Author: chinmoy
Date: 2009-06-26 10:32:04 -0700 (Fri, 26 Jun 2009)
New Revision: 17109
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/Phylotree.java
Log:
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
2009-06-26 15:33:11 UTC (rev 17108)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
2009-06-26 17:32:04 UTC (rev 17109)
@@ -13,269 +13,326 @@
public class PhylipTreeImpl implements Phylotree {
-
- private String treeStr;
- private LinkedList<PhylotreeNode> nodeList = null;
-
- // Constructors
-
- /*
- * Reads a PHYLIP string
- */
-
- public PhylipTreeImpl(String pTreeStr){
- this.treeStr = pTreeStr;
- nodeList = new LinkedList<PhylotreeNode>();
- parse();
- }
-
- /*
- * Reads a PHYLIP file
- */
-
- public PhylipTreeImpl(File pTreeFile){
-
- treeStr = getTreeTextFromFile(pTreeFile);
- parse();
- }
+ private String treeStr; // The tree in string format
+ private List<PhylotreeNode> nodeList = null; // List of all nodes in
the tree
- private String getTreeTextFromFile(File pTreeFile){
- String retStr = null;
-
- try{
-
- BufferedReader reader = new BufferedReader(new
FileReader(pTreeFile));
- retStr = reader.readLine();
- return retStr;
- }
- catch(IOException l)
- {
- return null;
- }
-
- catch(NullPointerException l)
- {
- return null;
- }
-
-
-
- //open the TreeFile, read its content
- // retStr = read the text from file
-
-
- }
-
- private void parse(){
- //This is the core of the parser
- //Parse the treeStr, and populate the data items,
-
-
- Stack <String> stack = new Stack<String>();
- LinkedList<String> list = new LinkedList<String>();
- LinkedList<PhylipNode> childNodeList = new LinkedList<PhylipNode>();
- LinkedList<Double> branchLengthList = new LinkedList<Double>();
-
- LinkedList<PhylipEdge> allEdges = new LinkedList<PhylipEdge>();
-
- Iterator<String> iterator;
- Iterator<PhylipNode> childNodeListIterator;
- Iterator<Double> branchLengthListIterator;
- Double branchLength = 0.0;
- // Split the input string into a list
- String [] substrings = treeStr.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++)
- {
+ // Constructors
- 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("\\(+");
+ /*
+ * Constructor that accepts a string as an argument
+ */
+ public PhylipTreeImpl(String pTreeStr){
+ this.treeStr = pTreeStr;
+ nodeList = new LinkedList<PhylotreeNode>();
+ parse();
+ }
- list.add(tempSub[1]);
- break;
+ /*
+ * Constructor that accepts a file as an argument
+ */
+ public PhylipTreeImpl(File pTreeFile){
+ treeStr = getTreeTextFromFile(pTreeFile);
+ parse();
+ }
- }
- }
- }
+ /*
+ * Reads a PHYLIP file and returns the tree in string format
+ */
+ private String getTreeTextFromFile(File pTreeFile){
+ String retStr = null;
- 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(")");
- }
+ try
+ {
+ // Read the file to obtain the tree
+ BufferedReader reader = new BufferedReader(new
FileReader(pTreeFile));
+ retStr = reader.readLine();
+ return retStr;
+ }
+ catch(IOException l)
+ {
+ // Error reading file
+ return null;
+ }
+ catch(NullPointerException l)
+ {
+ // File not found
+ return null;
+ }
- }
+ }
-
- // 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();
+ /*
+ * parse()
+ * Traverses the tree string 'treeStr'and creates appropriate nodes and
edges
+ */
+ private void parse()
+ {
+ Stack <String> stack = new Stack<String>();
+ Stack<PhylipNode> parentNodeStack = new Stack<PhylipNode>();
+ List<String> list = new LinkedList<String>();
+ List<PhylipNode> childNodeList = new LinkedList<PhylipNode>();
+ // ChildNodeList records the children of a node for the purpose
of creating edges.
