Author: mes
Date: 2010-09-23 16:50:19 -0700 (Thu, 23 Sep 2010)
New Revision: 22042
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/AbstractSelectTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsNodeViewTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTaskFactory.java
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
Log:
updated select tasks so that they are network tasks
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/AbstractSelectTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/AbstractSelectTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/AbstractSelectTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -31,15 +31,24 @@
import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.work.AbstractTask;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.task.AbstractNetworkTask;
import org.cytoscape.work.TaskMonitor;
-public abstract class AbstractSelectTask extends AbstractTask {
+public abstract class AbstractSelectTask extends AbstractNetworkTask {
protected CyNetworkManager netmgr;
- public AbstractSelectTask(CyNetworkManager netmgr) {
+ public AbstractSelectTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net);
this.netmgr = netmgr;
}
+
+ protected final void updateView() {
+ CyNetworkView view = netmgr.getNetworkView(net.getSUID());
+ if ( view != null )
+ view.updateView();
+ }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -38,25 +38,17 @@
package org.cytoscape.task.internal.select;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
public class DeselectAllEdgesTask extends AbstractSelectTask {
- public DeselectAllEdgesTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public DeselectAllEdgesTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor tm) {
- final CyNetwork n = netmgr.getCurrentNetwork();
- final CyNetworkView v = netmgr.getNetworkView( n.getSUID() );
- SelectUtils.setSelectedEdges( n.getEdgeList(), false);
-
- v.updateView();
+ SelectUtils.setSelectedEdges( net.getEdgeList(), false);
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllEdgesTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class DeselectAllEdgesTaskFactory implements TaskFactory {
+public class DeselectAllEdgesTaskFactory extends AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
public DeselectAllEdgesTaskFactory(CyNetworkManager netmgr) {
@@ -43,6 +44,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new DeselectAllEdgesTask(netmgr));
+ return new TaskIterator(new DeselectAllEdgesTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -37,25 +37,17 @@
package org.cytoscape.task.internal.select;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
public class DeselectAllNodesTask extends AbstractSelectTask {
- public DeselectAllNodesTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public DeselectAllNodesTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor tm) {
- final CyNetwork n = netmgr.getCurrentNetwork();
- final CyNetworkView v = netmgr.getNetworkView( n.getSUID() );
- SelectUtils.setSelectedNodes( n.getNodeList(), false);
-
- v.updateView();
+ SelectUtils.setSelectedNodes( net.getNodeList(), false);
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllNodesTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class DeselectAllNodesTaskFactory implements TaskFactory {
+public class DeselectAllNodesTaskFactory extends AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
@@ -44,6 +45,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new DeselectAllNodesTask(netmgr));
+ return new TaskIterator(new DeselectAllNodesTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -38,27 +38,18 @@
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
-
public class DeselectAllTask extends AbstractSelectTask {
- public DeselectAllTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public DeselectAllTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor tm) {
- final CyNetwork n = netmgr.getCurrentNetwork();
- final CyNetworkView v = netmgr.getNetworkView( n.getSUID() );
- SelectUtils.setSelectedEdges( n.getEdgeList(), false);
- SelectUtils.setSelectedNodes( n.getNodeList(), false);
-
- v.updateView();
+ SelectUtils.setSelectedEdges( net.getEdgeList(), false);
+ SelectUtils.setSelectedNodes( net.getNodeList(), false);
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/DeselectAllTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class DeselectAllTaskFactory implements TaskFactory {
+public class DeselectAllTaskFactory extends AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
@@ -44,6 +45,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new DeselectAllTask(netmgr));
+ return new TaskIterator(new DeselectAllTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -39,29 +39,23 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
public class InvertSelectedEdgesTask extends AbstractSelectTask {
- public InvertSelectedEdgesTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public InvertSelectedEdgesTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor tm) {
- final CyNetwork cyNetwork = netmgr.getCurrentNetwork();
