From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 16 Aug 2016 14:15:15 +0000 (+0100)
Subject: JAL-2154 always resolve dataset sequences when creating a mapping for a DBRefEntry
X-Git-Tag: Release_2_10_0~47^2~4^2~43^2~42
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=22abbe2e23f5e82e27fa7fa5dbbb4d7885a6fc3a;p=jalview.git

JAL-2154 always resolve dataset sequences when creating a mapping for a DBRefEntry
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 1edc9e5..355f46a 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -675,24 +675,28 @@ 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;
         }
       }