X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FInterProScanHelper.java;h=91f001822d13b379b0ac503128ea526c5281959d;hb=eca4795050a0f7eca3d5dece68eaa54987cebd15;hp=c05593f5a2b6a9951dca3c81e509d4b513a01d65;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git
diff --git a/src/jalview/io/gff/InterProScanHelper.java b/src/jalview/io/gff/InterProScanHelper.java
index c05593f..91f0018 100644
--- a/src/jalview/io/gff/InterProScanHelper.java
+++ b/src/jalview/io/gff/InterProScanHelper.java
@@ -73,13 +73,20 @@ public class InterProScanHelper extends Gff3Helper
}
/**
- *
- */
+ * An override that
+ *
+ * - uses Source (column 2) as feature type instead of the default column
+ * 3
+ * - sets "InterProScan" as the feature group
+ * - extracts "signature_desc" attribute as the feature description
+ *
+ */
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map> 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
@@ -91,13 +98,6 @@ public class InterProScanHelper extends Gff3Helper
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;
}