JAL-2403 removed remaining jvCalcMode references from PCA

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

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index fa4b747..0121e5c 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -21,9 +21,9 @@
 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;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequencePoint;
@@ -51,24 +51,31 @@ public class PCAModel
 
   private boolean jvCalcMode = true;
 
-  public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
-          boolean nucleotide2)
-  {
-    seqstrings = seqstrings2;
-    seqs = seqs2;
-    nucleotide = nucleotide2;
-    scoreModel = ScoreModels.getInstance().getDefaultModel(!nucleotide);
-  }
+  private SimilarityParamsI similarityParams;
 
-  public boolean isJvCalcMode()
+  /**
+   * 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, ScoreModelI sm,
+          SimilarityParamsI params)
   {
-    return jvCalcMode;
+    seqstrings = seqData;
+    seqs = sqs;
+    nucleotide = nuc;
+    scoreModel = sm;
+    similarityParams = params;
   }
 
   public void run()
   {
-    pca = new PCA(seqstrings, scoreModel);
-    pca.setJvCalcMode(jvCalcMode);
+    pca = new PCA(seqstrings, scoreModel, similarityParams);
     pca.run();
 
     // Now find the component coordinates