X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencemapping.java;h=160f5e27c5b3947fd58f75f7f64997a20a97a70d;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=550d0ff0237edb9dae2c4a49b21c64161526383e;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 550d0ff..160f5e2 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,14 +20,15 @@
  */
 package jalview.io.vamsas;
 
-import java.util.Vector;
-
 import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
 import jalview.gui.Desktop;
 import jalview.io.VamsasAppDatastore;
-import uk.ac.vamsas.client.Vobject;
+
+import java.util.Vector;
+
 import uk.ac.vamsas.objects.core.AlignmentSequence;
 import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.Sequence;
@@ -283,12 +284,12 @@ public class Sequencemapping extends Rangetype
       jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
       return;
     }
-    mobj = this.getvObj2jv((Vobject) sdloc);
+    mobj = this.getvObj2jv(sdloc);
     if (mobj instanceof SequenceI)
     {
       from = (SequenceI) mobj;
     }
-    mobj = this.getvObj2jv((Vobject) sdmap);
+    mobj = this.getvObj2jv(sdmap);
     if (mobj instanceof SequenceI)
     {
       to = (SequenceI) mobj;
@@ -325,19 +326,17 @@ public class Sequencemapping extends Rangetype
     }
     // create mapping storage object and make each dataset alignment reference
     // it.
-    jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc
-            .getV_parent());
-    jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap
-            .getV_parent());
-    AlignedCodonFrame afc = new AlignedCodonFrame(0);
+    AlignmentI dsLoc = (AlignmentI) getvObj2jv(sdloc.getV_parent());
+    AlignmentI dsMap = (AlignmentI) getvObj2jv(sdmap.getV_parent());
+    AlignedCodonFrame acf = new AlignedCodonFrame();
 
     if (dsLoc != null && dsLoc != dsMap)
     {
-      dsLoc.addCodonFrame(afc);
+      dsLoc.addCodonFrame(acf);
     }
     if (dsMap != null)
     {
-      dsMap.addCodonFrame(afc);
+      dsMap.addCodonFrame(acf);
     }
     // create and add the new mapping to (each) dataset's codonFrame
 
@@ -350,24 +349,23 @@ public class Sequencemapping extends Rangetype
         mapping = new jalview.util.MapList(mapping.getToRanges(),
                 mapping.getFromRanges(), mapping.getToRatio(),
                 mapping.getFromRatio());
-        afc.addMap(to, from, mapping);
+        acf.addMap(to, from, mapping);
       }
       else
       {
         mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
-        afc.addMap(from, to, mapping);
+        acf.addMap(from, to, mapping);
       }
     }
     else
     {
       mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense
-      afc.addMap(from, to, mapping);
+      acf.addMap(from, to, mapping);
     }
     bindjvvobj(mapping, sequenceMapping);
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance).addMappings(
-                    new AlignedCodonFrame[]
-                    { afc });
+            .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.
@@ -388,7 +386,7 @@ 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())
       {
@@ -402,11 +400,11 @@ 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[] fdb = from.getDBRefs();
     jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
-            .getDBRef().length];
-    int tdblen = to.getDBRef().length;
-    System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
+            .getDBRefs().length];
+    int tdblen = to.getDBRefs().length;
+    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++)