Author: sfederow
Date: 2010-10-25 19:47:06 -0700 (Mon, 25 Oct 2010)
New Revision: 22432
Removed:
csplugins/trunk/soc/sfederow/CyAnimator/src/MetabolicModule.java
Log:
Deleted: csplugins/trunk/soc/sfederow/CyAnimator/src/MetabolicModule.java
===================================================================
--- csplugins/trunk/soc/sfederow/CyAnimator/src/MetabolicModule.java
2010-10-26 02:46:35 UTC (rev 22431)
+++ csplugins/trunk/soc/sfederow/CyAnimator/src/MetabolicModule.java
2010-10-26 02:47:06 UTC (rev 22432)
@@ -1,281 +0,0 @@
-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;
- }
-}
-
-
-
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