X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2Fvamsas%2FDbref.java;h=e8fedac52cfcba693ec2bfb64970557b5da1c8d3;hb=7897c6cb08b496285bcb5fa9ed2d9f7d887d0068;hp=c5ac44f689ce9719ae6f7d82df2d7102a690b313;hpb=2ac1013336a5ea08943daed3552acf4b7a8c18b2;p=jalview.git

diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index c5ac44f..e8fedac 100644
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -1,115 +1,158 @@
-package jalview.io.vamsas;
-
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.SequenceI;
-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
-{
-  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)
-  {
-    super(datastore);
-    dbref = (DbRef) getjv2vObj(dbentry);
-    sq = sq2;
-    sequence = sequence2;
-    this.dbentry = dbentry;
-    if (dbref==null)
-    {
-      add();
-    } else {
-      if (dbref.isUpdated())
-      {
-        conflict();
-      } else {
-        update();
-      }
-        
-    }
-    
-  }
-
-  public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq, SequenceI dsseq)
-  {
-    super(datastore);
-    dbref = ref;
-    sequence = vdseq;
-    sq = dsseq;
-    dbentry = (jalview.datamodel.DBRefEntry) getvObj2jv(dbref);
-    if (dbentry == null)
-    {
-      addFromDocument();
-    } else {
-      if (dbref.isUpdated())
-      {
-        update();
-      }
-    }
-  }
-
-  private void update()
-  {
-    // 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.");
-  }
-
-  private void conflict()
-  {
-    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)
-    {
-      // TODO: Jalview ignores all the other maps
-      if (dbref.getMapCount()>1)
-      {
-        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)));
-      dbentry.setMap(mp);
-    }
-    // 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();
-    bindjvvobj(dbentry, dbref);
-    dbref.setAccessionId(dbentry.getAccessionId());
-    dbref.setSource(dbentry.getSource());
-    dbref.setVersion(dbentry.getVersion());
-    if (dbentry.getMap()!=null)
-    {
-      jalview.datamodel.Mapping mp = dbentry.getMap();
-      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());
-      }
-    }
-    sequence.addDbRef(dbref);
-  }
-
-}
+/*
+ * 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;
+import jalview.datamodel.SequenceI;
+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
+{
+  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)
+  {
+    super(datastore);
+    dbref = (DbRef) getjv2vObj(dbentry);
+    sq = sq2;
+    sequence = sequence2;
+    this.dbentry = dbentry;
+    if (dbref == null)
+    {
+      add();
+    }
+    else
+    {
+      if (dbref.isUpdated())
+      {
+        conflict();
+      }
+      else
+      {
+        update();
+      }
+
+    }
+
+  }
+
+  public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
+          SequenceI dsseq)
+  {
+    super(datastore);
+    dbref = ref;
+    sequence = vdseq;
+    sq = dsseq;
+    dbentry = (jalview.datamodel.DBRefEntry) getvObj2jv(dbref);
+    if (dbentry == null)
+    {
+      addFromDocument();
+    }
+    else
+    {
+      if (dbref.isUpdated())
+      {
+        update();
+      }
+    }
+  }
+
+  private void update()
+  {
+    // 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.");
+  }
+
+  private void conflict()
+  {
+    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)
+    {
+      // TODO: Jalview ignores all the other maps
+      if (dbref.getMapCount() > 1)
+      {
+        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)));
+      dbentry.setMap(mp);
+    }
+    // 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();
+    bindjvvobj(dbentry, dbref);
+    dbref.setAccessionId(dbentry.getAccessionId());
+    dbref.setSource(dbentry.getSource());
+    dbref.setVersion(dbentry.getVersion());
+    if (dbentry.getMap() != null)
+    {
+      jalview.datamodel.Mapping mp = dbentry.getMap();
+      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());
+      }
+    }
+    sequence.addDbRef(dbref);
+  }
+
+}