Author: pwang
Date: 2011-10-20 15:39:10 -0700 (Thu, 20 Oct 2011)
New Revision: 27252
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/Component.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/Component.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/Component.java
2011-10-20 22:34:50 UTC (rev 27251)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/Component.java
2011-10-20 22:39:10 UTC (rev 27252)
@@ -6,8 +6,9 @@
//-----------------------------------------------------------------------------------
package csplugins.jActiveModules;
//-----------------------------------------------------------------------------------
-import giny.model.GraphPerspective;
-import giny.model.Node;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyEdge.Type;
import java.util.Arrays;
import java.util.Comparator;
@@ -17,11 +18,8 @@
import java.util.List;
import java.util.Set;
import java.util.Vector;
-
-import cern.colt.list.IntArrayList;
-import cern.colt.map.OpenIntDoubleHashMap;
-import cytoscape.Cytoscape;
-import cytoscape.data.Semantics;
+import java.util.ArrayList;
+//import cytoscape.data.Semantics;
//-----------------------------------------------------------------------------------
/**
* This object represent a set of connected nodes that we wish to score for
signficance.
@@ -117,7 +115,7 @@
* regional scoring
*/
//public static HashMap node2edges;
- public static GraphPerspective graph;
+ public static CyNetwork graph;
/**
* Creates an empty components
@@ -145,7 +143,7 @@
* @param nComponents the neighboring components
* @param current the node which is next to all these components
*/
- public Component(Set nComponents, Node current){
+ public Component(Set nComponents, CyNode current){
nodes = new Vector();
contains = new HashSet();
scored = false;
@@ -182,10 +180,10 @@
//add the nodes of the current node to the iterator
//Edge [] e_array = (Edge [])node2edges.get(current);
//for(int i = 0;i<e_array.length;i++){
- for(Iterator neighborIt =
graph.neighborsList(current).iterator();neighborIt.hasNext();){
+ for(Iterator neighborIt = graph.getNeighborList(current,
Type.ANY).iterator();neighborIt.hasNext();){
//Node currentNeighbor = e_array[i].opposite(current);
//Node currentNeighbor = (e_array[i].getSource().equals(current) ?
e_array[i].getTarget() : e_array[i].getSource());
- Node currentNeighbor = (Node)neighborIt.next();
+ CyNode currentNeighbor = (CyNode)neighborIt.next();
if(!contains.contains(currentNeighbor)){
//this neighbor is not in the component, so it
//must be in the neighborhood. Add it in and add in
@@ -206,7 +204,7 @@
//is not in the neighborhood
Iterator neighborIt = neighbor.neighborhood.iterator();
while(neighborIt.hasNext()){
- Node nodeNeighbor = (Node)neighborIt.next();
+ CyNode nodeNeighbor = (CyNode)neighborIt.next();
if(!neighborhood.add(nodeNeighbor)){
//the neighborhood didn't change as a result of this
//update, that means it must have been added before
@@ -273,13 +271,14 @@
neighborhood = new HashSet();
it = nodes.iterator();
while(it.hasNext()){
- Node current = (Node)it.next();
+ CyNode current = (CyNode)it.next();
//Edge [] e_array = (Edge [])node2edges.get(current);
//for(int i=0;i<e_array.length;i++){
//Node neighbor = e_array[i].opposite(current);
// Node neighbor = (e_array[i].getSource().equals(current) ?
e_array[i].getTarget() : e_array[i].getSource());
- for(Iterator neighborIt =
graph.neighborsList(current).iterator();neighborIt.hasNext();){
- Node neighbor = (Node)neighborIt.next();
+
+ for(Iterator neighborIt = graph.getNeighborList(current,
Type.ANY).iterator();neighborIt.hasNext();){
+ CyNode neighbor = (CyNode)neighborIt.next();
if(!contains.contains(neighbor) && !neighborhood.contains(neighbor)){
//found a new neighbor, add its score into the mix
//and add it to the neighbor hash
@@ -304,7 +303,7 @@
*in this path.
* @param node The node be added to this component
*/
- public void addNode(Node node){
+ public void addNode(CyNode node){
scored = false;
nodes.add(node);
contains.add(node);
@@ -331,8 +330,8 @@
//Edge [] e_array = (Edge[])node2edges.get(node);
//for(int i=0;i<e_array.length;i++){
//Node neighbor = e_array[i].opposite(node);
- for(Iterator neighborIt =
graph.neighborsList(node).iterator();neighborIt.hasNext();){
- Node neighbor = (Node)neighborIt.next();
+ for(Iterator neighborIt = graph.getNeighborList(node,
Type.ANY).iterator();neighborIt.hasNext();){
+ CyNode neighbor = (CyNode)neighborIt.next();
//Node neighbor = (e_array[i].getSource().equals(node) ?
e_array[i].getTarget() : e_array[i].getSource());
//if this is a new neighbor, need to add in its score
if(!contains.contains(neighbor) && !neighborhood.contains(neighbor)){
@@ -353,7 +352,7 @@
* connected component, or even if this node belong to this particular
* component.
