Author: pwang
Date: 2012-02-09 14:55:55 -0800 (Thu, 09 Feb 2012)
New Revision: 28223
Added:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryAction.java
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryPlugin.java
Removed:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/MyAction.java
Modified:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java
Log:
Rename class
Deleted:
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
2012-02-09 22:39:37 UTC (rev 28222)
+++
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/MyAction.java
2012-02-09 22:55:55 UTC (rev 28223)
@@ -1,230 +0,0 @@
-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;
- }
-}
Modified:
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
2012-02-09 22:39:37 UTC (rev 28222)
+++
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java
2012-02-09 22:55:55 UTC (rev 28223)
@@ -1,24 +1,207 @@
-
-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);
- }
-}
+package org.cytoscape.subnetwork;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+public class SubnetworkByCategory {
+
+ public void execute(CyNetwork net, String attributeName){
+ // 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;
+ }
+}
Copied:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryAction.java
(from rev 28222,
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/MyAction.java)
===================================================================
---
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryAction.java
(rev 0)
+++
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryAction.java
2012-02-09 22:55:55 UTC (rev 28223)
@@ -0,0 +1,54 @@
+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 SubnetworkByCategoryAction extends CytoscapeAction {
+
+ private static final long serialVersionUID =
123456789023451239L;
+
+ public SubnetworkByCategoryAction() {
+ // 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) {
+
+ String attributeName = "Category";// this is the
default attribute name
+ // get attributeName from user
+
+
+
+ //
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+
+
+ SubnetworkByCategory w = new SubnetworkByCategory();
+
+ w.execute(net, attributeName);
+
+ }
+}
Copied:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryPlugin.java
(from rev 28222,
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java)
===================================================================
---
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryPlugin.java
(rev 0)
+++
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryPlugin.java
2012-02-09 22:55:55 UTC (rev 28223)
@@ -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 SubnetworkByCategoryPlugin extends CytoscapePlugin {
+
+ public SubnetworkByCategoryPlugin() {
+ // Properly initializes things.
+ super();
+
+ // This action represents the actual behavior of the plugin.
+ SubnetworkByCategoryAction action = new
SubnetworkByCategoryAction();
+ Cytoscape.getDesktop().getCyMenus().addAction(action);
+ }
+}
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