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fix for JAL-2507 - resolve stockholm per residue annotation type by annotation label...
author
Jim Procter
<jprocter@issues.jalview.org>
Thu, 4 May 2017 10:37:19 +0000
(11:37 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Thu, 4 May 2017 10:37:19 +0000
(11:37 +0100)
src/jalview/io/StockholmFile.java
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diff --git
a/src/jalview/io/StockholmFile.java
b/src/jalview/io/StockholmFile.java
index
2061f29
..
3b0dab4
100644
(file)
--- a/
src/jalview/io/StockholmFile.java
+++ b/
src/jalview/io/StockholmFile.java
@@
-978,15
+978,19
@@
public class StockholmFile extends AlignFile
{
for (int j = 0; j < alAnot.length; j++)
{
{
for (int j = 0; j < alAnot.length; j++)
{
- if (ds.getSequenceFeatures() != null)
+
+ String key = type2id(alAnot[j].label);
+ boolean isrna = alAnot[j].isValidStruc();
+
+ if (isrna)
{
{
- feature = ds.getSequenceFeatures()[0].type;
+ // hardwire to secondary structure if there is RNA secondary
+ // structure on the annotation
+ key = "SS";
}
}
- // ?bug - feature may still have previous loop value
- String key = type2id(feature);
-
if (key == null)
{
if (key == null)
{
+
continue;
}
continue;
}
@@
-994,7
+998,6
@@
public class StockholmFile extends AlignFile
out.append(new Format("%-" + maxid + "s").form("#=GR "
+ printId(s[i], jvSuffix) + " " + key + " "));
ann = alAnot[j].annotations;
out.append(new Format("%-" + maxid + "s").form("#=GR "
+ printId(s[i], jvSuffix) + " " + key + " "));
ann = alAnot[j].annotations;
- boolean isrna = alAnot[j].isValidStruc();
String seq = "";
for (int k = 0; k < ann.length; k++)
{
String seq = "";
for (int k = 0; k < ann.length; k++)
{