Author: mes
Date: 2010-09-23 17:16:42 -0700 (Thu, 23 Sep 2010)
New Revision: 22043
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/AbstractCreationTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewEmptyNetworkTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTaskFactory.java
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
Log:
removed more getCurrentNetworks
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/AbstractCreationTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/AbstractCreationTask.java
2010-09-23 23:50:19 UTC (rev 22042)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/AbstractCreationTask.java
2010-09-24 00:16:42 UTC (rev 22043)
@@ -31,15 +31,19 @@
import org.cytoscape.session.CyNetworkManager;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
+// net can be null, so don't use AbstractNetworkTask
public abstract class AbstractCreationTask extends AbstractTask {
protected CyNetworkManager netmgr;
+ protected CyNetwork net;
- public AbstractCreationTask(CyNetworkManager netmgr) {
+ public AbstractCreationTask(CyNetwork net, CyNetworkManager netmgr) {
+ this.net = net;
this.netmgr = netmgr;
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2010-09-23 23:50:19 UTC (rev 22042)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2010-09-24 00:16:42 UTC (rev 22043)
@@ -50,16 +50,16 @@
public class CloneNetworkTask extends AbstractCreationTask {
- public CloneNetworkTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public CloneNetworkTask(CyNetwork net, CyNetworkManager netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor e) {
// TODO
System.out.println("NOT implemented");
/*
- CyNetwork origNet = Cytoscape.getCurrentNetwork();
- CyNetworkView origView = Cytoscape.getCurrentNetworkView();
+ CyNetwork origNet = net;
+ CyNetworkView origView = netmgr.getNetworkView(net.getSUID());
VisualStyle vs =
Cytoscape.getVisualMappingManager().getVisualStyle();
CyNetwork new_network =
Cytoscape.createNetwork(origNet.getNodeList(),
@@ -104,8 +104,4 @@
}
*/
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTaskFactory.java
2010-09-24 00:16:42 UTC (rev 22043)
@@ -33,17 +33,18 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class CloneNetworkTaskFactory implements TaskFactory {
+public class CloneNetworkTaskFactory extends AbstractNetworkTaskFactory {
- private CyNetworkManager netmgr;
+ private final CyNetworkManager netmgr;
public CloneNetworkTaskFactory(CyNetworkManager netmgr) {
this.netmgr = netmgr;
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new CloneNetworkTask(netmgr));
+ return new TaskIterator(new CloneNetworkTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
2010-09-23 23:50:19 UTC (rev 22042)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
2010-09-24 00:16:42 UTC (rev 22043)
@@ -67,8 +67,4 @@
taskMonitor.setStatusMessage("Network view successfully create
for: "
+ net.attrs().get("name", String.class));
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewEmptyNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewEmptyNetworkTask.java
2010-09-23 23:50:19 UTC (rev 22042)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewEmptyNetworkTask.java
2010-09-24 00:16:42 UTC (rev 22043)
@@ -56,7 +56,7 @@
private final CyNetworkViewFactory cnvf;
public NewEmptyNetworkTask(CyNetworkFactory cnf, CyNetworkViewFactory
cnvf, CyNetworkManager netmgr) {
- super(netmgr);
+ super(null,netmgr);
this.cnf = cnf;
this.cnvf = cnvf;
}
@@ -69,8 +69,4 @@
netmgr.addNetwork(newNet);
netmgr.addNetworkView(view);
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTask.java
2010-09-23 23:50:19 UTC (rev 22042)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTask.java
2010-09-24 00:16:42 UTC (rev 22043)
@@ -56,16 +56,16 @@
public class NewNetworkSelectedNodesEdgesTask extends AbstractCreationTask {
- public NewNetworkSelectedNodesEdgesTask(CyNetworkManager netmgr) {
- super(netmgr);
+ public NewNetworkSelectedNodesEdgesTask(CyNetwork net, CyNetworkManager
netmgr) {
+ super(net,netmgr);
}
public void run(TaskMonitor tm) {
//TODO
System.out.println("NOT implemented");
/*
- CyNetwork current_network = Cytoscape.getCurrentNetwork();
