X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FInterProScanHelper.java;h=0aa3b74cb2376333ff75f8094f6c5ad91b1c7c34;hb=00918171094ad58563bd0b82e18ecf19537ba132;hp=e1334e1df0a8b16c4178b2517e968d7c1b4dbf09;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git
diff --git a/src/jalview/io/gff/InterProScanHelper.java b/src/jalview/io/gff/InterProScanHelper.java
index e1334e1..0aa3b74 100644
--- 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
+ *
+ * - 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 +97,6 @@ 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;
}