X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;h=31fc4b5ecdcc7e0e20c18a12e1d647da09822628;hb=9f327c52e2dc32b445f87c1852b7f5ffa0196870;hp=728dd629bea2e1fd46a1b5e268ec01758d4915fc;hpb=89f0bcb459ed6acff9f7da0842bf967b8f941dee;p=jalview.git

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 728dd62..31fc4b5 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -67,12 +67,16 @@ public abstract class TreeBuilder
 
   double maxDistValue;
 
-  double maxheight;
+  double maxHeight;
 
   int ycount;
 
   Vector<SequenceNode> node;
 
+  protected ScoreModelI scoreModel;
+
+  protected SimilarityParamsI scoreParams;
+
   private AlignmentView seqStrings; // redundant? (see seqData)
 
   /**
@@ -125,20 +129,20 @@ public abstract class TreeBuilder
   {
     if (nd == null)
     {
-      return maxheight;
+      return maxHeight;
     }
 
     if ((nd.left() == null) && (nd.right() == null))
     {
       nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
 
-      if (nd.height > maxheight)
+      if (nd.height > maxHeight)
       {
         return nd.height;
       }
       else
       {
-        return maxheight;
+        return maxHeight;
       }
     }
     else
@@ -149,15 +153,15 @@ public abstract class TreeBuilder
       }
       else
       {
-        maxheight = 0;
+        maxHeight = 0;
         nd.height = (float) 0.0;
       }
 
-      maxheight = findHeight((SequenceNode) (nd.left()));
-      maxheight = findHeight((SequenceNode) (nd.right()));
+      maxHeight = findHeight((SequenceNode) (nd.left()));
+      maxHeight = findHeight((SequenceNode) (nd.right()));
     }
 
-    return maxheight;
+    return maxHeight;
   }
 
   /**
@@ -295,7 +299,11 @@ public abstract class TreeBuilder
    */
   protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
   {
-    distances = sm.findDistances(seqData, scoreOptions);
+
+    this.scoreModel = sm;
+    this.scoreParams = scoreOptions;
+
+    distances = scoreModel.findDistances(seqData, scoreParams);
 
     makeLeaves();
 
@@ -479,4 +487,14 @@ public abstract class TreeBuilder
     return seqStrings;
   }
 
+  public MatrixI getDistances()
+  {
+    return distances;
+  }
+
+  public AlignmentView getSeqData()
+  {
+    return seqData;
+  }
+
 }