JAL-2403 improved ScoreModelI hierarchy as per Kira's review suggestions

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

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 5381880..effef9a 100644 (file)
--- 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();