Author: scooter
Date: 2012-05-01 12:44:43 -0700 (Tue, 01 May 2012)
New Revision: 29060
Modified:
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java
core3/impl/trunk/app-impl/src/test/java/org/cytoscape/app/internal/CyAppAdapterImplTest.java
Log:
Added group-api interfaces
Modified:
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
2012-05-01 18:58:55 UTC (rev 29059)
+++
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyActivator.java
2012-05-01 19:44:43 UTC (rev 29060)
@@ -19,6 +19,9 @@
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.io.datasource.DataSourceManager;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.group.CyGroupFactory;
+import org.cytoscape.group.CyGroupManager;
+import org.cytoscape.group.data.CyGroupAggregationManager;
import org.cytoscape.io.write.PresentationWriterManager;
import org.cytoscape.view.presentation.RenderingEngineManager;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
@@ -119,6 +122,9 @@
CyApplicationManager cyApplicationManagerRef =
getService(bc,CyApplicationManager.class);
CyEventHelper cyEventHelperRef =
getService(bc,CyEventHelper.class);
+ CyGroupAggregationManager cyGroupAggregationManagerRef =
getService(bc,CyGroupAggregationManager.class);
+ CyGroupFactory cyGroupFactoryRef =
getService(bc,CyGroupFactory.class);
+ CyGroupManager cyGroupManagerRef =
getService(bc,CyGroupManager.class);
CyLayoutAlgorithmManager cyLayoutAlgorithmManagerRef =
getService(bc,CyLayoutAlgorithmManager.class);
CyNetworkFactory cyNetworkFactoryRef =
getService(bc,CyNetworkFactory.class);
CyNetworkManager cyNetworkManagerRef =
getService(bc,CyNetworkManager.class);
@@ -228,62 +234,100 @@
// End of core-task services
- CyAppAdapterImpl cyAppAdapter = new
CyAppAdapterImpl(cyApplicationManagerRef,cyEventHelperRef,cyLayoutAlgorithmManagerRef,cyNetworkFactoryRef,cyNetworkManagerRef,cyNetworkViewFactoryRef,cyNetworkViewManagerRef,cyNetworkViewReaderManagerRef,cyNetworkViewWriterManagerRef,cyPropertyRef,cyPropertyReaderManagerRef,cyPropertyWriterManagerRef,cyRootNetworkFactoryRef,cyServiceRegistrarRef,cySessionManagerRef,cySessionReaderManagerRef,cySessionWriterManagerRef,cySwingApplicationRef,cyTableFactoryRef,cyTableManagerRef,cyTableReaderManagerRef,cytoscapeVersionService,
dialogTaskManagerRef,panelTaskManagerRef,submenuTaskManagerRef,presentationWriterManagerRef,renderingEngineManagerRef,taskManagerRef,undoSupportRef,
vmfFactoryC, vmfFactoryD, vmfFactoryP,
visualMappingManagerRef,visualStyleFactoryRef, dataSourceManager,
- loadVizmapFileTaskFactory,
- loadNetworkFileTaskFactory,
- loadNetworkURLTaskFactory,
- deleteSelectedNodesAndEdgesTaskFactory,
- selectAllTaskFactory,
- selectAllEdgesTaskFactory,
- selectAllNodesTaskFactory,
- selectAdjacentEdgesTaskFactory,
- selectConnectedNodesTaskFactory,
- selectFirstNeighborsTaskFactory,
- selectFirstNeighborsTaskFactoryInEdge,
- selectFirstNeighborsTaskFactoryOutEdge,
- deselectAllTaskFactory,
- deselectAllEdgesTaskFactory,
- deselectAllNodesTaskFactory,
- invertSelectedEdgesTaskFactory,
- invertSelectedNodesTaskFactory,
- selectFromFileListTaskFactory,
- selectFirstNeighborsNodeViewTaskFactory,
- hideSelectedTaskFactory,
- hideSelectedNodesTaskFactory,
- hideSelectedEdgesTaskFactory,
- unHideAllTaskFactory,
- unHideAllNodesTaskFactory,
- unHideAllEdgesTaskFactory,
- newEmptyNetworkTaskFactory,
- cloneNetworkTaskFactory,
- newNetworkSelectedNodesEdgesTaskFactory,
- newNetworkSelectedNodesOnlyTaskFactory,
- destroyNetworkTaskFactory,
- destroyNetworkViewTaskFactory,
- newSessionTaskFactory,
- openSessionTaskFactory,
- saveSessionAsTaskFactory,
- editNetworkTitleTaskFactory,
