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JAL-1148 reinstate sequence references for annotation regardless of whether they...
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Tue, 28 Aug 2012 09:31:50 +0000
(10:31 +0100)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Tue, 28 Aug 2012 09:31:50 +0000
(10:31 +0100)
src/jalview/gui/Jalview2XML.java
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diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
ea5d5a7
..
6acd421
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-2306,24
+2306,20
@@
public class Jalview2XML
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot);
}
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot);
}
- if (autoForView)
+ // register new annotation
+ if (an[i].getId() != null)
{
{
- // register new annotation
- if (an[i].getId() != null)
- {
- annotationIds.put(an[i].getId(), jaa);
- jaa.annotationId = an[i].getId();
- }
- // recover sequence association
- if (an[i].getSequenceRef() != null)
+ annotationIds.put(an[i].getId(), jaa);
+ jaa.annotationId = an[i].getId();
+ }
+ // recover sequence association
+ if (an[i].getSequenceRef() != null)
+ {
+ if (al.findName(an[i].getSequenceRef()) != null)
{
{
- if (al.findName(an[i].getSequenceRef()) != null)
- {
- jaa.createSequenceMapping(
- al.findName(an[i].getSequenceRef()), 1, true);
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(
- jaa);
- }
+ jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
+ 1, true);
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
}
}
// and make a note of any group association
}
}
// and make a note of any group association