From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 15 Jun 2012 08:58:07 +0000 (+0100)
Subject: Merge branch 'JAL-1013_pca_rna_dna' into develop
X-Git-Tag: Jalview_2_9~463
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=9793a4e49836be392513c2a51e9fc71a0b0eb417

Merge branch 'JAL-1013_pca_rna_dna' into develop
---

9793a4e49836be392513c2a51e9fc71a0b0eb417
diff --cc src/jalview/appletgui/PCAPanel.java
index 6568b5b,3e87f17..37b4281
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@@ -59,9 -66,10 +66,10 @@@ public class PCAPanel extends EmbmenuFr
  
      this.av = av;
      seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+     useidentity=av.getAlignment().isNucleotide();
      if (av.getSelectionGroup() == null)
      {
 -      seqs = av.alignment.getSequencesArray();
 +      seqs = av.getAlignment().getSequencesArray();
      }
      else
      {
diff --cc src/jalview/gui/PCAPanel.java
index fe0c4f9,0941c7d..9dc73b7
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@@ -67,9 -72,10 +72,10 @@@ public class PCAPanel extends GPCAPane
      boolean sameLength = true;
  
      seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+     nucleotide=av.getAlignment().isNucleotide();
      if (av.getSelectionGroup() == null)
      {
 -      seqs = av.alignment.getSequencesArray();
 +      seqs = av.getAlignment().getSequencesArray();
      }
      else
      {