Author: mes
Date: 2012-04-23 16:42:44 -0700 (Mon, 23 Apr 2012)
New Revision: 28957
Removed:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/
core3/impl/trunk/core-task-impl/src/test/java/org/cytoscape/task/internal/quickstart/
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/ConnectSelectedNodesTaskFactory.java
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/networkobjects/DeleteSelectedNodesAndEdgesTaskFactory.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTaskFactoryImpl.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTaskFactoryImpl.java
Log:
some updates to core-task-api, cleanup of getCurrentNetwork and removal of the
unused quickstart code
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/ConnectSelectedNodesTaskFactory.java
===================================================================
---
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/ConnectSelectedNodesTaskFactory.java
2012-04-23 22:57:12 UTC (rev 28956)
+++
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/edit/ConnectSelectedNodesTaskFactory.java
2012-04-23 23:42:44 UTC (rev 28957)
@@ -1,11 +1,11 @@
package org.cytoscape.task.edit;
-import org.cytoscape.work.TaskFactory;
+import org.cytoscape.task.NetworkTaskFactory;
/**
* This interface provides a task iterator for connecting selected nodes.
* @CyAPI.Api.Interface
*/
-public interface ConnectSelectedNodesTaskFactory extends TaskFactory {
+public interface ConnectSelectedNodesTaskFactory extends NetworkTaskFactory {
}
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/networkobjects/DeleteSelectedNodesAndEdgesTaskFactory.java
===================================================================
---
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/networkobjects/DeleteSelectedNodesAndEdgesTaskFactory.java
2012-04-23 22:57:12 UTC (rev 28956)
+++
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/networkobjects/DeleteSelectedNodesAndEdgesTaskFactory.java
2012-04-23 23:42:44 UTC (rev 28957)
@@ -1,12 +1,12 @@
package org.cytoscape.task.networkobjects;
-import org.cytoscape.work.TaskFactory;
+import org.cytoscape.task.NetworkTaskFactory;
/**
* This interface provides a task iterator for deleting selected nodes and
edges.
* @CyAPI.Api.Interface
*
*/
-public interface DeleteSelectedNodesAndEdgesTaskFactory extends TaskFactory{
+public interface DeleteSelectedNodesAndEdgesTaskFactory extends
NetworkTaskFactory{
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2012-04-23 22:57:12 UTC (rev 28956)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2012-04-23 23:42:44 UTC (rev 28957)
@@ -84,10 +84,6 @@
import org.cytoscape.task.internal.loadvizmap.LoadVizmapFileTaskFactoryImpl;
import
org.cytoscape.task.internal.networkobjects.DeleteSelectedNodesAndEdgesTaskFactoryImpl;
import org.cytoscape.task.internal.proxysettings.ProxySettingsTaskFactoryImpl;
-import org.cytoscape.task.internal.quickstart.ImportTaskUtil;
-import org.cytoscape.task.internal.quickstart.datasource.BioGridPreprocessor;
-import
org.cytoscape.task.internal.quickstart.datasource.InteractionFilePreprocessor;
-import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderUtil;
import org.cytoscape.task.internal.select.DeselectAllEdgesTaskFactoryImpl;
import org.cytoscape.task.internal.select.DeselectAllNodesTaskFactoryImpl;
import org.cytoscape.task.internal.select.DeselectAllTaskFactoryImpl;
@@ -212,7 +208,7 @@
LoadNetworkFileTaskFactoryImpl loadNetworkFileTaskFactory = new
LoadNetworkFileTaskFactoryImpl(cyNetworkReaderManagerServiceRef,cyNetworkManagerServiceRef,cyNetworkViewManagerServiceRef,cyPropertyServiceRef,cyNetworkNamingServiceRef,
