X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;fp=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;h=effef9a405fe3140b0f47f439b81f0ed5d285f6a;hb=aba253e57b22ce7d1f4fe376935e42aeb4f6d591;hp=5381880e05d8b31c1894a1cbb1fe23084457a1b0;hpb=21d7606604dab27e62ed700a39425b983901cef1;p=jalview.git

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 5381880..effef9a 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -1,9 +1,7 @@
 package jalview.analysis;
 
-import jalview.api.analysis.DistanceScoreModelI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.SimilarityScoreModelI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.SeqCigar;
@@ -276,22 +274,7 @@ public abstract class TreeBuilder
    */
   protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
   {
-    if (sm instanceof DistanceScoreModelI)
-    {
-      distances = ((DistanceScoreModelI) sm).findDistances(seqData,
-              scoreOptions);
-    }
-    else if (sm instanceof SimilarityScoreModelI)
-    {
-      /*
-       * 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);
-      result.reverseRange(true);
-      distances = result;
-    }
+    distances = sm.findDistances(seqData, scoreOptions);
   
     makeLeaves();