- for ( CyEdge e : cyNetwork.getEdgeList() ) {
+ for ( CyEdge e : net.getEdgeList() ) {
if ( e.attrs().get("selected",Boolean.class) ) {
e.attrs().set("selected",false);
} else {
e.attrs().set("selected",true);
}
}
-
- netmgr.getNetworkView( cyNetwork.getSUID() ).updateView();
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedEdgesTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class InvertSelectedEdgesTaskFactory implements TaskFactory {
+public class InvertSelectedEdgesTaskFactory extends AbstractNetworkTaskFactory
{
private CyNetworkManager netmgr;
@@ -44,6 +45,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new InvertSelectedEdgesTask(netmgr));
+ return new TaskIterator(new
InvertSelectedEdgesTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -39,31 +39,24 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
public class InvertSelectedNodesTask extends AbstractSelectTask {
- public InvertSelectedNodesTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public InvertSelectedNodesTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor tm) {
- final CyNetwork cyNetwork = netmgr.getCurrentNetwork();
- for ( CyNode n : cyNetwork.getNodeList() ) {
+ for ( CyNode n : net.getNodeList() ) {
if ( n.attrs().get("selected",Boolean.class) ) {
n.attrs().set("selected",false);
} else {
n.attrs().set("selected",true);
}
}
-
- netmgr.getNetworkView( cyNetwork.getSUID() ).updateView();
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/InvertSelectedNodesTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class InvertSelectedNodesTaskFactory implements TaskFactory {
+public class InvertSelectedNodesTaskFactory extends AbstractNetworkTaskFactory
{
private CyNetworkManager netmgr;
public InvertSelectedNodesTaskFactory(CyNetworkManager netmgr) {
@@ -43,6 +44,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new InvertSelectedNodesTask(netmgr));
+ return new TaskIterator(new
InvertSelectedNodesTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -44,33 +44,25 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
public class SelectAdjacentEdgesTask extends AbstractSelectTask {
- public SelectAdjacentEdgesTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public SelectAdjacentEdgesTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor tm) {
- final CyNetwork network = netmgr.getCurrentNetwork();
- final CyNetworkView v = netmgr.getNetworkView(
network.getSUID() );
final Set<CyEdge> edgeSet = new HashSet<CyEdge>();
// Get the list of selected nodes
- for (CyNode node:
CyTableUtil.getNodesInState(network,"selected",true)) {
+ for (CyNode node:
CyTableUtil.getNodesInState(net,"selected",true)) {
// Get the list of edges connected to this node
- edgeSet.addAll(
network.getAdjacentEdgeList(node,CyEdge.Type.ANY) );
+ edgeSet.addAll(
net.getAdjacentEdgeList(node,CyEdge.Type.ANY) );
}
SelectUtils.setSelectedEdges(edgeSet,true);
-
- v.updateView();
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAdjacentEdgesTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class SelectAdjacentEdgesTaskFactory implements TaskFactory {
+public class SelectAdjacentEdgesTaskFactory extends AbstractNetworkTaskFactory
{
private CyNetworkManager netmgr;
@@ -44,6 +45,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new SelectAdjacentEdgesTask(netmgr));
+ return new TaskIterator(new
SelectAdjacentEdgesTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -38,25 +38,17 @@
package org.cytoscape.task.internal.select;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
public class SelectAllEdgesTask extends AbstractSelectTask {
- public SelectAllEdgesTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public SelectAllEdgesTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor tm) {
- final CyNetwork n = netmgr.getCurrentNetwork();
- final CyNetworkView v = netmgr.getNetworkView(n.getSUID());
- SelectUtils.setSelectedEdges(n.getEdgeList(), true);
-
- v.updateView();
+ SelectUtils.setSelectedEdges(net.getEdgeList(), true);
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllEdgesTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class SelectAllEdgesTaskFactory implements TaskFactory {
+public class SelectAllEdgesTaskFactory extends AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
@@ -44,6 +45,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new SelectAllEdgesTask(netmgr));
+ return new TaskIterator(new SelectAllEdgesTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -38,28 +38,17 @@
package org.cytoscape.task.internal.select;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
public class SelectAllNodesTask extends AbstractSelectTask {
- public SelectAllNodesTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public SelectAllNodesTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor tm) {
- final CyNetwork n = netmgr.getCurrentNetwork();
- final CyNetworkView v = netmgr.getNetworkView(n.getSUID());
- SelectUtils.setSelectedNodes(n.getNodeList(), true);
-
- v.updateView();
-
- System.out.println("All nodes of network \"" + n.getSUID()
- + "\" have been selected");
+ SelectUtils.setSelectedNodes(net.getNodeList(), true);
