X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=efb7c4ac1553193ea364dc4e1982abcbfb94cbc0;hb=50ff87bdae1829a7a7471ec393142ae659b40a11;hp=37f5e5c5b80e95c6f8ade149b3d048880d64b1bc;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 37f5e5c..efb7c4a 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,22 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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;
 
+import jalview.util.MessageManager;
 import jalview.util.ShiftList;
 
 import java.io.PrintStream;
@@ -45,6 +49,18 @@ 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
@@ -98,6 +114,7 @@ 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
@@ -225,8 +242,7 @@ public class AlignmentView
   {
     if (!seqcigararray.isSeqCigarArray())
     {
-      throw new Error(
-              "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
+      throw new Error(MessageManager.getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
     }
     // contigs = seqcigararray.applyDeletions();
     contigs = seqcigararray.getDeletedRegions();
@@ -636,7 +652,7 @@ public class AlignmentView
   {
     if (sequences == null || width <= 0)
     {
-      throw new Error("empty view cannot be updated.");
+      throw new Error(MessageManager.getString("error.empty_view_cannot_be_updated"));
     }
     if (nvismsa == null)
     {
@@ -666,11 +682,7 @@ public class AlignmentView
               j++;
               if (mseq.length != sequences.length)
               {
-                throw new Error(
-                        "Mismatch between number of sequences in block "
-                                + j + " (" + mseq.length
-                                + ") and the original view ("
-                                + sequences.length + ")");
+                throw new Error(MessageManager.formatMessage("error.mismatch_between_number_of_sequences_in_block", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(mseq.length).toString(),Integer.valueOf(sequences.length).toString() }));
               }
               swidth = mseq[0].getLength(); // JBPNote: could ensure padded
               // here.
@@ -823,7 +835,7 @@ public class AlignmentView
               else
               {
                 // place gaps.
-                throw new Error("Padding not yet implemented.");
+                throw new Error(MessageManager.getString("error.padding_not_yet_implemented"));
               }
             }
           }
@@ -836,9 +848,7 @@ public class AlignmentView
     {
       if (nvismsa.length != 1)
       {
-        throw new Error(
-                "Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="
-                        + nvismsa.length);
+        throw new Error(MessageManager.formatMessage("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", new String[]{Integer.valueOf(nvismsa.length).toString()}));
       }
       if (nvismsa[0] != null)
       {