(JAL-811) new 'annotation type' field for marking annotation rows generated by alignm...

[jalview.git] / src / jalview / appletgui / PairwiseAlignPanel.java

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index c122b3f..a1fb5ea 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.appletgui;
 
@@ -49,17 +48,17 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
 
     if (ap.av.getSelectionGroup() == null)
     {
-      seqs = ap.av.alignment.getSequencesArray();
+      seqs = ap.av.getAlignment().getSequencesArray();
     }
     else
     {
-      seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment);
+      seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.getAlignment());
     }
 
     float scores[][] = new float[seqs.length][seqs.length];
     double totscore = 0;
     int count = ap.av.getSelectionGroup().getSize();
-    String type = (ap.av.alignment.isNucleotide()) ? AlignSeq.DNA
+    String type = (ap.av.getAlignment().isNucleotide()) ? AlignSeq.DNA
             : AlignSeq.PEP;
     Sequence seq;