Author: chinmoy
Date: 2009-06-12 00:02:41 -0700 (Fri, 12 Jun 2009)
New Revision: 16943
Added:
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/Parser.class
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/Parser.java
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:
Working Parser object as well as Parser plugin
Added: csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/Parser.class
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/Parser.class
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/Parser.java
===================================================================
--- csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/Parser.java
(rev 0)
+++ csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/Parser.java
2009-06-12 07:02:41 UTC (rev 16943)
@@ -0,0 +1,165 @@
+package parser;
+import java.util.*;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+public class Parser {
+
+
+ String treeString;
+ LinkedList<CyNode> allNodes;
+ LinkedList<CyEdge> allEdges;
+
+ public Parser(String tree)
+ {
+ treeString = tree;
+ allNodes = new LinkedList<CyNode>();
+ allEdges = new LinkedList<CyEdge>();
+
+ }
+
+ public void parse()
+ {
+ Stack <String> stack = new Stack<String>();
+ LinkedList<String> list = new LinkedList<String>();
+ LinkedList<String> edgeList = new LinkedList<String>();
+
+ Iterator<String> iterator;
+ Iterator<String> edgeListIterator;
+
+ // 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++)
+ {
+
+ if (substrings[i].charAt(0) == '(')
+ {
+ list.add("(");
+ for (int k = 1; k<substrings[i].length(); k++)
+ {
+ if(substrings[i].charAt(k) == '(')
+ {
+ list.add("(");
+ }
+ else
+ {
+ String[] tempSub =
substrings[i].split("\\(+");
+
+ list.add(tempSub[1]);
+ break;
+
+
+ }
+ }
+ }
+
+ 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 node and edge lists 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);
+ allNodes.add(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);
+ allNodes.add(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++;
+ allEdges.add(edgeA);
+
+
+ }
+ edgeList.clear();
+
+ // Add the temporary Parent node back
into the stack
+ stack.push(tempNodeLabel);
+
+
+ }
+ }
+
+ }
+
+ }
+
+ public LinkedList<CyNode> getNodeList(){
+ return allNodes;
+
+ }
+
+ public LinkedList<CyEdge> getEdgeList(){
+ return allEdges;
+ }
+}
Copied:
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin$MyPluginAction.class
(from rev 16875,
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin$MyPluginAction.class)
===================================================================
(Binary files differ)
Copied:
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.class
(from rev 16875,
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.class)
===================================================================
(Binary files differ)
Copied:
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.java
(from rev 16875,
csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.java)
===================================================================
--- csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.java
(rev 0)
+++ csplugins/trunk/soc/chinmoy/phylotree/ParserPlugin/parser/ParserPlugin.java
2009-06-12 07:02:41 UTC (rev 16943)
@@ -0,0 +1,97 @@
+package parser;
+
+
+import java.awt.event.ActionEvent;
+import java.util.*;
+import java.io.*;
+import javax.swing.*;
+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) {
+
+ String treeString; // The variable that will contain
the string read from the file
+
+ JFileChooser chooser = new JFileChooser();
+ int option = chooser.showOpenDialog(null);
+ if (option == JFileChooser.APPROVE_OPTION) {
+ File file = chooser.getSelectedFile();
+
+
+ try{
+
+ BufferedReader in = new BufferedReader(new
FileReader(file));
+ treeString = in.readLine();
+ parser.Parser p = new Parser(treeString);
+ p.parse();
+ LinkedList<CyNode> nodes = p.getNodeList();
+ LinkedList<CyEdge> edges = p.getEdgeList();
+
+
+ CyNetwork cyNetwork =
Cytoscape.createNetwork("network", false);
+ Iterator<CyNode> iterator1 = nodes.iterator();
+ while(iterator1.hasNext())
+ {
+ cyNetwork.addNode(iterator1.next());
+
+ }
+
+ Iterator<CyEdge> iterator2 = edges.iterator();
+ while(iterator2.hasNext())
+ {
+ cyNetwork.addEdge(iterator2.next());
+
+ }
+
+ }
+
+
+ catch(IOException l)
+ {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Error
reading file: " + file.getName());
+ }
+
+ catch(NullPointerException l)
+ {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Error
reading file: " + file.getName());
+ }
+
+ }
+
+
+
+
+ }
+ }
+}
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