Author: ghannum
Date: 2010-07-28 16:45:31 -0700 (Wed, 28 Jul 2010)
New Revision: 21066
Added:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLParagraphBlock.java
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/PanGIAPlugin.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchParameters.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/collections/ListOps.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLPage.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLTextBlock.java
Log:
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
2010-07-28 23:26:56 UTC (rev 21065)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
2010-07-28 23:45:31 UTC (rev 21066)
@@ -93,7 +93,7 @@
/////////////// Node Attribute Names /////////////
// This is common prefix for all finders.
- private static final String MODULE_FINDER_PREFIX = "Module Finder.";
+ private static final String MODULE_FINDER_PREFIX = "PanGIA.";
// Number of nodes in a module
private static final String GENE_COUNT = MODULE_FINDER_PREFIX + "member
count";
@@ -140,20 +140,17 @@
final TypedLinkNetwork<String, Float> geneticNetwork,
final double cutoff, final TaskMonitor taskMonitor,
final float remainingPercentage,
- Map<TypedLinkNodeModule<String, BFEdge>,String>
module_name)
+ Map<TypedLinkNodeModule<String, BFEdge>,String>
module_name,
+ String networkName
+ )
{
// Network attributes created here is required for managing
Visual Styles.
final CyAttributes networkAttr =
Cytoscape.getNetworkAttributes();
moduleToCyNodeMap = new HashMap<TypedLinkNodeModule<String,
BFEdge>, CyNode>();
- final Set<CyEdge> selectedEdges = new HashSet<CyEdge>();
- final Set<CyNode> selectedNodes = new HashSet<CyNode>();
-
overviewNetwork = Cytoscape.createNetwork(
- findNextAvailableNetworkName("Module Search
Results: "
- + new java.util.Date()),
- /* create_view = */false);
+ findNextAvailableNetworkName(networkName),
/* create_view = */false);
networkAttr.setAttribute(overviewNetwork.getIdentifier(),
VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME, NetworkType.OVERVIEW.name());
networkAttr.setUserVisible(VisualStyleObserver.NETWORK_TYPE_ATTRIBUTE_NAME,
false);
@@ -234,27 +231,22 @@
final double pValue = edge.value().linkMerge();
edgeAttribs.setAttribute(newEdge.getIdentifier(),
EDGE_PVALUE, Double
.valueOf(pValue));
- if (pValue < cutoff) {
- selectedEdges.add(newEdge);
- selectedNodes.add((CyNode) newEdge.getSource());
- selectedNodes.add((CyNode) newEdge.getTarget());
- }
-
+
final int gConnectedness =
geneticNetwork.getConnectedness(
sourceModule.asStringSet(),
targetModule.asStringSet());
edgeAttribs.setAttribute(newEdge.getIdentifier(),
- "genetic interaction count",
Integer.valueOf(gConnectedness));
+ "PanGIA.genetic interaction count",
Integer.valueOf(gConnectedness));
final int pConnectedness =
physicalNetwork.getConnectedness(
sourceModule.asStringSet(),
targetModule.asStringSet());
edgeAttribs.setAttribute(newEdge.getIdentifier(),
- "physical interaction count",
Integer.valueOf(pConnectedness));
- edgeAttribs.setAttribute(newEdge.getIdentifier(),
"source size",
+ "PanGIA.physical interaction count",
Integer.valueOf(pConnectedness));
+ edgeAttribs.setAttribute(newEdge.getIdentifier(),
"PanGIA.source size",
Integer.valueOf(sourceModule.size()));
- edgeAttribs.setAttribute(newEdge.getIdentifier(),
"target size",
+ edgeAttribs.setAttribute(newEdge.getIdentifier(),
"PanGIA.target size",
Integer.valueOf(targetModule.size()));
final double density = edgeScore
/ (sourceModule.size() *
targetModule.size());
- edgeAttribs.setAttribute(newEdge.getIdentifier(),
"density", Double
+ edgeAttribs.setAttribute(newEdge.getIdentifier(),
"PanGIA.genetic interaction density", Double
.valueOf(density));
}
@@ -263,10 +255,6 @@
Cytoscape.createNetworkView(overviewNetwork);
applyNetworkLayout(overviewNetwork, cutoff, maxScore);
- // Visually mark selected edges and nodes:
- overviewNetwork.setSelectedEdgeState(selectedEdges, true);
- overviewNetwork.setSelectedNodeState(selectedNodes, true);
-
taskMonitor.setStatus("5. Generating network views");
int networkViewCount = 0;
NetworkAndScore network;
@@ -355,7 +343,7 @@
for (final CyEdge edge : edges)
{
nestedNetwork.addEdge(edge);
- cyEdgeAttrs.setAttribute(edge.getIdentifier(), "Module
Finder.Interaction Type", "Physical");
+ cyEdgeAttrs.setAttribute(edge.getIdentifier(),
"PanGIA.Interaction Type", "Physical");
}
// Add the edges induced by "origGenNetwork" to our new nested
network.
