Author: pwang
Date: 2011-10-31 14:37:25 -0700 (Mon, 31 Oct 2011)
New Revision: 27350
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
Log:
Bug fixed
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
2011-10-31 21:34:55 UTC (rev 27349)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
2011-10-31 21:37:25 UTC (rev 27350)
@@ -190,7 +190,11 @@
overviewNetwork.getCyRow().set("name",
findNextAvailableNetworkName(networkName));
//networkAttr.setAttribute(overviewNetwork.getIdentifier(),
VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME, NetworkType.OVERVIEW.name());
+
+
overviewNetwork.getDefaultNetworkTable().createColumn(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
String.class, false);
overviewNetwork.getCyRow().set(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
NetworkType.OVERVIEW.name());
+
+
//networkAttr.setUserVisible(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
false);
//networkAttr.setUserEditable(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
false);
@@ -204,7 +208,7 @@
final TypedLinkNodeModule<String, BFEdge> sourceModule
= edge.source().value();
CyNode sourceNode = moduleToCyNodeMap.get(sourceModule);
if (sourceNode == null) {
- final String nodeName =
getNodeName(overviewNetwork, sourceModule,nodeIndex,module_name,nodeAttrName);
+ final String nodeName =
getNodeName(origPhysNetwork, sourceModule,nodeIndex,module_name,nodeAttrName);
sourceNode = makeOverviewNode(nodeName,
sourceModule,physicalNetwork,geneticNetwork);
//moduleToCyNodeMap.put(sourceModule,
sourceNode);
++nodeIndex;
@@ -213,7 +217,7 @@
final TypedLinkNodeModule<String, BFEdge> targetModule
= edge.target().value();
CyNode targetNode = moduleToCyNodeMap.get(targetModule);
if (targetNode == null) {
- final String nodeName =
getNodeName(overviewNetwork, targetModule,nodeIndex,module_name,nodeAttrName);
+ final String nodeName =
getNodeName(origPhysNetwork, targetModule,nodeIndex,module_name,nodeAttrName);
targetNode = makeOverviewNode(nodeName,
targetModule,physicalNetwork,geneticNetwork);
//moduleToCyNodeMap.put(targetModule,
targetNode);
++nodeIndex;
@@ -225,6 +229,11 @@
newEdge.getCyRow().set("interaction",
COMPLEX_INTERACTION_TYPE);
//edgeAttribs.setAttribute(newEdge.getIdentifier(),
REFERENCE_NETWORK_NAME_ATTRIB, origPhysNetwork.getTitle() + "/" +
origGenNetwork.getTitle());
+
+ if
(overviewNetwork.getDefaultEdgeTable().getColumn(REFERENCE_NETWORK_NAME_ATTRIB)==
null){
+
overviewNetwork.getDefaultEdgeTable().createColumn(REFERENCE_NETWORK_NAME_ATTRIB,
String.class, false);
+ }
+
newEdge.getCyRow().set(REFERENCE_NETWORK_NAME_ATTRIB,
origPhysNetwork.getCyRow().get("name", String.class) + "/" +
origGenNetwork.getCyRow().get("name", String.class));
//overviewNetwork.addEdge(newEdge);
@@ -232,30 +241,69 @@
// Add various edge attributes.
