From 51103d869344aed06f20d48fcd210b20ffb9e542 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 18 Sep 2007 10:30:52 +0000
Subject: [PATCH] fix class-cast exception and added beginnings of DBRef
 inference mechanism

---
 src/jalview/io/vamsas/Sequencemapping.java |   87 +++++++++++++++++++++++++++-
 1 file changed, 85 insertions(+), 2 deletions(-)

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index a4ee585..4cede9a 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -28,7 +28,7 @@ public class Sequencemapping extends Rangetype
     } else {
       if (sequenceMapping.isUpdated())
       {
-        update((jalview.datamodel.Mapping) mjvmapping, sequenceMapping);
+        update((jalview.util.MapList) mjvmapping, sequenceMapping);
       }
     }
   }
@@ -144,9 +144,13 @@ public class Sequencemapping extends Rangetype
 
     jalview.bin.Cache.log.debug("Successfully created mapping "+sequenceMapping.getVorbaId());
   }
+  private void update(jalview.util.MapList mjvmapping, SequenceMapping sequenceMapping)
+  {
+    jalview.bin.Cache.log.error("Not implemented: Jalview Update Alcodon Mapping:TODO!"); 
+  }
   private void update(jalview.datamodel.Mapping mjvmapping, SequenceMapping sequenceMapping)
   {
-    jalview.bin.Cache.log.error("Not implemented: Jalview Update Mapping"); 
+    jalview.bin.Cache.log.error("Not implemented: Jalview Update Sequence DBRef Mapping"); 
   }
   /**
    * limitations: Currently, jalview only deals with mappings between dataset
@@ -193,6 +197,7 @@ public class Sequencemapping extends Rangetype
       jalview.bin.Cache.log.error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
       return;
     } 
+
     if (sdloc.getDictionary()
             .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
     {
@@ -241,5 +246,83 @@ public class Sequencemapping extends Rangetype
     }
     bindjvvobj(mapping, sequenceMapping);
     jalview.structure.StructureSelectionManager.getStructureSelectionManager().addMappings(new AlignedCodonFrame[] { afc });
+    // Try to link up any conjugate database references in the two sequences
+    // matchConjugateDBRefs(from, to,  mapping);
+    // Try to propagate any dbrefs across this mapping.
+
   }
+  /**
+   * Complete any 'to' references in jalview.datamodel.Mapping objects associated with conjugate DBRefEntry under given mapping  
+   * @param from sequence corresponding to from reference for sequence mapping
+   * @param to sequence correspondeing to to reference for sequence mapping
+   * @param smap maplist parsed in same sense as from and to
+   */
+  private void matchConjugateDBRefs(SequenceI from, SequenceI to,
+          jalview.util.MapList smap)
+  {
+    if (from.getDBRef()==null && to.getDBRef()==null)
+    {
+      if (jalview.bin.Cache.log.isDebugEnabled())
+      {
+        jalview.bin.Cache.log.debug("Not matching conjugate refs for "+from.getName()+" and "+to.getName());
+      }
+      return; 
+    }
+    if (jalview.bin.Cache.log.isDebugEnabled())
+    {
+      jalview.bin.Cache.log.debug("Matching conjugate refs for "+from.getName()+" and "+to.getName());
+    }
+    jalview.datamodel.DBRefEntry[] fdb = from.getDBRef();
+    jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to.getDBRef().length];
+    int tdblen = to.getDBRef().length;
+    System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
+    Vector matched = new Vector();
+    jalview.util.MapList smapI = smap.getInverse();
+    for (int f=0;f<fdb.length; f++)
+    {
+      jalview.datamodel.DBRefEntry fe = fdb[f];
+      jalview.datamodel.Mapping fmp = fe.getMap();
+      boolean fmpnnl = fmp!=null;
+      // if (fmpnnl && fmp.getTo()!=null)
+      //{
+      //  jalview.bin.Cache.log.debug("Not overwriting existing To reference in "+fe);
+      //  continue;
+      //}
+      // smap from maps from fe.local to fe.map
+      boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap()) : false;
+      // smap from maps from fe.map to fe.local.
+      boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap()) : false;
+      for (int t=0; t<tdblen; t++)
+      {
+        jalview.datamodel.DBRefEntry te = tdb[t];
+        if (te!=null)
+        {
+          if (fe.getSource().equals(te.getSource())
+              && fe.getAccessionId().equals(te.getAccessionId()))
+          {
+            jalview.datamodel.Mapping tmp = te.getMap();
+            boolean tmpnnl = tmp!=null;
+            if (tmpnnl && tmp.getTo()!=null)
+            {
+              
+            }
+            // smap to maps from te.local to te.map
+            boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap()) : false;
+            // smap to maps from te.map to te.local
+            boolean smaptotemap2local = (tmpnnl) ? smapI.equals(fmp.getMap()) : false;
+            if (smapfromlocal2fe && smaptotemap2local)
+            {
+              // smap implies mapping from to to from
+              fmp.setTo(to);
+              tmp.setTo(from);
+            } else 
+              if (smapfromfemap2local && smaptolocal2tm) {
+                fmp.setTo(to);
+              }
+            }
+            
+        }
+      }
+    }
+    }
 }
\ No newline at end of file
-- 
1.7.10.2