(JAL-1013) specify sequence type to ensure PCA calculation employs correct substituti...

[jalview.git] / src / jalview / gui / PCAPanel.java

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index ac37106..4948c22 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -52,6 +52,11 @@ public class PCAPanel extends GPCAPanel implements Runnable
   SequenceI[] seqs;
 
   /**
+   * use the identity matrix for calculating similarity between sequences. 
+   */
+  private boolean useidentity=false;
+
+  /**
    * Creates a new PCAPanel object.
    * 
    * @param av
@@ -67,6 +72,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     boolean sameLength = true;
 
     seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+    useidentity=av.getAlignment().isNucleotide();
     if (av.getSelectionGroup() == null)
     {
       seqs = av.alignment.getSequencesArray();
@@ -129,7 +135,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
   {
     try
     {
-      pca = new PCA(seqstrings.getSequenceStrings(' '));
+      pca = new PCA(seqstrings.getSequenceStrings(' '), useidentity);
       pca.run();
 
       // Now find the component coordinates