@@ -364,7 +352,7 @@
for (final CyEdge edge : edges)
{
nestedNetwork.addEdge(edge);
- cyEdgeAttrs.setAttribute(edge.getIdentifier(), "Module
Finder.Interaction Type", "Genetic");
+ cyEdgeAttrs.setAttribute(edge.getIdentifier(),
"PanGIA.Interaction Type", "Genetic");
}
if (createNetworkView) {
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/PanGIAPlugin.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/PanGIAPlugin.java
2010-07-28 23:26:56 UTC (rev 21065)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/PanGIAPlugin.java
2010-07-28 23:45:31 UTC (rev 21066)
@@ -35,6 +35,7 @@
private final VisualStyleObserver vsObserver;
private static final String PLUGIN_NAME = "PanGIA";
+ public static final String VERSION = "1.0";
public PanGIAPlugin() {
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchParameters.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchParameters.java
2010-07-28 23:26:56 UTC (rev 21065)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchParameters.java
2010-07-28 23:45:31 UTC (rev 21066)
@@ -176,6 +176,6 @@
public String getReportPath()
{
- return this.getReportPath();
+ return this.reportPath;
}
}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
2010-07-28 23:26:56 UTC (rev 21065)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
2010-07-28 23:45:31 UTC (rev 21066)
@@ -1,6 +1,8 @@
package org.idekerlab.PanGIAPlugin;
+import org.idekerlab.PanGIAPlugin.utilities.html.*;
+
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
@@ -13,12 +15,13 @@
import org.idekerlab.PanGIAPlugin.ModFinder.HCSearch2;
import org.idekerlab.PanGIAPlugin.ModFinder.SouravScore;
import org.idekerlab.PanGIAPlugin.ModFinder.BFEdge.InteractionType;
-import org.idekerlab.PanGIAPlugin.data.DoubleVector;
+import org.idekerlab.PanGIAPlugin.data.*;
import org.idekerlab.PanGIAPlugin.networks.SFNetwork;
import org.idekerlab.PanGIAPlugin.networks.SNodeModule;
import org.idekerlab.PanGIAPlugin.networks.hashNetworks.FloatHashNetwork;
import org.idekerlab.PanGIAPlugin.networks.linkedNetworks.*;
import org.idekerlab.PanGIAPlugin.utilities.collections.HashMapUtil;
+import org.idekerlab.PanGIAPlugin.utilities.collections.ListOps;
import org.idekerlab.PanGIAPlugin.utilities.collections.SetUtil;
import cytoscape.CyEdge;
@@ -32,6 +35,8 @@
import org.idekerlab.PanGIAPlugin.util.Scaler;
import org.idekerlab.PanGIAPlugin.util.ScalerFactory;
+import java.io.*;
+
import javax.swing.*;
/**
@@ -81,7 +86,38 @@
if (needsToHalt) return;
+
+ //Load trainingComplexes
+ List<SNodeModule> trainingComplexes = null;
+ if (parameters.getComplexTrainingPhysical() ||
parameters.getComplexTrainingGenetic() || parameters.getComplexAnnotation())
+ {
+ final CyAttributes nodeAttr =
Cytoscape.getNodeAttributes();
+ Map<String,Set<String>> annot_node = new
HashMap<String,Set<String>>(1000);
+
+ for (String gnode : geneticNetwork.nodeIterator())
+ for (Object annot :
nodeAttr.getListAttribute(gnode, parameters.getAnnotationAttrName()))
+ HashMapUtil.updateMapSet(annot_node,
annot.toString(), gnode);
+
+ trainingComplexes = new
ArrayList<SNodeModule>(annot_node.size());
