merge from 2_4_Release branch

[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 c4d72c3..e8fedac 100644 (file)
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, 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 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.
+ * 
+ * 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
+ */
 package jalview.io.vamsas;
 
 import jalview.datamodel.DBRefEntry;
@@ -10,32 +28,43 @@ import jalview.io.VamsasAppDatastore;
 public class Dbref extends Rangetype
 {
   jalview.datamodel.SequenceI sq = null;
+
   uk.ac.vamsas.objects.core.Sequence sequence = null;
+
   DbRef dbref = null;
-  DBRefEntry dbentry=null;
-  public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry, jalview.datamodel.SequenceI sq2, uk.ac.vamsas.objects.core.Sequence sequence2)
+
+  DBRefEntry dbentry = null;
+
+  public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
+          jalview.datamodel.SequenceI sq2,
+          uk.ac.vamsas.objects.core.Sequence sequence2)
   {
     super(datastore);
     dbref = (DbRef) getjv2vObj(dbentry);
     sq = sq2;
     sequence = sequence2;
     this.dbentry = dbentry;
-    if (dbref==null)
+    if (dbref == null)
     {
       add();
-    } else {
+    }
+    else
+    {
       if (dbref.isUpdated())
       {
         conflict();
-      } else {
+      }
+      else
+      {
         update();
       }
-        
+
     }
-    
+
   }
 
-  public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq, SequenceI dsseq)
+  public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
+          SequenceI dsseq)
   {
     super(datastore);
     dbref = ref;
@@ -45,7 +74,9 @@ public class Dbref extends Rangetype
     if (dbentry == null)
     {
       addFromDocument();
-    } else {
+    }
+    else
+    {
       if (dbref.isUpdated())
       {
         update();
@@ -58,38 +89,47 @@ public class Dbref extends Rangetype
     // TODO: verify and update dbrefs in vamsas document
     // there will be trouble when a dataset sequence is modified to
     // contain more residues than were originally referenced - we must
-    // then make a number of dataset sequence entries - this info is already stored 
-    jalview.bin.Cache.log.debug("TODO verify update of dataset sequence database references.");
+    // then make a number of dataset sequence entries - this info is already
+    // stored
+    jalview.bin.Cache.log
+            .debug("TODO verify update of dataset sequence database references.");
   }
 
   private void conflict()
   {
-    jalview.bin.Cache.log.debug("Conflict in dbentry update for "+dbref.getAccessionId()+dbref.getSource()+" "+dbref.getVorbaId());
+    jalview.bin.Cache.log.debug("Conflict in dbentry update for "
+            + dbref.getAccessionId() + dbref.getSource() + " "
+            + dbref.getVorbaId());
     // TODO Auto-generated method stub
-    
+
   }
+
   private void addFromDocument()
   {
     // add new dbref
-    sq.addDBRef(dbentry = new jalview.datamodel.DBRefEntry
-            (
-                    dbref.getSource().toString(),
-                 dbref.getVersion().toString(),
-                 dbref.getAccessionId().toString()));
-    if (dbref.getMapCount()>0)
+    sq.addDBRef(dbentry = new jalview.datamodel.DBRefEntry(dbref
+            .getSource().toString(), dbref.getVersion().toString(), dbref
+            .getAccessionId().toString()));
+    if (dbref.getMapCount() > 0)
     {
       // TODO: Jalview ignores all the other maps
-      if (dbref.getMapCount()>1)
+      if (dbref.getMapCount() > 1)
       {
-        jalview.bin.Cache.log.debug("Ignoring additional mappings on DbRef: "+dbentry.getSource()+":"+dbentry.getAccessionId());
+        jalview.bin.Cache.log
+                .debug("Ignoring additional mappings on DbRef: "
+                        + dbentry.getSource() + ":"
+                        + dbentry.getAccessionId());
       }
-      jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(parsemapType(dbref.getMap(0)));
+      jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
+              parsemapType(dbref.getMap(0)));
       dbentry.setMap(mp);
     }
-    // TODO: jalview ignores links and properties because it doesn't know what to do with them.
-    
+    // TODO: jalview ignores links and properties because it doesn't know what
+    // to do with them.
+
     bindjvvobj(dbentry, dbref);
   }
+
   private void add()
   {
     DbRef dbref = new DbRef();
@@ -97,16 +137,19 @@ public class Dbref extends Rangetype
     dbref.setAccessionId(dbentry.getAccessionId());
     dbref.setSource(dbentry.getSource());
     dbref.setVersion(dbentry.getVersion());
-    if (dbentry.getMap()!=null)
+    if (dbentry.getMap() != null)
     {
       jalview.datamodel.Mapping mp = dbentry.getMap();
-      if (mp.getMap()!=null)
+      if (mp.getMap() != null)
       {
         Map vMap = new Map();
         initMapType(vMap, mp.getMap(), true);
         dbref.addMap(vMap);
-      } else {
-        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "+dbentry.getSrcAccString());
+      }
+      else
+      {
+        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+                + dbentry.getSrcAccString());
       }
     }
     sequence.addDbRef(dbref);