+ // It is cleared after the edges for each node are created.
- while(!stackTop.equals("("))
- {
+ List<Double> branchLengthList = new LinkedList<Double>();
+ // Reflects the ChildNodeList but records the edge lengths
instead of the child nodes.
- try
- {
- branchLength = Double.parseDouble(stackTop);
- }
- catch(NumberFormatException f)
- {
- // Add a node
- PhylipNode nodeA = new PhylipNode(stackTop);
- nodeList.add(nodeA);
- // Store each node label into a list
+ // Iterators for lists
+ Iterator<String> iterator;
+ Iterator<PhylipNode> childNodeListIterator;
+ Iterator<Double> branchLengthListIterator;
- childNodeList.add(nodeA);
- branchLengthList.add(branchLength);
- }
+ Double branchLength = 0.0;
- stackTop = stack.pop();
- }
- if(stackTop.equals("("))
- {
- // Add a temporary parent node
- String tempNodeLabel = "tempNode"+tempNodeIndex;
- PhylipNode tempNode = new PhylipNode(tempNodeLabel);
-
- if(stack.isEmpty())
- {
- nodeList.add(tempNode);
-
- }
-
- tempNodeIndex++;
+ // Split the tree string into a list
+ String [] substrings = treeStr.split(":|,|;");
- // Add edges between the temporary parent and the children
- childNodeListIterator = childNodeList.iterator();
- branchLengthListIterator = branchLengthList.iterator();
- int tempEdgeIndex = 0;
- while(childNodeListIterator.hasNext())
- {
- PhylipNode childNode = childNodeListIterator.next();
- String tempEdgeLabel = "edge"+tempEdgeIndex;
-
- PhylipEdge edge = new PhylipEdge(tempNode, childNode);
- Double edgeLength = branchLengthListIterator.next();
- branchLengthListIterator.remove();
- edge.setEdgeLength(edgeLength);
-
System.out.println(edge.getSourceNode().getName()+"<-->"+edge.getTargetNode().getName()+":"+edgeLength);
- tempEdgeIndex++;
- allEdges.add(edge); // temporarily
-
- }
- childNodeList.clear();
- // Add the temporary Parent node back into the stack
- stack.push(tempNodeLabel);
-
+ // Parse the input into a list ignoring ',' but adding names,
lengths and parentheses
- }
- }
+ for(int i = 0; i<substrings.length; i++)
+ {
+ substrings[i] = substrings[i].trim();
- }
+ // For every parenthesis encountered, add it to the list
+ if (substrings[i].charAt(0) == '(')
+ {
+ list.add("(");
+ for (int k = 1; k<substrings[i].length(); k++)
+ {
+ if(substrings[i].charAt(k) == '(')
+ {
+ list.add("(");
+ }
+ else
+ {
+ // Split the remainder of the
string around the '(' if a name is encountered
+ // Add the name to the list
+ String[] tempSub =
substrings[i].split("\\(+");
-
- }
-
-
-
-
- // interface methods
- public LinkedList<PhylotreeNode> getNodeList(){
- return nodeList;
- }
-
- //Get the edges for given node
- public List<PhylotreeEdge> getEdges(PhylotreeNode pNode){
- Vector<PhylotreeEdge> retValue = new Vector<PhylotreeEdge>();
+ list.add(tempSub[1]);
+ break;
- // a node could have multiple edges
- //retValue.add(connectedNode1);
- //retValue.add(connectedNode2);
- //retValue.add(connectedNodeN);
-
- return retValue;
- }
-
- public List getEdgeAttribute(PhylotreeEdge pEdge){
- return null;
- }
-
-
- // inner classes
- class PhylipNode implements PhylotreeNode {
- private String nodeName = null;
-
- public PhylipNode(String pNodeName){
- this.nodeName = pNodeName;
- }
-
- public String getName(){
- return nodeName;
- }
- }
-
-
- class PhylipEdge implements PhylotreeEdge {