tunableSetterServiceRef);
LoadNetworkURLTaskFactoryImpl loadNetworkURLTaskFactory = new
LoadNetworkURLTaskFactoryImpl(cyNetworkReaderManagerServiceRef,cyNetworkManagerServiceRef,cyNetworkViewManagerServiceRef,cyPropertyServiceRef,cyNetworkNamingServiceRef,streamUtilRef,
synchronousTaskManagerServiceRef, tunableSetterServiceRef);
- DeleteSelectedNodesAndEdgesTaskFactoryImpl
deleteSelectedNodesAndEdgesTaskFactory = new
DeleteSelectedNodesAndEdgesTaskFactoryImpl(undoSupportServiceRef,cyApplicationManagerServiceRef,cyNetworkViewManagerServiceRef,visualMappingManagerServiceRef,cyEventHelperRef);
+ DeleteSelectedNodesAndEdgesTaskFactoryImpl
deleteSelectedNodesAndEdgesTaskFactory = new
DeleteSelectedNodesAndEdgesTaskFactoryImpl(undoSupportServiceRef,cyNetworkViewManagerServiceRef,visualMappingManagerServiceRef,cyEventHelperRef);
SelectAllTaskFactoryImpl selectAllTaskFactory = new
SelectAllTaskFactoryImpl(undoSupportServiceRef,cyNetworkViewManagerServiceRef,cyEventHelperRef);
SelectAllEdgesTaskFactoryImpl selectAllEdgesTaskFactory = new
SelectAllEdgesTaskFactoryImpl(undoSupportServiceRef,cyNetworkViewManagerServiceRef,cyEventHelperRef);
SelectAllNodesTaskFactoryImpl selectAllNodesTaskFactory = new
SelectAllNodesTaskFactoryImpl(undoSupportServiceRef,cyNetworkViewManagerServiceRef,cyEventHelperRef);
@@ -265,11 +261,8 @@
CopyValueToEntireColumnTaskFactoryImpl
copyValueToEntireColumnTaskFactory = new
CopyValueToEntireColumnTaskFactoryImpl(undoSupportServiceRef);
DeleteTableTaskFactoryImpl deleteTableTaskFactory = new
DeleteTableTaskFactoryImpl(cyTableManagerServiceRef);
ExportVizmapTaskFactoryImpl exportVizmapTaskFactory = new
ExportVizmapTaskFactoryImpl(vizmapWriterManagerServiceRef,visualMappingManagerServiceRef,
tunableSetterServiceRef);
- SubnetworkBuilderUtil subnetworkBuilderUtil = new
SubnetworkBuilderUtil(cyNetworkReaderManagerServiceRef,cyNetworkManagerServiceRef,cyNetworkViewManagerServiceRef,cyPropertyServiceRef,cyNetworkNamingServiceRef,streamUtilRef,cyEventHelperRef,cyApplicationManagerServiceRef,cyRootNetworkFactoryServiceRef,cyNetworkViewFactoryServiceRef,visualMappingManagerServiceRef,visualStyleFactoryServiceRef,cyLayoutsServiceRef,undoSupportServiceRef);
- ImportTaskUtil importTaskUtil = new
ImportTaskUtil(cyNetworkReaderManagerServiceRef,cyNetworkManagerServiceRef,cyNetworkViewManagerServiceRef,cyPropertyServiceRef,cyNetworkNamingServiceRef,streamUtilRef,cyDataTableReaderManagerServiceRef,cyApplicationManagerServiceRef);
- BioGridPreprocessor bioGridPreprocessor = new
BioGridPreprocessor(cyPropertyServiceRef,cyApplicationConfigurationServiceRef);
- ConnectSelectedNodesTaskFactoryImpl
connectSelectedNodesTaskFactory = new
ConnectSelectedNodesTaskFactoryImpl(undoSupportServiceRef,cyApplicationManagerServiceRef,cyEventHelperRef);
+ ConnectSelectedNodesTaskFactoryImpl
connectSelectedNodesTaskFactory = new
ConnectSelectedNodesTaskFactoryImpl(undoSupportServiceRef,cyEventHelperRef);
MapGlobalToLocalTableTaskFactoryImpl mapGlobal = new
MapGlobalToLocalTableTaskFactoryImpl(cyTableManagerServiceRef,
cyNetworkManagerServiceRef, tunableSetterServiceRef);
@@ -888,8 +881,6 @@
registerService(bc,deleteTableTaskFactory,TableTaskFactory.class, new
Properties());
registerService(bc,deleteTableTaskFactory,DeleteTableTaskFactory.class, new
Properties());
- registerAllServices(bc,bioGridPreprocessor, new Properties());
-
Properties connectSelectedNodesTaskFactoryProps = new
Properties();
connectSelectedNodesTaskFactoryProps.setProperty(PREFERRED_MENU,"Edit");
