Author: pwang
Date: 2012-06-01 17:11:46 -0700 (Fri, 01 Jun 2012)
New Revision: 29429
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePaths.java
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePathsFinder.java
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePathsTaskFactory.java
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/Component.java
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ComponentFinder.java
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/CyActivator.java
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ServicesUtil.java
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/util/SelectUtil.java
Log:
Updated because of the change of API
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
2012-06-01 23:07:03 UTC (rev 29428)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
2012-06-02 00:11:46 UTC (rev 29429)
@@ -15,8 +15,8 @@
import csplugins.jActiveModules.dialogs.ActivePathsParameterPanel;
import org.cytoscape.application.CyApplicationManager;
-import org.cytoscape.application.events.CytoscapeStartEvent;
-import org.cytoscape.application.events.CytoscapeStartListener;
+import org.cytoscape.application.events.CyStartEvent;
+import org.cytoscape.application.events.CyStartListener;
import org.cytoscape.application.swing.AbstractCyAction;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.application.swing.CytoPanel;
@@ -26,9 +26,9 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.property.CyProperty;
-import org.cytoscape.task.creation.LoadVisualStyles;
+//import org.cytoscape.task.creation.LoadVisualStyles;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -56,12 +56,12 @@
private final CytoPanel cytoPanelWest;
private static final Logger logger =
LoggerFactory.getLogger(ActiveModulesUI.class);
- private CyHelpBrokerImpl cyHelpBroker = new CyHelpBrokerImpl();
+ //private CyHelpBrokerImpl cyHelpBroker = new CyHelpBrokerImpl();
public ActiveModulesUI(ActivePathFinderParameters apfParams,
ActivePathsParameterPanel mainPanel) {
- super("jActiveModules...",
ServicesUtil.cyApplicationManagerServiceRef);
+ super("jActiveModules...",
ServicesUtil.cyApplicationManagerServiceRef, "network",
ServicesUtil.cyNetworkViewManagerServiceRef);
setPreferredMenu("Plugins.jActiveModules");
//setMenuGravity(2.0f);
@@ -114,7 +114,7 @@
try {
helpSetURL = HelpSet.findHelpSet(classLoader,
HELP_SET_NAME);
final HelpSet newHelpSet = new HelpSet(classLoader,
helpSetURL);
- cyHelpBroker.getHelpSet().add(newHelpSet);
+ //cyHelpBroker.getHelpSet().add(newHelpSet);
} catch (final Exception e) {
logger.warn("Could not find help set: \"" +
HELP_SET_NAME + "!");
}
@@ -194,7 +194,7 @@
// t.start();
ActivePathsTaskFactory factory = new
ActivePathsTaskFactory(activePaths);
- ServicesUtil.taskManagerServiceRef.execute(factory);
+
ServicesUtil.taskManagerServiceRef.execute(factory.createTaskIterator());
}
/**
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePaths.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePaths.java
2012-06-01 23:07:03 UTC (rev 29428)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePaths.java
2012-06-02 00:11:46 UTC (rev 29429)
@@ -49,6 +49,7 @@
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import csplugins.jActiveModules.ServicesUtil;
+import java.io.File;
//-----------------------------------------------------------------------------------
@@ -188,7 +189,7 @@
//activePaths = apf.findActivePaths();
ActivePathsTaskFactory factory = new
ActivePathsTaskFactory(apf);
- ServicesUtil.synchronousTaskManagerServiceRef.execute(factory);
+
ServicesUtil.synchronousTaskManagerServiceRef.execute(factory.createTaskIterator());
activePaths = new Component[activePathsVect.size()];
for (int i=0; i< activePathsVect.size(); i++){
@@ -220,13 +221,13 @@
taskMonitor.setStatusMessage("Create an overview network for
all nested network...");
//2. create an overview network for all nested network
- final CyNetwork overview =
ServicesUtil.cyNetworkFactoryServiceRef.getInstance();
- overview.getCyRow().set("name", "jActiveModules Search Result
