X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=00cc94b56a494747d1f14edfb39b77fc3a5d623c;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=bb1519d933e7ac67f774e9111f9dc54c888917bb;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index bb1519d..00cc94b 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -35,6 +35,7 @@ public class PCAModel
     seqstrings = seqstrings2;
     seqs = seqs2;
     nucleotide = nucleotide2;
+    score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
   }
 
   private volatile PCA pca;
@@ -44,6 +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.
@@ -62,7 +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();
 
@@ -224,4 +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;
+  }
+  
 }