- private PhylipNode sourceNode = null;
- private PhylipNode targetNode = null;
- private double edgeLength = 0.0;
-
- public PhylipEdge(PhylipNode pSourceNode, PhylipNode pTargetNode){
- this.sourceNode = pSourceNode;
- this.targetNode = pTargetNode;
- }
-
- public void setEdgeLength(double length){
- edgeLength = length;
- }
-
- public double getEdgeLength() {
- return edgeLength;
- }
- public PhylipNode getSourceNode() {
- return sourceNode;
- }
-
- public PhylipNode getTargetNode(){
- return targetNode;
- }
- }
+
+ }
+ }
+ }
+
+ // For every name/length encountered, splice off the
')' and add it to the list
+ else if(substrings[i].charAt(0) != '(' &&
substrings[i].charAt(0) != ')')
+ {
+ String[] tempSub2 = substrings[i].split("\\)");
+ list.add(tempSub2[0]);
+ }
+
+ // For every ')' encountered add it to the list
+ if(substrings[i].charAt(substrings[i].length()-1)== ')')
+ {
+ list.add(")");
+ }
+ }
+
+
+ // Traverse the list into node and edge lists using a stack
+
+ iterator = list.iterator();
+ int parentNodeIndex = 0;
+ while(iterator.hasNext())
+ {
+ String tempStr = iterator.next();
+
+ if(!tempStr.equals(")"))
+ {
+ stack.push(tempStr);
+ // Ignore
+ }
+ if(tempStr.equals(")"))
+ {
+ // Pop off items from the stack till '(' is
encountered.
+ // Appropriately populate node and edge lists
with names/branch lenghts
+
+ String stackTop = stack.pop();
+
+ while(!stackTop.equals("("))
+ {
+
+ try
+ {
+ // If the item popped off is a
branch length, store it in the branchLength variable
+ // so that it may be associated
with the edge later
+ branchLength =
Double.parseDouble(stackTop);
+ }
+ catch(NumberFormatException f)
+ {
+ // Failure to parseDouble()
indicates that the item is a node name
+ // Add a PhylipNode
+
+ PhylipNode nodeA;
+ if(!parentNodeStack.isEmpty()
&& stackTop.equals(parentNodeStack.peek().getName()))
+ {
+ // This scenario
indicates that the stackTop is a parentNode which has previous associated edges
+ nodeA =
parentNodeStack.pop();
+ nodeList.add(nodeA);
+
+ }
+ else{
+ // This scenario
indicates that stackTop is a previously unencountered node
+ nodeA = new
PhylipNode(stackTop);
+ nodeList.add(nodeA);
+ }
+ // Also store the node in the
childNodeList and its branch length in the branchLengthList
+ // for the purpose of adding
edges from the parent node when it is created
+
+ childNodeList.add(nodeA);
+
branchLengthList.add(branchLength);
+ branchLength = 0.0;
+ }
+
+ stackTop = stack.pop();
+ }
+ if(stackTop.equals("("))
+ {
+ // '(' indicates that a set of child
nodes has been parsed
+ // Add a parent node representing the
common ancestor of all the child nodes
+
+ String parentNodeLabel =
"parentNode"+parentNodeIndex;
+ PhylipNode parentNode = new
PhylipNode(parentNodeLabel);
+ // Add a parent node even when there
are only two nodes in the entire tree
+ if(stack.isEmpty())
+ {
+ nodeList.add(parentNode);
+ }
+
+ parentNodeIndex++;
+
+ // Add edges between the parent node
and the children
+ // Initialize iterators
+ childNodeListIterator =
childNodeList.iterator();
+ branchLengthListIterator =
branchLengthList.iterator();
+
+ while(childNodeListIterator.hasNext())
+ {
+ PhylipNode childNode =
childNodeListIterator.next();
+
+ // Create the edge
+ PhylipEdge edge = new
PhylipEdge(parentNode,childNode);