connectSelectedNodesTaskFactoryProps.setProperty(ENABLE_FOR,"network");
@@ -900,10 +891,6 @@
registerService(bc,connectSelectedNodesTaskFactory,TaskFactory.class,
connectSelectedNodesTaskFactoryProps);
registerService(bc,connectSelectedNodesTaskFactory,ConnectSelectedNodesTaskFactory.class,
connectSelectedNodesTaskFactoryProps);
-
registerServiceListener(bc,importTaskUtil,"addProcessor","removeProcessor",InteractionFilePreprocessor.class);
-
registerServiceListener(bc,subnetworkBuilderUtil,"addProcessor","removeProcessor",InteractionFilePreprocessor.class);
-
registerServiceListener(bc,subnetworkBuilderUtil,"addFactory","removeFactory",VisualMappingFunctionFactory.class);
-
GroupNodesTaskFactoryImpl groupNodesTaskFactory =
new GroupNodesTaskFactoryImpl(cyGroupManager,
cyGroupFactory);
Properties groupNodesTaskFactoryProps = new Properties();
@@ -965,4 +952,4 @@
Properties mapNetworkAttrTaskFactoryProps = new Properties();
registerService(bc,mapNetworkAttrTaskFactory,MapNetworkAttrTaskFactory.class,mapNetworkAttrTaskFactoryProps);
}
-}
\ No newline at end of file
+}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTaskFactoryImpl.java
2012-04-23 22:57:12 UTC (rev 28956)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/edit/ConnectSelectedNodesTaskFactoryImpl.java
2012-04-23 23:42:44 UTC (rev 28957)
@@ -4,30 +4,26 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.task.edit.ConnectSelectedNodesTaskFactory;
-import org.cytoscape.work.AbstractTaskFactory;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.undo.UndoSupport;
+import org.cytoscape.model.CyNetwork;
-public class ConnectSelectedNodesTaskFactoryImpl extends AbstractTaskFactory
implements ConnectSelectedNodesTaskFactory{
+public class ConnectSelectedNodesTaskFactoryImpl extends
AbstractNetworkTaskFactory implements ConnectSelectedNodesTaskFactory{
private final UndoSupport undoSupport;
- private final CyApplicationManager appManager;
private final CyEventHelper eventHelper;
public ConnectSelectedNodesTaskFactoryImpl(final UndoSupport
undoSupport,
- final CyApplicationManager
appManager,
final CyEventHelper eventHelper)
{
this.undoSupport = undoSupport;
- this.appManager = appManager;
this.eventHelper = eventHelper;
}
@Override
- public TaskIterator createTaskIterator() {
- return new TaskIterator(
- new ConnectSelectedNodesTask(undoSupport,
appManager.getCurrentNetwork(),
- eventHelper));
+ public TaskIterator createTaskIterator(CyNetwork network) {
+ return new TaskIterator( new
ConnectSelectedNodesTask(undoSupport, network, eventHelper));
}
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTask.java
2012-04-23 22:57:12 UTC (rev 28956)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTask.java
2012-04-23 23:42:44 UTC (rev 28957)
@@ -39,7 +39,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTableUtil;
import org.cytoscape.model.subnetwork.CySubNetwork;
-import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.AbstractTask;
@@ -48,18 +48,19 @@
public class DeleteSelectedNodesAndEdgesTask extends AbstractTask {
private final UndoSupport undoSupport;
- private final CyApplicationManager applicationManager;
private final CyNetworkViewManager networkViewManager;
private final CyEventHelper eventHelper;
private final VisualMappingManager visualMappingManager;
+ private final CyNetwork network;
- public DeleteSelectedNodesAndEdgesTask(
- final UndoSupport undoSupport, final CyApplicationManager
applicationManager,
- final CyNetworkViewManager networkViewManager,
- final VisualMappingManager visualMappingManager, final
