From 656fe31e8c71a0306b133e1d08d617bb7a56d4d8 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 22 Aug 2007 09:30:19 +0000
Subject: [PATCH] better 'main' test and support creation of treenodes for all
 or just 'associated' binarynodes.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@441 be28352e-c001-0410-b1a7-c7978e42abec
---
 .../ac/vamsas/objects/utils/trees/NewickFile.java  |   30 ++++++++++++++++----
 1 file changed, 25 insertions(+), 5 deletions(-)

diff --git a/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
index 2e1e893..f8e49aa 100644
--- a/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
+++ b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
@@ -203,13 +203,13 @@ public class NewickFile {
   String errormessage;
   java.io.BufferedReader dataIn=null;
   public String nextLine() throws IOException {
+    if (dataIn==null && newickFile==null)
+      throw new IOException("IMPLEMENTATION ERROR: NewickFile has not been initialised for reading a newick string.");
     if (dataIn==null)
     {
       dataIn = new BufferedReader(new StringReader(newickFile));
       error=false;
     }
-    else
-      throw new IOException("IMPLEMENTATION ERROR: NewickFile has not been initialised for reading a newick string.");
     if (!error)
       return dataIn.readLine();
     throw new IOException("Invalid Source Stream:" + errormessage);
@@ -744,6 +744,18 @@ public class NewickFile {
       System.out.println(trf.print(false, false));
       System.out.println("With bootstraps and with distances.\n");
       System.out.println(trf.print(true, true));
+      System.out.println("leaves.\n");
+      Vector lvs = new Vector();
+      trf.findLeaves(trf.root, lvs);
+      Enumeration lv =lvs.elements();
+      while (lv.hasMoreElements())
+      {
+        BinaryNode leave = (BinaryNode) lv.nextElement();
+        if (leave.getName()!=null)
+        {
+          System.out.println("Node:'"+leave.getName()+"'");
+        }
+      }      
     } catch (java.io.IOException e) {
       System.err.println("Exception\n" + e);
       e.printStackTrace();
@@ -786,9 +798,17 @@ public class NewickFile {
   /**
    * make tree node vector from a newick tree structure with associated vamsas objects
    * @param ntree
-   * @return
+   * @return Treenode definitions for nodes with associated objects
+   */
+  public Treenode[] makeTreeNodes() {
+    return makeTreeNodes(true);
+  }
+  /**
+   * make treenode vector for a parsed tree with/out leaf node associations 
+   * @param ignoreplaceholders if true means only associated nodes are returned
+   * @return treenode vector for associated or all leaves
    */
-  public Treenode[] makeTreeNodes() { 
+  public Treenode[] makeTreeNodes(boolean ignoreplaceholders) { 
     Vector leaves = new Vector();
     findLeaves(root, leaves);
     Vector tnv = new Vector();
@@ -799,7 +819,7 @@ public class NewickFile {
       BinaryNode tnode = (BinaryNode) l.nextElement();
       if (tnode instanceof SequenceNode)
       {
-        if (!((SequenceNode) tnode).isPlaceholder())
+        if (!(ignoreplaceholders && ((SequenceNode) tnode).isPlaceholder()))
         {
           Object assocseq = ((SequenceNode) tnode).element();
           if (assocseq instanceof Vobject)
-- 
1.7.10.2