Merge branch 'JAL-1013_pca_rna_dna' into develop

diff --cc src/jalview/analysis/PCA.java
Simple merge

diff --cc src/jalview/appletgui/PCAPanel.java
index 6568b5b,3e87f17..37b4281
--- 1/src/jalview/appletgui/PCAPanel.java
--- 2/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/datamodel/BinarySequence.java
Simple merge

diff --cc src/jalview/gui/PCAPanel.java
index fe0c4f9,0941c7d..9dc73b7
--- 1/src/jalview/gui/PCAPanel.java
--- 2/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
      {

diff --cc src/jalview/gui/RotatableCanvas.java
Simple merge

diff --cc src/jalview/jbgui/GPCAPanel.java
Simple merge

diff --cc src/jalview/schemes/ResidueProperties.java
Simple merge