X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=0623dab3388d85073a858adb0e83046d3c5e9dd6;hb=33984e02c5687dc011d13da4b17cb0815970e0f5;hp=9b050ef1736ee6d1265af939ea555204dcb575f3;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 9b050ef..0623dab 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -30,6 +30,13 @@ 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)
@@ -69,8 +76,9 @@ public class PCAModel
 
   public void run()
   {
-
-    pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide,
+    char gapChar = scoreGapAsAny ? (nucleotide ? 'N' : 'X') : ' ';
+    String[] sequenceStrings = seqstrings.getSequenceStrings(gapChar);
+    pca = new PCA(sequenceStrings, nucleotide,
             score_matrix);
     pca.setJvCalcMode(jvCalcMode);
     pca.run();
@@ -83,32 +91,23 @@ public class PCAModel
       ii++;
     }
 
-    double[][] comps = new double[ii][ii];
-
-    for (int i = 0; i < ii; i++)
-    {
-      if (pca.getEigenvalue(i) > 1e-4)
-      {
-        comps[i] = pca.component(i);
-      }
-    }
-
-    top = pca.getM().rows - 1;
+    int height = pca.getHeight();
+    // top = pca.getM().height() - 1;
+    top = height - 1;
 
     points = new Vector<SequencePoint>();
     float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
 
-    for (int i = 0; i < pca.getM().rows; i++)
+    for (int i = 0; i < height; i++)
     {
       SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
       points.addElement(sp);
     }
-
   }
 
   public void updateRc(RotatableCanvasI rc)
   {
-    rc.setPoints(points, pca.getM().rows);
+    rc.setPoints(points, pca.getHeight());
   }
 
   public boolean isNucleotide()
@@ -146,9 +145,9 @@ public class PCAModel
     // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
     float[][] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
 
-    for (int i = 0; i < pca.getM().rows; i++)
+    for (int i = 0; i < pca.getHeight(); i++)
     {
-      ((SequencePoint) points.elementAt(i)).coord = scores[i];
+      points.elementAt(i).coord = scores[i];
     }
   }