X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=5e7fca26507662e2235e774754c6abc8241ff9e9;hb=56da3dabe5fd0b8e68daca4ae742850bd763a207;hp=324c69a538bb0be5f9e0d886aaa43eb729ea4124;hpb=74c5bd7b1f98214a6d57d7c64d0548013530d397;p=jalview.git

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 324c69a..5e7fca2 100644
--- 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;
@@ -42,7 +41,7 @@ public class PCAModel
   SequenceI[] seqs;
 
   /*
-   * Score model used to calculate PCA
+   * Name of score model used to calculate PCA
    */
   ScoreModelI scoreModel;
 
@@ -50,39 +49,31 @@ public class PCAModel
 
   private Vector<SequencePoint> points;
 
-  private boolean jvCalcMode = true;
-
   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 modelName
    * @param params
    */
   public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
-          SimilarityParamsI params)
+          ScoreModelI modelName, SimilarityParamsI params)
   {
     seqstrings = seqData;
     seqs = sqs;
     nucleotide = nuc;
-    scoreModel = ScoreModels.getInstance().getDefaultModel(!nucleotide);
+    scoreModel = modelName;
     similarityParams = params;
   }
 
-  public boolean isJvCalcMode()
-  {
-    return jvCalcMode;
-  }
-
   public void run()
   {
     pca = new PCA(seqstrings, scoreModel, similarityParams);
-    pca.setJvCalcMode(jvCalcMode);
     pca.run();
 
     // Now find the component coordinates
@@ -229,11 +220,6 @@ public class PCAModel
     return pts;
   }
 
-  public void setJvCalcMode(boolean state)
-  {
-    jvCalcMode = state;
-  }
-
   public String getScoreModelName()
   {
     return scoreModel == null ? "" : scoreModel.getName();