X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDbref.java;h=a82d9d49f80bd0e0a953ba0aaf4bbce49c233b0c;hb=67b3acb8df1438ef37a756c04e14f5a3b8406808;hp=e247d9cba78a5be7dffdf0eb83eaccf3186a6913;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index e247d9c..a82d9d4 100644
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -1,42 +1,48 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * 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.bin.Cache;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
 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;
+import uk.ac.vamsas.objects.utils.SymbolDictionary;
 
 public class Dbref extends Rangetype
 {
-  jalview.datamodel.SequenceI sq = null;
+  SequenceI sq = null;
 
   uk.ac.vamsas.objects.core.Sequence sequence = null;
 
   DataSet ds;
 
   public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
-          jalview.datamodel.SequenceI sq2,
-          uk.ac.vamsas.objects.core.Sequence sequence2, DataSet dataset)
+          SequenceI sq2, uk.ac.vamsas.objects.core.Sequence sequence2,
+          DataSet dataset)
   {
     super(datastore, dbentry, DbRef.class);
     // initialise object specific attributes
@@ -51,7 +57,7 @@ public class Dbref extends Rangetype
   public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
           SequenceI dsseq)
   {
-    super(datastore, ref, jalview.datamodel.DBRefEntry.class);
+    super(datastore, ref, DBRefEntry.class);
     sequence = vdseq;
     sq = dsseq;
     ds = (DataSet) vdseq.getV_parent();
@@ -68,7 +74,7 @@ public class Dbref extends Rangetype
     if (jvobj.getMap() != null)
     {
       // Record mapping to external database coordinate system.
-      jalview.datamodel.Mapping mp = jvobj.getMap();
+      Mapping mp = jvobj.getMap();
       if (mp.getMap() != null)
       {
         Map vMap = null;
@@ -89,7 +95,7 @@ public class Dbref extends Rangetype
     }
     else
     {
-      jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+      Cache.log.debug("Ignoring mapless DbRef.Map "
               + jvobj.getSrcAccString());
     }
 
@@ -101,10 +107,9 @@ public class Dbref extends Rangetype
    * 
    * @param mp
    */
-  private void updateMapTo(jalview.datamodel.Mapping mp)
+  private void updateMapTo(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)
@@ -123,11 +128,11 @@ public class Dbref extends Rangetype
                   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),
+                          : ((mp.getMappedWidth() == 3) ? SymbolDictionary.STANDARD_NA
+                                  : SymbolDictionary.STANDARD_AA),
                   ds);
         }
-        // 
+        //
         // TODO: NOW add a mapping between new dataset sequence and sequence
         // associated with the database reference
 
@@ -156,12 +161,11 @@ public class Dbref extends Rangetype
       // TODO: Jalview ignores all the other maps
       if (vobj.getMapCount() > 1)
       {
-        jalview.bin.Cache.log
+        Cache.log
                 .debug("Ignoring additional mappings on DbRef: "
                         + jvobj.getSource() + ":" + jvobj.getAccessionId());
       }
-      jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
-              parsemapType(vobj.getMap(0)));
+      Mapping mp = new Mapping(parsemapType(vobj.getMap(0)));
       if (jvobj.getMap() == null || !mp.equals(jvobj.getMap()))
       {
         jvobj.setMap(mp);
@@ -173,7 +177,7 @@ 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 "
+    Cache.log.debug("Conflict in dbentry update for "
             + vobj.getAccessionId() + vobj.getSource() + " "
             + vobj.getVorbaId());
     // TODO Auto-generated method stub
@@ -185,7 +189,7 @@ 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()
+    sq.addDBRef(jvobj = new DBRefEntry(vobj.getSource()
             .toString(), vobj.getVersion().toString(), vobj
             .getAccessionId().toString()));
     if (vobj.getMapCount() > 0)
@@ -193,11 +197,11 @@ public class Dbref extends Rangetype
       // TODO: Jalview ignores all the other maps
       if (vobj.getMapCount() > 1)
       {
-        jalview.bin.Cache.log
+        Cache.log
                 .debug("Ignoring additional mappings on DbRef: "
                         + jvobj.getSource() + ":" + jvobj.getAccessionId());
       }
-      jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
+      Mapping mp = new Mapping(
               parsemapType(vobj.getMap(0)));
       jvobj.setMap(mp);
     }
@@ -218,7 +222,7 @@ public class Dbref extends Rangetype
     sequence.addDbRef(dbref);
     if (jvobj.getMap() != null)
     {
-      jalview.datamodel.Mapping mp = jvobj.getMap();
+      Mapping mp = jvobj.getMap();
       if (mp.getMap() != null)
       {
         Map vMap = new Map();
@@ -228,7 +232,7 @@ public class Dbref extends Rangetype
       }
       else
       {
-        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+        Cache.log.debug("Ignoring mapless DbRef.Map "
                 + jvobj.getSrcAccString());
       }
     }