X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=d8da4970bc3d8dcc6930a57cde99349d552caece;hb=11cce1c1e065d4430400ad414460ae643b51fbfe;hp=ca005328d12385eb7363dce7637b9cac1f6bea2b;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index ca00532..d8da497 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.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.analysis;
 
@@ -50,7 +49,7 @@ public class SeqsetUtils
    * Keys are Name, Start, End, SeqFeatures, PdbId
    * 
    * @param seq
-   *                SequenceI
+   *          SequenceI
    * @return Hashtable
    */
   public static Hashtable SeqCharacterHash(SequenceI seq)
@@ -85,9 +84,9 @@ public class SeqsetUtils
    * these methods with something more elegant.
    * 
    * @param sq
-   *                SequenceI
+   *          SequenceI
    * @param sqinfo
-   *                Hashtable
+   *          Hashtable
    * @return boolean true if name was not updated from sqinfo Name entry
    */
   public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
@@ -151,7 +150,7 @@ public class SeqsetUtils
    * ordered vector of sequences.
    * 
    * @param i
-   *                int
+   *          int
    * @return String
    */
   public static String unique_name(int i)
@@ -165,10 +164,10 @@ public class SeqsetUtils
    * name.
    * 
    * @param sequences
-   *                SequenceI[]
+   *          SequenceI[]
    * @param write_names
-   *                boolean set this to rename each of the sequences to its
-   *                unique_name(index) name
+   *          boolean set this to rename each of the sequences to its
+   *          unique_name(index) name
    * @return Hashtable to be passed to
    * @see deuniquify to recover original names (and properties) for renamed
    *      sequences
@@ -201,9 +200,9 @@ public class SeqsetUtils
    * 
    * @see uniquify(sequences,true)
    * @param map
-   *                Hashtable
+   *          Hashtable
    * @param sequences
-   *                SequenceI[]
+   *          SequenceI[]
    * @return boolean
    */
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
@@ -217,12 +216,12 @@ public class SeqsetUtils
    * 
    * @see uniquify(sequences,true)
    * @param map
-   *                Hashtable
+   *          Hashtable
    * @param sequences
-   *                SequenceI[]
+   *          SequenceI[]
    * @param quiet
-   *                when false, don't complain about sequences without any data
-   *                in the map.
+   *          when false, don't complain about sequences without any data in the
+   *          map.
    * @return boolean
    */
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
@@ -277,7 +276,7 @@ public class SeqsetUtils
    * contain at least one residue.
    * 
    * @param sequences
-   *                SequenceI[]
+   *          SequenceI[]
    * @return SequenceI[]
    */
   public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)