Author: pwang
Date: 2011-10-30 01:04:03 -0700 (Sun, 30 Oct 2011)
New Revision: 27347
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
Log:
refactored to work with Cy3
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
2011-10-29 22:22:15 UTC (rev 27346)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
2011-10-30 08:04:03 UTC (rev 27347)
@@ -17,6 +17,7 @@
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.model.CyRow;
/**
@@ -118,16 +119,16 @@
private CyNetwork overviewNetwork = null;
private Map<TypedLinkNodeModule<String, BFEdge>, CyNode>
moduleToCyNodeMap;
private int maxSize = 0;
- private final int MAX_NETWORK_VIEWS = PropUtil.getInt(CytoscapeInit
- .getProperties(), "moduleNetworkViewCreationThreshold",
0);
+ private int MAX_NETWORK_VIEWS = 5 ; //PropUtil.getInt(CytoscapeInit
+ //.getProperties(),
"moduleNetworkViewCreationThreshold", 0);
private final PriorityQueue<NetworkAndScore> networksOrderedByScores =
new PriorityQueue(
100);
// VisualStyle moduleVS =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().
//
getVisualStyle(VisualStyleObserver.VS_MODULE_NAME);
- private final CyTable nodeAttribs = Cytoscape.getNodeAttributes();
- private final CyTable edgeAttribs = Cytoscape.getEdgeAttributes();
+// private final CyTable nodeAttribs = Cytoscape.getNodeAttributes();
+// private final CyTable edgeAttribs = Cytoscape.getEdgeAttributes();
public static List<String> getEdgeAttributeNames()
{
@@ -171,8 +172,15 @@
String geneticEdgeAttrName
)
{
+ try {
+ MAX_NETWORK_VIEWS = new
Integer(ServicesUtil.cytoscapePropertiesServiceRef.getProperties().getProperty("moduleNetworkViewCreationThreshold")).intValue();
+ }
+ catch (Exception e){
+ MAX_NETWORK_VIEWS = 5;
+ }
+
// Network attributes created here is required for managing
Visual Styles.
- final CyTable networkAttr = Cytoscape.getNetworkAttributes();
+ //final CyTable networkAttr = Cytoscape.getNetworkAttributes();
moduleToCyNodeMap = new HashMap<TypedLinkNodeModule<String,
BFEdge>, CyNode>();
@@ -195,8 +203,8 @@
final TypedLinkNodeModule<String, BFEdge> sourceModule
= edge.source().value();
CyNode sourceNode = moduleToCyNodeMap.get(sourceModule);
if (sourceNode == null) {
- final String nodeName =
getNodeName(sourceModule,nodeIndex,module_name,nodeAttrName);
- sourceNode = makeOverviewNode(nodeName,
sourceModule,nodeAttribs,physicalNetwork,geneticNetwork);
+ final String nodeName =
getNodeName(overviewNetwork, sourceModule,nodeIndex,module_name,nodeAttrName);
+ sourceNode = makeOverviewNode(nodeName,
sourceModule,physicalNetwork,geneticNetwork);
//moduleToCyNodeMap.put(sourceModule,
sourceNode);
++nodeIndex;
}
@@ -204,8 +212,8 @@
final TypedLinkNodeModule<String, BFEdge> targetModule
= edge.target().value();
CyNode targetNode = moduleToCyNodeMap.get(targetModule);
if (targetNode == null) {
- final String nodeName =
getNodeName(targetModule,nodeIndex,module_name,nodeAttrName);
- targetNode = makeOverviewNode(nodeName,
targetModule,nodeAttribs,physicalNetwork,geneticNetwork);
+ final String nodeName =
getNodeName(overviewNetwork, targetModule,nodeIndex,module_name,nodeAttrName);
+ targetNode = makeOverviewNode(nodeName,
targetModule,physicalNetwork,geneticNetwork);
//moduleToCyNodeMap.put(targetModule,
targetNode);
++nodeIndex;
}
@@ -213,7 +221,7 @@
//final CyEdge newEdge =
Cytoscape.getCyEdge(sourceNode, targetNode, Semantics.INTERACTION,
COMPLEX_INTERACTION_TYPE, /* create = */true);
CyEdge newEdge = overviewNetwork.addEdge(sourceNode,
targetNode, false);
- newEdge.getCyRow().set(Semantics.INTERACTION,
COMPLEX_INTERACTION_TYPE);
+ newEdge.getCyRow().set("interaction",
COMPLEX_INTERACTION_TYPE);
//edgeAttribs.setAttribute(newEdge.getIdentifier(),