final double edgeScore = edge.value().link();
//edgeAttribs.setAttribute(newEdge.getIdentifier(),
EDGE_SCORE,Double.valueOf(edgeScore));
+ if
(overviewNetwork.getDefaultEdgeTable().getColumn(EDGE_SCORE)== null){
+
overviewNetwork.getDefaultEdgeTable().createColumn(EDGE_SCORE, Double.class,
false);
+ }
+
newEdge.getCyRow().set(EDGE_SCORE,
Double.valueOf(edgeScore));
if (edgeScore > maxScore)
maxScore = edgeScore;
final double pValue = edge.value().linkMerge();
//edgeAttribs.setAttribute(newEdge.getIdentifier(),
EDGE_PVALUE, Double.valueOf(pValue));
+
+ if
(overviewNetwork.getDefaultEdgeTable().getColumn(EDGE_PVALUE)== null){
+
overviewNetwork.getDefaultEdgeTable().createColumn(EDGE_PVALUE, Double.class,
false);
+ }
+
newEdge.getCyRow().set(EDGE_PVALUE,
Double.valueOf(pValue));
final int gConnectedness =
geneticNetwork.getConnectedness(sourceModule.asStringSet(),
targetModule.asStringSet());
//edgeAttribs.setAttribute(newEdge.getIdentifier(),EDGE_GEN_EDGE_COUNT,
Integer.valueOf(gConnectedness));
+
+
+ if
(overviewNetwork.getDefaultEdgeTable().getColumn(EDGE_GEN_EDGE_COUNT)== null){
+
overviewNetwork.getDefaultEdgeTable().createColumn(EDGE_GEN_EDGE_COUNT,
Integer.class, false);
+ }
+
newEdge.getCyRow().set(EDGE_GEN_EDGE_COUNT,
Integer.valueOf(gConnectedness));
final int pConnectedness =
physicalNetwork.getConnectedness(sourceModule.asStringSet(),
targetModule.asStringSet());
//edgeAttribs.setAttribute(newEdge.getIdentifier(),EDGE_PHYS_EDGE_COUNT,
Integer.valueOf(pConnectedness));
+
+
+ if
(overviewNetwork.getDefaultEdgeTable().getColumn(EDGE_PHYS_EDGE_COUNT)== null){
+
overviewNetwork.getDefaultEdgeTable().createColumn(EDGE_PHYS_EDGE_COUNT,
Integer.class, false);
+ }
+
newEdge.getCyRow().set(EDGE_PHYS_EDGE_COUNT,
Integer.valueOf(pConnectedness));
//edgeAttribs.setAttribute(newEdge.getIdentifier(),
EDGE_SOURCE_SIZE, Integer.valueOf(sourceModule.size()));
+
+
+ if
(overviewNetwork.getDefaultEdgeTable().getColumn(EDGE_SOURCE_SIZE)== null){
+
overviewNetwork.getDefaultEdgeTable().createColumn(EDGE_SOURCE_SIZE,
Integer.class, false);
+ }
+
newEdge.getCyRow().set(EDGE_SOURCE_SIZE,
Integer.valueOf(sourceModule.size()));
//edgeAttribs.setAttribute(newEdge.getIdentifier(),
EDGE_TARGET_SIZE, Integer.valueOf(targetModule.size()));
+
+
+ if
(overviewNetwork.getDefaultEdgeTable().getColumn(EDGE_TARGET_SIZE)== null){
+
overviewNetwork.getDefaultEdgeTable().createColumn(EDGE_TARGET_SIZE,
Integer.class, false);
+ }
+
newEdge.getCyRow().set(EDGE_TARGET_SIZE,
Integer.valueOf(targetModule.size()));
final double density = edgeScore / (sourceModule.size()
* targetModule.size());
//edgeAttribs.setAttribute(newEdge.getIdentifier(),
EDGE_GEN_DENSITY, Double.valueOf(density));
+
+
+ if
(overviewNetwork.getDefaultEdgeTable().getColumn(EDGE_GEN_DENSITY)== null){
+
overviewNetwork.getDefaultEdgeTable().createColumn(EDGE_GEN_DENSITY,
Double.class, false);
+ }
+
newEdge.getCyRow().set(EDGE_GEN_DENSITY,
Double.valueOf(density));
}
@@ -266,12 +314,17 @@
NetworkAndScore network;
final float percentIncrement = remainingPercentage /
networksOrderedByScores.size();
float percentCompleted = 100.0f - remainingPercentage;
