JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / io / vamsas / Dbref.java

diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index d930f14..3e2f4e5 100644 (file)
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -1,31 +1,33 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io.vamsas;
 
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+
 import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Map;
 import uk.ac.vamsas.objects.core.Sequence;
-import uk.ac.vamsas.objects.core.SequenceType;
-import jalview.io.VamsasAppDatastore;
 
 public class Dbref extends Rangetype
 {
@@ -104,8 +106,7 @@ public class Dbref extends Rangetype
    */
   private void updateMapTo(jalview.datamodel.Mapping mp)
   {
-    log
-            .info("Performing updateMapTo remove this message when we know what we're doing.");
+    log.info("Performing updateMapTo remove this message when we know what we're doing.");
     // TODO determine how sequences associated with database mappings are stored
     // in the document
     if (mp != null && mp.getTo() != null)
@@ -128,10 +129,10 @@ public class Dbref extends Rangetype
                                   : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA),
                   ds);
         }
-        // 
+        //
         // TODO: NOW add a mapping between new dataset sequence and sequence
         // associated with the database reference
-        
+
         // dna mappings only...
         // new jalview.io.vamsas.Sequencemapping(datastore, mp, sequence, ds);