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JAL-3063 correct handling of absent choice element in DBRef Mapping
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 23 Jan 2019 09:15:52 +0000
(09:15 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 23 Jan 2019 09:15:52 +0000
(09:15 +0000)
src/jalview/project/Jalview2XML.java
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diff --git
a/src/jalview/project/Jalview2XML.java
b/src/jalview/project/Jalview2XML.java
index
74b6bf0
..
e57dd01
100644
(file)
--- 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());
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))
{
if (m.getDseqFor() != null)
{
String dsfor = m.getDseqFor();
if (seqRefIds.containsKey(dsfor))
{
- /**
+ /*
* recover from hash
*/
jmap.setTo(seqRefIds.get(dsfor));
* recover from hash
*/
jmap.setTo(seqRefIds.get(dsfor));
@@
-5847,9
+5848,9
@@
public class Jalview2XML
frefedSequence.add(newMappingRef(dsfor, jmap));
}
}
frefedSequence.add(newMappingRef(dsfor, jmap));
}
}
- else
+ else if (m.getSequence() != null)
{
{
- /**
+ /*
* local sequence definition
*/
Sequence ms = m.getSequence();
* local sequence definition
*/
Sequence ms = m.getSequence();