- CyNetworkView current_network_view = Cytoscape.getCurrentNetworkView();
+ CyNetwork current_network = net;
+ CyNetworkView current_network_view =
netmgr.getNetworkView(net.getSUID());
if ((current_network == null) || (current_network ==
Cytoscape.getNullNetwork()))
return;
@@ -103,8 +103,4 @@
vmm.setVisualStyle(vsName);
*/
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesEdgesTaskFactory.java
2010-09-24 00:16:42 UTC (rev 22043)
@@ -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 NewNetworkSelectedNodesEdgesTaskFactory implements TaskFactory {
+public class NewNetworkSelectedNodesEdgesTaskFactory extends
AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
@@ -44,6 +45,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new
NewNetworkSelectedNodesEdgesTask(netmgr));
+ return new TaskIterator(new
NewNetworkSelectedNodesEdgesTask(net,netmgr));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTask.java
2010-09-23 23:50:19 UTC (rev 22042)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTask.java
2010-09-24 00:16:42 UTC (rev 22043)
@@ -70,11 +70,11 @@
private final VisualMappingManager vmm;
private final CyNetworkNaming cyNetworkNaming;
- public NewNetworkSelectedNodesOnlyTask(final CyRootNetworkFactory
cyroot,
+ public NewNetworkSelectedNodesOnlyTask(final CyNetwork net, final
CyRootNetworkFactory cyroot,
final CyNetworkViewFactory cnvf, final CyNetworkManager
netmgr,
final CyNetworkNaming cyNetworkNaming,
final VisualMappingManager vmm) {
- super(netmgr);
+ super(net,netmgr);
this.cyroot = cyroot;
this.cnvf = cnvf;
this.cyNetworkNaming = cyNetworkNaming;
@@ -83,7 +83,7 @@
public void run(TaskMonitor tm) {
- CyNetwork current_network = netmgr.getCurrentNetwork();
+ CyNetwork current_network = net;
if (current_network == null)
return;
@@ -147,8 +147,4 @@
vmm.setVisualStyle(newVS, new_view);
}
}
-
- @Override
- public void cancel() {
- }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTaskFactory.java
2010-09-23 23:50:19 UTC (rev 22042)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/NewNetworkSelectedNodesOnlyTaskFactory.java
2010-09-24 00:16:42 UTC (rev 22043)
@@ -37,9 +37,10 @@
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.task.AbstractNetworkTaskFactory;
-public class NewNetworkSelectedNodesOnlyTaskFactory implements TaskFactory {
+public class NewNetworkSelectedNodesOnlyTaskFactory extends
AbstractNetworkTaskFactory {
private CyNetworkManager netmgr;
private CyRootNetworkFactory crnf;
@@ -59,6 +60,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new
NewNetworkSelectedNodesOnlyTask(crnf, cnvf, netmgr, naming, vmm));
+ return new TaskIterator(new
NewNetworkSelectedNodesOnlyTask(net,crnf, cnvf, netmgr, naming, vmm));
}
}
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 23:50:19 UTC (rev 22042)
+++
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-09-24 00:16:42 UTC (rev 22043)
@@ -285,7 +285,7 @@
<osgi:service id="newNetworkSelectedNodesEdgesTaskFactoryService"
ref="newNetworkSelectedNodesEdgesTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="From selected nodes, selected
edges" />
<entry key="preferredMenu" value="File.New.Network" />
@@ -296,7 +296,7 @@
<osgi:service id="newNetworkSelectedNodesOnlyTaskFactoryService"
ref="newNetworkSelectedNodesOnlyTaskFactory"
- interface="org.cytoscape.work.TaskFactory">
+ interface="org.cytoscape.task.NetworkTaskFactory">
<osgi:service-properties>
<entry key="title" value="From selected nodes, all
edges" />
<entry key="preferredMenu" value="File.New.Network" />
@@ -305,6 +305,16 @@
</osgi:service-properties>
</osgi:service>
+ <osgi:service id="cloneNetworkTaskFactoryService"
+ ref="cloneNetworkTaskFactory"
+ interface="org.cytoscape.task.NetworkTaskFactory">
+ <osgi:service-properties>
+ <entry key="title" value="Clone Current Network" />
+ <entry key="preferredMenu" value="File.New.Network" />
+ <entry key="enableFor" value="selectedNetworkObjs" />
+ </osgi:service-properties>
+ </osgi:service>
+
<!-- destruction -->
<osgi:service id="destroyNetworkTaskFactoryService"
ref="destroyNetworkTaskFactory"
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