Merge branch 'develop' into features/JAL-2094_colourInterface

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index aefc6f8..1295b46 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -390,6 +390,37 @@ public class CrossRef
     SequenceI[] retrieved = null;
     SequenceI dss = seq.getDatasetSequence() == null ? seq : seq
             .getDatasetSequence();
+    // first filter in case we are retrieving crossrefs that have already been
+    // retrieved. this happens for cases where a database record doesn't yield
+    // protein products for CDS
+    DBRefEntry[] dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
+    for (SequenceI sq : dataset.getSequences())
+    {
+      boolean dupeFound = false;
+      // !fromDna means we are looking only for nucleotide sequences, not
+      // protein
+      if (sq.isProtein() == fromDna)
+      {
+        for (DBRefEntry dbr : sq.getPrimaryDBRefs())
+        {
+          for (DBRefEntry found : DBRefUtils.searchRefs(dbrSourceSet, dbr))
+          {
+            sourceRefs.remove(found);
+            dupeFound = true;
+          }
+        }
+      }
+      if (dupeFound)
+      {
+        dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
+      }
+    }
+    if (sourceRefs.size() == 0)
+    {
+      // no more work to do! We already had all requested sequence records in
+      // the dataset.
+      return;
+    }
     try
     {
       retrieved = sftch.getSequences(sourceRefs, !fromDna);
@@ -836,8 +867,8 @@ public class CrossRef
    *          </ul>
    * @return true if relationship found and sequence added.
    */
-  boolean searchDataset(boolean fromDna, SequenceI fromSeq,
-          DBRefEntry xrf, List<SequenceI> foundSeqs, AlignedCodonFrame mappings,
+  boolean searchDataset(boolean fromDna, SequenceI fromSeq, DBRefEntry xrf,
+          List<SequenceI> foundSeqs, AlignedCodonFrame mappings,
           boolean direct)
   {
     boolean found = false;
@@ -898,37 +929,38 @@ public class CrossRef
           // }
           if (!cands.isEmpty())
           {
-            if (!foundSeqs.contains(nxt))
+            if (foundSeqs.contains(nxt))
             {
-              found = true;
-              foundSeqs.add(nxt);
-              if (mappings != null && !direct)
+              continue;
+            }
+            found = true;
+            foundSeqs.add(nxt);
+            if (mappings != null && !direct)
+            {
+              /*
+               * if the matched sequence has mapped dbrefs to
+               * protein product / cdna, add equivalent mappings to
+               * our source sequence
+               */
+              for (DBRefEntry candidate : cands)
               {
-                /*
-                 * if the matched sequence has mapped dbrefs to
-                 * protein product / cdna, add equivalent mappings to
-                 * our source sequence
-                 */
-                for (DBRefEntry candidate : cands)
+                Mapping mapping = candidate.getMap();
+                if (mapping != null)
                 {
-                  Mapping mapping = candidate.getMap();
-                  if (mapping != null)
+                  MapList map = mapping.getMap();
+                  if (mapping.getTo() != null
+                          && map.getFromRatio() != map.getToRatio())
                   {
-                    MapList map = mapping.getMap();
-                    if (mapping.getTo() != null
-                            && map.getFromRatio() != map.getToRatio())
+                    /*
+                     * add a mapping, as from dna to peptide sequence
+                     */
+                    if (map.getFromRatio() == 3)
                     {
-                      /*
-                       * add a mapping, as from dna to peptide sequence
-                       */
-                      if (map.getFromRatio() == 3)
-                      {
-                        mappings.addMap(nxt, fromSeq, map);
-                      }
-                      else
-                      {
-                        mappings.addMap(nxt, fromSeq, map.getInverse());
-                      }
+                      mappings.addMap(nxt, fromSeq, map);
+                    }
+                    else
+                    {
+                      mappings.addMap(nxt, fromSeq, map.getInverse());
                     }
                   }
                 }