{
private static final String ALLELES = "alleles";
- private static final List<String> CROSS_REFERENCES = Arrays
- .asList(new String[] { "CCDS", "Uniprot/SWISSPROT",
- "Uniprot/SPTREMBL" });
-
protected static final String CONSEQUENCE_TYPE = "consequence_type";
protected static final String PARENT = "Parent";
}
EnsemblXref xrefFetcher = new EnsemblXref(getDomain());
- List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName(),
- getCrossReferenceDatabases());
+ List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName());
for (DBRefEntry xref : xrefs)
{
seq.addDBRef(xref);
}
/**
- * Returns a list of database names to be used when fetching cross-references.
- * Specifically, the names are used to filter data returned by the Ensembl
- * xrefs REST service on the value in field 'dbname'.
- *
- * @return
- */
- protected List<String> getCrossReferenceDatabases()
- {
- return CROSS_REFERENCES;
- }
-
- /**
* Fetches sequences for the list of accession ids and adds them to the
* alignment. Returns the extended (or created) alignment.
*