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mikekuceramikekucera
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Publication-Ready toggle. Closes #134.
1 parent 2655500 commit c9d5937

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4 files changed

+635
-478
lines changed

4 files changed

+635
-478
lines changed

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

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@@ -18,6 +18,7 @@
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import org.baderlab.csplugins.enrichmentmap.autoannotate.action.DisplayOptionsPanelAction;
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import org.baderlab.csplugins.enrichmentmap.commands.EnrichmentMapGSEACommandHandlerTaskFactory;
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import org.baderlab.csplugins.enrichmentmap.task.BuildEnrichmentMapTuneableTaskFactory;
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import org.baderlab.csplugins.enrichmentmap.task.CreatePublicationVisualStyleTaskRunner;
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import org.baderlab.csplugins.enrichmentmap.task.EdgeWidthTableColumnTaskFactory;
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import org.baderlab.csplugins.enrichmentmap.view.BulkEMCreationPanel;
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import org.baderlab.csplugins.enrichmentmap.view.EnrichmentMapInputPanel;
@@ -121,7 +122,8 @@ public void start(BundleContext bc) {
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//create two instances of the heatmap panel
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HeatMapPanel heatMapPanel_node = new HeatMapPanel(true, cySwingApplicationRef, fileUtil, cyApplicationManagerRef, openBrowserRef,dialogTaskManager,streamUtil);
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HeatMapPanel heatMapPanel_edge = new HeatMapPanel(false, cySwingApplicationRef, fileUtil, cyApplicationManagerRef, openBrowserRef,dialogTaskManager,streamUtil);
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ParametersPanel paramsPanel = new ParametersPanel(openBrowserRef, cyApplicationManagerRef);
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CreatePublicationVisualStyleTaskRunner taskRunner = new CreatePublicationVisualStyleTaskRunner(cyApplicationManagerRef, visualMappingManagerRef, visualStyleFactoryRef, eventHelper, dialogTaskManager);
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ParametersPanel paramsPanel = new ParametersPanel(openBrowserRef, cyApplicationManagerRef, taskRunner);
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//Get an instance of EM manager
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EnrichmentMapManager manager = EnrichmentMapManager.getInstance();

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

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@@ -0,0 +1,90 @@
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package org.baderlab.csplugins.enrichmentmap.task;
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import java.awt.Color;
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import org.cytoscape.application.CyApplicationManager;
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import org.cytoscape.event.CyEventHelper;
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import org.cytoscape.view.model.CyNetworkView;
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import org.cytoscape.view.presentation.property.BasicVisualLexicon;
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import org.cytoscape.view.vizmap.VisualMappingManager;
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import org.cytoscape.view.vizmap.VisualStyle;
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import org.cytoscape.view.vizmap.VisualStyleFactory;
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import org.cytoscape.work.AbstractTask;
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import org.cytoscape.work.TaskMonitor;
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public class CreatePublicationVisualStyleTask extends AbstractTask {
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private static final String SUFFIX = "_publication";
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private final CyApplicationManager applicationManager;
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private final VisualMappingManager visualMappingManager;
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private final VisualStyleFactory visualStyleFactory;
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private final CyEventHelper eventHelper;
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public CreatePublicationVisualStyleTask(
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CyApplicationManager applicationManager,
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VisualMappingManager visualMappingManager,
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VisualStyleFactory visualStyleFactory,
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CyEventHelper eventHelper) {
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this.applicationManager = applicationManager;
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this.visualMappingManager = visualMappingManager;
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this.visualStyleFactory = visualStyleFactory;
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this.eventHelper = eventHelper;
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}
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private VisualStyle attemptToGetExistingStyle(String vs_name) {
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for(VisualStyle vs : visualMappingManager.getAllVisualStyles()) {
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if(vs.getTitle() != null && vs.getTitle().equals(vs_name)) {
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return vs;
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}
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}
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return null;
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}
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@Override
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public void run(TaskMonitor taskMonitor) {
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taskMonitor.setTitle("EnrichmentMap");
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taskMonitor.setStatusMessage("Create Publication-Ready Visual Style");
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VisualStyle currentStyle = visualMappingManager.getCurrentVisualStyle();
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if(currentStyle == null)
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return;
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String currentTitle = currentStyle.getTitle();
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// If the current visual style is publication then attempt to switch back
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if(currentTitle.endsWith(SUFFIX)) {
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String title = currentTitle.substring(0, currentTitle.length() - SUFFIX.length());
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VisualStyle existingStyle = attemptToGetExistingStyle(title);
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if(existingStyle != null) {
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visualMappingManager.setCurrentVisualStyle(existingStyle);
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}
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}
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else {
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String title = currentTitle + SUFFIX;
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VisualStyle visualStyle = attemptToGetExistingStyle(title);
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if(visualStyle == null) {
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// create a copy of the current style
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visualStyle = visualStyleFactory.createVisualStyle(currentStyle);
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visualStyle.setTitle(title);
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// Remove node labels
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visualStyle.removeVisualMappingFunction(BasicVisualLexicon.NODE_LABEL);
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visualStyle.setDefaultValue(BasicVisualLexicon.NODE_LABEL, "");
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// Make background white
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visualStyle.removeVisualMappingFunction(BasicVisualLexicon.NETWORK_BACKGROUND_PAINT);
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visualStyle.setDefaultValue(BasicVisualLexicon.NETWORK_BACKGROUND_PAINT, Color.WHITE);
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visualMappingManager.addVisualStyle(visualStyle);
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}
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visualMappingManager.setCurrentVisualStyle(visualStyle);
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}
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eventHelper.flushPayloadEvents(); // view won't update properly without this
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CyNetworkView view = applicationManager.getCurrentNetworkView();
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view.updateView();
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}
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}

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

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package org.baderlab.csplugins.enrichmentmap.task;
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import java.awt.event.ActionEvent;
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import java.awt.event.ActionListener;
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import org.cytoscape.application.CyApplicationManager;
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import org.cytoscape.event.CyEventHelper;
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import org.cytoscape.view.vizmap.VisualMappingManager;
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import org.cytoscape.view.vizmap.VisualStyleFactory;
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import org.cytoscape.work.TaskIterator;
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import org.cytoscape.work.TaskManager;
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public class CreatePublicationVisualStyleTaskRunner implements ActionListener {
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private final CyApplicationManager applicationManager;
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private final VisualMappingManager visualMappingManager;
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private final VisualStyleFactory visualStyleFactory;
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private final CyEventHelper eventHelper;
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private final TaskManager<?,?> taskManager;
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public CreatePublicationVisualStyleTaskRunner(
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CyApplicationManager applicationManager,
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VisualMappingManager visualMappingManager,
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VisualStyleFactory visualStyleFactory,
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CyEventHelper eventHelper,
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TaskManager<?,?> taskManager) {
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this.applicationManager = applicationManager;
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this.visualMappingManager = visualMappingManager;
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this.visualStyleFactory = visualStyleFactory;
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this.eventHelper = eventHelper;
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this.taskManager = taskManager;
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}
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public void run() {
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taskManager.execute(new TaskIterator(new CreatePublicationVisualStyleTask(applicationManager, visualMappingManager, visualStyleFactory, eventHelper)));
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}
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@Override
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public void actionPerformed(ActionEvent e) {
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run();
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}
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}

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