JAL-2759 Rename findColumnPosition and adjustForHiddenColumns (yay!)

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

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index f216009..5e7fca2 100644 (file)
--- 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;
 
   /**
@@ -60,28 +58,22 @@ 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,
-          SimilarityParamsI params)
+  public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+          ScoreModelI modelName, SimilarityParamsI params)
   {
     seqstrings = seqData;
     seqs = sqs;
     nucleotide = nuc;
-    scoreModel = sm;
+    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
@@ -228,11 +220,6 @@ public class PCAModel
     return pts;
   }
 
-  public void setJvCalcMode(boolean state)
-  {
-    jvCalcMode = state;
-  }
-
   public String getScoreModelName()
   {
     return scoreModel == null ? "" : scoreModel.getName();