Author: pwang
Date: 2011-10-31 03:57:02 -0700 (Mon, 31 Oct 2011)
New Revision: 27348
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
Log:
Use subnetwork for nestedNetwork
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
2011-10-30 08:04:03 UTC (rev 27347)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
2011-10-31 10:57:02 UTC (rev 27348)
@@ -18,6 +18,7 @@
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.model.CyRow;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
/**
@@ -398,53 +399,76 @@
// First, create network without view.
//final CyNetwork nestedNetwork =
Cytoscape.createNetwork(networkName, overviewNetwork, false);
- final CyNetwork nestedNetwork =
ServicesUtil.cyNetworkFactoryServiceRef.getInstance();
+ //final CyNetwork nestedNetwork =
ServicesUtil.cyNetworkFactoryServiceRef.getInstance();
+
+
+ // Add the nodes to our new nested network.
+// final List<CyNode> nodes = new ArrayList<CyNode>();
+// for (final String nodeName : nodeNames) {
+// final CyNode node = nestedNetwork.addNode();
//Cytoscape.getCyNode(nodeName, /* create = */false);
+// node.getCyRow().set("name", nodeName);
+// if (node == null) {
+// System.err.println("in
NestedNetworkCreator.generateNestedNetwork() (in the PanGIA plug-in): unknown
node: \"" + nodeName + "\"!");
+// throw new IllegalStateException("unknown node:
\"" + nodeName + "\"!");
+// }
+// //nestedNetwork.addNode(node);
+// nodes.add(node);
+// //nodeAttributes.setAttribute(node.getIdentifier(),
VisualStyleObserver.PARENT_MODULE_ATTRIBUTE_NAME, networkName);
+//
node.getCyRow().set(VisualStyleObserver.PARENT_MODULE_ATTRIBUTE_NAME,
networkName);
+// }
+
- //networkAttr.setAttribute(nestedNetwork.getIdentifier(),
VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME, NetworkType.MODULE.name());
-
nestedNetwork.getCyRow().set(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
NetworkType.MODULE.name());
+ // Find the list of nodes
- //CyTable nodeAttributes = Cytoscape.getNodeAttributes();
+ HashMap<String,CyNode> name_node_map = new
HashMap<String,CyNode>();
+ Iterator<CyNode> node_it =
origPhysNetwork.getNodeList().iterator();
+ while(node_it.hasNext()){
+ CyNode node = node_it.next();
+ String name = node.getCyRow().get("name", String.class);
+ name_node_map.put(name, node);
+ }
- // Add the nodes to our new nested network.
final List<CyNode> nodes = new ArrayList<CyNode>();
for (final String nodeName : nodeNames) {
- final CyNode node = nestedNetwork.addNode();
//Cytoscape.getCyNode(nodeName, /* create = */false);
- node.getCyRow().set("name", nodeName);
- if (node == null) {
- System.err.println("in
NestedNetworkCreator.generateNestedNetwork() (in the PanGIA plug-in): unknown
node: \"" + nodeName + "\"!");
- throw new IllegalStateException("unknown node:
\"" + nodeName + "\"!");
- }
- //nestedNetwork.addNode(node);
- nodes.add(node);
- //nodeAttributes.setAttribute(node.getIdentifier(),
VisualStyleObserver.PARENT_MODULE_ATTRIBUTE_NAME, networkName);
+ CyNode node = name_node_map.get(nodeName);
+ nodes.add(node);
+ }
+
+ List<CyNode> nodeList = getIntersectingNodes(origPhysNetwork,
nodes);
+ Iterator<CyNode> it = nodeList.iterator();
+ while(it.hasNext()){
+
+ CyNode node = it.next();
node.getCyRow().set(VisualStyleObserver.PARENT_MODULE_ATTRIBUTE_NAME,
networkName);
}
-
- //CyTable cyEdgeAttrs = Cytoscape.getEdgeAttributes();
// Add the edges induced by "origPhysNetwork" to our new nested
network.
- List<CyEdge> edges = (List<CyEdge>)
origPhysNetwork.getConnectingEdgeList(getIntersectingNodes(origPhysNetwork,
nodes));
-
+ //List<CyEdge> edges = (List<CyEdge>)
origPhysNetwork..getConnectingEdgeList(nodeList);
+ List<CyEdge> edges =
getConnectingEdges(origPhysNetwork,nodeList);
+
for (final CyEdge edge : edges)
{
if
(physicalNetwork.containsEdge(edge.getSource().getCyRow().get("name",
String.class),edge.getTarget().getCyRow().get("name", String.class)))
{
//nestedNetwork.addEdge(edge);
- nestedNetwork.addEdge(edge.getSource(),
edge.getTarget(), false);
//cyEdgeAttrs.setAttribute(edge.getIdentifier(), "PanGIA.Interaction Type",
"Physical");
edge.getCyRow().set("PanGIA.Interaction Type",
"Physical");
}
}
// Add the edges induced by "origGenNetwork" to our new nested
network.
- edges = (List<CyEdge>)
origGenNetwork.getConnectingEdges(getIntersectingNodes(origGenNetwork, nodes));
- for (final CyEdge edge : edges)
+ //edges = (List<CyEdge>)
origGenNetwork.getConnectingEdges(getIntersectingNodes(origGenNetwork, nodes));
+
+ List<CyNode> nodeList2 = getIntersectingNodes(origGenNetwork,
nodes);
+ List<CyEdge >edges2 = getConnectingEdges(origGenNetwork,
nodeList2);
+
+
+ for (final CyEdge edge : edges2)
{
if
(geneticNetwork.containsEdge(edge.getSource().getCyRow().get("name",
String.class),edge.getTarget().getCyRow().get("name", String.class)))
{
//nestedNetwork.addEdge(edge);
- nestedNetwork.addEdge(edge.getSource(),
edge.getTarget(), false);
//Object existingAttribute =
cyEdgeAttrs.getAttribute(edge.getIdentifier(), "PanGIA.Interaction Type");
Object existingAttribute =
edge.getCyRow().getRaw("PanGIA.Interaction Type");
if (existingAttribute==null ||
!existingAttribute.equals("Physical"))
@@ -486,6 +510,16 @@
}
}
+ //Merge two edge list
+ edges.addAll(edges2);
+
+ //
+ CyRootNetwork rootNetwork =
ServicesUtil.cyRootNetworkFactory.convert(origPhysNetwork);
+ CyNetwork nestedNetwork =
rootNetwork.addSubNetwork(getIntersectingNodes(origPhysNetwork, nodes), edges);
+
+
nestedNetwork.getCyRow().set(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
NetworkType.MODULE.name());
+
+
if (createNetworkView) {
CyNetworkView theView =
ServicesUtil.cyNetworkViewFactoryServiceRef.getNetworkView(nestedNetwork);
@@ -604,4 +638,19 @@
return commonNodes;
}
+
+ private List<CyEdge> getConnectingEdges(CyNetwork network,List<CyNode>
nodeList)
+ {
+ HashSet<CyEdge> edgeSet = new HashSet<CyEdge>();
+ Iterator<CyNode> it = nodeList.iterator();
+ while(it.hasNext()){
+ CyNode node = it.next();
+ List<CyEdge> edgeList =
network.getAdjacentEdgeList(node, CyEdge.Type.ANY);
+ edgeSet.addAll(edgeList);
+ }
+
+ return new ArrayList<CyEdge>(edgeSet);
+ }
+
+
}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