REFERENCE_NETWORK_NAME_ATTRIB, origPhysNetwork.getTitle() + "/" +
origGenNetwork.getTitle());
newEdge.getCyRow().set(REFERENCE_NETWORK_NAME_ATTRIB,
origPhysNetwork.getCyRow().get("name", String.class) + "/" +
origGenNetwork.getCyRow().get("name", String.class));
@@ -259,9 +267,24 @@
float percentCompleted = 100.0f - remainingPercentage;
while ((network = networksOrderedByScores.poll()) != null) {
final boolean createView = networkViewCount++ <
MAX_NETWORK_VIEWS;
- final CyNetwork nestedNetwork =
generateNestedNetwork(network.getNodeName(), network.getGenes(),
origPhysNetwork, origGenNetwork, physicalNetwork,geneticNetwork, createView,
networkAttr, isGNetSigned, geneticEdgeAttrName);
- final CyNode node =
Cytoscape.getCyNode(network.getNodeName(), false);
- node.setNetwork(nestedNetwork);
+ final CyNetwork nestedNetwork =
generateNestedNetwork(network.getNodeName(), network.getGenes(),
origPhysNetwork, origGenNetwork, physicalNetwork,geneticNetwork, createView,
isGNetSigned, geneticEdgeAttrName);
+
+
+ Collection<CyRow> rows =
overviewNetwork.getDefaultNodeTable().getMatchingRows("name",
network.getNodeName());
+
+ Iterator<CyNode> nodeIt=
overviewNetwork.getNodeList().iterator();
+
+ while (nodeIt.hasNext()){
+ CyNode aNode = nodeIt.next();
+ String nodeName = aNode.getCyRow().get("name",
String.class);
+ if
(nodeName.equalsIgnoreCase(network.getNodeName())){
+ aNode.setNetwork(nestedNetwork);
+ break;
+ }
+ }
+
+ //final CyNode node =
Cytoscape.getCyNode(network.getNodeName(), false);
+ //node.setNetwork(nestedNetwork);
percentCompleted += percentIncrement;
taskMonitor.setProgress(Math.round(percentCompleted)/100.0);
@@ -274,7 +297,7 @@
}
- private String getNodeName(TypedLinkNodeModule<String, BFEdge> module,
int nodeIndex, Map<TypedLinkNodeModule<String, BFEdge>,String> module_name,
String nodeAttrName)
+ private String getNodeName(CyNetwork network,
TypedLinkNodeModule<String, BFEdge> module, int nodeIndex,
Map<TypedLinkNodeModule<String, BFEdge>,String> module_name, String
nodeAttrName)
{
@@ -282,19 +305,31 @@
if (module.size()<=2)
{
Iterator<String> genes =
module.getMemberValues().iterator();
- String newName =
"["+String.valueOf(nodeAttribs.getAttribute(genes.next(),nodeAttrName));
- while (genes.hasNext()) newName+=",
"+String.valueOf(nodeAttribs.getAttribute(genes.next(),nodeAttrName));
- return findNextAvailableNodeName(newName+"]");
+
+
+ //String newName =
"["+String.valueOf(nodeAttribs.getAttribute(genes.next(),nodeAttrName));
+ CyRow[] rows= (CyRow[])
network.getDefaultNodeTable().getMatchingRows(nodeAttrName,
genes.next()).toArray();
+ 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();
+ String newName1 = "["+String.valueOf(rows1[0]);
+
+ newName+=", "+String.valueOf(newName1);
+ }
+ return findNextAvailableNodeName(network, newName+"]");
}
//Annotate large complexes
if (module_name!=null)
{
String name = module_name.get(module);
- if (name!=null) return findNextAvailableNodeName(name);
+ if (name!=null) return
findNextAvailableNodeName(network, name);
}
- return findNextAvailableNodeName("Module" + nodeIndex);
+ return findNextAvailableNodeName(network, "Module" + nodeIndex);
}
CyNetwork getOverviewNetwork() {
@@ -306,14 +341,18 @@
*/
private CyNode makeOverviewNode(final String nodeName,
final TypedLinkNodeModule<String, BFEdge> module,
- final CyTable nodeAttribs, TypedLinkNetwork<String,
Float> physicalNetwork, TypedLinkNetwork<String, Float> geneticNetwork) {
+ TypedLinkNetwork<String, Float> physicalNetwork,
TypedLinkNetwork<String, Float> geneticNetwork) {
- final CyNode newNode = Cytoscape.getCyNode(nodeName, true); //
create=true
+ //final CyNode newNode = Cytoscape.getCyNode(nodeName, true);
