From 322373e3ca9cef7843be21e01032cf9c0c9a5c12 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 21 Aug 2007 12:43:54 +0000
Subject: [PATCH] newickfile class moved into its own package ready for
 refactoring public methods into Trees class.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@437 be28352e-c001-0410-b1a7-c7978e42abec
---
 src/uk/ac/vamsas/objects/utils/Trees.java          |    5 +
 .../objects/utils/{ => trees}/NewickFile.java      |  139 +++++++++++++++++++-
 2 files changed, 143 insertions(+), 1 deletion(-)
 create mode 100644 src/uk/ac/vamsas/objects/utils/Trees.java
 rename src/uk/ac/vamsas/objects/utils/{ => trees}/NewickFile.java (84%)

diff --git a/src/uk/ac/vamsas/objects/utils/Trees.java b/src/uk/ac/vamsas/objects/utils/Trees.java
new file mode 100644
index 0000000..45d4e99
--- /dev/null
+++ b/src/uk/ac/vamsas/objects/utils/Trees.java
@@ -0,0 +1,5 @@
+package uk.ac.vamsas.objects.utils;
+
+public class Trees {
+
+}
diff --git a/src/uk/ac/vamsas/objects/utils/NewickFile.java b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
similarity index 84%
rename from src/uk/ac/vamsas/objects/utils/NewickFile.java
rename to src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
index 058bca9..db62ef9 100644
--- a/src/uk/ac/vamsas/objects/utils/NewickFile.java
+++ b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
@@ -23,15 +23,20 @@
 // TODO: Implement Basic NHX tag parsing and preservation
 // TODO: http://evolution.genetics.wustl.edu/eddy/forester/NHX.html
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
-package uk.ac.vamsas.objects.utils;
+package uk.ac.vamsas.objects.utils.trees;
 
 import java.io.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.client.VorbaId;
 import uk.ac.vamsas.objects.core.SequenceType;
+import uk.ac.vamsas.objects.core.Treenode;
+import uk.ac.vamsas.objects.core.Vref;
 
 /**
  * DOCUMENT ME!
@@ -1131,4 +1136,136 @@ public class NewickFile {
       e.printStackTrace();
     }
   }
+  /**
+   * Search for leaf nodes.
+   *
+   * @param node root node to search from
+   * @param leaves Vector of leaves to add leaf node objects too.
+   *
+   * @return Vector of leaf nodes on binary tree
+   */
+  public Vector findLeaves(SequenceNode node, Vector leaves)
+  { 
+    if (node == null)
+    {
+      return leaves;
+    }
+
+    if ( (node.left() == null) && (node.right() == null)) // Interior node detection
+    {
+      leaves.addElement(node);
+
+      return leaves;
+    }
+    else
+    {
+/*  TODO: Identify internal nodes...    if (node.isSequenceLabel())
+      {
+        leaves.addElement(node);
+      }*/
+      findLeaves( (SequenceNode) node.left(), leaves);
+      findLeaves( (SequenceNode) node.right(), leaves);
+    }
+
+    return leaves;
+  }
+
+  /**
+   * make tree node vector from a newick tree structure with associated vamsas objects
+   * @param ntree
+   * @return
+   */
+  public Treenode[] makeTreeNodes() { // NJTree ntree) {
+    Vector leaves = new Vector();
+    findLeaves(root, leaves);
+    Vector tnv = new Vector();
+    Enumeration l = leaves.elements();
+    int i=0;
+    Hashtable nodespecs = new Hashtable();
+    while (l.hasMoreElements())
+    {
+      BinaryNode tnode = (BinaryNode) l.nextElement();
+      if (tnode instanceof SequenceNode)
+      {
+        if (!((SequenceNode) tnode).isPlaceholder())
+        {
+          Object assocseq = ((SequenceNode) tnode).element();
+          if (assocseq instanceof Vobject)
+          {
+            Vobject vobj = (Vobject) assocseq;
+            if (vobj!=null)
+            {
+              Treenode node = new Treenode();
+              node.setNodespec(makeNodeSpec(nodespecs, tnode));
+              node.setName(tnode.getName());
+              Vref vr = new Vref();
+              vr.addRefs(vobj);
+              node.addVref(vr);
+              tnv.addElement(node);
+            }
+            else
+            {
+              System.err.println("WARNING: Unassociated treeNode "+tnode.element().toString()+" "
+                      +((tnode.getName()!=null) ? " label "+tnode.getName() : ""));
+            }
+          }
+        }
+      }
+    }
+    if (tnv.size()>0)
+    {
+      Treenode[] tn = new Treenode[tnv.size()];
+      tnv.copyInto(tn);  
+      return tn;
+    }
+    return new Treenode[] {};
+  }
+  private String makeNodeSpec(Hashtable nodespecs, BinaryNode tnode)
+  { 
+    String nname = new String(tnode.getName());
+    Integer nindx = (Integer) nodespecs.get(nname);
+    if (nindx==null)
+    {
+      nindx = new Integer(1);
+    }
+    nname = nindx.toString()+" "+nname;
+    return nname;
+  }
+  /**
+   * call to match up Treenode specs to NJTree parsed from document object.
+   * 
+   * @param nodespec
+   * @param leaves
+   *          as returned from NJTree.findLeaves( .., ..) ..
+   * @return
+   */
+  private BinaryNode findNodeSpec(String nodespec, Vector leaves)
+  {
+    int occurence=-1;
+    String nspec = nodespec.substring(nodespec.indexOf(' ')+1);
+    String oval = nodespec.substring(0, nodespec.indexOf(' '));
+    try {
+      occurence = new Integer(oval).intValue();
+    }
+    catch (Exception e)
+    {
+      System.err.println("Invalid nodespec '"+nodespec+"'");
+      return null;
+    }
+    BinaryNode bn = null;
+    
+    int nocc = 0;
+    Enumeration en = leaves.elements();
+    while (en.hasMoreElements() && nocc<occurence)
+    {
+      bn = (BinaryNode) en.nextElement();
+      if (bn instanceof SequenceNode && bn.getName().equals(nspec))
+      {
+         --occurence;
+      } else 
+        bn=null;
+    }
+    return bn;
+  }
+
 }
-- 
1.7.10.2