1 package jalview.ext.ensembl;
3 import jalview.datamodel.AlignmentI;
4 import jalview.datamodel.SequenceFeature;
8 import com.stevesoft.pat.Regex;
11 * A client to fetch protein translated sequence for an Ensembl identifier
16 public class EnsemblProtein extends EnsemblSeqProxy
19 * accepts ENSP with 11 digits
20 * or ENSMUSP or similar for other species
21 * or CCDSnnnnn.nn with at least 3 digits
23 private static final Regex ACCESSION_REGEX = new Regex(
24 "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
27 * Default constructor (to use rest.ensembl.org)
29 public EnsemblProtein()
35 * Constructor given the target domain to fetch data from
39 public EnsemblProtein(String d)
45 public String getDbName()
47 return "ENSEMBL (Protein)";
51 protected EnsemblSeqType getSourceEnsemblType()
53 return EnsemblSeqType.PROTEIN;
57 * Returns false, as this fetcher does not retrieve DNA sequences.
60 public boolean isDnaCoding()
66 * Test query is to the protein translation of transcript ENST00000288602
69 public String getTestQuery()
71 return "ENSP00000288602";
75 * Overrides base class method to do nothing - genomic features are not
76 * applicable to the protein product sequence
79 protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
84 protected EnsemblFeatureType[] getFeaturesToFetch()
86 // not applicable - can't fetch genomic features for a protein sequence
91 protected boolean identifiesSequence(SequenceFeature sf, String accId)
93 // not applicable - protein sequence is not a 'subset' of genomic sequence
98 public Regex getAccessionValidator()
100 return ACCESSION_REGEX;
104 * Returns an accession id for a query, including conversion of ENST* to
105 * ENSP*. This supports querying for the protein sequence for a transcript
106 * (ENST identifier) and returning the ENSP identifier.
109 public String getAccessionIdFromQuery(String query)
111 String accId = super.getAccessionIdFromQuery(query);
114 * ensure last character before (11) digits is P
115 * ENST00000288602 -> ENSP00000288602
116 * ENSMUST00000288602 -> ENSMUSP00000288602
118 if (accId != null && accId.length() >= 12)
120 char[] chars = accId.toCharArray();
121 chars[chars.length - 12] = 'P';
122 accId = new String(chars);