apply version 2.7 copyright

[jalview.git] / src / jalview / util / DBRefUtils.java

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 411a7b9..42fbef6 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.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 2.7)
+ * Copyright (C) 2011 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.util;
 
@@ -30,9 +29,9 @@ public class DBRefUtils
   /**
    * 
    * @param dbrefs
-   *                Vector of DBRef objects to search
+   *          Vector of DBRef objects to search
    * @param sources
-   *                String[] array of source DBRef IDs to retrieve
+   *          String[] array of source DBRef IDs to retrieve
    * @return Vector
    */
   public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
@@ -79,9 +78,9 @@ public class DBRefUtils
    * isDasCoordinateSystem
    * 
    * @param string
-   *                String
+   *          String
    * @param dBRefEntry
-   *                DBRefEntry
+   *          DBRefEntry
    * @return boolean true if Source DBRefEntry is compatible with DAS
    *         CoordinateSystem name
    */
@@ -152,9 +151,9 @@ public class DBRefUtils
    * attributes.
    * 
    * @param ref
-   *                Set of references to search
+   *          Set of references to search
    * @param entry
-   *                pattern to collect - null any entry for wildcard match
+   *          pattern to collect - null any entry for wildcard match
    * @return
    */
   public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
@@ -304,8 +303,8 @@ public class DBRefUtils
             if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
                     || (refb.getMap().getMap() != null
                             && refa.getMap().getMap() != null && refb
-                            .getMap().getMap().getInverse().equals(
-                                    refa.getMap().getMap())))
+                            .getMap().getMap().getInverse()
+                            .equals(refa.getMap().getMap())))
             {
               return true;
             }
@@ -362,8 +361,8 @@ public class DBRefUtils
   {
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-//      System.err.println("Comparing A: "+refa.getSrcAccString()+(refa.hasMap()?" has map.":"."));
-//      System.err.println("Comparing B: "+refb.getSrcAccString()+(refb.hasMap()?" has map.":"."));
+      // System.err.println("Comparing A: "+refa.getSrcAccString()+(refa.hasMap()?" has map.":"."));
+      // System.err.println("Comparing B: "+refb.getSrcAccString()+(refb.hasMap()?" has map.":"."));
       if (refa.getSource() != null && refb.getSource() != null
               && refb.getSource().equals(refa.getSource()))
       {
@@ -382,9 +381,9 @@ public class DBRefUtils
                   && (refb.getMap().getMap() == null && refa.getMap()
                           .getMap() == null)
                   || (refb.getMap().getMap() != null
-                          && refa.getMap().getMap() != null && 
-                          (refb
-                          .getMap().getMap().equals(refa.getMap().getMap())))) { // getMap().getMap().containsEither(false,refa.getMap().getMap())
+                          && refa.getMap().getMap() != null && (refb
+                          .getMap().getMap().equals(refa.getMap().getMap()))))
+          { // getMap().getMap().containsEither(false,refa.getMap().getMap())
             return true;
           }
         }
@@ -401,7 +400,7 @@ public class DBRefUtils
    * @param version
    * @param acn
    * @param seq
-   *                where to anotate with reference
+   *          where to anotate with reference
    * @return parsed version of entry that was added to seq (if any)
    */
   public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,