
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//AutoAnnotationManager.getInstance().flushPayloadEvents();
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break;
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}//end of if
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}//end of for
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}//end of if unselectedcluster
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}//end of For going through all clusters
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//if there are clusters to add or to remove only do it once we have gone through all the clusters - to avoid race conditions.
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clusterListSelectionModel.setValueIsAdjusting(false);
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* intialize the parameters needed for this instance of the action
102+
*/
103+
private EnrichmentMap getAndInitializeEnrichmentMap(CyNetwork network) {
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// get the static enrichment map manager.
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EnrichmentMapManager manager = EnrichmentMapManager.getInstance();
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EnrichmentMap map = manager.getMap(network.getSUID());
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if (map != null) {
108+
if (map.getParams().isData() && map.getParams().getHmParams() == null) {
109+
// create a heatmap parameters instance for this action listener
110+
HeatMapParameters hmParams = new HeatMapParameters(edgeOverlapPanel, nodeOverlapPanel);
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// If there are two distinct datasets intialize the theme and range for the heatmap coloring separately.
112+
if (map.getParams().isData2() && map.getDataset(EnrichmentMap.DATASET2).getExpressionSets() != null && !map.getDataset(EnrichmentMap.DATASET1).getExpressionSets().getFilename().equalsIgnoreCase(map.getDataset(EnrichmentMap.DATASET2).getExpressionSets().getFilename()))
113+
hmParams.initColorGradients(map.getDataset(EnrichmentMap.DATASET1).getExpressionSets(), map.getDataset(EnrichmentMap.DATASET2).getExpressionSets());
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else
115+
hmParams.initColorGradients(map.getDataset(EnrichmentMap.DATASET1).getExpressionSets());
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// associate the newly created heatmap parameters with the current enrichment map paramters
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map.getParams().setHmParams(hmParams);
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}
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}
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return map;
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}
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}
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}
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}
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}
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}//end of if e.getSource check
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heatMapUpdating = false;
300-
}
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/**
125+
* Handle network action. This method handles edge or node selection or unselections.
126+
*/
127+
public void handleEvent(RowsSetEvent e) {
128+
// TODO: improve performance of calculating the Union of genesets (Nodes) and intersection of overlaps (Edges)
129+
// Meanwhile we have a flag to skip the updating of the Heatmap, which can be toggled by a check-mark in the EM-Menu
130+
boolean override_revalidate_heatmap = EnrichmentMapManager.getInstance().isOverrideHeatmapRevalidation();
131+
132+
CyNetwork network = this.applicationManager.getCurrentNetwork();
133+
134+
// only handle event if it is a selected node
135+
if (network != null && e != null && (e.getSource() == network.getDefaultEdgeTable() || e.getSource() == network.getDefaultNodeTable())) {
136+
final EnrichmentMap map = getAndInitializeEnrichmentMap(network);
137+
if (map != null) {
138+
139+
// There is no flag to indicate that this is only an edge/node selection
140+
// After select get the nodes and the edges that were selected.
141+
if (!override_revalidate_heatmap) {
142+
143+
List<CyNode> selectedNodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
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List<CyEdge> selectedEdges = CyTableUtil.getEdgesInState(network, CyNetwork.SELECTED, true);
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final List<CyNode> Nodes = map.getParams().getSelectedNodes();
147+
final List<CyEdge> Edges = map.getParams().getSelectedEdges();
148+
149+
Nodes.clear();
150+
Nodes.addAll(selectedNodes);
151+
152+
Edges.clear();
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Edges.addAll(selectedEdges);
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// Once we have amalgamated all the nodes and edges, launch a task to update the heatmap.
156+
// Start the task in a separate thread to avoid Cytoscape deadlock bug (redmine issue #3370)
157+
new Thread() {
158+
public void run() {
159+
UpdateHeatMapTask updateHeatmap = new UpdateHeatMapTask(map, Nodes, Edges, edgeOverlapPanel, nodeOverlapPanel, cytoPanelSouth, applicationManager);
160+
syncTaskManager.execute(new TaskIterator(updateHeatmap));
161+
}
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}.start();
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}
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}
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} // end of if e.getSource check
166+
}
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}

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