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllNodesTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class SelectAllNodesTaskFactory implements TaskFactory {
+public class SelectAllNodesTaskFactory extends AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
public SelectAllNodesTaskFactory(CyNetworkManager netmgr) {
@@ -43,6 +44,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new SelectAllNodesTask(netmgr));
+ return new TaskIterator(new SelectAllNodesTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -38,26 +38,18 @@
package org.cytoscape.task.internal.select;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
public class SelectAllTask extends AbstractSelectTask {
- public SelectAllTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public SelectAllTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor monitor) {
- CyNetwork n = netmgr.getCurrentNetwork();
- CyNetworkView v = netmgr.getNetworkView( n.getSUID() );
- SelectUtils.setSelectedNodes( n.getNodeList(), true);
- SelectUtils.setSelectedEdges( n.getEdgeList(), true);
-
- v.updateView();
+ SelectUtils.setSelectedNodes( net.getNodeList(), true);
+ SelectUtils.setSelectedEdges( net.getEdgeList(), true);
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectAllTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class SelectAllTaskFactory implements TaskFactory {
+public class SelectAllTaskFactory extends AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
@@ -44,6 +45,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new SelectAllTask(netmgr));
+ return new TaskIterator(new SelectAllTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -45,21 +45,17 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
public class SelectConnectedNodesTask extends AbstractSelectTask {
- public SelectConnectedNodesTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public SelectConnectedNodesTask(CyNetwork net, CyNetworkManager netmgr)
{
+ super(net,netmgr);
}
public void run(TaskMonitor tm) {
- final CyNetwork currentNetwork = netmgr.getCurrentNetwork();
- final CyNetworkView v =
netmgr.getNetworkView(currentNetwork.getSUID());
- final List<CyEdge> selectedEdges = CyTableUtil.getEdgesInState(
- currentNetwork, "selected", true);
+ final List<CyEdge> selectedEdges =
CyTableUtil.getEdgesInState(net, "selected", true);
final Set<CyNode> nodes = new HashSet<CyNode>();
for (CyEdge edge : selectedEdges) {
@@ -68,11 +64,6 @@
}
SelectUtils.setSelectedNodes(nodes, true);
-
- v.updateView();
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectConnectedNodesTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class SelectConnectedNodesTaskFactory implements TaskFactory {
+public class SelectConnectedNodesTaskFactory extends
AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
public SelectConnectedNodesTaskFactory(CyNetworkManager netmgr) {
@@ -43,6 +44,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new SelectConnectedNodesTask(netmgr));
+ return new TaskIterator(new
SelectConnectedNodesTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsNodeViewTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsNodeViewTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsNodeViewTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -36,6 +36,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
import java.util.Set;
import java.util.HashSet;
@@ -65,8 +66,4 @@
netView.updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -39,35 +39,24 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.session.CyNetworkManager;
public class SelectFirstNeighborsTask extends AbstractSelectTask {
- public SelectFirstNeighborsTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public SelectFirstNeighborsTask(CyNetwork net, CyNetworkManager netmgr)
{
+ super(net,netmgr);
}
@Override
public void run(TaskMonitor tm) {
- final CyNetwork currentNetwork = netmgr.getCurrentNetwork();
- final CyNetworkView view = netmgr.getNetworkView(currentNetwork
- .getSUID());
- final List<CyNode> selectedNodes = CyTableUtil.getNodesInState(
- currentNetwork, "selected", true);
+ final List<CyNode> selectedNodes =
CyTableUtil.getNodesInState(net, "selected", true);
final Set<CyNode> nodes = new HashSet<CyNode>();
for (CyNode currentNode : selectedNodes)
- nodes.addAll(currentNetwork.getNeighborList(currentNode,
- CyEdge.Type.ANY));
+ nodes.addAll(net.getNeighborList(currentNode,
CyEdge.Type.ANY));
SelectUtils.setSelectedNodes(nodes, true);
-
- view.updateView();
+ updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFirstNeighborsTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class SelectFirstNeighborsTaskFactory implements TaskFactory {
+public class SelectFirstNeighborsTaskFactory extends
AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
@@ -44,6 +45,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new SelectFirstNeighborsTask(netmgr));
+ return new TaskIterator(new
SelectFirstNeighborsTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTask.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -37,15 +37,13 @@
package org.cytoscape.task.internal.select;
