X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=b4d75f9d4ef23f3759669465fa1cd39d1fd9a82a;hb=8f767dbd2ec39bd1c06167c7a1da00f413b7a899;hp=2b5a0e214f10cbdf3528e045cfdeebed326c9a9d;hpb=29d4809e01ace4e6ac449ec944bfeec70070ac81;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 2b5a0e2..b4d75f9 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -68,11 +68,6 @@ public class CrossRef
   List<SequenceI> rseqs;
 
   /**
-   * mappings constructed
-   */
-  AlignedCodonFrame cf;
-
-  /**
    * Constructor
    * 
    * @param seqs
@@ -213,7 +208,7 @@ public class CrossRef
   {
 
     rseqs = new ArrayList<SequenceI>();
-    cf = new AlignedCodonFrame();
+    AlignedCodonFrame cf = new AlignedCodonFrame();
     matcher = new SequenceIdMatcher(
             dataset.getSequences());
 
@@ -286,21 +281,23 @@ public class CrossRef
               refIterator.remove();
               continue;
             }
+            // TODO: need to determine if this should be a deriveSequence
             SequenceI rsq = new Sequence(mappedTo);
             rseqs.add(rsq);
-            if (xref.getMap().getMap().getFromRatio() != xref.getMap()
-                    .getMap().getToRatio())
+            if (xref.getMap().getMap().isTripletMap())
             {
               // get sense of map correct for adding to product alignment.
               if (fromDna)
               {
                 // map is from dna seq to a protein product
-                cf.addMap(dss, rsq, xref.getMap().getMap());
+                cf.addMap(dss, rsq, xref.getMap().getMap(), xref.getMap()
+                        .getMappedFromId());
               }
               else
               {
                 // map should be from protein seq to its coding dna
-                cf.addMap(rsq, dss, xref.getMap().getMap().getInverse());
+                cf.addMap(rsq, dss, xref.getMap().getMap().getInverse(),
+                        xref.getMap().getMappedFromId());
               }
             }
           }
@@ -336,7 +333,7 @@ public class CrossRef
        */
       if (!sourceRefs.isEmpty())
       {
-        retrieveCrossRef(sourceRefs, seq, xrfs, fromDna);
+        retrieveCrossRef(sourceRefs, seq, xrfs, fromDna, cf);
       }
     }
 
@@ -353,7 +350,7 @@ public class CrossRef
   }
 
   private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
-          DBRefEntry[] xrfs, boolean fromDna)
+          DBRefEntry[] xrfs, boolean fromDna, AlignedCodonFrame cf)
   {
     ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
     SequenceI[] retrieved = null;
@@ -621,14 +618,14 @@ public class CrossRef
   void updateDbrefMappings(SequenceI mapFrom, DBRefEntry[] xrefs,
           SequenceI[] retrieved, AlignedCodonFrame acf, boolean fromDna)
   {
-    SequenceIdMatcher matcher = new SequenceIdMatcher(retrieved);
+    SequenceIdMatcher idMatcher = new SequenceIdMatcher(retrieved);
     for (DBRefEntry xref : xrefs)
     {
       if (!xref.hasMap())
       {
         String targetSeqName = xref.getSource() + "|"
                 + xref.getAccessionId();
-        SequenceI[] matches = matcher.findAllIdMatches(targetSeqName);
+        SequenceI[] matches = idMatcher.findAllIdMatches(targetSeqName);
         if (matches == null)
         {
           return;
@@ -705,6 +702,20 @@ public class CrossRef
       return false;
     }
     xref.setMap(new Mapping(mapTo, mapping));
+
+    /*
+     * and add a reverse DbRef with the inverse mapping
+     */
+    if (mapFrom.getDatasetSequence() != null
+            && mapFrom.getDatasetSequence().getSourceDBRef() != null)
+    {
+      DBRefEntry dbref = new DBRefEntry(mapFrom.getDatasetSequence()
+              .getSourceDBRef());
+      dbref.setMap(new Mapping(mapFrom.getDatasetSequence(), mapping
+              .getInverse()));
+      mapTo.addDBRef(dbref);
+    }
+
     if (fromDna)
     {
       AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);