1 package jalview.ext.ensembl;
3 import jalview.datamodel.AlignmentI;
4 import jalview.datamodel.SequenceFeature;
6 import java.util.Arrays;
9 public class EnsemblProtein extends EnsemblSeqProxy
12 private static final List<String> CROSSREFS = Arrays.asList(new String[] {
13 "PDB", "Uniprot/SPTREMBL", "Uniprot/SWISSPROT" });
15 public EnsemblProtein()
21 public String getDbName()
23 return "ENSEMBL (Protein)";
27 protected EnsemblSeqType getSourceEnsemblType()
29 return EnsemblSeqType.PROTEIN;
33 * Returns false, as this fetcher does not retrieve DNA sequences.
36 public boolean isDnaCoding()
42 * Test query is to the protein translation of transcript ENST00000288602
45 public String getTestQuery()
47 return "ENSP00000288602";
51 * Overrides base class method to do nothing - genomic features are not
52 * applicable to the protein product sequence
55 protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
60 protected EnsemblFeatureType[] getFeaturesToFetch()
62 // not applicable - can't fetch genomic features for a protein sequence
67 protected boolean identifiesSequence(SequenceFeature sf, String accId)
69 // not applicable - protein sequence is not a 'subset' of genomic sequence
74 protected List<String> getCrossReferenceDatabases()