1 package jalview.ext.ensembl;
3 import jalview.datamodel.AlignmentI;
4 import jalview.datamodel.SequenceFeature;
5 import jalview.datamodel.SequenceI;
7 public class EnsemblProtein extends EnsemblSeqProxy
10 public EnsemblProtein()
16 public String getDbName()
18 return "ENSEMBL (Protein)";
22 protected EnsemblSeqType getSourceEnsemblType()
24 return EnsemblSeqType.PROTEIN;
28 * Returns false, as this fetcher does not retrieve DNA sequences.
31 public boolean isDnaCoding()
37 * Test query is to the protein translation of transcript ENST00000288602
40 public String getTestQuery()
42 return "ENSP00000288602";
46 * Overrides base class method to do nothing - genomic features are not
47 * applicable to the protein product sequence
50 protected void addFeaturesAndProduct(String accId, AlignmentI alignment,
51 SequenceI genomicSequence)
56 protected EnsemblFeatureType[] getFeaturesToFetch()
58 // not applicable - can't fetch genomic features for a protein sequence
63 protected boolean identifiesSequence(SequenceFeature sf, String accId)
65 // not applicable - protein sequence is not a 'subset' of genomic sequence