+
+ for (String annot : annot_node.keySet())
+ trainingComplexes.add(new
SNodeModule(annot,annot_node.get(annot)));
+ }
+
+ if (needsToHalt) return;
+
+ //Perform training
+ if (parameters.getComplexTrainingPhysical()) physicalNetwork =
ComplexRegression.complexRegress(physicalNetwork, trainingComplexes, true);
+ if (parameters.getComplexTrainingGenetic()) geneticNetwork =
ComplexRegression.complexRegress(geneticNetwork, trainingComplexes, true);
+
+
+ if (needsToHalt) return;
+
//Apply the degree filter
+ int pnetNodes1 = physicalNetwork.numNodes();
+ int pnetEdges1 = physicalNetwork.numEdges();
+
+
int degreeFilter = parameters.getPhysicalNetworkFilterDegree();
if (degreeFilter!=-1)
{
@@ -89,6 +125,9 @@
Set<String> pnodes = physicalNetwork.getNodes();
physicalNetwork = new
FloatHashNetwork(ptlnet.subNetwork(pnodes, degreeFilter));
}
+
+ int pnetNodes2 = physicalNetwork.numNodes();
+ int pnetEdges2 = physicalNetwork.numEdges();
if (needsToHalt) return;
@@ -109,32 +148,7 @@
if (needsToHalt) return;
- //Load trainingComplexes
- List<SNodeModule> trainingComplexes = null;
- if (parameters.getComplexTrainingPhysical() ||
parameters.getComplexTrainingGenetic() || parameters.getComplexAnnotation())
- {
- final CyAttributes nodeAttr =
Cytoscape.getNodeAttributes();
- Map<String,Set<String>> annot_node = new
HashMap<String,Set<String>>(1000);
-
- for (String gnode : geneticNetwork.nodeIterator())
- for (Object annot :
nodeAttr.getListAttribute(gnode, parameters.getAnnotationAttrName()))
- HashMapUtil.updateMapSet(annot_node,
annot.toString(), gnode);
-
- trainingComplexes = new
ArrayList<SNodeModule>(annot_node.size());
-
- for (String annot : annot_node.keySet())
- trainingComplexes.add(new
SNodeModule(annot,annot_node.get(annot)));
- }
- if (needsToHalt) return;
-
- //Perform training
- if (parameters.getComplexTrainingPhysical()) physicalNetwork =
ComplexRegression.complexRegress(physicalNetwork, trainingComplexes, true);
- if (parameters.getComplexTrainingGenetic()) geneticNetwork =
ComplexRegression.complexRegress(geneticNetwork, trainingComplexes, true);
-
-
- if (needsToHalt) return;
-
//Initialize the scoring function
final HCScoringFunction hcScoringFunction =
new SouravScore(physicalNetwork, geneticNetwork,
@@ -234,10 +248,11 @@
final TypedLinkNetwork<String, Float> pNet =
physicalNetwork.asTypedLinkNetwork();
final TypedLinkNetwork<String, Float> gNet =
geneticNetwork.asTypedLinkNetwork();
+ String networkName = "PanGIA Results: "+ new java.util.Date();
final NestedNetworkCreator nnCreator =
new NestedNetworkCreator(results, physicalInputNetwork,
geneticInputNetwork,
pNet, gNet, pValueThreshold,
taskMonitor,
- 100.0f -
COMPUTE_SIG_PERCENTAGE, module_name);
+ 100.0f -
COMPUTE_SIG_PERCENTAGE, module_name, networkName);
setStatus("Search finished!\n\n" + "Number of modules = "
+ nnCreator.getOverviewNetwork().getNodeCount() +
"\n\n"
@@ -262,7 +277,7 @@
}
//Generate report
- if (!parameters.getReportPath().equals(""))
generateReport(parameters.getReportPath());
+ if (!parameters.getReportPath().equals(""))
