String atts = gff[ATTRIBUTES_COL];
Map<String, List<String>> attributes = parseNameValuePairs(atts);
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
if (so.isA(soTerm, SequenceOntologyI.PROTEIN_MATCH))
{
sf = processProteinMatch(attributes, seq, gff, align, newseqs,
desc = target.split(" ")[0];
}
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
String type = sf.getType();
if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
{