JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 542f15e..7140867 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -21,7 +21,7 @@
 package jalview.analysis;
 
 import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.DistanceModelI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.BinaryNode;
 import jalview.datamodel.CigarArray;
@@ -224,7 +224,7 @@ public class NJTree
    *          DOCUMENT ME!
    */
   public NJTree(SequenceI[] sequence, AlignmentView seqData, String type,
-          String pwtype, ScoreModelI sm, int start, int end)
+          String pwtype, DistanceModelI sm, int start, int end)
   {
     this.sequence = sequence;
     this.node = new Vector<SequenceNode>();
@@ -736,7 +736,7 @@ public class NJTree
    * 
    * @return similarity matrix used to compute tree
    */
-  public float[][] findDistances(ScoreModelI _pwmatrix)
+  public float[][] findDistances(DistanceModelI _pwmatrix)
   {
 
     float[][] dist = new float[noseqs][noseqs];