Author: pwang
Date: 2012-02-09 12:14:14 -0800 (Thu, 09 Feb 2012)
New Revision: 28219
Added:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/pom.xml
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/MyAction.java
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/resources/
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/resources/plugin.props
Log:
Original creation
Added: csplugins/trunk/ucsd/pwang/subnetworkByCategory/pom.xml
===================================================================
--- csplugins/trunk/ucsd/pwang/subnetworkByCategory/pom.xml
(rev 0)
+++ csplugins/trunk/ucsd/pwang/subnetworkByCategory/pom.xml 2012-02-09
20:14:14 UTC (rev 28219)
@@ -0,0 +1,58 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape</groupId>
+
+ <parent>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>parent</artifactId>
+ <version>2.8.3-SNAPSHOT</version>
+ </parent>
+
+
+ <artifactId>subnetworkbycategory</artifactId>
+ <packaging>jar</packaging>
+ <name>SubnetworkByCategory</name>
+
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots
-->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <archive>
+ <manifestEntries>
+
<Cytoscape-Plugin>org.cytoscape.subnetwork.SubnetworkByCategory</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
\ No newline at end of file
Added:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/MyAction.java
===================================================================
---
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/MyAction.java
(rev 0)
+++
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/MyAction.java
2012-02-09 20:14:14 UTC (rev 28219)
@@ -0,0 +1,230 @@
+package org.cytoscape.subnetwork;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.util.CytoscapeAction;
+import java.awt.event.ActionEvent;
+
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.CyEdge;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.Vector;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * A simple action. Change the names as appropriate and
+ * then fill in your expected behavior in the actionPerformed()
+ * method.
+ */
+public class MyAction extends CytoscapeAction {
+
+ private static final long serialVersionUID =
123456789023451239L;
+
+ public MyAction() {
+ // Give your action a name here
+ super("Subnetwork by Category");
+
+ // Set the menu you'd like here. Plugins don't need
+ // to live in the Plugins menu, so choose whatever
+ // is appropriate!
+ setPreferredMenu("Plugins");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ // Do something useful here!
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+ String attributeName = "Category";
+
+ // 1. get the node list for each category
+ HashMap categoryMap = getNodeCategoryMap(net,
attributeName);
+
+ // 2. create subnetwork for each category
+ CyNetwork[] subnetworks = createSubnetworks(net,
categoryMap);
+
+ //3. create an overview network for all nested network
+ Set overview_nodes = new HashSet();
+ for (int i=0; i< subnetworks.length; i++){
+ CyNode newNode
=Cytoscape.getCyNode(subnetworks[i].getTitle(), true);
+ newNode.setNestedNetwork(subnetworks[i]);
+ overview_nodes.add(newNode);
+ }
+
+ Set overview_edges = getOverviewEdges(net,
overview_nodes);
+ final CyNetwork overview =
Cytoscape.createNetwork(overview_nodes, overview_edges, "Overview of category
", net, false);
+
+ // 4. Create a view for overview network
+ Cytoscape.createNetworkView(overview,
overview.getTitle());
+ }
+
+
+ //
+ private Set getOverviewEdges(CyNetwork parentNetwork, Set
overview_nodes){
+
+ HashSet overview_edgeSet = new HashSet();
+
+ //1. Build node and edge set for each subnetwork
+ int overview_nodeCount = overview_nodes.size();
+ CyNode[] overview_nodeArray = new
CyNode[overview_nodeCount];
+
+ HashSet[] nodeSet = new HashSet[overview_nodeCount];
+ HashSet[] edgeSet = new HashSet[overview_nodeCount];
+
+ Iterator it = overview_nodes.iterator();
+ int i=0;
+ while(it.hasNext()){
+ CyNode node = (CyNode)it.next();
+ overview_nodeArray[i] = node;
+ CyNetwork subnetwork =
(CyNetwork)node.getNestedNetwork();
+
+ // build node set
+ List subnetworkNodeList =
subnetwork.nodesList();
+ nodeSet[i] = new HashSet();
+ Iterator nodeIt = subnetworkNodeList.iterator();
+ while (nodeIt.hasNext()){
+ nodeSet[i].add(nodeIt.next());
+ }
+
+ //build edge set
+ List subnetworkEdgeList =
subnetwork.edgesList();
+ edgeSet[i] = new HashSet();
+ Iterator edgeIt = subnetworkEdgeList.iterator();
+ while (edgeIt.hasNext()){
+ edgeSet[i].add(edgeIt.next());
+ }
+
+ i++;
+ }
+
+ //2.Build outgoing edge set for each subnetwork
+ HashSet[] outgoing_edgeSet = new
HashSet[overview_nodeCount];
+
+ // build edge set for parent network
+ //HashSet parentEdgeSet = new HashSet();
+ Iterator parentEdgeIt =
parentNetwork.edgesList().iterator();
+ while (parentEdgeIt.hasNext()){
+ //parentEdgeSet.add(parentEdgeIt.next());;
+ CyEdge edge = (CyEdge)parentEdgeIt.next();
+
+ // Check if edge is an outing edge for each
subnetwork
+ for (int k=0; k< overview_nodeCount; k++){
+ if
(nodeSet[k].contains(edge.getSource()) &&
!nodeSet[k].contains(edge.getTarget()) ||
+
(!nodeSet[k].contains(edge.getSource()) &&
nodeSet[k].contains(edge.getTarget()))){
+ if (outgoing_edgeSet[k] ==
null){
+ outgoing_edgeSet[k] =