generateReport(parameters.getReportPath(), networkName, pnetNodes1, pnetNodes2,
pnetEdges1, pnetEdges2, geneticNetwork.numNodes(), geneticNetwork.numEdges(),
trainingComplexes);
}
private static int getNumberOfSharedNodes(CyNetwork networkA, CyNetwork
networkB){
@@ -501,8 +516,64 @@
return scaledEdgeAttribValues;
}
- private static void generateReport(String path)
+ private void generateReport(String path, String networkName, int
pnetNodes1, int pnetNodes2, int pnetEdges1, int pnetEdges2, int gnetNodes, int
gnetEdges, List<SNodeModule> trainingComplexes)
{
+ HTMLPage report = new HTMLPage();
+ report.setTitle("PanGIA report: "+networkName);
+ HTMLParagraphBlock b = new HTMLParagraphBlock(10);
+ b.add("PanGIA v. "+PanGIAPlugin.VERSION);
+ b.add("Please cite! ...");
+ b.add(networkName);
+ b.add("");
+ b.add("Physical network:");
+ b.add(parameters.getPhysicalNetwork().getIdentifier());
+ boolean isBinary = parameters.getPhysicalEdgeAttrName() == null
|| parameters.getPhysicalEdgeAttrName().length() == 0;
+ if (isBinary) b.add(parameters.getPhysicalEdgeAttrName()+"
(binary)");
+ else b.add(parameters.getPhysicalEdgeAttrName()+" (numeric,
scaling="+parameters.getPhysicalScalingMethod()+")");
+ b.add("Nodes: "+pnetNodes1+", Edges: "+pnetEdges1+"");
+ int nfd = parameters.getPhysicalNetworkFilterDegree();
+ if (nfd==-1) b.add("Network filter degree: None");
+ else b.add("Network filter degree: "+nfd+" (Nodes:
"+pnetNodes2+", Edges: "+pnetEdges2+")");
+ b.add("");
+
+ b.add("Genetic network:");
+ b.add(parameters.getGeneticNetwork().getIdentifier());
+ isBinary = parameters.getGeneticEdgeAttrName() == null ||
parameters.getGeneticEdgeAttrName().length() == 0;
+ if (isBinary) b.add(parameters.getGeneticEdgeAttrName()+"
(binary)");
+ else b.add(parameters.getGeneticEdgeAttrName()+" (numeric,
scaling="+parameters.getGeneticScalingMethod()+")");
+ b.add("Nodes: "+gnetNodes+", Edges: "+gnetEdges+"");
+ b.add("");
+
+ if (parameters.getComplexTrainingPhysical() ||
parameters.getComplexTrainingGenetic() || parameters.getComplexAnnotation())
+ {
+ b.add("Annotation:
"+parameters.getAnnotationAttrName()+" ("+trainingComplexes.size()+"
entries)");
+ b.add("");
+
+ if (parameters.getComplexTrainingPhysical())
+ {
+ b.add("Physical interaction annotation
enrichment");
+ float[] x = new
FloatVector(DoubleVector.getScale(0,100,2).getData()).getData();
+ float[] y = new
FloatVector(DoubleVector.times(DoubleVector.rUnif(51),100)).getData();
+
+ b.add("<IMG
src=\"http://chart.apis.google.com/chart?cht=lxy&chs=500x300&chd=t:"+ListOps.collectionToString(x,",")+"|"+ListOps.collectionToString(y,",")+"&chxr=0,-25,10,5&chxt=x,x,y,y&chxl=1:|Interaction_Score|2:|10^-2|10^-1|10^0|10^1|10^2|10^3|3:|Enrichment&chxp=1,60|3,50&chco=0000FF&chxs=0,000000,12,0,lt|1,000000,12,1,lt|2,000000,12,2,lt|3,000000,12,3,lt&chg=0,100,3,3,0,40\">");
+ b.add("");
+ }
+
+
+ }
+
+
+ b.add("Search parameters: alpha="+parameters.getAlpha()+",
alphaMultiplier="+parameters.getAlphaMultiplier());
+ b.add("Edge filtering:
pval="+parameters.getPValueThreshold()+",
samples="+parameters.getNumberOfSamples());
+
+ //What else to report?
