sfs = sequence.getFeatures()
.getFeaturesByOntology(term);
for (SequenceFeature sf : sfs)
{
String parent = (String) sf.getValue(PARENT);
if (parent != null && parent.equalsIgnoreCase(parentId))
{
result.add(sf);
}
}
return result;
}
/**
* Answers true if the feature type is either 'NMD_transcript_variant' or
* 'transcript' (or one of its sub-types in the Sequence Ontology). This is
* because NMD_transcript_variant behaves like 'transcript' in Ensembl
* although strictly speaking it is not (it is a sub-type of
* sequence_variant).
*
* (This test was needed when fetching transcript features as GFF. As we are
* now fetching as JSON, all features have type 'transcript' so the check for
* NMD_transcript_variant is redundant. Left in for any future case arising.)
*
* @param featureType
* @return
*/
public static boolean isTranscript(String featureType)
{
return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
|| SequenceOntologyFactory.getInstance().isA(featureType,
SequenceOntologyI.TRANSCRIPT);
}
}