JAL-2154 regression warning - should never recover a sequence ‘like’ an xref’s mappin...

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 288d60e..81fad27 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -271,20 +271,45 @@ public class CrossRef
              * but findInDataset() matches ENSP when looking for Uniprot...
              */
             SequenceI matchInDataset = findInDataset(xref);
+            if (matchInDataset != null && xref.getMap().getTo() != null
+                    && matchInDataset != xref.getMap().getTo())
+            {
+              System.err
+                      .println("Implementation problem (reopen JAL-2154): CrossRef.findInDataset seems to have recovered a different sequence than the one explicitly mapped for xref."
+                              + "Found:"
+                              + matchInDataset
+                              + "\nExpected:"
+                              + xref.getMap().getTo()
+                              + "\nFor xref:"
+                              + xref);
+            }
             /*matcher.findIdMatch(mappedTo);*/
             if (matchInDataset != null)
             {
               if (!rseqs.contains(matchInDataset))
               {
                 rseqs.add(matchInDataset);
+                // need to try harder to only add unique mappings
+                if (xref.getMap().getMap().isTripletMap()
+                        && dataset.getMapping(seq, matchInDataset) == null
+                        && cf.getMappingBetween(seq, matchInDataset) == null)
+                {
+                  // materialise a mapping for highlighting between these sequences
+                  if (fromDna)
+                  {
+                    cf.addMap(dss, matchInDataset, xref.getMap().getMap(), xref.getMap().getMappedFromId());
+                  } else {
+                    cf.addMap(matchInDataset, dss, xref.getMap().getMap().getInverse(), xref.getMap().getMappedFromId());
+                  }
+                }
               }
               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)
@@ -413,6 +438,7 @@ public class CrossRef
                 }
                 else
                 {
+                  dataset.addSequence(map.getTo());
                   matcher.add(map.getTo());
                 }
                 try
@@ -662,24 +688,28 @@ public class CrossRef
           DBRefEntry xref, AlignedCodonFrame mappings, boolean fromDna)
   {
     MapList mapping = null;
-
+    SequenceI dsmapFrom = mapFrom.getDatasetSequence() == null ? mapFrom
+            : mapFrom.getDatasetSequence();
+    SequenceI dsmapTo = mapFrom.getDatasetSequence() == null ? mapTo
+            : mapTo.getDatasetSequence();
     /*
-     * look for a reverse mapping, if found make its inverse
+     * look for a reverse mapping, if found make its inverse. 
+     * Note - we do this on dataset sequences only.
      */
-    if (mapTo.getDBRefs() != null)
+    if (dsmapTo.getDBRefs() != null)
     {
-      for (DBRefEntry dbref : mapTo.getDBRefs())
+      for (DBRefEntry dbref : dsmapTo.getDBRefs())
       {
         String name = dbref.getSource() + "|" + dbref.getAccessionId();
-        if (dbref.hasMap() && mapFrom.getName().startsWith(name))
+        if (dbref.hasMap() && dsmapFrom.getName().startsWith(name))
         {
           /*
            * looks like we've found a map from 'mapTo' to 'mapFrom'
            * - invert it to make the mapping the other way 
            */
           MapList reverse = dbref.getMap().getMap().getInverse();
-          xref.setMap(new Mapping(mapTo, reverse));
-          mappings.addMap(mapFrom, mapTo, reverse);
+          xref.setMap(new Mapping(dsmapTo, reverse));
+          mappings.addMap(mapFrom, dsmapTo, reverse);
           return true;
         }
       }