X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;h=c4a94eb87763acc47f216fc860f8f82a1fcd99cf;hb=98b3b695032b6af0c35443044b6d3d00390b3c22;hp=b794368bd94d631633f0e069cacc75ad7ec357fd;hpb=833fafa77f2f63bea98ce1d6e1e4ee3e46e7bd53;p=jalview.git

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index b794368..c4a94eb 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -67,13 +67,19 @@ public abstract class TreeBuilder
 
   double maxDistValue;
 
-  double maxheight;
+  double maxHeight;
 
   int ycount;
 
   Vector<SequenceNode> node;
 
-  private AlignmentView seqStrings;
+  protected ScoreModelI scoreModel;
+
+  protected SimilarityParamsI scoreParams;
+
+  private AlignmentViewport avport;
+
+  private AlignmentView seqStrings; // redundant? (see seqData)
 
   /**
    * Constructor
@@ -86,6 +92,7 @@ public abstract class TreeBuilder
           SimilarityParamsI scoreParameters)
   {
     int start, end;
+    avport = av;
     boolean selview = av.getSelectionGroup() != null
             && av.getSelectionGroup().getSize() > 1;
     seqStrings = av.getAlignmentView(selview);
@@ -125,20 +132,20 @@ 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 +156,15 @@ 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 +302,11 @@ 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 +490,24 @@ public abstract class TreeBuilder
     return seqStrings;
   }
 
+  public MatrixI getDistances()
+  {
+    return distances;
+  }
+
+  public ScoreModelI getScoreModel()
+  {
+    return scoreModel;
+  }
+
+  public SimilarityParamsI getScoreParams()
+  {
+    return scoreParams;
+  }
+
+  public AlignmentViewport getAvport()
+  {
+    return avport;
+  }
+
 }