new HashSet();
+ }
+ outgoing_edgeSet[k].add(edge);
+ }
+ }
+ }
+
+ // determine if there are any edge between
overview_node and its attribute "overlapCount"
+ for (int m=0; m<overview_nodeArray.length; m++ ){
+ for (int n=m+1; n< overview_nodeArray.length;
n++){
+ int overlapCount =
getEdgeSetOverlapCount(outgoing_edgeSet[m], outgoing_edgeSet[n]);
+
+ // Create an edge if edge overlapCount
is more than 0
+ if (overlapCount >0){
+ CyEdge newEdge
=Cytoscape.getCyEdge(overview_nodeArray[m], overview_nodeArray[n],
+
Semantics.INTERACTION, "pp", true);
+ // add an attribute
"overlapCount" for this edge
+
Cytoscape.getEdgeAttributes().setAttribute(newEdge.getIdentifier(),
"overlapCount", new Integer(overlapCount));
+
+ overview_edgeSet.add(newEdge);
+ }
+ }
+ }
+
+ return overview_edgeSet;
+ }
+
+
+ //
+ private int getEdgeSetOverlapCount(HashSet edgeSetA, HashSet
edgeSetB){
+
+ int overlapCount = 0;
+
+ Iterator it = edgeSetA.iterator();
+ while (it.hasNext()){
+ CyEdge edge = (CyEdge)it.next();
+ if (edgeSetB.contains(edge)){
+ overlapCount++;
+ }
+ }
+
+ return overlapCount;
+ }
+
+
+ //
+ private CyNetwork[] createSubnetworks(CyNetwork parentNet,
HashMap categoryMap) {
+ CyNetwork[] subnetworks = new
CyNetwork[categoryMap.keySet().size()];
+
+ Iterator it = categoryMap.keySet().iterator();
+
+ int i=0;
+ while (it.hasNext()){
+ String categoryName = it.next().toString();
+
+ // 1. get node set for this subnetwork
+ Vector nodeVect =
(Vector)categoryMap.get(categoryName);
+
+ Set nodeSet = new HashSet();
+ for (int j = 0; j < nodeVect.size(); j++) {
+ CyNode oneNode = (CyNode)
nodeVect.elementAt(j);
+ if (oneNode != null)
+ nodeSet.add(oneNode);
+ }
+
+ // 2. get edge set for this subnetwork
+ Set edgeSet = new HashSet();
+ Iterator iterator = parentNet.edgesIterator();
+ while (iterator.hasNext()) {
+ CyEdge edge = (CyEdge) iterator.next();
+ if (nodeSet.contains(edge.getSource())
&& nodeSet.contains(edge.getTarget()))
+ edgeSet.add(edge);
+ }
+
+ // 3. Create subnetwork based on given nodeSet
and EdgeSet
+ subnetworks[i++] =
Cytoscape.createNetwork(nodeSet, edgeSet, categoryName, parentNet, false);
+ }
+
+ return subnetworks;
+ }
+
+
+ //////
+ private HashMap getNodeCategoryMap(CyNetwork net, String
attributeName){
+ HashMap categoryMap = new HashMap();
+
+ int[] nodeIndices = net.getNodeIndicesArray();
+ CyAttributes attributes = Cytoscape.getNodeAttributes();
+
+ for (int i=0; i< nodeIndices.length; i++){
+ CyNode node = (CyNode)
Cytoscape.getRootGraph().getNode(nodeIndices[i]);
+ String nodeId = node.getIdentifier();
+
+ if (attributes.getAttribute(nodeId,
attributeName.toLowerCase()) == null){
+ continue;
+ }
+
+ String attValue =
attributes.getAttribute(nodeId, attributeName.toLowerCase()).toString();
+
+ if
(categoryMap.containsKey(attValue.toLowerCase())){
+ Vector nodeVect =
(Vector)categoryMap.get(attValue.toLowerCase());
+ nodeVect.add(node);
+ }
+ else {// It is a new category
+ Vector nodeVect = new Vector();
+ nodeVect.add(node);
+ categoryMap.put(attValue.toLowerCase(),
nodeVect);
+ }
+ }
+
+ return categoryMap;
+ }
+}
Added:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java
===================================================================
---
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java
(rev 0)
+++
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java
2012-02-09 20:14:14 UTC (rev 28219)
@@ -0,0 +1,24 @@
+
+package org.cytoscape.subnetwork;
+
+import cytoscape.Cytoscape;
+import cytoscape.plugin.CytoscapePlugin;
+
+
+/**
+ * This class is used to instantiate your plugin. Put whatever initialization
code
+ * you need into the no argument constructor (the only one that will be
called).
+ * The actual functionality of your plugin can be in this class, but should
+ * probably be separated into separted classes that get instantiated here.
+ */
+public class SubnetworkByCategory extends CytoscapePlugin {
+
+ public SubnetworkByCategory() {
+ // Properly initializes things.
+ super();
+
+ // This action represents the actual behavior of the plugin.
+ MyAction action = new MyAction();
+ Cytoscape.getDesktop().getCyMenus().addAction(action);
+ }
+}
Added:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/resources/plugin.props
===================================================================
---
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/resources/plugin.props
(rev 0)
+++
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/resources/plugin.props
2012-02-09 20:14:14 UTC (rev 28219)
@@ -0,0 +1,26 @@
+# This props file would be filled out and included in the plugin jar file.
+# This props file will be used to put information into the Plugin Manager
+# about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=MyPlugin
+
+# Description used to give users information about the plugin such as what it
does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=My example Plugin.
+
+# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Other
+
+# List of authors. Note each author and institution pair are separated by a :
(colon)
+# each additional author institution pair must be separated from other pairs
bye a ; (semicolon)
+pluginAuthorsIntsitutions=Your Name:Your Institution
+
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