Author: chinmoy
Date: 2009-06-11 23:58:55 -0700 (Thu, 11 Jun 2009)
New Revision: 16942
Removed:
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin$MyPluginAction.class
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.class
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.java
Log:
Deleted:
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin$MyPluginAction.class
===================================================================
(Binary files differ)
Deleted:
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.class
===================================================================
(Binary files differ)
Deleted:
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.java
===================================================================
--- csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.java
2009-06-12 03:16:49 UTC (rev 16941)
+++ csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.java
2009-06-12 06:58:55 UTC (rev 16942)
@@ -1,178 +0,0 @@
-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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