X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;h=5347ba23cb8a9723b8f2d31ab49d05561c92bc85;hb=a58c1f3005f962f3d48043e38fd5e621081eb9b0;hp=f28c6bc4acd381e4db3884d047f031efcf764944;hpb=a547c517480867ed1bbb2334ee7c51e642588a41;p=jalview.git

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index f28c6bc..5347ba2 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -55,6 +55,8 @@ public abstract class TreeBuilder
 
   Vector<SequenceNode> node;
 
+  private AlignmentView seqStrings;
+
   /**
    * Constructor
    * 
@@ -68,7 +70,7 @@ public abstract class TreeBuilder
     int start, end;
     boolean selview = av.getSelectionGroup() != null
             && av.getSelectionGroup().getSize() > 1;
-    AlignmentView seqStrings = av.getAlignmentView(selview);
+    seqStrings = av.getAlignmentView(selview);
     if (!selview)
     {
       start = 0;
@@ -277,6 +279,7 @@ public abstract class TreeBuilder
     {
       /*
        * compute similarity and invert it to give a distance measure
+       * reverseRange(true) converts maximum similarity to zero distance
        */
       MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
               seqData, scoreOptions);
@@ -458,4 +461,9 @@ public abstract class TreeBuilder
     }
   }
 
+  public AlignmentView getOriginalData()
+  {
+    return seqStrings;
+  }
+
 }