X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=65e84d124422fe9a5e372960ac6169b35727d002;hb=5b05749cab04092671551fbbcdc80406b53da7d0;hp=db95c713e635367ff2d88c92d25db37e8b9638a6;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index db95c71..65e84d1 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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.datamodel;
 
@@ -107,7 +106,7 @@ public class AlignmentView
    * regions
    * 
    * @param gapCharacter
-   *                char
+   *          char
    * @return Object[] { SequenceI[], ColumnSelection}
    */
   public Object[] getAlignmentAndColumnSelection(char gapCharacter)
@@ -124,7 +123,7 @@ public class AlignmentView
    * getSequenceStrings
    * 
    * @param c
-   *                char
+   *          char
    * @return String[]
    */
   public String[] getSequenceStrings(char c)
@@ -170,7 +169,7 @@ public class AlignmentView
    * get the contiguous subalignments in an alignment view.
    * 
    * @param gapCharacter
-   *                char
+   *          char
    * @return SequenceI[][]
    */
   public SequenceI[][] getVisibleContigs(char gapCharacter)
@@ -193,7 +192,7 @@ public class AlignmentView
           njobs++;
         }
         fwidth += contigs[contig + 2]; // end up with full region width
-                                        // (including hidden regions)
+        // (including hidden regions)
         start = contigs[contig + 1] + contigs[contig + 2];
       }
       if (start < fwidth)
@@ -247,9 +246,9 @@ public class AlignmentView
    * sub alignments
    * 
    * @param nvismsa
-   *                SequenceI[][]
+   *          SequenceI[][]
    * @param orders
-   *                AlignmentOrder[] corresponding to each SequenceI[] block.
+   *          AlignmentOrder[] corresponding to each SequenceI[] block.
    * @return Object[]
    */
   public Object[] getUpdatedView(SequenceI[][] nvismsa,
@@ -294,7 +293,7 @@ public class AlignmentView
                                 + sequences.length + ")");
               }
               swidth = mseq[0].getLength(); // JBPNote: could ensure padded
-                                            // here.
+              // here.
               for (int s = 0; s < mseq.length; s++)
               {
                 if (alignment[s] == null)
@@ -495,7 +494,7 @@ public class AlignmentView
           nvis++;
         }
         fwidth += contigs[contig + 2]; // end up with full region width
-                                        // (including hidden regions)
+        // (including hidden regions)
         start = contigs[contig + 1] + contigs[contig + 2];
       }
       if (start < fwidth)