// create=true
+ CyNode newNode = overviewNetwork.addNode();
+ newNode.getCyRow().set("name", nodeName);
+
+
moduleToCyNodeMap.put(module, newNode);
- overviewNetwork.addNode(newNode);
+ //overviewNetwork.addNode(newNode);
//Add attributes
final Set<String> genes = module.getMemberValues();
@@ -352,43 +391,47 @@
private CyNetwork generateNestedNetwork(final String networkName,
final Set<String> nodeNames, final CyNetwork
origPhysNetwork,
final CyNetwork origGenNetwork,
TypedLinkNetwork<String, Float> physicalNetwork, TypedLinkNetwork<String,
Float> geneticNetwork, final boolean createNetworkView,
- final CyTable networkAttr, boolean isGNetSigned, String
geneticEdgeAttrName)
+ boolean isGNetSigned, String geneticEdgeAttrName)
{
if (nodeNames.isEmpty())
return null;
// First, create network without view.
- final CyNetwork nestedNetwork =
Cytoscape.createNetwork(networkName, overviewNetwork, false);
+ //final CyNetwork nestedNetwork =
Cytoscape.createNetwork(networkName, overviewNetwork, false);
+ final CyNetwork nestedNetwork =
ServicesUtil.cyNetworkFactoryServiceRef.getInstance();
//networkAttr.setAttribute(nestedNetwork.getIdentifier(),
VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME, NetworkType.MODULE.name());
- nestedNetwork.getCyRow().set(
VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME, NetworkType.MODULE.name());
+
nestedNetwork.getCyRow().set(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
NetworkType.MODULE.name());
- CyTable nodeAttributes = Cytoscape.getNodeAttributes();
+ //CyTable nodeAttributes = Cytoscape.getNodeAttributes();
// Add the nodes to our new nested network.
final List<CyNode> nodes = new ArrayList<CyNode>();
for (final String nodeName : nodeNames) {
- final CyNode node = Cytoscape.getCyNode(nodeName, /*
create = */false);
+ 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);
+ //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);
}
- CyTable cyEdgeAttrs = Cytoscape.getEdgeAttributes();
+ //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));
+
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);
+ nestedNetwork.addEdge(edge.getSource(),
edge.getTarget(), false);
//cyEdgeAttrs.setAttribute(edge.getIdentifier(), "PanGIA.Interaction Type",
"Physical");
edge.getCyRow().set("PanGIA.Interaction Type",
"Physical");
}
@@ -400,7 +443,8 @@
{
if
(geneticNetwork.containsEdge(edge.getSource().getCyRow().get("name",
String.class),edge.getTarget().getCyRow().get("name", String.class)))
{
- nestedNetwork.addEdge(edge);
+ //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"))
@@ -489,17 +533,21 @@
* The node name we'd like to use, if it is available. If
not we
* use it as a prefix instead.
*/
- private String findNextAvailableNodeName(final String
initialPreference) {
+ private String findNextAvailableNodeName(CyNetwork network, final
String initialPreference) {
// Try the preferred choice first:
- CyNode node = Cytoscape
- .getCyNode(initialPreference, /* create =
*/false);
- if (node == null)
+ //CyNode node = Cytoscape
+ // .getCyNode(initialPreference, /* create =
*/false);
+
+ if (network.getDefaultNodeTable().getMatchingRows("name",
initialPreference).isEmpty())
+ //if (node == null)
return initialPreference;
for (int suffix = 1; true; ++suffix) {
final String titleCandidate = initialPreference + "-" +
suffix;
- node = Cytoscape.getCyNode(titleCandidate, /* create =
*/false);
- if (node == null)
+
+ if
(network.getDefaultNodeTable().getMatchingRows("name",
titleCandidate).isEmpty())
+ //node = Cytoscape.getCyNode(titleCandidate, /* create
= */false);
+ //if (node == null)
return titleCandidate;
}
}
--
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.
