}
/**
- *
- */
+ * 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)
{
- 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
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;
}
*/
public static boolean recognises(String[] columns)
{
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
String type = columns[TYPE_COL];
if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
|| (".".equals(columns[SOURCE_COL])