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Removed AutoAnnotate
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@mikekucera
mikekucera committed Jan 13, 2016
1 parent c29a525 commit 36500ce
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Showing 38 changed files with 143 additions and 6,106 deletions.
33 changes: 1 addition & 32 deletions EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -13,9 +13,6 @@
import org.baderlab.csplugins.enrichmentmap.actions.LoadPostAnalysisPanelAction;
import org.baderlab.csplugins.enrichmentmap.actions.ShowAboutPanelAction;
import org.baderlab.csplugins.enrichmentmap.actions.ShowEdgeWidthDialogAction;
import org.baderlab.csplugins.enrichmentmap.autoannotate.AutoAnnotationManager;
import org.baderlab.csplugins.enrichmentmap.autoannotate.action.AutoAnnotationPanelAction;
import org.baderlab.csplugins.enrichmentmap.autoannotate.action.DisplayOptionsPanelAction;
import org.baderlab.csplugins.enrichmentmap.commands.EnrichmentMapGSEACommandHandlerTaskFactory;
import org.baderlab.csplugins.enrichmentmap.task.BuildEnrichmentMapTuneableTaskFactory;
import org.baderlab.csplugins.enrichmentmap.task.CreatePublicationVisualStyleTaskFactory;
Expand All @@ -28,7 +25,6 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.events.SetCurrentNetworkListener;
import org.cytoscape.application.events.SetCurrentNetworkViewListener;
import org.cytoscape.application.events.SetSelectedNetworkViewsListener;
import org.cytoscape.application.swing.CyAction;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.command.CommandExecutorTaskFactory;
Expand All @@ -40,9 +36,6 @@
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.events.ColumnCreatedListener;
import org.cytoscape.model.events.ColumnDeletedListener;
import org.cytoscape.model.events.ColumnNameChangedListener;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
import org.cytoscape.model.events.RowsSetListener;
import org.cytoscape.service.util.AbstractCyActivator;
Expand All @@ -57,7 +50,6 @@
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.model.events.NetworkViewAboutToBeDestroyedListener;
import org.cytoscape.view.presentation.annotations.AnnotationFactory;
import org.cytoscape.view.presentation.annotations.AnnotationManager;
import org.cytoscape.view.presentation.annotations.ShapeAnnotation;
Expand Down Expand Up @@ -137,37 +129,15 @@ public void start(BundleContext bc) {
EnrichmentMapActionListener EMActionListener = new EnrichmentMapActionListener(heatMapPanel_node,heatMapPanel_edge, cyApplicationManagerRef, cySwingApplicationRef,fileUtil,streamUtil,syncTaskManager);
registerService(bc,EMActionListener, RowsSetListener.class, new Properties());

// Set up autoAnnotationManager, hand it all of the services it needs
AutoAnnotationManager autoAnnotationManager = AutoAnnotationManager.getInstance();
autoAnnotationManager.initialize(cySwingApplicationRef, tableManager, commandExecutor, dialogTaskManager, syncTaskManager, annotationManager, layoutManager, shapeFactory, textFactory, groupFactory, groupManager, heatMapPanel_node, EMActionListener, eventHelper,cyApplicationManagerRef);
//register network/table events to autoAnnotationManager
registerService(bc, autoAnnotationManager, SetSelectedNetworkViewsListener.class, new Properties());
registerService(bc, autoAnnotationManager, NetworkViewAboutToBeDestroyedListener.class, new Properties());
registerService(bc, autoAnnotationManager, ColumnCreatedListener.class, new Properties());
registerService(bc, autoAnnotationManager, ColumnDeletedListener.class, new Properties());
registerService(bc, autoAnnotationManager, ColumnNameChangedListener.class, new Properties());
registerService(bc, autoAnnotationManager, RowsSetListener.class, new Properties());

//Create each Action within Enrichment map as a service
Map<String,String> serviceProperties;

//About Action
serviceProperties = new HashMap<>();
serviceProperties.put("inMenuBar", "true");
serviceProperties.put("preferredMenu", "Apps.EnrichmentMap");
ShowAboutPanelAction aboutAction = new ShowAboutPanelAction(serviceProperties,cyApplicationManagerRef ,cyNetworkViewManagerRef, cySwingApplicationRef, openBrowserRef);

//Auto-annotate Panel Action - opens Annotation panel
serviceProperties = new HashMap<>();
serviceProperties.put("inMenuBar", "true");
serviceProperties.put("preferredMenu", "Apps.EnrichmentMap");
AutoAnnotationPanelAction autoAnnotationPanelAction = new AutoAnnotationPanelAction(serviceProperties,cyApplicationManagerRef, cyNetworkViewManagerRef, cySwingApplicationRef, annotationManager, registrar);

//Auto-annotate Display Options Panel Action - opens display options panel
serviceProperties = new HashMap<>();
DisplayOptionsPanelAction displayOptionsPanelAction = new DisplayOptionsPanelAction(serviceProperties,cyApplicationManagerRef, cyNetworkViewManagerRef, cySwingApplicationRef, annotationManager, registrar);
autoAnnotationManager.setDisplayOptionsPanelAction(displayOptionsPanelAction);

//Build Enrichment Map Action - opens EM panel
serviceProperties = new HashMap<>();
serviceProperties.put("inMenuBar", "true");
Expand All @@ -193,14 +163,13 @@ public void start(BundleContext bc) {

//register the services
registerService(bc, LoadEnrichmentMapInputPanelAction, CyAction.class, new Properties());
registerService(bc, autoAnnotationPanelAction, CyAction.class, new Properties());
registerService(bc, BulkEMInputPanelAction, CyAction.class, new Properties());
registerService(bc, loadPostAnalysisAction, CyAction.class, new Properties());
registerService(bc, edgeWidthPanelAction, CyAction.class, new Properties());
registerService(bc, aboutAction, CyAction.class,new Properties());

//register the session save and restore
EnrichmentMapSessionAction sessionAction = new EnrichmentMapSessionAction(cyNetworkManagerRef, sessionManager, cyApplicationManagerRef, streamUtil, autoAnnotationPanelAction);
EnrichmentMapSessionAction sessionAction = new EnrichmentMapSessionAction(cyNetworkManagerRef, sessionManager, cyApplicationManagerRef, streamUtil);
registerService(bc,sessionAction,SessionAboutToBeSavedListener.class, new Properties());
registerService(bc,sessionAction,SessionLoadedListener.class, new Properties());

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