Author: chinmoy
Date: 2009-06-08 19:55:33 -0700 (Mon, 08 Jun 2009)
New Revision: 16874
Added:
csplugins/trunk/soc/chinmoy/phylotree/.classpath
csplugins/trunk/soc/chinmoy/phylotree/.project
csplugins/trunk/soc/chinmoy/phylotree/parser/
csplugins/trunk/soc/chinmoy/phylotree/parser/ParserPlugin$MyPluginAction.class
csplugins/trunk/soc/chinmoy/phylotree/parser/ParserPlugin.class
csplugins/trunk/soc/chinmoy/phylotree/parser/ParserPlugin.java
Log:
Added: csplugins/trunk/soc/chinmoy/phylotree/.classpath
===================================================================
--- csplugins/trunk/soc/chinmoy/phylotree/.classpath
(rev 0)
+++ csplugins/trunk/soc/chinmoy/phylotree/.classpath 2009-06-09 02:55:33 UTC
(rev 16874)
@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" path=""/>
+ <classpathentry kind="con"
path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/cytoscape.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/activation.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/biojava-1.4.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/colt.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/coltginy.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/commons-cli-1.x-cytoscape-custom.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/com-nerius-math-xform.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/concurrent.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/cytoscape-cruft-obo.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/cytoscape-geom-rtree.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/cytoscape-geom-spacial.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/cytoscape-graph-dynamic.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/cytoscape-graph-fixed.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/cytoscape-render-export.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/cytoscape-render-immed.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/cytoscape-render-stateful.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/cytoscape-task.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/cytoscape-util-intr.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/ding.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/FastInfoset.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/fing.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-export-2.1.1.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-graphics2d-2.1.1.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-graphicsio-2.1.1.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-graphicsio-java-2.1.1.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-graphicsio-ps-2.1.1.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-graphicsio-svg-2.1.1.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-io-2.0.2.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-jas-plotter-2.2.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-swing-2.0.3.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-util-2.0.2.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/freehep-xml-2.1.1.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/giny.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/glf.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/http.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/i4jruntime.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/itext-2.0.4.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jaxb-api.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jaxb-impl.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jaxws-api.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jaxws-rt.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jaxws-tools.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jdom-1.0.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jhall.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jnlp.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jsr173_1.0_api.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jsr181-api.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/jsr250-api.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/junit.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/l2fprod-common-all.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/looks-2.1.4.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/phoebe.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/piccolo.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/resolver.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/saaj-api.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/saaj-impl.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/sjsxp.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/stax-ex.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/streambuffer.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/swing-layout-1.0.1.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/swingx-2006_10_27.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/tclib.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/undo.support.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/violinstrings-1.0.2.jar"/>
+ <classpathentry kind="lib" path="C:/Program
Files/Cytoscape_v2.6.2/lib/wizard.jar"/>
+ <classpathentry kind="output" path=""/>
+</classpath>
Added: csplugins/trunk/soc/chinmoy/phylotree/.project
===================================================================
--- csplugins/trunk/soc/chinmoy/phylotree/.project
(rev 0)
+++ csplugins/trunk/soc/chinmoy/phylotree/.project 2009-06-09 02:55:33 UTC
(rev 16874)
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>ParserPlugin</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ </natures>
+</projectDescription>
Added:
csplugins/trunk/soc/chinmoy/phylotree/parser/ParserPlugin$MyPluginAction.class
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/soc/chinmoy/phylotree/parser/ParserPlugin$MyPluginAction.class
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/soc/chinmoy/phylotree/parser/ParserPlugin.class
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/soc/chinmoy/phylotree/parser/ParserPlugin.class
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/soc/chinmoy/phylotree/parser/ParserPlugin.java
===================================================================
--- csplugins/trunk/soc/chinmoy/phylotree/parser/ParserPlugin.java
(rev 0)
+++ csplugins/trunk/soc/chinmoy/phylotree/parser/ParserPlugin.java
2009-06-09 02:55:33 UTC (rev 16874)
@@ -0,0 +1,178 @@
+package parser;
+
+
+import java.awt.event.ActionEvent;
+import java.util.*;
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.util.CytoscapeAction;
+/**
+ * Plugin to parse a phylogenetic tree into a network
+ *
+ */
+
+public class ParserPlugin extends CytoscapePlugin {
+
+ /**
+ * Parser a string representation of a PHYLIP phylogenetic tree
+ * into a Cytoscape network.