"+ runCount++);
+ final CyNetwork overview =
ServicesUtil.cyNetworkFactoryServiceRef.createNetwork();
+ overview.getRow(overview).set("name", "jActiveModules Search
Result "+ runCount++);
Set<CyNode> path_nodes = new HashSet<CyNode>();
for (int i=0; i< subnetworks.length; i++){
CyNode newNode = overview.addNode();
//Cytoscape.getCyNode(subnetworks[i].getTitle(), true);
- newNode.getCyRow().set("name",
subnetworks[i].getCyRow().get("name", String.class));
+ overview.getRow(newNode).set("name",
subnetworks[i].getRow(subnetworks[i]).get("name", String.class));
path_nodes.add(newNode);
newNode.setNetworkPointer(subnetworks[i]);
// create an attribute for this new node
@@ -235,7 +236,7 @@
if
(overview.getDefaultNodeTable().getColumn(NODE_SCORE)== null){
overview.getDefaultNodeTable().createColumn(NODE_SCORE, Double.class, false);
}
- newNode.getCyRow().set(NODE_SCORE, new
Double(activePaths[i].getScore()));
+ overview.getRow(newNode).set(NODE_SCORE, new
Double(activePaths[i].getScore()));
}
ServicesUtil.cyNetworkManagerServiceRef.addNetwork(overview);
@@ -265,13 +266,13 @@
aEdge.getTarget().getNetworkPointer().getNodeCount());
//cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
"jActiveModules_nodeCount_min_two", minNodeCount);
-
aEdge.getCyRow().set("jActiveModules_nodeCount_min_two", minNodeCount);
+
overview.getRow(aEdge).set("jActiveModules_nodeCount_min_two", minNodeCount);
//cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
"jActiveModules_nodeOverlapCount", NumberOfSharedNodes);
- aEdge.getCyRow().set("jActiveModules_nodeOverlapCount",
NumberOfSharedNodes);
+
overview.getRow(aEdge).set("jActiveModules_nodeOverlapCount",
NumberOfSharedNodes);
double overlapScore =
(double)NumberOfSharedNodes/minNodeCount;
//cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
EDGE_SCORE, overlapScore);
- aEdge.getCyRow().set(EDGE_SCORE, overlapScore);
+ overview.getRow(aEdge).set(EDGE_SCORE, overlapScore);
}
taskMonitor.setProgress(0.8);
@@ -279,12 +280,15 @@
//4. Create a view for overview network and apply visual style
//Cytoscape.createNetworkView(overview,
overview.getIdentifier(), tuning(), null);
- final CyNetworkView newView =
ServicesUtil.cyNetworkViewFactoryServiceRef.getNetworkView(overview);
+ final CyNetworkView newView =
ServicesUtil.cyNetworkViewFactoryServiceRef.createNetworkView(overview);
ServicesUtil.cyNetworkViewManagerServiceRef.addNetworkView(newView);
// Apply layout for overview
- layoutAlgorithm.setNetworkView(newView);
-
this.insertTasksAfterCurrentTask(layoutAlgorithm.getTaskIterator());
+// layoutAlgorithm.setNetworkView(newView);
+//
this.insertTasksAfterCurrentTask(layoutAlgorithm.getTaskIterator());
+ Object context = layoutAlgorithm.getDefaultLayoutContext();
+
insertTasksAfterCurrentTask(layoutAlgorithm.createTaskIterator(newView,
context, CyLayoutAlgorithm.ALL_NODE_VIEWS,""));
+
// this.visualMappingManager.setVisualStyle(overviewVS, newView);
// newView.updateView();
@@ -305,11 +309,12 @@
}
for (int i=0; i<n; i++){
- CyNetworkView theView =
ServicesUtil.cyNetworkViewFactoryServiceRef.getNetworkView(subnetworks[i]);
+ CyNetworkView theView =
ServicesUtil.cyNetworkViewFactoryServiceRef.createNetworkView(subnetworks[i]);
ServicesUtil.cyNetworkViewManagerServiceRef.addNetworkView(theView);
- layoutAlgorithm.setNetworkView(theView);
-
this.insertTasksAfterCurrentTask(layoutAlgorithm.getTaskIterator());
+// layoutAlgorithm.setNetworkView(theView);
+//
this.insertTasksAfterCurrentTask(layoutAlgorithm.getTaskIterator());
+
insertTasksAfterCurrentTask(layoutAlgorithm.createTaskIterator(theView,
context, CyLayoutAlgorithm.ALL_NODE_VIEWS,""));
//
this.visualMappingManager.setVisualStyle(moduleVS, theView);
// theView.updateView();
@@ -395,7 +400,7 @@
CySubNetwork[] subnetworks2 = new
CySubNetwork[activePaths.length];
- CyRootNetwork rootNetwork =
ServicesUtil.cyRootNetworkFactory.convert(cyNetwork);
+ CyRootNetwork rootNetwork =
ServicesUtil.cyRootNetworkFactory.getRootNetwork(cyNetwork);
for (int i = 0; i < activePaths.length; i++) {
Component thePath = activePaths[i];
