List<SequenceI> seqs = parseSequenceJson(ids);
if (seqs == null)
- return alignment;
+ {
+ return alignment;
+ }
if (seqs.isEmpty())
{
Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK);
Map<String, Object> val = (Map<String, Object>) getJSON(null, ids, -1, MODE_MAP, null);
if (val == null)
- return null;
+ {
+ return null;
+ }
Object s = val.get("desc");
String desc = s == null ? null : s.toString();
s = val.get("id");
* for sequence_variant on reverse strand, have to convert the allele
* values to their complements
*/
- if (!forwardStrand && SequenceOntologyFactory.getInstance()
+ if (!forwardStrand && SequenceOntologyFactory.getSequenceOntology()
.isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
{
reverseComplementAlleles(copy);
public static boolean isTranscript(String featureType)
{
return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
- || SequenceOntologyFactory.getInstance().isA(featureType,
+ || SequenceOntologyFactory.getSequenceOntology().isA(featureType,
SequenceOntologyI.TRANSCRIPT);
}
}