Author: scooter
Date: 2009-11-05 20:07:07 -0800 (Thu, 05 Nov 2009)
New Revision: 18371
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
Log:
Modified to handle numeric node names
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
2009-11-06 01:39:29 UTC (rev 18370)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
2009-11-06 04:07:07 UTC (rev 18371)
@@ -13,12 +13,15 @@
import javax.swing.JOptionPane;
+import cytoscape.logger.CyLogger;
+
public class PhylipTreeImpl implements Phylotree {
private String treeStr; // The tree in string format
private List<PhylotreeNode> nodeList = null; // List of all nodes in
the tree
+ private CyLogger logger = CyLogger.getLogger("phylotree.parser");
// Constructors
@@ -46,13 +49,14 @@
* Reads a PHYLIP file and returns the tree in string format
*/
public String getTreeTextFromFile(File pTreeFile){
- String retStr = null;
+ String retStr = "";
try
{
// Read the file to obtain the tree
BufferedReader reader = new BufferedReader(new
FileReader(pTreeFile));
- retStr = reader.readLine();
+ String line = null;
+ while ((line = reader.readLine()) != null) retStr +=
line;
return retStr;
}
catch(IOException l)
@@ -83,36 +87,37 @@
{
while(str.charAt(i)!='(' &&
str.charAt(i)!=')'&& str.charAt(i)!=';')
{
-
// Create multiple words for those
separated by a ','
if(str.charAt(i)==',')
{
-
break;
}
-
-
-
word = word+str.charAt(i);
i++;
-
if(i>=str.length())
break;
-
}
// Add the word to the list
if(!word.equals(""))
{
+ // System.out.println("See word:
"+word);
if(word.charAt(0)!=':'){
+ // OK, we've got a word, but it
doesn't start with a colon. If
+ // we see a colon, then we have
a name:length pair
String [] subWords =
word.split(":");
- for(int x = 0;
x<subWords.length; x++)
- {
-
if(!subWords[x].equals(""))
- {
-
//System.out.println(subWords[x]);
+ if (subWords.length > 0) {
+ // Do we have a name?
+ if
(!subWords[0].equals("")) {
+
list.add(subWords[0].trim()); // Yes, add it as a string
+ //
System.out.println("Added: "+subWords[0].trim());
+ }
-
list.add(subWords[x].trim());
+ // Do we have a number?
+ if (subWords.length ==
2 && !subWords[1].equals("")) {
+ list.add(":");
+
list.add(subWords[1].trim());
+ //
System.out.println("Added: "+": + "+subWords[1].trim());
}
}
}
@@ -121,14 +126,12 @@
{
String [] lengths =
word.split(":");
list.add(":");
- list.add(lengths[1]);
+ list.add(lengths[1].trim());
}
}
-
word = "";
}
-
// End of the tree string
else if(i<str.length() && str.charAt(i)==';')
break;
@@ -137,44 +140,47 @@
else
{
list.add(""+str.charAt(i));
-
i++;
-
if(i>=str.length())
break;
}
-
}
+ // For debugging
+ // System.out.println("Node List before refinement: ");
+ // for (String s: list)
+ // System.out.println("Node: "+s);
+
// Refine the list
ListIterator<String> ite = list.listIterator();
-
List<Integer> replaceList = new LinkedList<Integer>();
List<Integer> ancestorList = new LinkedList<Integer>();
// Get indices of unnamed nodes
while(ite.hasNext())
{
-
int previousIndex = 0;
int index = 0;
if(ite.hasPrevious())
previousIndex = ite.previousIndex();
+
String listEle = ite.next();
+ // System.out.println("List refine - 1. Element =
"+listEle+", previous element = "+list.get(previousIndex));
-
- if((listEle.equals(",") &&
list.get(previousIndex).equals("(")) ||(listEle.equals(":") &&
list.get(previousIndex).equals("(")))
+ if((listEle.equals(",") &&
list.get(previousIndex).equals("(")) ||
+ (listEle.equals(":") &&
list.get(previousIndex).equals("(")))
{
index = ite.nextIndex();
replaceList.add(index);
+ // System.out.println("Adding
"+list.get(index)+" to replaceList");
}
else if ((listEle.equals(")")||listEle.equals(":")) &&
list.get(previousIndex).equals(","))