@@ -421,7 +426,7 @@
//subnetworks[i] = Cytoscape.createNetwork(nodeSet,
edgeSet, pathName, cyNetwork, false);
subnetworks2[i] = rootNetwork.addSubNetwork(nodeSet,
edgeSet);
- subnetworks2[i].getCyRow().set("name", pathName);
+ subnetworks2[i].getRow(subnetworks2[i]).set("name",
pathName);
// if(i < MAX_NETWORK_VIEWS) {
// //final CyNetworkView moduleView =
Cytoscape.createNetworkView(subnetworks[i], subnetworks[i].getTitle(),
tuning());
@@ -475,7 +480,7 @@
final Double[][] attribValues = new
Double[attrNames.length][geneList.size()];
final Map<String, Integer> geneNameToIndexMap = new
HashMap<String, Integer>();
for (int i = 0; i < geneList.size(); i++) {
- final String geneName =
geneList.get(i).getCyRow().get("name", String.class); //.getIdentifier();
+ final String geneName =
this.cyNetwork.getRow(geneList.get(i)).get("name", String.class);
//.getIdentifier();
geneNameToIndexMap.put(geneName, new Integer(i));
for (int j = 0; j < attrNames.length; j++)
@@ -503,7 +508,7 @@
CyNode shuffle = shuffledList.get(i);
// If randomizing, you'll get p-values for a different
gene.
- String canonicalName = shuffle.getCyRow().get("name",
String.class); //.getIdentifier();
+ String canonicalName =
this.cyNetwork.getRow(shuffle).get("name", String.class); //.getIdentifier();
double[] tempArray = new double[attrNames.length];
for (int j = 0; j < attrNames.length; j++) {
@@ -514,12 +519,12 @@
double sigValue = d.doubleValue();
if (sigValue < MIN_SIG) {
sigValue = MIN_SIG;
- logger.warn("Warning: value for
" + current.getCyRow().get("name", String.class)+ //.getIdentifier() +
+ logger.warn("Warning: value for
" + this.cyNetwork.getRow(current).get("name", String.class)+
//.getIdentifier() +
" (" +
canonicalName + ") adjusted to " + MIN_SIG);
}
if (sigValue > MAX_SIG) {
sigValue = MAX_SIG;
- logger.warn("Warning: value for
" + current.getCyRow().get("name", String.class)+ //.getIdentifier() +
+ logger.warn("Warning: value for
" + this.cyNetwork.getRow(current).get("name", String.class)+
//.getIdentifier() +
" (" +
canonicalName + ") adjusted to " + MAX_SIG);
}
@@ -663,18 +668,21 @@
Iterator<CyNode> it =
this.cyNetwork.getNodeList().iterator();
while (it.hasNext()){
CyNode node = it.next();
- node.getCyRow().set(CyNetwork.SELECTED, false);
+
this.cyNetwork.getRow(node).set(CyNetwork.SELECTED, false);
}
}
//filter.setSelectedNodes(activePath.getDisplayNodesGeneric(),
true);
Iterator<CyNode> it2 =
activePath.getDisplayNodesGeneric().iterator();
while (it2.hasNext()){
CyNode node2 = it2.next();
- node2.getCyRow().set(CyNetwork.SELECTED, true);
+ this.cyNetwork.getRow(node2).set(CyNetwork.SELECTED,
true);
}
// cyNetwork.setFlaggedNodes(activePath.getNodes(),true);
-
ServicesUtil.cyNetworkViewManagerServiceRef.getNetworkView(ServicesUtil.cyApplicationManagerServiceRef.getCurrentNetwork().getSUID()).updateView();
+
+ Collection<CyNetworkView> views =
ServicesUtil.cyNetworkViewManagerServiceRef.getNetworkViews(ServicesUtil.cyApplicationManagerServiceRef.getCurrentNetwork());
+ Iterator<CyNetworkView> it = views.iterator();
+ it.next().updateView();
//Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
}
//
------------------------------------------------------------------------------
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePathsFinder.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePathsFinder.java
2012-06-01 23:07:03 UTC (rev 29428)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePathsFinder.java
2012-06-02 00:11:46 UTC (rev 29429)
@@ -440,7 +440,7 @@
//gst.start();
//threadVector.add(gst);
ActivePathsTaskFactory factory = new
ActivePathsTaskFactory(gst);
-
ServicesUtil.synchronousTaskManagerServiceRef.execute(factory);
+
ServicesUtil.synchronousTaskManagerServiceRef.execute(factory.createTaskIterator());
}
// // wait for the threads to finish
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePathsTaskFactory.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePathsTaskFactory.java
2012-06-01 23:07:03 UTC (rev 29428)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePathsTaskFactory.java
