Author: scooter
Date: 2010-01-30 18:17:38 -0800 (Sat, 30 Jan 2010)
New Revision: 19082
Modified:
cytoscape/trunk/src/cytoscape/CyMain.java
cytoscape/trunk/src/cytoscape/Cytoscape.java
cytoscape/trunk/src/cytoscape/data/readers/XGMMLReader.java
Log:
Group fixes
Modified: cytoscape/trunk/src/cytoscape/CyMain.java
===================================================================
--- cytoscape/trunk/src/cytoscape/CyMain.java 2010-01-30 06:08:39 UTC (rev
19081)
+++ cytoscape/trunk/src/cytoscape/CyMain.java 2010-01-31 02:17:38 UTC (rev
19082)
@@ -305,7 +305,7 @@
* For Mac: move menue bar to OS X default bar
(next to Apple
* icon)
*/
-
System.setProperty("apple.laf.useScreenMenuBar", "true");
+
System.setProperty("apple.laf.useScreenMenuBar", "true");
} else {
/*
Modified: cytoscape/trunk/src/cytoscape/Cytoscape.java
===================================================================
--- cytoscape/trunk/src/cytoscape/Cytoscape.java 2010-01-30 06:08:39 UTC
(rev 19081)
+++ cytoscape/trunk/src/cytoscape/Cytoscape.java 2010-01-31 02:17:38 UTC
(rev 19082)
@@ -79,6 +79,8 @@
import cytoscape.ding.DingNetworkView;
import cytoscape.giny.CytoscapeFingRootGraph;
import cytoscape.giny.CytoscapeRootGraph;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupManager;
import cytoscape.init.CyInitParams;
import cytoscape.layout.CyLayoutAlgorithm;
import cytoscape.layout.CyLayouts;
@@ -716,14 +718,19 @@
if (create && attribute instanceof String &&
attribute.equals(Semantics.INTERACTION)) {
// create the edge
- CyEdge edge = (CyEdge) Cytoscape.getRootGraph()
-
.getEdge(Cytoscape.getRootGraph()
-
.createEdge(source, target));
+ int rootEdge =
Cytoscape.getRootGraph().createEdge(source, target);
+ // System.out.println("Created edge: "+rootEdge+"from
"+source.getRootGraphIndex()+" to "+target.getRootGraphIndex());
+ //CyEdge edge = (CyEdge) Cytoscape.getRootGraph()
+ //
.getEdge(Cytoscape.getRootGraph()
+ //
.createEdge(source, target));
+ CyEdge edge = (CyEdge)
Cytoscape.getRootGraph().getEdge(rootEdge);
+
// create the edge id
String edge_name =
CyEdge.createIdentifier(source.getIdentifier(),
(String)
attribute_value,
target.getIdentifier());
+ // System.out.println("Setting ID for edge:
"+edge_name);
edge.setIdentifier(edge_name);
edgeAttributes.setAttribute(edge_name,
Semantics.INTERACTION, (String) attribute_value);
@@ -1865,6 +1872,12 @@
* Clear all networks and attributes and start a new session.
*/
public static void createNewSession() {
+ // Clear groups
+ List<CyGroup>groups = CyGroupManager.getGroupList();
+ for (CyGroup group: groups) {
+ CyGroupManager.removeGroup(group);
+ }
+
// Destroy all networks
Set<CyNetwork> netSet = getNetworkSet();
Modified: cytoscape/trunk/src/cytoscape/data/readers/XGMMLReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/XGMMLReader.java 2010-01-30
06:08:39 UTC (rev 19081)
+++ cytoscape/trunk/src/cytoscape/data/readers/XGMMLReader.java 2010-01-31
02:17:38 UTC (rev 19082)
@@ -688,6 +688,7 @@
CyGroup newGroup = null;
String viewer = null;
+
for (CyNode groupNode : groupMap.keySet()) {
List<CyNode> childList =
groupMap.get(groupNode);
viewer =
nodeAttributes.getStringAttribute(groupNode.getIdentifier(),
CyGroup.GROUP_VIEWER_ATTR);
@@ -718,7 +719,7 @@
}
}
- if (view == Cytoscape.getNullNetworkView())
+ if (view == null || view == Cytoscape.getNullNetworkView())
return;
// Apply visual style before updateView().
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