JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to

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

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 4ad6d48..fa4b747 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -21,7 +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.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequencePoint;
@@ -30,23 +32,6 @@ import java.util.Vector;
 
 public class PCAModel
 {
-  /*
-   * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
-   * for pairwise scoring; 2.10.2 uses gap score (last column) in
-   * score matrix (JAL-2397)
-   * Set this flag to true (via Groovy) for 2.10.1 behaviour
-   */
-  private static boolean scoreGapAsAny = false;
-
-  public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
-          boolean nucleotide2)
-  {
-    seqstrings = seqstrings2;
-    seqs = seqs2;
-    nucleotide = nucleotide2;
-    score_matrix = nucleotide2 ? "DNA" : "BLOSUM62";
-  }
-
   private volatile PCA pca;
 
   int top;
@@ -55,20 +40,26 @@ public class PCAModel
 
   SequenceI[] seqs;
 
-  /**
-   * Score matrix used to calculate PC
+  /*
+   * Score model used to calculate PCA
    */
-  String score_matrix;
+  ScoreModelI scoreModel;
 
-  /**
-   * use the identity matrix for calculating similarity between sequences.
-   */
   private boolean nucleotide = false;
 
   private Vector<SequencePoint> points;
 
   private boolean jvCalcMode = true;
 
+  public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
+          boolean nucleotide2)
+  {
+    seqstrings = seqstrings2;
+    seqs = seqs2;
+    nucleotide = nucleotide2;
+    scoreModel = ScoreModels.getInstance().getDefaultModel(!nucleotide);
+  }
+
   public boolean isJvCalcMode()
   {
     return jvCalcMode;
@@ -76,10 +67,7 @@ public class PCAModel
 
   public void run()
   {
-    char gapChar = scoreGapAsAny ? (nucleotide ? 'N' : 'X') : ' ';
-    String[] sequenceStrings = seqstrings.getSequenceStrings(gapChar);
-    pca = new PCA(sequenceStrings, nucleotide,
-            score_matrix);
+    pca = new PCA(seqstrings, scoreModel);
     pca.setJvCalcMode(jvCalcMode);
     pca.run();
 
@@ -232,14 +220,14 @@ public class PCAModel
     jvCalcMode = state;
   }
 
-  public String getScore_matrix()
+  public String getScoreModelName()
   {
-    return score_matrix;
+    return scoreModel == null ? "" : scoreModel.getName();
   }
 
-  public void setScore_matrix(String score_matrix)
+  public void setScoreModel(ScoreModelI sm)
   {
-    this.score_matrix = score_matrix;
+    this.scoreModel = sm;
   }
 
 }