JAL-1925 update source version in license

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

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index aa90b93..9b050ef 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,12 +1,32 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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;
-
 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
 {
@@ -17,6 +37,7 @@ public class PCAModel
     seqstrings = seqstrings2;
     seqs = seqs2;
     nucleotide = nucleotide2;
+    score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
   }
 
   private volatile PCA pca;
@@ -28,6 +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;
@@ -44,7 +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();
 
@@ -206,4 +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;
+  }
+
 }