String atts = gff[ATTRIBUTES_COL];
Map<String, List<String>> attributes = parseNameValuePairs(atts);
- if (SequenceOntology.getInstance().isProteinMatch(soTerm))
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ if (so.isA(soTerm, SequenceOntologyI.PROTEIN_MATCH))
{
- sf = processProteinMatch(attributes, seq, gff, align,
- newseqs, relaxedIdMatching);
+ sf = processProteinMatch(attributes, seq, gff, align, newseqs,
+ relaxedIdMatching);
}
- else if (SequenceOntology.getInstance().isNucleotideMatch(soTerm))
+ else if (so.isA(soTerm, SequenceOntologyI.NUCLEOTIDE_MATCH))
{
sf = processNucleotideMatch(attributes, seq, gff, align,
newseqs, relaxedIdMatching);
desc = target.split(" ")[0];
}
- SequenceOntology so = SequenceOntology.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
String type = sf.getType();
- if (so.isSequenceVariant(type))
+ if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
{
/*
* Ensembl returns dna variants as 'alleles'