2012-06-02 00:11:46 UTC (rev 29429)
@@ -1,18 +1,18 @@
package csplugins.jActiveModules;
import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.AbstractTaskFactory;
import org.cytoscape.work.Task;
-public class ActivePathsTaskFactory implements TaskFactory {
+public class ActivePathsTaskFactory extends AbstractTaskFactory {
private Task task;
public ActivePathsTaskFactory(Task task){
this.task = task;
}
- public TaskIterator getTaskIterator() {
+ public TaskIterator createTaskIterator() {
return new TaskIterator(task);
}
}
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/Component.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/Component.java
2012-06-01 23:07:03 UTC (rev 29428)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/Component.java
2012-06-02 00:11:46 UTC (rev 29429)
@@ -583,12 +583,14 @@
}
}
- public String [] getNodeNames(){
+ public String [] getNodeNames(CyNetwork network){
String [] result = new String[nodes.size()];
Iterator it = displayNodes.iterator();
for(int i=0;i<result.length;i++){
- //result[i] =
(String)Cytoscape.getNodeAttributeValue((Node)it.next(),Semantics.CANONICAL_NAME);
- result[i] = ((CyNode)it.next()).getCyRow().get("name", String.class);
//.getIdentifier();
+ //result[i] =
(String)Cytoscape.getNodeAttributeValue((Node)it.next(),Semantics.CANONICAL_NAME);
+ //result[i] = ((CyNode)it.next()).getCyRow().get("name",
String.class); //.getIdentifier();
+ CyNode node = (CyNode)it.next();
+ result[i] = network.getDefaultNodeTable().getRow(node).get("name",
String.class);
}
return result;
@@ -664,7 +666,7 @@
CyNode current = (CyNode)nodeIt.next();
tempComponent.addNode(current);
double new_score = tempComponent.getScore();
- node2Increase.put(current.getIndex()
/*.getRootGraphIndex()*/,new_score-previous_score);
+
node2Increase.put(current.getSUID().intValue()/*.getRootGraphIndex()*/,new_score-previous_score);
tempComponent.removeNode(current);
}
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ComponentFinder.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ComponentFinder.java
2012-06-01 23:07:03 UTC (rev 29428)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ComponentFinder.java
2012-06-02 00:11:46 UTC (rev 29429)
@@ -72,7 +72,7 @@
//call back to postVisit after it is done searching any node. This is
//where we will update the status of that node
if(!valid.contains(nodes.get(start))){
- throw new RuntimeException("Starting node for a component search was
not present in the graph, this is an ActiveModules
bug."+((CyNode)nodes.get(start)).getCyRow().get("name", String.class));
//.getIdentifier());
+ throw new RuntimeException("Starting node for a component search was
not present in the graph, this is an ActiveModules
bug."/*((CyNode)nodes.get(start)).getCyRow().get("name", String.class)*/);
//.getIdentifier());
}
search((CyNode)nodes.get(start));
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/CyActivator.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/CyActivator.java
2012-06-01 23:07:03 UTC (rev 29428)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/CyActivator.java
2012-06-02 00:11:46 UTC (rev 29429)
@@ -4,7 +4,7 @@
import org.cytoscape.work.TaskManager;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.property.CyProperty;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -20,13 +20,11 @@
import org.osgi.framework.BundleContext;
import org.cytoscape.service.util.AbstractCyActivator;
-import org.cytoscape.task.creation.LoadVisualStyles;
-
+import org.cytoscape.task.read.LoadVizmapFileTaskFactory;
import java.util.Properties;
import csplugins.jActiveModules.dialogs.ActivePathsParameterPanel;
import csplugins.jActiveModules.data.ActivePathFinderParameters;
-import org.cytoscape.util.swing.NetworkSelectorPanel;
-import org.cytoscape.task.creation.LoadVisualStyles;
+import csplugins.jActiveModules.util.swing.NetworkSelectorPanel;
public class CyActivator extends AbstractCyActivator {
public CyActivator() {
@@ -49,11 +47,11 @@
VisualMappingManager visualMappingManagerRef =
getService(bc,VisualMappingManager.class);