{
index = ite.nextIndex();
-
replaceList.add(index);
+ // System.out.println("Adding
"+list.get(index)+" to replaceList");
}
// And the unnamed parents as well
else if((listEle.equals(",") &&
list.get(previousIndex).equals(")"))
@@ -183,13 +189,10 @@
{
index = ite.nextIndex();
ancestorList.add(index-1);
-
+ // System.out.println("Adding
"+list.get(index-1)+" to ancestor list");
}
-
-
}
-
// Add unnamed nodes to marked indices
ListIterator<Integer> ite2 = replaceList.listIterator();
@@ -197,6 +200,7 @@
{
int addIndex = ite2.next();
list.add(addIndex+unIndex+ancestorNumber, "Unnamed
Node"+unIndex);
+ // System.out.println("Adding Unnamed Node"+unIndex+"
to list");
unIndex++;
}
@@ -204,8 +208,8 @@
while(ite2.hasNext())
{
int ancestorIndex = ite2.next();
-
list.add(ancestorIndex+ancestorNumber+unIndex,
"Ancestor"+ancestorNumber);
+ // System.out.println("Adding
Ancestor"+ancestorNumber+" to list");
ancestorNumber++;
}
@@ -215,11 +219,16 @@
{
String ele = ite.next();
- if(ele.equals(",")||ele.equals(":"))
+ if(ele.equals(","))
ite.remove();
}
// list.add(";");
+ // For debugging
+ // System.out.println("Node List after refinement: ");
+ // for (String s: list)
+ // System.out.println("Node: "+s);
+
return list;
}
else
@@ -241,7 +250,6 @@
List<Double> branchLengthList = new LinkedList<Double>();
// Reflects the ChildNodeList but records the edge lengths
instead of the child nodes.
-
// Iterators for lists
ListIterator<String> iterator;
Iterator<PhylipNode> childNodeListIterator;
@@ -251,17 +259,17 @@
iterator = list.listIterator();
+ // System.out.println("Creating stack");
//stack.push("Root Node"); // Something for the highest
ancestor to connect to
while(iterator.hasNext())
{
-
String tempStr = iterator.next();
-
//if(!tempStr.equals(")")&&!tempStr.equals(";"))
if(!tempStr.equals(")"))
{
+ // System.out.println("Push "+tempStr);
stack.push(tempStr);
// Ignore
}
@@ -274,17 +282,29 @@
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
+ // System.out.println("stackTop
"+stackTop);
+
+ // See if this is a branch length
+ if (stack.peek().equals(":")) {
+ //
System.out.println("BranchLength = "+stackTop);
+ 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)
+ {
+ logger.warning("Can't
parse branch length: "+f.getMessage(), f);
+ }
+ // Skip over the ":" and get it
+ if(!stack.isEmpty()) {
+ stackTop = stack.pop();
+ }
+ } else {
// Add a PhylipNode
PhylipNode nodeA;
@@ -293,12 +313,13 @@
// This scenario
indicates that the stackTop is a parentNode which has previous associated edges
nodeA =
parentNodeStack.pop();
nodeList.add(nodeA);
-
+ //
System.out.println("Added parent node "+nodeA.getName());
}
else{
// This scenario
indicates that stackTop is a previously unencountered node
nodeA = new
PhylipNode(stackTop);
nodeList.add(nodeA);
+ //
System.out.println("Added new node "+nodeA.getName());
}
// 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
@@ -330,6 +351,7 @@
ancestor = "Root Node";
}
PhylipNode parentNode = new
PhylipNode(ancestor);
+ // System.out.println("Added new parent
node "+parentNode.getName());
// Add a parent node even when there
are only two nodes in the entire tree
if(stack.isEmpty())
{
@@ -359,9 +381,7 @@
childNode.nodeEdges.add(edge);
//Used during development
- //
System.out.println(edge.getSourceNode().getName()+"<-->"+edge.getTargetNode().getName()+":"+edgeLength);
-
-
+ //
System.out.println(edge.getSourceNode().getName()+"<-->"+edge.getTargetNode().getName()+":"+edgeLength);
}
childNodeList.clear();
@@ -390,8 +410,6 @@
if(list!=null)
// Traverse the list into node and edge lists using a
stack
readListIntoStack(list);
-
-
}
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