+
while ((network = networksOrderedByScores.poll()) != null) {
final boolean createView = networkViewCount++ <
MAX_NETWORK_VIEWS;
+
+ System.out.println("\tBBBBBBBBBBBBBBBBBBB: 1");
+
final CyNetwork nestedNetwork =
generateNestedNetwork(network.getNodeName(), network.getGenes(),
origPhysNetwork, origGenNetwork, physicalNetwork,geneticNetwork, createView,
isGNetSigned, geneticEdgeAttrName);
+ System.out.println("\tBBBBBBBBBBBBBBBB: 2");
- Collection<CyRow> rows =
overviewNetwork.getDefaultNodeTable().getMatchingRows("name",
network.getNodeName());
+ //Collection<CyRow> rows =
overviewNetwork.getDefaultNodeTable().getMatchingRows("name",
network.getNodeName());
Iterator<CyNode> nodeIt=
overviewNetwork.getNodeList().iterator();
@@ -283,14 +336,16 @@
break;
}
}
-
+ System.out.println("DDDDDDDDDDDDDD: 1");
+
//final CyNode node =
Cytoscape.getCyNode(network.getNodeName(), false);
//node.setNetwork(nestedNetwork);
percentCompleted += percentIncrement;
-
taskMonitor.setProgress(Math.round(percentCompleted)/100.0);
+ taskMonitor.setProgress(Math.round(percentCompleted));
}
-
+ System.out.println("EEEEEEEEEEEEEEE: 1");
+
//Cytoscape.createNetworkView(overviewNetwork);
ServicesUtil.cyNetworkViewFactoryServiceRef.getNetworkView(overviewNetwork);
applyNetworkLayout(overviewNetwork, cutoff, maxScore);
@@ -307,15 +362,20 @@
{
Iterator<String> genes =
module.getMemberValues().iterator();
+ //String newName =
"["+String.valueOf(nodeAttribs.getAttribute(genes.next(),nodeAttrName));
+ Collection<CyRow> rowsCollection =
network.getDefaultNodeTable().getMatchingRows(nodeAttrName, genes.next());
- //String newName =
"["+String.valueOf(nodeAttribs.getAttribute(genes.next(),nodeAttrName));
- CyRow[] rows= (CyRow[])
network.getDefaultNodeTable().getMatchingRows(nodeAttrName,
genes.next()).toArray();
+ CyRow[] rows= rowsCollection.toArray(new CyRow[0]);
+
String newName = "["+String.valueOf(rows[0]);
while (genes.hasNext())
{
//newName+=",
"+String.valueOf(nodeAttribs.getAttribute(genes.next(),nodeAttrName));
- CyRow[] rows1= (CyRow[])
network.getDefaultNodeTable().getMatchingRows(nodeAttrName,
genes.next()).toArray();
+
+ Collection<CyRow> rowsCollection1=
network.getDefaultNodeTable().getMatchingRows(nodeAttrName, genes.next());
+ rowsCollection1.toArray(new CyRow[0]);
+ CyRow[] rows1= rowsCollection1.toArray(new
CyRow[0]); ;//(CyRow[])
network.getDefaultNodeTable().getMatchingRows(nodeAttrName,
genes.next()).toArray();
String newName1 = "["+String.valueOf(rows1[0]);
newName+=", "+String.valueOf(newName1);
@@ -359,14 +419,29 @@
final Set<String> genes = module.getMemberValues();
final Integer geneCount = Integer.valueOf(genes.size());
//nodeAttribs.setAttribute(newNode.getIdentifier(), GENE_COUNT,
geneCount);
+
+
+ if
(overviewNetwork.getDefaultNodeTable().getColumn(GENE_COUNT)== null){
+
overviewNetwork.getDefaultNodeTable().createColumn(GENE_COUNT, Integer.class,
false);
+ }
+
newNode.getCyRow().set(GENE_COUNT, geneCount);
//nodeAttribs.setAttribute(newNode.getIdentifier(),
GENE_COUNT_SQRT, Math.sqrt(geneCount));
+
+ if
(overviewNetwork.getDefaultNodeTable().getColumn(GENE_COUNT_SQRT)== null){
