Author: sfederow
Date: 2010-10-25 13:06:03 -0700 (Mon, 25 Oct 2010)
New Revision: 22375
Added:
csplugins/trunk/soc/sfederow/CyAnimator/src/MetabolicModule.java
Modified:
csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimator.java
Log:
Modified: csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimator.java
===================================================================
--- csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimator.java 2010-10-25
19:59:22 UTC (rev 22374)
+++ csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimator.java 2010-10-25
20:06:03 UTC (rev 22375)
@@ -28,10 +28,10 @@
class CyAnimatorAction extends CytoscapeAction {
- public CyAnimatorAction() {super("CyAnimatorrr"); }
+ public CyAnimatorAction() {super("CyAnimator"); }
public void actionPerformed(ActionEvent e) {
- System.out.println("WWDDDWWWWWWWWW");
+ //create the dialog
CyAnimatorDialog animationDialog = new
CyAnimatorDialog();
// Pop it up
animationDialog.actionPerformed(e);
Added: csplugins/trunk/soc/sfederow/CyAnimator/src/MetabolicModule.java
===================================================================
--- csplugins/trunk/soc/sfederow/CyAnimator/src/MetabolicModule.java
(rev 0)
+++ csplugins/trunk/soc/sfederow/CyAnimator/src/MetabolicModule.java
2010-10-25 20:06:03 UTC (rev 22375)
@@ -0,0 +1,281 @@
+package CyAnimator;
+
+import giny.model.Edge;
+import giny.model.Node;
+import giny.view.EdgeView;
+import giny.view.NodeView;
+
+import javax.swing.JFileChooser;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.view.CyNetworkView;
+import cytoscape.CyNode;
+import cytoscape.visual.LineStyle;
+
+import java.awt.Color;
+import java.awt.Paint;
+import java.awt.Stroke;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.regex.*;
+
+public class MetabolicModule {
+ private CyNetworkView networkView = null;
+ private CyNetwork network = null;
+ private FrameManager frameManager = null;
+
+ private List<Node> nodeList = null;
+ private List<Edge> edgeList = null;
+ private List<NodeView> nodeViewList = null;
+ private List<EdgeView> edgeViewList = null;
+ private Map<String, Integer> concMap = null;
+ private Map<String, Integer> fluxMap = null;
+
+
+ public MetabolicModule(String filePath) throws IOException{
+ System.out.println(filePath);
+ String pathConc = filePath+"/concentrations.tab";
+ String pathFlux = filePath+"/fluxes.tab";
+ String pathS = filePath+"/S.tab";
+ String pathRxns = filePath+"/rxns.tab";
+ String pathMets = filePath+"/mets.tab";
+ int rxncount = 50;
+ int metcount = 32;
+ int timepoints = 20;
+ concMap = new HashMap<String,Integer>();
+ fluxMap = new HashMap<String,Integer>();
+ BufferedReader readConcbuffer = new BufferedReader(new
FileReader(pathConc));
+ String strRead;
+
+ double concProfile[][] = new double[metcount][timepoints];
+ double fluxProfile[][] = new double[rxncount][timepoints];
+
+
+ //Read in the concentrations from a tab delimited file where
each metabolite is a row
+ //and each column is a timepoint in the simulation
+ int i = 0;
+ while ((strRead=readConcbuffer.readLine()) != null){
+
+
+
+ String splitarray[] = strRead.split("\t");
+ //System.out.println(splitarray[0]);
+
+ double normfactor = 0;
+ for(int k=0;k<timepoints;k++){
+ if(Math.abs(Double.parseDouble(splitarray[k]))
> normfactor){
+ normfactor =
Math.abs(Double.parseDouble(splitarray[k]));
+ }
+ }
+
+ for(int j=0;j<timepoints;j++){
+ //System.out.println(splitarray[j]);
+ concProfile[i][j] =
Double.parseDouble(splitarray[j]);
+ }
+ i++;
+ //String firstentry = splitarray[0];
+ //String secondentry = splitarray[1];
+
+ }
+
+ BufferedReader readSbuffer = new BufferedReader(new
FileReader(pathS));
+
+ i = 0;
+ while ((strRead=readSbuffer.readLine()) != null){
+ String splitarray[] = strRead.split("\t");
+ if(i==0){
+ for(int j=0;j<splitarray.length;j++){
+
//System.out.println(splitarray[j]+"\t"+j);
+ fluxMap.put(splitarray[j],j);
+ }
+ }
+ concMap.put(splitarray[0], i);
+ i++;
+ }
+
+ BufferedReader readFluxbuffer = new BufferedReader(new
FileReader(pathFlux));
+ i = 0;
+ while ((strRead=readFluxbuffer.readLine()) != null){
+ String splitarray[] = strRead.split("\t");
+
+ double normfactor = 0;
+ for(int k=0;k<timepoints;k++){
+ if(Math.abs(Double.parseDouble(splitarray[k]))
