Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh...

[jalview.git] / src / jalview / analysis / TreeBuilder.java

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 30b83b3..c4a94eb 100644 (file)
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -53,8 +53,6 @@ public abstract class TreeBuilder
 
   protected MatrixI distances;
 
-  public MatrixI testDistances;
-
   protected int mini;
 
   protected int minj;
@@ -79,6 +77,8 @@ public abstract class TreeBuilder
 
   protected SimilarityParamsI scoreParams;
 
+  private AlignmentViewport avport;
+
   private AlignmentView seqStrings; // redundant? (see seqData)
 
   /**
@@ -92,6 +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);
@@ -305,8 +306,8 @@ public abstract class TreeBuilder
     this.scoreModel = sm;
     this.scoreParams = scoreOptions;
 
-    testDistances = scoreModel.findDistances(seqData, scoreParams);
     distances = scoreModel.findDistances(seqData, scoreParams);
+
     makeLeaves();
 
     noClus = clusters.size();
@@ -494,11 +495,6 @@ public abstract class TreeBuilder
     return distances;
   }
 
-  public AlignmentView getSeqData()
-  {
-    return seqData;
-  }
-
   public ScoreModelI getScoreModel()
   {
     return scoreModel;
@@ -509,4 +505,9 @@ public abstract class TreeBuilder
     return scoreParams;
   }
 
+  public AlignmentViewport getAvport()
+  {
+    return avport;
+  }
+
 }