1 package jalview.ext.ensembl;
3 import jalview.datamodel.AlignmentI;
4 import jalview.datamodel.SequenceFeature;
6 public class EnsemblProtein extends EnsemblSeqProxy
9 public EnsemblProtein()
15 public String getDbName()
17 return "ENSEMBL (Protein)";
21 protected EnsemblSeqType getSourceEnsemblType()
23 return EnsemblSeqType.PROTEIN;
27 * Returns false, as this fetcher does not retrieve DNA sequences.
30 public boolean isDnaCoding()
36 * Test query is to the protein translation of transcript ENST00000288602
39 public String getTestQuery()
41 return "ENSP00000288602";
45 * Overrides base class method to do nothing - genomic features are not
46 * applicable to the protein product sequence
49 protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
54 protected EnsemblFeatureType[] getFeaturesToFetch()
56 // not applicable - can't fetch genomic features for a protein sequence
61 protected boolean identifiesSequence(SequenceFeature sf, String accId)
63 // not applicable - protein sequence is not a 'subset' of genomic sequence