Merge branch 'develop' into features/JAL-2393customMatrices

[jalview.git] / src / jalview / viewmodel / PCAModel.java

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 324c69a..f216009 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -21,7 +21,6 @@
 package jalview.viewmodel;
 
 import jalview.analysis.PCA;
-import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.RotatableCanvasI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
@@ -55,22 +54,22 @@ public class PCAModel
   private SimilarityParamsI similarityParams;
 
   /**
-   * Constructor given sequence data and score calculation parameter options.
-   * The initial state is to compute PCA using a default score model (BLOSUM62
-   * for peptide, DNA for nucleotide).
+   * Constructor given sequence data, score model and score calculation
+   * parameter options.
    * 
    * @param seqData
    * @param sqs
    * @param nuc
+   * @param sm
    * @param params
    */
-  public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+  public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc, ScoreModelI sm,
           SimilarityParamsI params)
   {
     seqstrings = seqData;
     seqs = sqs;
     nucleotide = nuc;
-    scoreModel = ScoreModels.getInstance().getDefaultModel(!nucleotide);
+    scoreModel = sm;
     similarityParams = params;
   }