CyEventHelper eventHelper)
+ public DeleteSelectedNodesAndEdgesTask(final CyNetwork network,
+ final UndoSupport undoSupport,
+ final CyNetworkViewManager
networkViewManager,
+ final VisualMappingManager
visualMappingManager,
+ final CyEventHelper eventHelper)
{
+ this.network = network;
this.undoSupport = undoSupport;
- this.applicationManager = applicationManager;
this.networkViewManager = networkViewManager;
this.visualMappingManager = visualMappingManager;
this.eventHelper = eventHelper;
@@ -67,15 +68,13 @@
@Override
public void run(final TaskMonitor taskMonitor) {
- taskMonitor.setProgress(0.0);
- CyNetworkView myView =
applicationManager.getCurrentNetworkView();
- if (myView == null){
+ if (network == null)
return;
- }
+
+ taskMonitor.setProgress(0.0);
// Delete from the base network so that our changes can be
undone:
- final CySubNetwork network = (CySubNetwork) myView.getModel();
final List<CyNode> selectedNodes =
CyTableUtil.getNodesInState(network, "selected", true);
taskMonitor.setProgress(0.1);
final Set<CyEdge> selectedEdges = new
HashSet<CyEdge>(CyTableUtil.getEdgesInState(network, "selected", true));
@@ -87,16 +86,13 @@
taskMonitor.setProgress(0.3);
undoSupport.postEdit(
- new DeleteEdit(network, selectedNodes, selectedEdges,
+ new DeleteEdit((CySubNetwork)network, selectedNodes,
selectedEdges,
networkViewManager,
visualMappingManager, eventHelper));
// Delete the actual nodes and edges:
network.removeNodes(selectedNodes);
- taskMonitor.setProgress(0.5);
- network.removeEdges(selectedEdges);
taskMonitor.setProgress(0.7);
- myView.updateView();
-
+ network.removeEdges(selectedEdges);
taskMonitor.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTaskFactoryImpl.java
2012-04-23 22:57:12 UTC (rev 28956)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/networkobjects/DeleteSelectedNodesAndEdgesTaskFactoryImpl.java
2012-04-23 23:42:44 UTC (rev 28957)
@@ -35,34 +35,32 @@
import
org.cytoscape.task.networkobjects.DeleteSelectedNodesAndEdgesTaskFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.vizmap.VisualMappingManager;
-import org.cytoscape.work.AbstractTaskFactory;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.undo.UndoSupport;
-public class DeleteSelectedNodesAndEdgesTaskFactoryImpl extends
AbstractTaskFactory implements DeleteSelectedNodesAndEdgesTaskFactory {
+public class DeleteSelectedNodesAndEdgesTaskFactoryImpl extends
AbstractNetworkTaskFactory implements DeleteSelectedNodesAndEdgesTaskFactory {
private final UndoSupport undoSupport;
- private final CyApplicationManager applicationManager;
private final CyNetworkViewManager networkViewManager;
private final VisualMappingManager visualMappingManager;
private final CyEventHelper eventHelper;
public DeleteSelectedNodesAndEdgesTaskFactoryImpl(final UndoSupport
undoSupport,
- final
CyApplicationManager applicationManager,
final
CyNetworkViewManager networkViewManager,
final
VisualMappingManager visualMappingManager,
final CyEventHelper
eventHelper)
{
this.undoSupport = undoSupport;
- this.applicationManager = applicationManager;
this.networkViewManager = networkViewManager;
this.visualMappingManager = visualMappingManager;
this.eventHelper = eventHelper;
}
- public TaskIterator createTaskIterator() {
+ public TaskIterator createTaskIterator(CyNetwork network) {
return new TaskIterator(
- new DeleteSelectedNodesAndEdgesTask(undoSupport,
applicationManager,
+ new DeleteSelectedNodesAndEdgesTask(network,
undoSupport,
networkViewManager,
visualMappingManager, eventHelper));
}
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