package jalview.ext.ensembl;
-import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+import jalview.datamodel.SequenceFeature;
public class EnsemblGenome extends EnsemblSeqProxy
{
+ /*
+ * fetch transcript features on genomic sequence (to identify the transcript
+ * regions) and cds, exon and variation features (to retain)
+ */
+ private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
+ EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
+ EnsemblFeatureType.cds, EnsemblFeatureType.variation };
- public EnsemblGenome() throws Exception
+ public EnsemblGenome()
{
super();
}
return EnsemblSeqType.GENOMIC;
}
+ @Override
+ protected EnsemblFeatureType[] getFeaturesToFetch()
+ {
+ return FEATURES_TO_FETCH;
+ }
+
+ /**
+ * Answers true unless the feature type is 'transcript' (or a sub-type of
+ * transcript in the Sequence Ontology), or has a parent other than the given
+ * accession id. Transcript features are only retrieved in order to identify
+ * the transcript sequence range, and are redundant information on the
+ * transcript sequence itself.
+ */
+ @Override
+ protected boolean retainFeature(SequenceFeature sf, String accessionId)
+ {
+ if (isTranscript(sf.getType()))
+ {
+ return false;
+ }
+ return featureMayBelong(sf, accessionId);
+ }
+
+ /**
+ * Answers true if the sequence feature type is 'transcript' (or a subtype of
+ * transcript in the Sequence Ontology), and the ID of the feature is the
+ * transcript we are retrieving
+ */
+ @Override
+ protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ {
+ if (isTranscript(sf.getType()))
+ {
+ String id = (String) sf.getValue(ID);
+ if (("transcript:" + accId).equals(id))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
}