From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 23 Jan 2019 09:15:52 +0000 (+0000)
Subject: JAL-3063 correct handling of absent choice element in DBRef Mapping
X-Git-Tag: Release_2_11_1_0~68^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c93f0b25cf06af3e8f65426acc0b0c82ba281d69;p=jalview.git

JAL-3063 correct handling of absent choice element in DBRef Mapping
---

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 74b6bf0..e57dd01 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -5829,15 +5829,16 @@ public class Jalview2XML
     jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
             fto, m.getMapFromUnit().intValue(),
             m.getMapToUnit().intValue());
-    // if (m.getMappingChoice() != null)
-    // {
-    // MappingChoice mc = m.getMappingChoice();
+
+    /*
+     * (optional) choice of dseqFor or Sequence
+     */
     if (m.getDseqFor() != null)
     {
       String dsfor = m.getDseqFor();
       if (seqRefIds.containsKey(dsfor))
       {
-        /**
+        /*
          * recover from hash
          */
         jmap.setTo(seqRefIds.get(dsfor));
@@ -5847,9 +5848,9 @@ public class Jalview2XML
         frefedSequence.add(newMappingRef(dsfor, jmap));
       }
     }
-    else
+    else if (m.getSequence() != null)
     {
-      /**
+      /*
        * local sequence definition
        */
       Sequence ms = m.getSequence();