CyNetworkFactory cyNetworkFactoryServiceRef =
getService(bc,CyNetworkFactory.class);
- CyRootNetworkFactory cyRootNetworkFactory =
getService(bc,CyRootNetworkFactory.class);
+ CyRootNetworkManager cyRootNetworkFactory =
getService(bc,CyRootNetworkManager.class);
CyNetworkViewFactory cyNetworkViewFactoryServiceRef =
getService(bc,CyNetworkViewFactory.class);
CyLayoutAlgorithmManager cyLayoutsServiceRef =
getService(bc,CyLayoutAlgorithmManager.class);
- LoadVisualStyles loadVizmapFileTaskFactory =
getService(bc,LoadVisualStyles.class);
+ LoadVizmapFileTaskFactory loadVizmapFileTaskFactory =
getService(bc,LoadVizmapFileTaskFactory.class);
SynchronousTaskManager synchronousTaskManagerServiceRef =
getService(bc,SynchronousTaskManager.class);
//
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ServicesUtil.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ServicesUtil.java
2012-06-01 23:07:03 UTC (rev 29428)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ServicesUtil.java
2012-06-02 00:11:46 UTC (rev 29429)
@@ -7,10 +7,10 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.property.CyProperty;
import org.cytoscape.service.util.CyServiceRegistrar;
-import org.cytoscape.task.creation.LoadVisualStyles;
+import org.cytoscape.task.read.LoadVizmapFileTaskFactory;
//import org.cytoscape.task.creation.LoadVisualStylesFromFileFactory;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -36,11 +36,11 @@
public static VisualMappingManager visualMappingManagerRef;
public static CyNetworkFactory cyNetworkFactoryServiceRef;
- public static CyRootNetworkFactory cyRootNetworkFactory;
+ public static CyRootNetworkManager cyRootNetworkFactory;
public static CyNetworkViewFactory cyNetworkViewFactoryServiceRef;
public static CyLayoutAlgorithmManager cyLayoutsServiceRef;
- public static LoadVisualStyles loadVizmapFileTaskFactory;
+ public static LoadVizmapFileTaskFactory loadVizmapFileTaskFactory;
public static SynchronousTaskManager synchronousTaskManagerServiceRef;
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
2012-06-01 23:07:03 UTC (rev 29428)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
2012-06-02 00:11:46 UTC (rev 29429)
@@ -69,8 +69,7 @@
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTable;
//import cytoscape.view.CyHelpBroker;
-import org.cytoscape.util.swing.NetworkSelectorPanel;
-
+import csplugins.jActiveModules.util.swing.NetworkSelectorPanel;
import java.awt.Component;
import javax.swing.table.TableColumn;
import javax.swing.JComboBox;
@@ -178,7 +177,7 @@
private NetworkSelectorPanel networkPanel;
//private final CySwingApplication cySwingApplicationServiceRef;
- private CyHelpBrokerImpl cyHelpBroker = new CyHelpBrokerImpl();
+ //private CyHelpBrokerImpl cyHelpBroker = new CyHelpBrokerImpl();
//
-----------------------------------------------------------------------------
public ActivePathsParameterPanel(ActivePathFinderParameters
incomingApfParams,NetworkSelectorPanel networkSelectorPanel){
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/util/SelectUtil.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/util/SelectUtil.java
2012-06-01 23:07:03 UTC (rev 29428)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/util/SelectUtil.java
2012-06-02 00:11:46 UTC (rev 29429)
@@ -8,20 +8,21 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
-import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyTable;
public class SelectUtil {
public static Set<CyNode> getSelectedNodes(CyNetwork cyNetwork) {
- return getSelected(cyNetwork.getNodeList());
+ return getSelected(cyNetwork.getNodeList(), cyNetwork);
}
- static <T extends CyTableEntry> Set<T> getSelected(Collection<T> items)
{
+ static <T extends CyIdentifiable> Set<T> getSelected(Collection<T>
items, CyNetwork network) {
Set<T> entries = new HashSet<T>();
for (T item : items) {
- CyRow row = item.getCyRow();
+ //CyRow row = item.getCyRow();
+ CyRow row = network.getRow(item);
if (row.get(CyNetwork.SELECTED, Boolean.class)) {
entries.add(item);
}
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