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JAL-1199 JAL-1569 incremental patch allow non-standard annotation to be output
author
Jim Procter
<jprocter@dundee.ac.uk>
Mon, 1 Dec 2014 21:49:16 +0000
(21:49 +0000)
committer
Jim Procter
<jprocter@dundee.ac.uk>
Mon, 1 Dec 2014 21:49:16 +0000
(21:49 +0000)
src/jalview/io/StockholmFile.java
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diff --git
a/src/jalview/io/StockholmFile.java
b/src/jalview/io/StockholmFile.java
index
96c462c
..
3b9fb00
100644
(file)
--- a/
src/jalview/io/StockholmFile.java
+++ b/
src/jalview/io/StockholmFile.java
@@
-1027,13
+1027,21
@@
public class StockholmFile extends AlignFile
}
else
{
}
else
{
- label = (key = type2id(aa.label.toLowerCase())) + "_cons";
+ key = type2id(aa.label.toLowerCase());
+ if (key == null)
+ {
+ label = aa.label;
+ }
+ else
+ {
+ label = key + "_cons";
+ }
}
}
-
if (label == null)
{
label = aa.label;
}
if (label == null)
{
label = aa.label;
}
+ label = label.replace(" ", "_");
out.append(new Format("%-" + maxid + "s").form("#=GC " + label
+ " "));
out.append(new Format("%-" + maxid + "s").form("#=GC " + label
+ " "));
@@
-1067,7
+1075,7
@@
public class StockholmFile extends AlignFile
String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
.toString(sequenceI.getCharAt(k)))
: annot.displayCharacter;
String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
.toString(sequenceI.getCharAt(k)))
: annot.displayCharacter;
- if (key.equals("SS"))
+ if (key != null && key.equals("SS"))
{
if (annot == null)
{
{
if (annot == null)
{