*/
- public void removeNode(Node node){
+ public void removeNode(CyNode node){
scored = false;
if(!regionScoring){
@@ -371,8 +370,8 @@
//it's neighbors and see if any of them are in the component
//Edge [] e_array = (Edge [])node2edges.get(node);
//for(int i=0;i<e_array.length;i++){
- for(Iterator neighborIt =
graph.neighborsList(node).iterator();neighborIt.hasNext();){
- Node nextNeighbor = (Node)neighborIt.next();
+ for(Iterator neighborIt = graph.getNeighborList(node,
Type.ANY).iterator();neighborIt.hasNext();){
+ CyNode nextNeighbor = (CyNode)neighborIt.next();
//Node nextNeighbor = e_array[i].opposite(node);
//Node nextNeighbor = (e_array[i].getSource().equals(node) ?
e_array[i].getTarget() : e_array[i].getSource());
//only do this for nodes that are in the component
@@ -380,9 +379,9 @@
//Edge [] next_array = (Edge [])node2edges.get(nextNeighbor);
boolean stillNeighbor=false;
//int j = 0;
- for(Iterator nextIt =
graph.neighborsList(nextNeighbor).iterator();nextIt.hasNext() &&
!stillNeighbor;){
+ for(Iterator nextIt = graph.getNeighborList(nextNeighbor,
Type.ANY).iterator();nextIt.hasNext() && !stillNeighbor;){
//while(!stillNeighbor && j<next_array.length){
- Node myNode = (Node)nextIt.next();
+ CyNode myNode = (CyNode)nextIt.next();
//Node myNode = (next_array[j].getSource().equals(nextNeighbor) ?
next_array[j].getTarget() : next_array[j].getSource());
if(contains.contains(myNode)){
stillNeighbor = true;
@@ -409,7 +408,7 @@
* @param node The specified node
* @return true if the component contains node
*/
- public boolean contains(Node node){
+ public boolean contains(CyNode node){
return contains.contains(node);
}
/**
@@ -588,7 +587,7 @@
Iterator it = displayNodes.iterator();
for(int i=0;i<result.length;i++){
//result[i] =
(String)Cytoscape.getNodeAttributeValue((Node)it.next(),Semantics.CANONICAL_NAME);
- result[i] = ((Node)it.next()).getIdentifier();
+ result[i] = ((CyNode)it.next()).getCyRow().get("name", String.class);
//.getIdentifier();
}
return result;
@@ -616,12 +615,12 @@
return displayNodes;
}
- public List<Node> getDisplayNodesGeneric()
+ public List<CyNode> getDisplayNodesGeneric()
{
- List<Node> list = new java.util.ArrayList(displayNodes.size());
+ List<CyNode> list = new java.util.ArrayList(displayNodes.size());
Iterator iterator = displayNodes.iterator();
while (iterator.hasNext())
- list.add((Node) iterator.next());
+ list.add((CyNode) iterator.next());
return list;
}
@@ -661,10 +660,10 @@
OpenIntDoubleHashMap node2Increase = new
OpenIntDoubleHashMap(neighborhood.size());
double previous_score = tempComponent.getScore();
for(Iterator nodeIt =
neighborhood.iterator();nodeIt.hasNext();){
- Node current = (Node)nodeIt.next();
+ CyNode current = (CyNode)nodeIt.next();
tempComponent.addNode(current);
double new_score = tempComponent.getScore();
-
node2Increase.put(current.getRootGraphIndex(),new_score-previous_score);
+ node2Increase.put(current.getSUID()
/*.getRootGraphIndex()*/,new_score-previous_score);
tempComponent.removeNode(current);
}
@@ -675,7 +674,7 @@
int idy = 0;
double score_increase = 1.0;
while(idy < neighborNodes.size() && score_increase > 0){
- Node current = graph.getNode(neighborNodes.get(idy));
+ CyNode current =
graph.getNode(neighborNodes.get(idy));
tempComponent.addNode(current);
double new_score = tempComponent.getScore();
score_increase = new_score - previous_score;
@@ -700,6 +699,49 @@
}
+
+ // replace "cern.colt.list.OpenIntDoubleHashMap"
+ private class OpenIntDoubleHashMap {
+ private HashMap hashMap = new HashMap();
+ private int size =-1;
+
+ public OpenIntDoubleHashMap(int size){
+ this.size = size;
+ }
+
+ public void put(Long index, double score){
+ this.hashMap.put(index, score);
+ }
+
+ public void keysSortedByValue(IntArrayList arrayList){
+ //???????????????
+ }
+ }
+
+ // replace "cern.colt.list.IntArrayList"
+ private class IntArrayList {
+ private ArrayList<Integer> intArray;
+ public IntArrayList(int size){
+ this.intArray = new ArrayList<Integer>(size);
+ }
+
+ public int size(){
+ return intArray.size();
+ }
+
+ public int get(int index){
+ return this.intArray.get(index);
+ }
+
+ public void reverse(){
+ int size = this.intArray.size();
+ ArrayList<Integer> tmpList = new ArrayList<Integer>(size);
+ for (int i=0; i< size; i++){
+ tmpList.set(i, this.intArray.get(size-1-i));
+ }
+ this.intArray = tmpList;
+ }
+ }
}
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