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 36a8caf..c4a94eb 100644 (file)
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -73,6 +73,12 @@ public abstract class TreeBuilder
 
   Vector<SequenceNode> node;
 
+  protected ScoreModelI scoreModel;
+
+  protected SimilarityParamsI scoreParams;
+
+  private AlignmentViewport avport;
+
   private AlignmentView seqStrings; // redundant? (see seqData)
 
   /**
@@ -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);
@@ -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();
 
@@ -484,9 +495,19 @@ public abstract class TreeBuilder
     return distances;
   }
 
-  public AlignmentView getSeqData()
+  public ScoreModelI getScoreModel()
+  {
+    return scoreModel;
+  }
+
+  public SimilarityParamsI getScoreParams()
+  {
+    return scoreParams;
+  }
+
+  public AlignmentViewport getAvport()
   {
-    return seqData;
+    return avport;
   }
 
 }