TreeBuilder now stores the used ScoreModel and ScoreParams

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

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 36a8caf..31fc4b5 100644 (file)
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -73,6 +73,10 @@ public abstract class TreeBuilder
 
   Vector<SequenceNode> node;
 
+  protected ScoreModelI scoreModel;
+
+  protected SimilarityParamsI scoreParams;
+
   private AlignmentView seqStrings; // redundant? (see seqData)
 
   /**
@@ -295,7 +299,11 @@ 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();