X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDbref.java;h=bdef00f9ff65e862a41525af12ebe564285d86de;hb=ed581b841fe9361bfe80bb006df190a29df264fb;hp=d930f14b18d6804ac27fd6b630d9d156a7e3bcc3;hpb=29ea678048298c63f589674ff35f6c026497550c;p=jalview.git

diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index d930f14..bdef00f 100644
--- 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
 {
@@ -90,8 +92,8 @@ public class Dbref extends Rangetype
     }
     else
     {
-      jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
-              + jvobj.getSrcAccString());
+      jalview.bin.Cache.log.debug(
+              "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
     }
 
   }
@@ -104,8 +106,8 @@ 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)
@@ -119,19 +121,18 @@ public class Dbref extends Rangetype
           // sync the dataset sequence, if it hasn't been done already.
           // TODO: ensure real dataset sequence corresponding to getTo is
           // recovered
-          dssync = new Datasetsequence(
-                  datastore,
-                  mp.getTo(),
-                  (mp.getMappedWidth() == mp.getWidth()) ? sequence
-                          .getDictionary()
-                          : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+          dssync = new Datasetsequence(datastore, mp.getTo(),
+                  (mp.getMappedWidth() == mp.getWidth())
+                          ? sequence.getDictionary()
+                          : ((mp.getMappedWidth() == 3)
+                                  ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
                                   : 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);
 
@@ -174,9 +175,9 @@ public class Dbref extends Rangetype
   {
     DbRef vobj = (DbRef) this.vobj;
     DBRefEntry jvobj = (DBRefEntry) this.jvobj;
-    jalview.bin.Cache.log.debug("Conflict in dbentry update for "
-            + vobj.getAccessionId() + vobj.getSource() + " "
-            + vobj.getVorbaId());
+    jalview.bin.Cache.log
+            .debug("Conflict in dbentry update for " + vobj.getAccessionId()
+                    + vobj.getSource() + " " + vobj.getVorbaId());
     // TODO Auto-generated method stub
 
   }
@@ -186,9 +187,9 @@ public class Dbref extends Rangetype
     DbRef vobj = (DbRef) this.vobj;
     DBRefEntry jvobj = (DBRefEntry) this.jvobj;
     // add new dbref
-    sq.addDBRef(jvobj = new jalview.datamodel.DBRefEntry(vobj.getSource()
-            .toString(), vobj.getVersion().toString(), vobj
-            .getAccessionId().toString()));
+    sq.addDBRef(jvobj = new jalview.datamodel.DBRefEntry(
+            vobj.getSource().toString(), vobj.getVersion().toString(),
+            vobj.getAccessionId().toString()));
     if (vobj.getMapCount() > 0)
     {
       // TODO: Jalview ignores all the other maps
@@ -229,8 +230,8 @@ public class Dbref extends Rangetype
       }
       else
       {
-        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
-                + jvobj.getSrcAccString());
+        jalview.bin.Cache.log.debug(
+                "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
       }
     }
   }