+
overviewNetwork.getDefaultNodeTable().createColumn(GENE_COUNT_SQRT,
Double.class, false);
+ }
+
newNode.getCyRow().set(GENE_COUNT_SQRT, Math.sqrt(geneCount));
if (genes.size() > maxSize)
maxSize = genes.size();
final double score = Double.valueOf(module.score());
//nodeAttribs.setAttribute(newNode.getIdentifier(), SCORE,
score);
+ if (overviewNetwork.getDefaultNodeTable().getColumn(SCORE)==
null){
+
overviewNetwork.getDefaultNodeTable().createColumn(SCORE, Double.class, false);
+ }
+
newNode.getCyRow().set( SCORE, score);
StringBuilder members = new StringBuilder();
@@ -376,11 +451,27 @@
members.append(gene);
}
//nodeAttribs.setAttribute(newNode.getIdentifier(), MEMBERS,
members.toString());
+
+ if (overviewNetwork.getDefaultNodeTable().getColumn(MEMBERS)==
null){
+
overviewNetwork.getDefaultNodeTable().createColumn(MEMBERS, String.class,
false);
+ }
+
newNode.getCyRow().set(MEMBERS, members.toString());
//nodeAttribs.setAttribute(newNode.getIdentifier(),
PHYS_EDGE_COUNT, physicalNetwork.subNetwork(module.asStringSet()).numEdges());
+
+ if
(overviewNetwork.getDefaultNodeTable().getColumn(PHYS_EDGE_COUNT)== null){
+
overviewNetwork.getDefaultNodeTable().createColumn(PHYS_EDGE_COUNT,
Integer.class, false);
+ }
+
newNode.getCyRow().set(PHYS_EDGE_COUNT,
physicalNetwork.subNetwork(module.asStringSet()).numEdges());
//nodeAttribs.setAttribute(newNode.getIdentifier(),
GEN_EDGE_COUNT, geneticNetwork.subNetwork(module.asStringSet()).numEdges());
+
+
+ if
(overviewNetwork.getDefaultNodeTable().getColumn(GEN_EDGE_COUNT)== null){
+
overviewNetwork.getDefaultNodeTable().createColumn(GEN_EDGE_COUNT,
Integer.class, false);
+ }
+
newNode.getCyRow().set(GEN_EDGE_COUNT,
geneticNetwork.subNetwork(module.asStringSet()).numEdges());
//Add to network
@@ -394,6 +485,8 @@
final CyNetwork origGenNetwork,
TypedLinkNetwork<String, Float> physicalNetwork, TypedLinkNetwork<String,
Float> geneticNetwork, final boolean createNetworkView,
boolean isGNetSigned, String geneticEdgeAttrName)
{
+ System.out.println("Entering generateNestedNetwork()...");
+
if (nodeNames.isEmpty())
return null;
@@ -417,7 +510,6 @@
//
node.getCyRow().set(VisualStyleObserver.PARENT_MODULE_ATTRIBUTE_NAME,
networkName);
// }
-
// Find the list of nodes
HashMap<String,CyNode> name_node_map = new
HashMap<String,CyNode>();
@@ -427,7 +519,6 @@
String name = node.getCyRow().get("name", String.class);
name_node_map.put(name, node);
}
-
final List<CyNode> nodes = new ArrayList<CyNode>();
for (final String nodeName : nodeNames) {
CyNode node = name_node_map.get(nodeName);
@@ -439,20 +530,31 @@
while(it.hasNext()){
CyNode node = it.next();
+ if
(origPhysNetwork.getDefaultNodeTable().getColumn(VisualStyleObserver.PARENT_MODULE_ATTRIBUTE_NAME)
== null){
+
origPhysNetwork.getDefaultNodeTable().createColumn(VisualStyleObserver.PARENT_MODULE_ATTRIBUTE_NAME,
String.class, false);
+ }
node.getCyRow().set(VisualStyleObserver.PARENT_MODULE_ATTRIBUTE_NAME,
networkName);
}
+ System.out.println("\tRRRRRRRRRRRRRRRRRRRRRRR..nodeList.size()
= "+ nodeList.size());
// Add the edges induced by "origPhysNetwork" to our new nested
network.