-import org.cytoscape.session.CyNetworkManager;
//import cytoscape.data.Semantics;
-
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
+import org.cytoscape.session.CyNetworkManager;
import java.io.BufferedReader;
import java.io.FileReader;
@@ -60,8 +58,8 @@
@Tunable(description="Node selection file")
public File file;
- public SelectFromFileListTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public SelectFromFileListTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor tm) throws Exception {
@@ -69,8 +67,6 @@
if ( file == null )
throw new Exception("You must specify a file to load!");
- CyNetwork network = netmgr.getCurrentNetwork();
-
try {
FileReader fin = new FileReader(file);
BufferedReader bin = new BufferedReader(fin);
@@ -89,10 +85,10 @@
// loop through all the node of the graph
// selecting those in the file
- List<CyNode> nodeList = network.getNodeList();
+ List<CyNode> nodeList = net.getNodeList();
for ( CyNode node : nodeList ) {
- //List<String> synonyms =
Semantics.getAllSynonyms(node, network);
+ //List<String> synonyms =
Semantics.getAllSynonyms(node, net);
//for ( String syn : synonyms ) {
//if ( fileNodes.contains(syn) ) {
@@ -102,15 +98,10 @@
}
//}
}
+ updateView();
} catch (Exception e) {
throw new Exception("Error reading file: " +
file.getAbsolutePath(), e);
}
-
- netmgr.getNetworkView(network.getSUID()).updateView();
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTaskFactory.java
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/select/SelectFromFileListTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
@@ -33,9 +33,10 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class SelectFromFileListTaskFactory implements TaskFactory {
+public class SelectFromFileListTaskFactory extends AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
@@ -44,6 +45,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new SelectFromFileListTask(netmgr));
+ return new TaskIterator(new SelectFromFileListTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-09-23 23:07:36 UTC (rev 22041)
+++
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-09-23 23:50:19 UTC (rev 22042)
@@ -91,7 +91,7 @@
<!-- selection -->
<osgi:service id="selectAllTaskFactoryService"
ref="selectAllTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="Select all nodes and edges" />
<entry key="preferredMenu" value="Select" />
@@ -101,7 +101,7 @@
</osgi:service>
<osgi:service id="selectAllEdgesTaskFactoryService"
ref="selectAllEdgesTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="Select all edges" />
<entry key="preferredMenu" value="Select.Edges" />
@@ -111,7 +111,7 @@
</osgi:service>
<osgi:service id="selectAllNodesTaskFactoryService"
ref="selectAllNodesTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="Select all nodes" />
<entry key="preferredMenu" value="Select.Nodes" />
@@ -122,7 +122,7 @@
<osgi:service id="selectAdjacentEdgesTaskFactoryService"
ref="selectAdjacentEdgesTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="Select adjacent edges" />
<entry key="preferredMenu" value="Select.Edges" />
@@ -132,7 +132,7 @@
</osgi:service>
<osgi:service id="selectConnectedNodesTaskFactoryService"
ref="selectConnectedNodesTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="Nodes connected by selected
edges" />
<entry key="preferredMenu" value="Select.Nodes" />
@@ -142,7 +142,7 @@
</osgi:service>
<osgi:service id="selectFirstNeighborsTaskFactoryService"
ref="selectFirstNeighborsTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="First neighbors of selected
nodes" />
<entry key="preferredMenu" value="Select.Nodes" />
@@ -153,7 +153,7 @@
<osgi:service id="deselectAllTaskFactoryService"
ref="deselectAllTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="Deselect all nodes and edges"
/>
<entry key="preferredMenu" value="Select" />
@@ -163,7 +163,7 @@
</osgi:service>
<osgi:service id="deselectAllEdgesTaskFactoryService"
ref="deselectAllEdgesTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="Deselect all edges" />
<entry key="preferredMenu" value="Select.Edges" />
@@ -173,7 +173,7 @@
</osgi:service>
<osgi:service id="deselectAllNodesTaskFactoryService"
ref="deselectAllNodesTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="Deselect all nodes" />
<entry key="preferredMenu" value="Select.Nodes" />
@@ -183,7 +183,7 @@
</osgi:service>
<osgi:service id="invertSelectedEdgesTaskFactoryService"
ref="invertSelectedEdgesTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="Invert edge selection" />
<entry key="preferredMenu" value="Select.Edges" />
@@ -193,7 +193,7 @@
</osgi:service>
<osgi:service id="invertSelectedNodesTaskFactoryService"
ref="invertSelectedNodesTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="Invert node selection" />
<entry key="preferredMenu" value="Select.Nodes" />
@@ -203,7 +203,7 @@
</osgi:service>
<osgi:service id="selectFromFileListTaskFactoryService"
ref="selectFromFileListTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="From file..." />
<entry key="preferredMenu" value="Select.Nodes" />
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