Author: scooter
Date: 2011-06-24 23:09:03 -0700 (Fri, 24 Jun 2011)
New Revision: 25941
Modified:
cytoscape/trunk/application/src/main/java/cytoscape/data/readers/XGMMLParser.java
cytoscape/trunk/application/src/main/java/cytoscape/data/readers/XGMMLReader.java
cytoscape/trunk/application/src/main/java/cytoscape/data/writers/XGMMLWriter.java
Log:
Some fixes to handle complex group cases.
Modified:
cytoscape/trunk/application/src/main/java/cytoscape/data/readers/XGMMLParser.java
===================================================================
---
cytoscape/trunk/application/src/main/java/cytoscape/data/readers/XGMMLParser.java
2011-06-25 04:38:44 UTC (rev 25940)
+++
cytoscape/trunk/application/src/main/java/cytoscape/data/readers/XGMMLParser.java
2011-06-25 06:09:03 UTC (rev 25941)
@@ -153,6 +153,7 @@
private HashMap<String,CyNode> idMap = null;
/* Map of group nodes to children */
private HashMap<CyNode,List<CyNode>> groupMap = null;
+ private HashMap<CyNode,List<CyEdge>> groupEdgeMap = null;
/* List of nodes we weren't able to resolve */
private HashMap<CyNode, CyEdge> unresolvedNodeMap = null;
/* List of edges we weren't able to resolve */
@@ -623,7 +624,11 @@
return groupMap;
}
+ HashMap<CyNode, List<CyEdge>> getGroupEdgeMap() {
+ return groupEdgeMap;
+ }
+
void setMetaData(CyNetwork network) {
MetadataParser mdp = new MetadataParser(network);
if (RDFType != null)
@@ -972,6 +977,13 @@
} else if (sourceAlias != null && targetAlias != null) {
currentEdge = createEdge(sourceAlias,
targetAlias, interaction, label);
}
+
+ // If we're part of a group, this edge needs to be
remembered as (possibly) an
+ // inner or outer edge
+ if (currentGroupNode != null) {
+ List<CyEdge> groupEdges =
groupEdgeMap.get(currentGroupNode);
+ groupEdges.add(currentEdge);
+ }
return current;
}
@@ -1024,9 +1036,11 @@
class handleGroup implements Handler {
public ParseState handle(String tag, Attributes atts,
ParseState current) throws SAXException {
if (groupMap == null) groupMap = new HashMap<CyNode,
List<CyNode>>();
+ if (groupEdgeMap == null) groupEdgeMap = new
HashMap<CyNode, List<CyEdge>>();
if (currentGroupNode != null)
groupStack.push(currentGroupNode);
currentGroupNode = currentNode;
groupMap.put(currentGroupNode, new ArrayList<CyNode>());
+ groupEdgeMap.put(currentGroupNode, new
ArrayList<CyEdge>());
// logger.debug("Found group: "+currentNode);
return current;
}
Modified:
cytoscape/trunk/application/src/main/java/cytoscape/data/readers/XGMMLReader.java
===================================================================
---
cytoscape/trunk/application/src/main/java/cytoscape/data/readers/XGMMLReader.java
2011-06-25 04:38:44 UTC (rev 25940)
+++
cytoscape/trunk/application/src/main/java/cytoscape/data/readers/XGMMLReader.java
2011-06-25 06:09:03 UTC (rev 25941)
@@ -714,6 +714,7 @@
// we don't create views by default, but groups should still
// exist even when we don't create the view
Map<CyNode,List<CyNode>>groupMap = parser.getGroupMap();
+ Map<CyNode,List<CyEdge>>groupEdgeMap = parser.getGroupEdgeMap();
if (groupMap != null) {
CyAttributes nodeAttributes =
Cytoscape.getNodeAttributes();
@@ -722,6 +723,8 @@
for (CyNode groupNode : groupMap.keySet()) {
List<CyNode> childList =
groupMap.get(groupNode);
+ List<CyEdge> edgeList =
groupEdgeMap.get(groupNode);
+
viewer =
nodeAttributes.getStringAttribute(groupNode.getIdentifier(),
CyGroup.GROUP_VIEWER_ATTR);
CyGroupViewer groupViewer =
CyGroupManager.getGroupViewer(viewer);
boolean isLocal = false;
@@ -758,6 +761,14 @@
if (groupViewer == null)
network.hideNode(groupNode);
}
+
+ // OK, make sure we have all of our inner and
outer edges added
+ for (CyEdge edge: edgeList) {
+ if
(childList.contains(edge.getSource()) && childList.contains(edge.getTarget()))
+ newGroup.addInnerEdge(edge);
+ else
+ newGroup.addOuterEdge(edge);
+ }
}
// If we have a view, notify the group viewer
Modified:
cytoscape/trunk/application/src/main/java/cytoscape/data/writers/XGMMLWriter.java
===================================================================
---
cytoscape/trunk/application/src/main/java/cytoscape/data/writers/XGMMLWriter.java
2011-06-25 04:38:44 UTC (rev 25940)
+++
cytoscape/trunk/application/src/main/java/cytoscape/data/writers/XGMMLWriter.java
2011-06-25 06:09:03 UTC (rev 25941)
@@ -665,10 +665,10 @@
}
for (CyEdge edge: group.getOuterEdges()) {
logger.debug("Writing outer edge
"+edge.getIdentifier()+" for group "+group);
- if (!edgeMap.containsKey(edge)) {
+ // if (!edgeMap.containsKey(edge)) {
edgeMap.put(edge,edge);
writeEdge(edge, false);
- }
+ // }
}
depth--; writeElement("</graph>\n");
--
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