X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=0623dab3388d85073a858adb0e83046d3c5e9dd6;hb=ad66d7d56acd4063655df6a845e217683b88523e;hp=a9c87872d4962c6e5a16f6656d17a4de318fd0d4;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index a9c8787..0623dab 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,33 +1,42 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 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.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.viewmodel;
 
-import java.util.Vector;
-
 import jalview.analysis.PCA;
+import jalview.api.RotatableCanvasI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequencePoint;
-import jalview.api.RotatableCanvasI;
+
+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)
@@ -45,7 +54,7 @@ public class PCAModel
   AlignmentView seqstrings;
 
   SequenceI[] seqs;
-  
+
   /**
    * Score matrix used to calculate PC
    */
@@ -67,8 +76,10 @@ public class PCAModel
 
   public void run()
   {
-
-    pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide, score_matrix);
+    char gapChar = scoreGapAsAny ? (nucleotide ? 'N' : 'X') : ' ';
+    String[] sequenceStrings = seqstrings.getSequenceStrings(gapChar);
+    pca = new PCA(sequenceStrings, nucleotide,
+            score_matrix);
     pca.setJvCalcMode(jvCalcMode);
     pca.run();
 
@@ -80,32 +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()
@@ -143,9 +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];
     }
   }
 
@@ -239,5 +241,5 @@ public class PCAModel
   {
     this.score_matrix = score_matrix;
   }
-  
+
 }