From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 30 Sep 2016 16:44:32 +0000 (+0100)
Subject: JAL-2210 some DBRef xref/ref correspondences may add sequence but have no mapping... 
X-Git-Tag: Release_2_10_0~20^2~21
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=56a55873956da91d4301cbab320c69873f2329ab;p=jalview.git

JAL-2210 some DBRef xref/ref correspondences may add sequence but have no mapping (e.g. ENSG->Uniprot), so always check if mappings have been added even if xref’ed sequence has already been added to set to be shown to user.
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index a729334..4a7a41b 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -296,20 +296,28 @@ public class CrossRef
               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)
+              }
+              // even if rseqs contained matchInDataset - check mappings between
+              // these seqs are added
+              // 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)
                 {
-                  // 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());
-                  }
+                  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;
             }