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JAL-2602 check for null or empty description when copying consensus
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 27 Jun 2017 13:03:09 +0000
(14:03 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 27 Jun 2017 13:03:09 +0000
(14:03 +0100)
src/jalview/gui/AlignViewport.java
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diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
86e1144
..
288f261
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-34,6
+34,7
@@
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
@@
-330,15
+331,18
@@
public class AlignViewport extends AlignmentViewport implements
StringBuffer seqs = new StringBuffer();
for (int i = 0; i < consensus.annotations.length; i++)
{
StringBuffer seqs = new StringBuffer();
for (int i = 0; i < consensus.annotations.length; i++)
{
- if (consensus.annotations[i] != null)
+ Annotation annotation = consensus.annotations[i];
+ if (annotation != null)
{
{
- if (consensus.annotations[i].description.charAt(0) == '[')
+ String description = annotation.description;
+ if (description != null && description.startsWith("["))
{
{
- seqs.append(consensus.annotations[i].description.charAt(1));
+ // consensus is a tie - just pick the first one
+ seqs.append(description.charAt(1));
}
else
{
}
else
{
- seqs.append(consensus.annotations[i].displayCharacter);
+ seqs.append(annotation.displayCharacter);
}
}
}
}
}
}