patch fixes JAL-1558

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

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 31fce15..a9c8787 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.viewmodel;
 
@@ -34,6 +35,7 @@ public class PCAModel
     seqstrings = seqstrings2;
     seqs = seqs2;
     nucleotide = nucleotide2;
+    score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
   }
 
   private volatile PCA pca;
@@ -43,6 +45,11 @@ public class PCAModel
   AlignmentView seqstrings;
 
   SequenceI[] seqs;
+  
+  /**
+   * Score matrix used to calculate PC
+   */
+  String score_matrix;
 
   /**
    * use the identity matrix for calculating similarity between sequences.
@@ -61,7 +68,7 @@ public class PCAModel
   public void run()
   {
 
-    pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
+    pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide, score_matrix);
     pca.setJvCalcMode(jvCalcMode);
     pca.run();
 
@@ -223,4 +230,14 @@ public class PCAModel
     jvCalcMode = state;
   }
 
+  public String getScore_matrix()
+  {
+    return score_matrix;
+  }
+
+  public void setScore_matrix(String score_matrix)
+  {
+    this.score_matrix = score_matrix;
+  }
+  
 }