+
+
+
+
+ report.addToBody(b);
+
+ report.write(path);
}
}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
2010-07-28 23:26:56 UTC (rev 21065)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
2010-07-28 23:45:31 UTC (rev 21066)
@@ -734,10 +734,10 @@
private void
reportPathButtionActionPerformed(java.awt.event.ActionEvent evt) {
JFileChooser reportFileChooser = new JFileChooser(".");
-
reportFileChooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
+ reportFileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
reportFileChooser.setMultiSelectionEnabled(false);
- reportFileChooser.setDialogTitle("Choose a report folder path");
- reportFileChooser.setSelectedFile(new File("PanGIA_Report"));
+ reportFileChooser.setDialogTitle("Choose a report path");
+ reportFileChooser.setSelectedFile(new File(new
File("PanGIA_Report.html").getAbsoluteFile().getName()));
int returnVal =
reportFileChooser.showSaveDialog(reportPathButton);
if (returnVal==JFileChooser.APPROVE_OPTION)
@@ -755,6 +755,8 @@
reportPathTextField.setToolTipText("");
reportPathTextField.setEnabled(false);
}
+
+ updateSearchButtonState();
}
@@ -829,7 +831,7 @@
private JLabel reportPathLabel;
private JTextField reportPathTextField;
private JButton reportPathButton;
- private String reportPath;
+ private String reportPath="";
private JLabel parameterErrorLabel;
// End of variables declaration
@@ -1171,7 +1173,14 @@
}
}
+ if (!reportPath.equals("") && new File(reportPath).exists() &&
new File(reportPath).isDirectory())
+ {
+ searchButton.setEnabled(false);
+ parameterErrorLabel.setText("Error: Report path cannot
be a directory.");
+ return;
+ }
+
parameterErrorLabel.setText("");
searchButton.setEnabled(true);
}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/collections/ListOps.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/collections/ListOps.java
2010-07-28 23:26:56 UTC (rev 21065)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/collections/ListOps.java
2010-07-28 23:45:31 UTC (rev 21066)
@@ -201,7 +201,33 @@
return out;
}
+
+
+ public static String collectionToString(double[] st, String delim) {
+ if (st.length == 0)
+ return "";
+
+ String out = String.valueOf(st[0]);
+
+ for (int i = 1; i < st.length; i++)
+ out += delim + st[i];
+
+ return out;
+ }
+
+ public static String collectionToString(float[] st, String delim) {
+ if (st.length == 0)
+ return "";
+
+ String out = String.valueOf(st[0]);
+
+ for (int i = 1; i < st.length; i++)
+ out += delim + st[i];
+
+ return out;
+ }
+
public static String collectionToString(Collection<String> st, String
delim) {
String out = "";
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLPage.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLPage.java
2010-07-28 23:26:56 UTC (rev 21065)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLPage.java
2010-07-28 23:45:31 UTC (rev 21066)
@@ -30,6 +30,11 @@
body.add(new HTMLTable(st,border,al,width));
}
+ public void addToBody(HTMLBlock b)
+ {
+ body.add(b);
+ }
+
public void write(String file)
{
BufferedWriter bw = FileUtil.getBufferedWriter(file, false);
Added:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLParagraphBlock.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLParagraphBlock.java
(rev 0)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLParagraphBlock.java
2010-07-28 23:45:31 UTC (rev 21066)
@@ -0,0 +1,34 @@
+package org.idekerlab.PanGIAPlugin.utilities.html;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+
+public class HTMLParagraphBlock extends HTMLTextBlock
+{
+
+ public HTMLParagraphBlock()
+ {
+ super();
+ }
+
+ public HTMLParagraphBlock(int numLines)
+ {
+ super(numLines);
+ }
+
+ protected void write(BufferedWriter bw, int depth)
+ {
+ String tabs = "";
+ for (int i=0;i<depth;i++) tabs+="\t";
+
+ try
+ {
+ bw.write(tabs+"<P>\n");
+
+ for (String line : text)
+ bw.write(tabs+line+"<BR>\n");
+
+ bw.write(tabs+"</P>\n");
+ }catch (IOException e) {e.printStackTrace();}
+ }
+}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLTextBlock.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLTextBlock.java
2010-07-28 23:26:56 UTC (rev 21065)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/html/HTMLTextBlock.java
2010-07-28 23:45:31 UTC (rev 21066)
@@ -38,6 +38,6 @@
{
for (String line : text)
bw.write(tabs+line+"\n");
- }catch (IOException e) {System.out.println("Error
HTMLPage.write(String): "+e);System.exit(0);}
+ }catch (IOException e) {e.printStackTrace();}
}
}
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