- createNetworkViewTaskFactory,
- exportNetworkImageTaskFactory,
- exportNetworkViewTaskFactory,
- exportSelectedTableTaskFactory,
- exportTableTaskFactory,
- applyPreferredLayoutTaskFactory,
- deleteColumnTaskFactory,
- renameColumnTaskFactory,
- deleteTableTaskFactory,
- exportVizmapTaskFactory,
- connectSelectedNodesTaskFactory,
- mapGlobal,
- applyVisualStyleTaskFactory,
- mapNetworkAttrTaskFactory,
- groupNodesTaskFactory,
- unGroupTaskFactory,
- collapseGroupTaskFactory,
- expandGroupTaskFactory,
- unGroupNodesTaskFactory
- );
+ CyAppAdapterImpl cyAppAdapter = new
CyAppAdapterImpl(cyApplicationManagerRef,
+
cyEventHelperRef,
+
cyGroupAggregationManagerRef,
+
cyGroupFactoryRef,
+
cyGroupManagerRef,
+
cyLayoutAlgorithmManagerRef,
+
cyNetworkFactoryRef,
+
cyNetworkManagerRef,
+
cyNetworkViewFactoryRef,
+
cyNetworkViewManagerRef,
+
cyNetworkViewReaderManagerRef,
+
cyNetworkViewWriterManagerRef,
+
cyPropertyRef,
+
cyPropertyReaderManagerRef,
+
cyPropertyWriterManagerRef,
+
cyRootNetworkFactoryRef,
+
cyServiceRegistrarRef,
+
cySessionManagerRef,
+
cySessionReaderManagerRef,
+
cySessionWriterManagerRef,
+
cySwingApplicationRef,
+
cyTableFactoryRef,
+
cyTableManagerRef,
+
cyTableReaderManagerRef,
+
cytoscapeVersionService,
+
dialogTaskManagerRef,
+
panelTaskManagerRef,
+
submenuTaskManagerRef,
+
presentationWriterManagerRef,
+
renderingEngineManagerRef,
+
taskManagerRef,
+
undoSupportRef,
+
vmfFactoryC,
+
vmfFactoryD,
+
vmfFactoryP,
+
visualMappingManagerRef,
+
visualStyleFactoryRef,
+
dataSourceManager,
+ // from
core-task-api
+
loadVizmapFileTaskFactory,
+
loadNetworkFileTaskFactory,
+
loadNetworkURLTaskFactory,
+
deleteSelectedNodesAndEdgesTaskFactory,
+
selectAllTaskFactory,
+
selectAllEdgesTaskFactory,
+
selectAllNodesTaskFactory,
+
selectAdjacentEdgesTaskFactory,
+
selectConnectedNodesTaskFactory,
+
selectFirstNeighborsTaskFactory,
+
selectFirstNeighborsTaskFactoryInEdge,
+
selectFirstNeighborsTaskFactoryOutEdge,
+
deselectAllTaskFactory,
+
deselectAllEdgesTaskFactory,
+
deselectAllNodesTaskFactory,
+
invertSelectedEdgesTaskFactory,
+
invertSelectedNodesTaskFactory,
+
selectFromFileListTaskFactory,
+
selectFirstNeighborsNodeViewTaskFactory,
+
hideSelectedTaskFactory,
+
hideSelectedNodesTaskFactory,
+
hideSelectedEdgesTaskFactory,
+
unHideAllTaskFactory,
+
unHideAllNodesTaskFactory,
+
unHideAllEdgesTaskFactory,
+
newEmptyNetworkTaskFactory,
+
cloneNetworkTaskFactory,
+
newNetworkSelectedNodesEdgesTaskFactory,
+
newNetworkSelectedNodesOnlyTaskFactory,
+
destroyNetworkTaskFactory,
+
destroyNetworkViewTaskFactory,
+
newSessionTaskFactory,
+
openSessionTaskFactory,
+
saveSessionAsTaskFactory,
+
editNetworkTitleTaskFactory,
+
createNetworkViewTaskFactory,
+
exportNetworkImageTaskFactory,
+
exportNetworkViewTaskFactory,
+
exportSelectedTableTaskFactory,
+
exportTableTaskFactory,
+
applyPreferredLayoutTaskFactory,
+
deleteColumnTaskFactory,
+
renameColumnTaskFactory,
+
deleteTableTaskFactory,
+
exportVizmapTaskFactory,
+
connectSelectedNodesTaskFactory,
+ mapGlobal,
+
applyVisualStyleTaskFactory,
+
mapNetworkAttrTaskFactory,
+
groupNodesTaskFactory,
+
unGroupTaskFactory,
+
collapseGroupTaskFactory,
+
expandGroupTaskFactory,
+
unGroupNodesTaskFactory
+ );
AppLoaderTaskFactory appLoaderTaskFactory = new
AppLoaderTaskFactory(cyAppAdapter);
AppManagerAction appManagerAction = new AppManagerAction(
Modified:
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java
===================================================================
---
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java
2012-05-01 18:58:55 UTC (rev 29059)
+++
