X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=29838518818a35700f935afe1f2c893fe49d5750;hb=a94284081155efc1183fac5d8254826db542a933;hp=bb1519d933e7ac67f774e9111f9dc54c888917bb;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index bb1519d..2983851 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 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;
@@ -35,6 +37,7 @@ public class PCAModel
     seqstrings = seqstrings2;
     seqs = seqs2;
     nucleotide = nucleotide2;
+    score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
   }
 
   private volatile PCA pca;
@@ -46,6 +49,11 @@ public class PCAModel
   SequenceI[] seqs;
 
   /**
+   * Score matrix used to calculate PC
+   */
+  String score_matrix;
+
+  /**
    * use the identity matrix for calculating similarity between sequences.
    */
   private boolean nucleotide = false;
@@ -62,7 +70,8 @@ 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();
 
@@ -224,4 +233,14 @@ public class PCAModel
     jvCalcMode = state;
   }
 
+  public String getScore_matrix()
+  {
+    return score_matrix;
+  }
+
+  public void setScore_matrix(String score_matrix)
+  {
+    this.score_matrix = score_matrix;
+  }
+
 }