X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencemapping.java;h=0a582e5f3b85bfc0aed151aa65d962b45acddbbd;hb=66993ec5b2bbc67ed10836d2288d938f6c368076;hp=4929a06b2278e1aa4d7bcafa68e9ca82c42119ac;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 4929a06..0a582e5 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -22,11 +22,14 @@ package jalview.io.vamsas;
 
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
 import jalview.gui.Desktop;
 import jalview.io.VamsasAppDatastore;
 
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Vector;
 
 import uk.ac.vamsas.objects.core.AlignmentSequence;
@@ -102,10 +105,8 @@ public class Sequencemapping extends Rangetype
     if (ds != null && sequenceMapping.is__stored_in_document()
             && sequenceMapping.getV_parent() != ds)
     {
-      jalview.bin.Cache.log
-              .warn("Probable IMPLEMENTATION ERROR: "
-                      + ds
-                      + " doesn't match the parent of the bound sequence mapping object.");
+      jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + ds
+              + " doesn't match the parent of the bound sequence mapping object.");
     }
   }
 
@@ -152,8 +153,8 @@ public class Sequencemapping extends Rangetype
     SequenceType to = (SequenceType) getjv2vObj(jvto);
     if (to == null)
     {
-      jalview.bin.Cache.log
-              .warn("FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
+      jalview.bin.Cache.log.warn(
+              "FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
       return;
     }
     SequenceMapping sequenceMapping = new SequenceMapping();
@@ -183,8 +184,8 @@ public class Sequencemapping extends Rangetype
 
     if (!dnaToProt)
     {
-      jalview.bin.Cache.log
-              .warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
+      jalview.bin.Cache.log.warn(
+              "Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
       return;
     }
     if (ds == null)
@@ -211,8 +212,8 @@ public class Sequencemapping extends Rangetype
               true);
     }
     ds.addSequenceMapping(sequenceMapping);
-    sequenceMapping.setProvenance(this
-            .dummyProvenance("user defined coding region translation")); // TODO:
+    sequenceMapping.setProvenance(
+            this.dummyProvenance("user defined coding region translation")); // TODO:
     // correctly
     // construct
     // provenance
@@ -223,8 +224,8 @@ public class Sequencemapping extends Rangetype
     // mapping
     bindjvvobj(mjvmapping.getMap(), sequenceMapping);
 
-    jalview.bin.Cache.log.debug("Successfully created mapping "
-            + sequenceMapping.getVorbaId());
+    jalview.bin.Cache.log.debug(
+            "Successfully created mapping " + sequenceMapping.getVorbaId());
   }
 
   // private void update(jalview.util.MapList mjvmapping,
@@ -244,8 +245,8 @@ public class Sequencemapping extends Rangetype
   private void update(jalview.datamodel.Mapping mjvmapping,
           SequenceMapping sequenceMapping)
   {
-    jalview.bin.Cache.log
-            .error("Not implemented: Jalview Update Sequence DBRef Mapping");
+    jalview.bin.Cache.log.error(
+            "Not implemented: Jalview Update Sequence DBRef Mapping");
   }
 
   /**
@@ -297,8 +298,8 @@ public class Sequencemapping extends Rangetype
     if (from == null || to == null)
     {
 
-      jalview.bin.Cache.log
-              .error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
+      jalview.bin.Cache.log.error(
+              "Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
       return;
     }
 
@@ -364,7 +365,8 @@ public class Sequencemapping extends Rangetype
     }
     bindjvvobj(mapping, sequenceMapping);
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance).addMapping(acf);
+            .getStructureSelectionManager(Desktop.instance)
+            .registerMapping(acf);
     // Try to link up any conjugate database references in the two sequences
     // matchConjugateDBRefs(from, to, mapping);
     // Try to propagate any dbrefs across this mapping.
@@ -385,7 +387,7 @@ public class Sequencemapping extends Rangetype
   private void matchConjugateDBRefs(SequenceI from, SequenceI to,
           jalview.util.MapList smap)
   {
-    if (from.getDBRef() == null && to.getDBRef() == null)
+    if (from.getDBRefs() == null && to.getDBRefs() == null)
     {
       if (jalview.bin.Cache.log.isDebugEnabled())
       {
@@ -399,18 +401,25 @@ public class Sequencemapping extends Rangetype
       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);
+    List<DBRefEntry> fdb = from.getDBRefs();
+    List<DBRefEntry> tdb = new ArrayList<DBRefEntry>(to.getDBRefs());
+    int tdblen = to.getDBRefs().size();
+//    
+//    
+//    YOWSER
+//    
+//    System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
+//    
+//    
+//    
+//    
     Vector matched = new Vector();
     jalview.util.MapList smapI = smap.getInverse();
-    for (int f = 0; f < fdb.length; f++)
+    for (int f = 0, fn = fdb.size(); f < fn; f++)
     {
-      jalview.datamodel.DBRefEntry fe = fdb[f];
+      jalview.datamodel.DBRefEntry fe = fdb.get(f);
       jalview.datamodel.Mapping fmp = fe.getMap();
-      boolean fmpnnl = fmp != null;
+      boolean fmpnnl = (fmp != null);
       // if (fmpnnl && fmp.getTo()!=null)
       // {
       // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
@@ -425,7 +434,7 @@ public class Sequencemapping extends Rangetype
               : false;
       for (int t = 0; t < tdblen; t++)
       {
-        jalview.datamodel.DBRefEntry te = tdb[t];
+        jalview.datamodel.DBRefEntry te = tdb.get(t);
         if (te != null)
         {
           if (fe.getSource().equals(te.getSource())
@@ -441,8 +450,9 @@ public class Sequencemapping extends Rangetype
             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;
+            boolean smaptotemap2local = (tmpnnl)
+                    ? smapI.equals(fmp.getMap())
+                    : false;
             if (smapfromlocal2fe && smaptotemap2local)
             {
               // smap implies mapping from to to from