> normfactor){
+ normfactor =
Math.abs(Double.parseDouble(splitarray[k]));
+ }
+ }
+ for(int j=0;j<timepoints;j++){
+
+ fluxProfile[i][j] =
Double.parseDouble(splitarray[j])/normfactor;
+ }
+ i++;
+ }
+
+
+
+ //SmatrixToCyNetwork converter = new
SmatrixToCyNetwork(pathS,pathRxns,pathMets);
+
+ network = Cytoscape.getCurrentNetwork();
+ networkView = Cytoscape.getCurrentNetworkView();
+
+
+
+ nodeList = network.nodesList();
+ edgeList = network.edgesList();
+ frameManager = new FrameManager();
+
+ Pattern edgeSyntax = Pattern.compile("\\w+ \\((\\w+)\\) \\w+");
+ Matcher tmp = null;
+ /*
+ for(int m=0;m<concProfile.length;m++){
+ for(int n=0;n<concProfile[m].length;n++){
+ System.out.println(concProfile[m][n]);
+ }
+ }
+ */
+ /*
+ for(int m=0;m<fluxProfile.length;m++){
+ for(int n=0;n<fluxProfile[m].length;n++){
+ System.out.println(fluxProfile[m][n]);
+ }
+ }
+ */
+ /*
+ for(Edge edge: edgeList){
+ EdgeView edgeView = networkView.getEdgeView(edge);
+ edgeView.setStrokeWidth(50);
+ edgeView.setLineType(1);
+
+
+ }
+ */
+
+
+
+ networkView.updateView();
+ Paint origColor = null;
+ for(int k=1;k<timepoints;k++){
+
+
+ for(Node node: nodeList){
+ NodeView nodeView =
networkView.getNodeView(node);
+ if(k==1){ origColor =
nodeView.getUnselectedPaint();}
+ int col = fluxMap.get(node.getIdentifier());
+
//System.out.println(node.getIdentifier()+"\t"+nodeView.getHeight()+"\t"+nodeView.getWidth());
+
+ if(fluxProfile[col][k] < 0){
nodeView.setUnselectedPaint(Color.RED); }
+ else{
nodeView.setUnselectedPaint(Color.GREEN);}//origColor); }
+
+ //if(fluxProfile[col][k] < .05){
+ //fluxProfile[col][k] =
Math.abs(fluxProfile[col][k])*100;
+ //}
+ System.out.println(fluxProfile[col][k]);
+ if(fluxProfile[col][k] == 0){
fluxProfile[col][k] = 1; }
+
nodeView.setHeight(Math.abs(fluxProfile[col][k])*35);
+
nodeView.setWidth(Math.abs(fluxProfile[col][k])*35);
+
+
+ }
+
+ for(Edge edge: edgeList){
+ EdgeView edgeView =
networkView.getEdgeView(edge);
+ tmp = edgeSyntax.matcher(edge.getIdentifier());
+
+
+
+ //edgeView.setUnselectedPaint(Color.GRAY);
+ //System.out.println(edgeView.getStrokeWidth());
+ //System.out.println(edgeView.getLineType());
+ if(tmp.find()){
+
+ int row = concMap.get(tmp.group(1));
+ Stroke oldStroke = edgeView.getStroke();
+ try{
+ Stroke newStroke =
LineStyle.extractLineStyle(oldStroke).getStroke(Float.parseFloat(concProfile[row][k]+"")*3);
+
+ edgeView.setStroke(newStroke);
+
edgeView.setStrokeWidth(Float.parseFloat(concProfile[row][k]+"")*5);
+ }catch (Exception excp) {
+
System.out.println("hey"+excp.getMessage());
+ }
+
//System.out.println(tmp.group(1)+"\t"+row+"\t"+k);
+
//edgeView.setStrokeWidth(100*(float)concProfile[row][k]);
+
//System.out.println(concProfile[row][k]);
+ }
+ }
+
+ frameManager.addKeyFrame();
+
+ }
+
+ //networkView.updateView();
+ ArrayList<CyFrame> adjFrames = new ArrayList<CyFrame>();
+ ArrayList<CyFrame> frameList = frameManager.getKeyFrameList();
+ for(CyFrame frame: frameList){
+ frame.setInterCount(10);
+ adjFrames.add(frame);
+ }
+ frameManager.setKeyFrameList(adjFrames);
+ frameManager.play();
+
+
+
+ }
+
+
+ class SmatrixToCyNetwork{
+
+ String[] rxns;
+ String[] mets;
+
+
+ public SmatrixToCyNetwork(String pathS, String pathRxns,String
pathMets) throws Exception{
+ BufferedReader readRxnbuffer = new BufferedReader(new
FileReader(pathRxns));
+ String strRead;
+
+ while((strRead=readRxnbuffer.readLine()) != null){
+
+ rxns = strRead.split("\t");
+ }
+
+
+ BufferedReader readMetbuffer = new BufferedReader(new
FileReader(pathMets));
+
+ while ((strRead=readMetbuffer.readLine()) != null){
+
+ mets = strRead.split("\t");
+ }
+
+ }
+
+
+
+ CyNetwork network = Cytoscape.createNetwork("S_matrix");
+
+ //rxns.length;i++){
+ //CyNode node = Cytoscape.getCyNode(rxns[i], true);
+
+ //network.addNode(node);
+ //}
+ /*
+ System.out.println(network.getNodeCount());
+ */
+ public CyNetwork returnS(){
+ return null;
+ }
+
+ }
+ public FrameManager getFrameManager(){
+ return frameManager;
+ }
+}
+
+
+
Property changes on:
csplugins/trunk/soc/sfederow/CyAnimator/src/MetabolicModule.java
___________________________________________________________________
Name: svn:executable
+ *
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