//List<CyEdge> edges = (List<CyEdge>)
origPhysNetwork..getConnectingEdgeList(nodeList);
List<CyEdge> edges =
getConnectingEdges(origPhysNetwork,nodeList);
+ System.out.println("\tTTTTTTTTTTTTTTTTTTT");
+
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);
//cyEdgeAttrs.setAttribute(edge.getIdentifier(), "PanGIA.Interaction Type",
"Physical");
+
+ if
(origPhysNetwork.getDefaultEdgeTable().getColumn("PanGIA.Interaction Type") ==
null){
+
origPhysNetwork.getDefaultEdgeTable().createColumn("PanGIA.Interaction Type",
String.class, false);
+ }
+
edge.getCyRow().set("PanGIA.Interaction Type",
"Physical");
}
}
@@ -461,13 +563,19 @@
//edges = (List<CyEdge>)
origGenNetwork.getConnectingEdges(getIntersectingNodes(origGenNetwork, nodes));
List<CyNode> nodeList2 = getIntersectingNodes(origGenNetwork,
nodes);
+
List<CyEdge >edges2 = getConnectingEdges(origGenNetwork,
nodeList2);
+ System.out.println("\tUUUUUUUUUUUUUUUUUUU...edges2.size()="+
edges2.size());
for (final CyEdge edge : edges2)
{
+ System.out.println("\tIIIIIIIIIIIIIIIIIIIIIIII...");
+
if
(geneticNetwork.containsEdge(edge.getSource().getCyRow().get("name",
String.class),edge.getTarget().getCyRow().get("name", String.class)))
{
+
System.out.println("\t\tOOOOOOOOOOOOOOOOOOOOOOOOOOO...");
+
//nestedNetwork.addEdge(edge);
//Object existingAttribute =
cyEdgeAttrs.getAttribute(edge.getIdentifier(), "PanGIA.Interaction Type");
Object existingAttribute =
edge.getCyRow().getRaw("PanGIA.Interaction Type");
@@ -513,13 +621,24 @@
//Merge two edge list
edges.addAll(edges2);
+ System.out.println("\tLLLLLLLLLLLLL...........edges.size() =
"+edges.size());
+
//
CyRootNetwork rootNetwork =
ServicesUtil.cyRootNetworkFactory.convert(origPhysNetwork);
- CyNetwork nestedNetwork =
rootNetwork.addSubNetwork(getIntersectingNodes(origPhysNetwork, nodes), edges);
+ System.out.println("\tLLLLLLLLLLLLL...........1 ");
+
+ CyNetwork nestedNetwork =
rootNetwork.addSubNetwork(getIntersectingNodes(origPhysNetwork, nodes), edges);
x
+
+ System.out.println("\tLLLLLLLLLLLLL...........2 ");
+
+ if
(nestedNetwork.getDefaultNetworkTable().getColumn(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME)==
null){
+
nestedNetwork.getDefaultNetworkTable().createColumn(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
String.class, false);
+ }
nestedNetwork.getCyRow().set(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
NetworkType.MODULE.name());
-
+ System.out.println("\tLLLLLLLLLLLLL...........3 ");
+
if (createNetworkView) {
CyNetworkView theView =
ServicesUtil.cyNetworkViewFactoryServiceRef.getNetworkView(nestedNetwork);
@@ -532,6 +651,8 @@
ServicesUtil.taskManagerServiceRef.execute(alg);
}
+ System.out.println("\tExiting generateNestedNetwork ... ");
+
return nestedNetwork;
}
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