+
+ // Associate the edge length
with the edge
+ Double edgeLength =
branchLengthListIterator.next();
+
branchLengthListIterator.remove();
+ edge.setEdgeLength(edgeLength);
+
+ // Record the edge in each
node's respective list of edges
+
//System.out.println(parentNode.nodeEdges);
+ parentNode.nodeEdges.add(edge);
+ childNode.nodeEdges.add(edge);
+
+ //Used during development
+
//System.out.println(edge.getSourceNode().getName()+"<-->"+edge.getTargetNode().getName()+":"+edgeLength);
+
+
+ }
+ childNodeList.clear();
+
+ // Add the label of the parent node
back into the stack so it is connected to the rest of the tree
+ // Also add the parentNode into a
separate stack so that its associated edges are preserved
+
+ stack.push(parentNodeLabel);
+ parentNodeStack.push(parentNode);
+
+ }
+ }
+
+ }
+
+
+ }
+
+
+
+
+ // Interface methods
+ public List<PhylotreeNode> getNodeList(){
+ return nodeList;
+ }
+
+ // Get the edges for given node
+ public List<PhylotreeEdge> getEdges(PhylotreeNode pNode){
+
+ // Obtain a list of edges for the node
+ PhylipNode phylipNode = (PhylipNode)pNode;
+ List<PhylipEdge> edges = phylipNode.nodeEdges;
+
+ // Add each edge to the vector to be returned
+ Vector<PhylotreeEdge> retValue = new Vector<PhylotreeEdge>();
+ Iterator<PhylipEdge> iterator = edges.iterator();
+ while(iterator.hasNext())
+ {
+ // A node could have multiple edges
+ PhylipEdge pEdge = iterator.next();
+ retValue.add(pEdge);
+ }
+ return retValue;
+ }
+
+/* Return a list of all the edge attributes
+ * The order of attributes is {edgeLength,}
+ */
+ public List<Object> getEdgeAttribute(PhylotreeEdge pEdge){
+
+ List<Object> edgeAttributes = new LinkedList<Object> ();
+
+ PhylipEdge phyEdge = (PhylipEdge)pEdge;
+
+ edgeAttributes.add(phyEdge.getEdgeLength());
+ return edgeAttributes;
+ }
+
+
+ // Inner classes
+ class PhylipNode implements PhylotreeNode {
+ private String nodeName = null;
+ public List<PhylipEdge> nodeEdges; // List of all edges
connected to this node
+
+ public PhylipNode(String pNodeName){
+ this.nodeName = pNodeName;
+ this.nodeEdges = new LinkedList<PhylipEdge>();
+ }
+
+ public String getName(){
+ return nodeName;
+ }
+ }
+
+
+ class PhylipEdge implements PhylotreeEdge {
+ private PhylipNode sourceNode = null;
+ private PhylipNode targetNode = null;
+ private double edgeLength = 0.0;
+
+ public PhylipEdge(PhylipNode pSourceNode, PhylipNode
pTargetNode){
+ this.sourceNode = pSourceNode;
+ this.targetNode = pTargetNode;
+ }
+
+ public void setEdgeLength(double length){
+ edgeLength = length;
+ }
+
+ public double getEdgeLength() {
+ return edgeLength;
+ }
+ public PhylipNode getSourceNode() {
+ return sourceNode;
+ }
+
+ public PhylipNode getTargetNode(){
+ return targetNode;
+ }
+ }
}
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/Phylotree.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/Phylotree.java
2009-06-26 15:33:11 UTC (rev 17108)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/Phylotree.java
2009-06-26 17:32:04 UTC (rev 17109)
@@ -20,6 +20,6 @@
* @param layout DOCUMENT ME!
* @return List of Edges (Node pairs)
*/
- public List getEdgeAttribute(PhylotreeEdge pEdge);
+ public List<Object> getEdgeAttribute(PhylotreeEdge pEdge);
}
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