X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=8f3483d37a27c0918a2a83f88c52ba02215caebf;hb=9270f5adbff6622400c8fc933ebdb652cbb760f5;hp=7324b6c02bfb3341feb93c23e97285cdc540eac9;hpb=25b52338f677d211c04f6b60980188badf83db00;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 7324b6c..8f3483d 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -5,6 +5,8 @@ import jalview.util.*;
 import jalview.schemes.ResidueProperties;
 import java.util.*;
 
+import jalview.io.NewickFile;
+
 public class NJTree {
 
   Vector cluster;
@@ -44,6 +46,73 @@ public class NJTree {
   public NJTree(SequenceNode node) {
     top = node;
     maxheight = findHeight(top);
+
+  }
+  // Private SequenceID class to do fuzzy .equals() method for Hashtable.
+
+  private class SeqIdname {
+    String id;
+
+    SeqIdname(String s) {
+      id = new String(s);
+    }
+    public int hashCode() {
+      return (id.substring(0,4).hashCode());
+    }
+    public boolean equals(Object s) {
+      if (s instanceof SeqIdname) {
+        return this.equals((SeqIdname) s);
+      } else {
+        if (s instanceof String) {
+          return this.equals((String) s);
+        }
+      }
+      return false;
+    }
+
+
+    public boolean equals(SeqIdname s) {
+      if (id.startsWith(s.id) || s.id.startsWith(id)) {
+        return true;
+      }
+      return false;
+    }
+
+    public boolean equals(String s) {
+      if (id.startsWith(s) || s.startsWith(id)) {
+        return true;
+      }
+      return false;
+    }
+  }
+
+  public NJTree(SequenceI[] seqs, NewickFile treefile) {
+    top = treefile.getTree();
+    maxheight = findHeight(top);
+    Hashtable names = new Hashtable();
+    for (int i = 0; i < seqs.length; i++)
+    {
+      names.put(new SeqIdname(seqs[i].getDisplayId()), seqs[i]);
+    }
+    Vector leaves = new Vector();
+    findLeaves(top, leaves);
+    int i = 0;
+    int namesleft = seqs.length;
+    SequenceNode j;
+    SeqIdname nam;
+    while (i < leaves.size())
+    {
+      j = (SequenceNode) leaves.elementAt(i++);
+      nam = new SeqIdname(j.getName());
+      if ((namesleft>-1)
+          && names.containsKey(nam))
+      {
+        j.setElement(names.get(nam));
+        namesleft--;
+      } else {
+        j.setElement(new Sequence(nam.id, "THISISAPLACEHLDER"));
+      }
+    }
   }
 
   public NJTree(SequenceI[] sequence,int start, int end) {
@@ -469,8 +538,8 @@ public class NJTree {
 
       float dist = ((SequenceNode)node).dist;
       if (dist > maxDistValue) {
-	  maxdist      = (SequenceNode)node;
-	  maxDistValue = dist;
+          maxdist      = (SequenceNode)node;
+          maxDistValue = dist;
       }
     } else {
       findMaxDist((SequenceNode)node.left());
@@ -478,10 +547,10 @@ public class NJTree {
     }
   }
     public Vector getGroups() {
-	return groups;
+        return groups;
     }
     public float getMaxHeight() {
-	return maxheight;
+        return maxheight;
     }
   public void  groupNodes(SequenceNode node, float threshold) {
     if (node == null) {
@@ -570,8 +639,8 @@ public class NJTree {
   }
 
     public void reCount(SequenceNode node) {
-	ycount = 0;
-	_reCount(node);
+        ycount = 0;
+        _reCount(node);
     }
   public void _reCount(SequenceNode node) {
     if (node == null) {
@@ -595,13 +664,13 @@ public class NJTree {
 
   }
     public void swapNodes(SequenceNode node) {
-	if (node == null) {
-	    return;
-	}
-	SequenceNode tmp = (SequenceNode)node.left();
+        if (node == null) {
+            return;
+        }
+        SequenceNode tmp = (SequenceNode)node.left();
 
-	node.setLeft(node.right());
-	node.setRight(tmp);
+        node.setLeft(node.right());
+        node.setRight(tmp);
     }
   public void changeDirection(SequenceNode node, SequenceNode dir) {
     if (node == null) {
@@ -641,13 +710,13 @@ public class NJTree {
     }
   }
     public void setMaxDist(SequenceNode node) {
-	this.maxdist = maxdist;
+        this.maxdist = maxdist;
     }
     public SequenceNode getMaxDist() {
-	return maxdist;
+        return maxdist;
     }
     public SequenceNode getTopNode() {
-	return top;
+        return top;
     }
 
 }