From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 4 Aug 2016 19:59:46 +0000 (+0100)
Subject: JAL-2154 make sure codon mappings between sequences discovered via database cross... 
X-Git-Tag: Release_2_10_0~47^2~4^2~43^2~56
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cc9619f850c707b183d2c1e7528ca5b4579e9e78;p=jalview.git

JAL-2154 make sure codon mappings between sequences discovered via database cross-reference matching are added to the codonframe.
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index b4d75f9..1edc9e5 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -277,6 +277,19 @@ 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)
+                {
+                  // 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;