+ @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(SequenceFeature sf, String accessionId)
+ {
+ if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+ SequenceOntologyI.CDS))
+ {
+ return false;
+ }
+ return featureMayBelong(sf, accessionId);
+ }
+
+ /**
+ * 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 (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+ SequenceOntologyI.CDS))
+ {
+ String parentFeature = (String) sf.getValue(PARENT);
+ if (("transcript:" + accId).equals(parentFeature))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Overrides this method to trivially return a range which is the whole of the
+ * nucleotide sequence. This is both faster than scanning for CDS features,
+ * and also means we don't need to keep CDS features on CDS sequence (where
+ * they are redundant information).
+ */
+ protected List<int[]> getCdsRanges(SequenceI dnaSeq)
+ {
+ int len = dnaSeq.getLength();
+ List<int[]> ranges = new ArrayList<int[]>();
+ ranges.add(new int[] { 1, len });
+ return ranges;
+ }
+