JAL-1683 replace year/version strings with tokens in source

[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 c27bc9a..aacdecf 100644 (file)
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -1,20 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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;
 
@@ -87,40 +89,61 @@ public class Dbref extends Rangetype
         updateMapTo(mp);
       }
     }
-      else
-      {
-        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
-                + jvobj.getSrcAccString());
-      }
-    
+    else
+    {
+      jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+              + jvobj.getSrcAccString());
+    }
+
   }
+
   /**
-   * ugly hack to try to get the embedded sequences within a database reference to be stored in the document's dataset.
+   * ugly hack to try to get the embedded sequences within a database reference
+   * to be stored in the document's dataset.
+   * 
    * @param mp
    */
   private void updateMapTo(jalview.datamodel.Mapping mp)
   {
     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)
+    // TODO determine how sequences associated with database mappings are stored
+    // in the document
+    if (mp != null && mp.getTo() != null)
     {
       if (mp.getTo().getDatasetSequence() == null)
       {
-        // sync the dataset sequence, if it hasn't been done already.
-        Datasetsequence dssync = new Datasetsequence(
-                datastore, mp.getTo(),
-                (mp.getMappedWidth() == mp.getWidth()) ? sequence
-                        .getDictionary()
-                        : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA
-                                : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA),
-                ds);
-        // add a mapping between new dataset sequence and sequence associated with the database reference
-        
-      } else {
-        log.debug("Ignoring non-dataset sequence mapping.");
+        // TODO: fix this hinky sh!t
+        DatastoreItem dssync = dsReg.getDatastoreItemFor(mp.getTo());
+        if (dssync == null)
+        {
+          // 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
+                                  : 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);
+
       }
+
+    }
+    else
+    {
+      log.debug("Ignoring non-dataset sequence mapping.");
     }
   }
+
   public void updateFromDoc()
   {
     DbRef vobj = (DbRef) this.vobj;
@@ -140,13 +163,13 @@ public class Dbref extends Rangetype
       }
       jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
               parsemapType(vobj.getMap(0)));
-      if (jvobj.getMap()==null || !mp.equals(jvobj.getMap()))
+      if (jvobj.getMap() == null || !mp.equals(jvobj.getMap()))
       {
         jvobj.setMap(mp);
       }
     }
   }
-  
+
   public void conflict()
   {
     DbRef vobj = (DbRef) this.vobj;
@@ -193,6 +216,7 @@ public class Dbref extends Rangetype
     dbref.setAccessionId(jvobj.getAccessionId());
     dbref.setSource(jvobj.getSource());
     dbref.setVersion(jvobj.getVersion());
+    sequence.addDbRef(dbref);
     if (jvobj.getMap() != null)
     {
       jalview.datamodel.Mapping mp = jvobj.getMap();
@@ -201,6 +225,7 @@ public class Dbref extends Rangetype
         Map vMap = new Map();
         initMapType(vMap, mp.getMap(), true);
         dbref.addMap(vMap);
+        updateMapTo(mp);
       }
       else
       {
@@ -208,7 +233,6 @@ public class Dbref extends Rangetype
                 + jvobj.getSrcAccString());
       }
     }
-    sequence.addDbRef(dbref);
   }
 
 }