core3/impl/trunk/app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java
2012-05-01 19:44:43 UTC (rev 29060)
@@ -12,6 +12,9 @@
import org.cytoscape.io.datasource.DataSourceManager;
import org.cytoscape.equations.AbstractFunction;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.group.CyGroupFactory;
+import org.cytoscape.group.CyGroupManager;
+import org.cytoscape.group.data.CyGroupAggregationManager;
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.read.CyNetworkReader;
import org.cytoscape.io.read.CyNetworkReaderManager;
@@ -135,6 +138,9 @@
//
private final CyApplicationManager cyApplicationManager;
private final CyEventHelper cyEventHelper;
+ private final CyGroupAggregationManager cyGroupAggregationManager;
+ private final CyGroupFactory cyGroupFactory;
+ private final CyGroupManager cyGroupManager;
private final CyLayoutAlgorithmManager cyLayoutAlgorithmManager;
private final CyNetworkFactory cyNetworkFactory;
private final CyNetworkManager cyNetworkManager;
@@ -280,6 +286,9 @@
//
CyAppAdapterImpl( final CyApplicationManager cyApplicationManager,
final CyEventHelper cyEventHelper,
+ final CyGroupAggregationManager
cyGroupAggregationManager,
+ final CyGroupFactory cyGroupFactory,
+ final CyGroupManager cyGroupManager,
final CyLayoutAlgorithmManager
cyLayoutAlgorithmManager,
final CyNetworkFactory cyNetworkFactory,
final CyNetworkManager cyNetworkManager,
@@ -386,6 +395,9 @@
{
this.cyApplicationManager = cyApplicationManager;
this.cyEventHelper = cyEventHelper;
+ this.cyGroupAggregationManager = cyGroupAggregationManager;
+ this.cyGroupFactory = cyGroupFactory;
+ this.cyGroupManager = cyGroupManager;
this.cyLayoutAlgorithmManager = cyLayoutAlgorithmManager;
this.cyNetworkFactory = cyNetworkFactory;
this.cyNetworkManager = cyNetworkManager;
@@ -485,6 +497,9 @@
//
public CyApplicationManager getCyApplicationManager() { return
cyApplicationManager; }
public CyEventHelper getCyEventHelper() { return cyEventHelper; }
+ @Override public CyGroupAggregationManager
getCyGroupAggregationManager() { return cyGroupAggregationManager; }
+ @Override public CyGroupFactory getCyGroupFactory() { return
cyGroupFactory; }
+ @Override public CyGroupManager getCyGroupManager() { return
cyGroupManager; }
public CyLayoutAlgorithmManager getCyLayoutAlgorithmManager() { return
cyLayoutAlgorithmManager; }
public CyNetworkFactory getCyNetworkFactory() { return
cyNetworkFactory; }
public CyNetworkManager getCyNetworkManager() { return
cyNetworkManager; }
Modified:
core3/impl/trunk/app-impl/src/test/java/org/cytoscape/app/internal/CyAppAdapterImplTest.java
===================================================================
---
core3/impl/trunk/app-impl/src/test/java/org/cytoscape/app/internal/CyAppAdapterImplTest.java
2012-05-01 18:58:55 UTC (rev 29059)
+++
core3/impl/trunk/app-impl/src/test/java/org/cytoscape/app/internal/CyAppAdapterImplTest.java
2012-05-01 19:44:43 UTC (rev 29060)
@@ -24,6 +24,9 @@
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
+import org.cytoscape.group.CyGroupFactory;
+import org.cytoscape.group.CyGroupManager;
+import org.cytoscape.group.data.CyGroupAggregationManager;
//import org.cytoscape.app.CyAppAdapterTest;
import org.cytoscape.app.CyAppAdapter;
import org.cytoscape.property.CyProperty;
@@ -103,6 +106,9 @@
CyAppAdapter adapter = new CyAppAdapterImpl(
mock(CyApplicationManager.class),
mock(CyEventHelper.class),
+ mock(CyGroupAggregationManager.class),
+ mock(CyGroupFactory.class),
+ mock(CyGroupManager.class),
mock(CyLayoutAlgorithmManager.class),
mock(CyNetworkFactory.class),
mock(CyNetworkManager.class),
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