X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;h=c4a94eb87763acc47f216fc860f8f82a1fcd99cf;hb=c58f08345070f16bdc228c5e272db1bfd9cb6241;hp=0cd340e88b57dde048bb634f1e244fbce244e131;hpb=24003ce252e653972ece110e077acd16ed47fe15;p=jalview.git

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 0cd340e..c4a94eb 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -77,6 +77,8 @@ public abstract class TreeBuilder
 
   protected SimilarityParamsI scoreParams;
 
+  private AlignmentViewport avport;
+
   private AlignmentView seqStrings; // redundant? (see seqData)
 
   /**
@@ -90,6 +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);
@@ -492,11 +495,6 @@ public abstract class TreeBuilder
     return distances;
   }
 
-  public AlignmentView getSeqData()
-  {
-    return seqData;
-  }
-
   public ScoreModelI getScoreModel()
   {
     return scoreModel;
@@ -507,4 +505,9 @@ public abstract class TreeBuilder
     return scoreParams;
   }
 
+  public AlignmentViewport getAvport()
+  {
+    return avport;
+  }
+
 }