X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=928d35e46ccc5199bf76dfa03a5506c2f9d48d62;hb=19e044a2ce25aa395f9cf22f15c7378221636d21;hp=0121e5c8d7ec209c113c61aa0ce1ed6d1f7f0b9e;hpb=3e49bcba7b477c8f016f5b073a0cd2808739a944;p=jalview.git

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 0121e5c..928d35e 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -41,7 +41,7 @@ public class PCAModel
   SequenceI[] seqs;
 
   /*
-   * Score model used to calculate PCA
+   * Name of score model used to calculate PCA
    */
   ScoreModelI scoreModel;
 
@@ -49,8 +49,6 @@ public class PCAModel
 
   private Vector<SequencePoint> points;
 
-  private boolean jvCalcMode = true;
-
   private SimilarityParamsI similarityParams;
 
   /**
@@ -60,16 +58,17 @@ public class PCAModel
    * @param seqData
    * @param sqs
    * @param nuc
-   * @param sm
+   * @param modelName
    * @param params
    */
-  public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc, ScoreModelI sm,
+  public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+          ScoreModelI modelName,
           SimilarityParamsI params)
   {
     seqstrings = seqData;
     seqs = sqs;
     nucleotide = nuc;
-    scoreModel = sm;
+    scoreModel = modelName;
     similarityParams = params;
   }
 
@@ -222,11 +221,6 @@ public class PCAModel
     return pts;
   }
 
-  public void setJvCalcMode(boolean state)
-  {
-    jvCalcMode = state;
-  }
-
   public String getScoreModelName()
   {
     return scoreModel == null ? "" : scoreModel.getName();