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JAL-3187 update alignAs code and unit tests for 'shared dataset' case
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
InterProScanHelper.java
diff --git
a/src/jalview/io/gff/InterProScanHelper.java
b/src/jalview/io/gff/InterProScanHelper.java
index
c05593f
..
948cdd2
100644
(file)
--- a/
src/jalview/io/gff/InterProScanHelper.java
+++ b/
src/jalview/io/gff/InterProScanHelper.java
@@
-73,13
+73,19
@@
public class InterProScanHelper extends Gff3Helper
}
/**
}
/**
- *
- */
+ * An override that
+ * <ul>
+ * <li>uses Source (column 2) as feature type instead of the default column 3</li>
+ * <li>sets "InterProScan" as the feature group</li>
+ * <li>extracts "signature_desc" attribute as the feature description</li>
+ * </ul>
+ */
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map<String, List<String>> attributes)
{
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map<String, List<String>> attributes)
{
- SequenceFeature sf = super.buildSequenceFeature(gff, attributes);
+ SequenceFeature sf = super.buildSequenceFeature(gff, SOURCE_COL,
+ INTER_PRO_SCAN, attributes);
/*
* signature_desc is a more informative source of description
/*
* signature_desc is a more informative source of description
@@
-91,13
+97,6
@@
public class InterProScanHelper extends Gff3Helper
sf.setDescription(description);
}
sf.setDescription(description);
}
- /*
- * Set sequence feature group as 'InterProScan', and type as the source
- * database for this match (e.g. 'Pfam')
- */
- sf.setType(gff[SOURCE_COL]);
- sf.setFeatureGroup(INTER_PRO_SCAN);
-
return sf;
}
return sf;
}