package jalview.ext.ensembl;
-import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+import jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntology;
public class EnsemblCds extends EnsemblSeqProxy
{
+ /*
+ * fetch cds features on genomic sequence (to identify the CDS regions)
+ * and variation features (to retain)
+ */
+ private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
+ EnsemblFeatureType.cds, EnsemblFeatureType.variation };
+ /**
+ * Constructor
+ */
public EnsemblCds()
{
super();
return EnsemblSeqType.CDS;
}
+ @Override
+ protected EnsemblFeatureType[] getFeaturesToFetch()
+ {
+ return FEATURES_TO_FETCH;
+ }
+
+ /**
+ * Answers true unless the feature type is 'CDS' (or a sub-type of CDS in the
+ * Sequence Ontology). CDS features are only retrieved in order to identify
+ * the cds sequence range, and are redundant information on the cds sequence
+ * itself.
+ */
+ @Override
+ protected boolean retainFeature(String type)
+ {
+ return !SequenceOntology.getInstance().isA(type, SequenceOntology.CDS);
+ }
+
+ /**
+ * Answers true if the sequence feature type is 'CDS' (or a subtype of CDS in
+ * the Sequence Ontology), and the Parent of the feature is the transcript we
+ * are retrieving
+ */
+ @Override
+ protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ {
+ if (SequenceOntology.getInstance().isA(sf.getType(),
+ SequenceOntology.CDS))
+ {
+ String parentFeature = (String) sf.getValue("Parent");
+ if (("transcript:" + accId).equals(parentFeature))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
}