JAL-1517 source formatting

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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index ea0fbe0..6c4cfae 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
@@ -46,6 +48,18 @@ 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 +113,7 @@ 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