+ /**
+ * Returns false, as this fetcher does not retrieve DNA sequences.
+ */
+ @Override
+ public boolean isDnaCoding()
+ {
+ return false;
+ }
+
+ /**
+ * Test query is to the protein translation of transcript ENST00000288602
+ */
+ @Override
+ public String getTestQuery()
+ {
+ return "ENSP00000288602";
+ }
+
+ /**
+ * Overrides base class method to do nothing - genomic features are not
+ * applicable to the protein product sequence
+ */
+ @Override
+ protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
+ {
+ }
+
+ @Override
+ protected EnsemblFeatureType[] getFeaturesToFetch()
+ {
+ // not applicable - can't fetch genomic features for a protein sequence
+ return null;
+ }
+
+ @Override
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
+ {
+ return new ArrayList<>();
+ }
+
+ @Override
+ public Regex getAccessionValidator()
+ {
+ return ACCESSION_REGEX;
+ }
+
+ /**
+ * Returns an accession id for a query, including conversion of ENST* to
+ * ENSP*. This supports querying for the protein sequence for a transcript
+ * (ENST identifier) and returning the ENSP identifier.
+ */
+ @Override
+ public String getAccessionIdFromQuery(String query)
+ {
+ String accId = super.getAccessionIdFromQuery(query);
+
+ /*
+ * ensure last character before (11) digits is P
+ * ENST00000288602 -> ENSP00000288602
+ * ENSMUST00000288602 -> ENSMUSP00000288602
+ */
+ if (accId != null && accId.length() >= 12)
+ {
+ char[] chars = accId.toCharArray();
+ chars[chars.length - 12] = 'P';
+ accId = new String(chars);
+ }
+ return accId;
+ }
+