X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=37b4281b79a331df7bfb8cda98127c5d5a1878af;hb=9793a4e49836be392513c2a51e9fc71a0b0eb417;hp=6568b5b18407e7fca22859c271cfd611890fd3cf;hpb=1a4b77f5614636b009e9a4cf2924ad00f4e8cb79;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 6568b5b..37b4281 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -36,9 +36,16 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
 
   AlignViewport av;
 
+  AlignmentView seqstrings;
+
   SequenceI[] seqs;
 
-  AlignmentView seqstrings;
+  
+  /**
+   * use the identity matrix for calculating similarity between sequences. 
+   */
+  private boolean useidentity=false;
+
 
   public PCAPanel(AlignViewport av)
   {
@@ -59,6 +66,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
 
     this.av = av;
     seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+    useidentity=av.getAlignment().isNucleotide();
     if (av.getSelectionGroup() == null)
     {
       seqs = av.getAlignment().getSequencesArray();
@@ -96,7 +104,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
    */
   public void run()
   {
-    pca = new PCA(seqstrings.getSequenceStrings(' '));
+    pca = new PCA(seqstrings.getSequenceStrings(' '), useidentity);
     pca.run();
 
     // Now find the component coordinates