X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=a9c87872d4962c6e5a16f6656d17a4de318fd0d4;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=aa90b93f9009485a12fa9d3ac4cc294442458e15;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index aa90b93..a9c8787 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.viewmodel;
 
 import java.util.Vector;
@@ -17,6 +35,7 @@ public class PCAModel
     seqstrings = seqstrings2;
     seqs = seqs2;
     nucleotide = nucleotide2;
+    score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
   }
 
   private volatile PCA pca;
@@ -26,6 +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.
@@ -44,7 +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();
 
@@ -206,4 +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;
+  }
+  
 }