X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDbref.java;h=91bf66625105a910dcf8f08894503fe7042db554;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=d4aafe82b1b1d3593924de1867a6263baae26056;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git

diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index d4aafe8..91bf666 100644
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -1,29 +1,34 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.Console;
 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 jalview.io.VamsasAppDatastore;
 
 public class Dbref extends Rangetype
 {
@@ -88,8 +93,8 @@ public class Dbref extends Rangetype
     }
     else
     {
-      jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
-              + jvobj.getSrcAccString());
+      Console.debug(
+              "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
     }
 
   }
@@ -102,7 +107,8 @@ 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)
@@ -116,12 +122,11 @@ 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);
         }
@@ -154,8 +159,7 @@ public class Dbref extends Rangetype
       // TODO: Jalview ignores all the other maps
       if (vobj.getMapCount() > 1)
       {
-        jalview.bin.Cache.log
-                .debug("Ignoring additional mappings on DbRef: "
+        Console.debug("Ignoring additional mappings on DbRef: "
                         + jvobj.getSource() + ":" + jvobj.getAccessionId());
       }
       jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
@@ -171,9 +175,8 @@ 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());
+    Console.debug("Conflict in dbentry update for " + vobj.getAccessionId()
+                    + vobj.getSource() + " " + vobj.getVorbaId());
     // TODO Auto-generated method stub
 
   }
@@ -183,16 +186,15 @@ 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
       if (vobj.getMapCount() > 1)
       {
-        jalview.bin.Cache.log
-                .debug("Ignoring additional mappings on DbRef: "
+        Console.debug("Ignoring additional mappings on DbRef: "
                         + jvobj.getSource() + ":" + jvobj.getAccessionId());
       }
       jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
@@ -226,8 +228,8 @@ public class Dbref extends Rangetype
       }
       else
       {
-        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
-                + jvobj.getSrcAccString());
+        Console.debug(
+                "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
       }
     }
   }