JAL-1473 refactor score matrices and tree score calculations to interface/api and...

[jalview.git] / src / jalview / datamodel / AlignmentView.java

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index ea0fbe0..273a685 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -46,6 +46,16 @@ public class AlignmentView
    */
   private Vector scGroups;
 
+  private boolean isNa=false;
+  /**
+   * false if the view concerns peptides
+   * @return
+   */
+  public boolean isNa()
+  {
+    return isNa;
+  }
+
   /**
    * Group defined over SeqCigars. Unlike AlignmentI associated groups, each
    * SequenceGroup hold just the essential properties for the group, but no
@@ -99,6 +109,7 @@ public class AlignmentView
             (selectedRegionOnly ? selection : null)),
             (selectedRegionOnly && selection != null) ? selection
                     .getStartRes() : 0);
+    isNa = alignment.isNucleotide();
     // walk down SeqCigar array and Alignment Array - optionally restricted by
     // selected region.
     // test group membership for each sequence in each group, store membership