JAL-1632 JAL-2416 load score matrices from file, as float[][]

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

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index cb6deed..9383166 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,30 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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
 {
@@ -35,7 +37,7 @@ public class PCAModel
     seqstrings = seqstrings2;
     seqs = seqs2;
     nucleotide = nucleotide2;
-    score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
+    score_matrix = nucleotide2 ? "DNA" : "BLOSUM62";
   }
 
   private volatile PCA pca;
@@ -45,7 +47,7 @@ public class PCAModel
   AlignmentView seqstrings;
 
   SequenceI[] seqs;
-  
+
   /**
    * Score matrix used to calculate PC
    */
@@ -68,7 +70,8 @@ public class PCAModel
   public void run()
   {
 
-    pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide, score_matrix);
+    pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide,
+            score_matrix);
     pca.setJvCalcMode(jvCalcMode);
     pca.run();
 
@@ -145,7 +148,7 @@ public class PCAModel
 
     for (int i = 0; i < pca.getM().rows; i++)
     {
-      ((SequencePoint) points.elementAt(i)).coord = scores[i];
+      points.elementAt(i).coord = scores[i];
     }
   }
 
@@ -239,5 +242,5 @@ public class PCAModel
   {
     this.score_matrix = score_matrix;
   }
-  
+
 }