+ * Edit the String treeString to try different phylogenetic trees
+ *
+ */
+ public ParserPlugin() {
+ // Create an Action, add the action to Cytoscape menu
+ MyPluginAction action = new MyPluginAction(this);
+
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
action);
+ }
+
+ public class MyPluginAction extends CytoscapeAction {
+
+ public MyPluginAction(ParserPlugin myPlugin) {
+ // Add the menu item under menu pulldown "Plugins"
+ super("ParserPlugin");
+ setPreferredMenu("Plugins");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+
+ // Pick a string represenation of a phylogenetic tree
+ // These have all been obtained from the PHYLIP site
+
+ // String treeString= "";
+
+ String treeString =
"(Bovine:0.69395,(Gibbon:0.36079,(Orang:0.33636,(Gorilla:0.17147,(Chimp:0.19268,
Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460)";
+
+ // String treeString =
"(Bovine:0.69395,(Hylobates:0.36079,(Pongo:0.33636,(G._Gorilla:0.17147,
(P._paniscus:0.19268,H._sapiens:0.11927):0.08386):0.06124):0.15057):0.54939,
Rodent:1.21460)";
+ // String treeString =
"((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700,seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201,weasel:18.87953):2.09460):3.87382,dog:25.46154)";
+
+
+ //String treeString = "(B,(A,C,E),D)";
+
+ Stack <String> stack = new Stack<String>();
+ LinkedList<String> list = new LinkedList<String>();
+ LinkedList<String> edgeList = new
LinkedList<String>();
+
+ Iterator<String> iterator;
+ Iterator<String> edgeListIterator;
+
+ CyNetwork cyNetwork =
Cytoscape.createNetwork("network", false);
+
+
+ // Split the input string into a list
+ String [] substrings = treeString.split(":|,");
+ for(int i =0; i<substrings.length;i++)
+ {
+ substrings[i] = substrings[i].trim();
+ }
+
+ // Parse the input into a list
+ for(int i = 0; i<substrings.length; i++)
+ {
+ substrings[i].trim();
+ if (substrings[i].charAt(0) == '(')
+ {
+ list.add("(");
+ String[] tempSub = substrings[i].split("\\(");
+ list.add(tempSub[1]);
+ }
+ else if(substrings[i].charAt(0) != '(' &&
substrings[i].charAt(0) != ')')
+ {
+ String[] tempSub2 = substrings[i].split("\\)");
+ list.add(tempSub2[0]);
+ }
+
if(substrings[i].charAt(substrings[i].length()-1)== ')')
+ {
+ list.add(")");
+ }
+
+ }
+
+
+ // Parse the list into a CyNetwork using a stack
+
+ iterator = list.iterator();
+ int tempNodeIndex = 0;
+ while(iterator.hasNext())
+ {
+ Object tempObj = iterator.next();
+ String tempStr = (String) tempObj;
+
+ if(!tempStr.equals(")"))
+ {
+ stack.push(tempStr);
+ // Ignore (
+ }
+ if(tempStr.equals(")"))
+ {
+ String stackTop = stack.pop();
+ while(!stackTop.equals("("))
+ {
+
+ try
+ {
+ Double branchLength =
Double.parseDouble(stackTop);
+ // @DEVELOP_ME
+ // Find a way to store the branch length
with the node
+ // so that the layout is actually
representative of the
+ // edge distances
+ }
+ catch(NumberFormatException f)
+ {
+ // Add a node
+
+ CyNode nodeA =
Cytoscape.getCyNode(stackTop, true);
+ cyNetwork.addNode(nodeA);
+
+
+ // Store each node label into a list
+
+ edgeList.add(stackTop);
+ }
+
+ stackTop = stack.pop();
+ }
+ if(stackTop.equals("("))
+ {
+ // Add a temporary parent node
+ String tempNodeLabel =
"tempNode"+tempNodeIndex;
+ CyNode tempNode =
Cytoscape.getCyNode(tempNodeLabel, true);
+ cyNetwork.addNode(tempNode);
+ tempNodeIndex++;
+
+ // Add edges between the temporary
parent and the children
+ edgeListIterator = edgeList.iterator();
+ int tempEdgeIndex = 0;
+
while(edgeListIterator.hasNext())
+ {
+ Object tempEdgeListObj
= edgeListIterator.next();
+ String tempEdgeListStr
= (String) tempEdgeListObj;
+ String tempEdgeLabel =
"edge"+tempEdgeIndex;
+ CyEdge edgeA =
Cytoscape.getCyEdge(tempNodeLabel, tempEdgeLabel, tempEdgeListStr, "pp");
+ tempEdgeIndex++;
+
cyNetwork.addEdge(edgeA);
+
+
+ }
+ edgeList.clear();
+
+ // Add only the tempNode back to the
edgeList so that its parent can make an edge to it.
+ edgeList.add(tempNodeLabel);
+ }
+ }
+
+ }
+
+
+ // remove a node
+ //cyNetwork.removeNode(node1.getRootGraphIndex(), true);
+
//Cytoscape.firePropertyChange(Cytoscape.NETWORK_MODIFIED, null, cyNetwork);
+
+ // destroy the network
+ //Cytoscape.destroyNetwork(cyNetwork);
+
//Cytoscape.firePropertyChange(Cytoscape.NETWORK_DESTROYED, cyNetwork, null);
+ }
+ }
+}
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