package jalview.ext.ensembl; import jalview.datamodel.SequenceFeature; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; import com.stevesoft.pat.Regex; /** * A client to fetch CDNA sequence from Ensembl (i.e. that part of the genomic * sequence that is transcribed to RNA, but not necessarily translated to * protein) * * @author gmcarstairs * */ public class EnsemblCdna extends EnsemblSeqProxy { /* * accepts ENST or ENSTG with 11 digits * or ENSMUST or similar for other species * or CCDSnnnnn.nn with at least 3 digits */ private static final Regex ACCESSION_REGEX = new Regex( "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)"); /* * fetch exon features on genomic sequence (to identify the cdna regions) * and cds and variation features (to retain) */ private static final EnsemblFeatureType[] FEATURES_TO_FETCH = { EnsemblFeatureType.exon, EnsemblFeatureType.cds, EnsemblFeatureType.variation }; /** * Default constructor (to use rest.ensembl.org) */ public EnsemblCdna() { super(); } /** * Constructor given the target domain to fetch data from * * @param d */ public EnsemblCdna(String d) { super(d); } @Override public String getDbName() { return "ENSEMBL (CDNA)"; } @Override protected EnsemblSeqType getSourceEnsemblType() { return EnsemblSeqType.CDNA; } @Override public Regex getAccessionValidator() { return ACCESSION_REGEX; } @Override protected EnsemblFeatureType[] getFeaturesToFetch() { return FEATURES_TO_FETCH; } /** * Answers true unless the feature type is 'transcript' (or a sub-type in the * Sequence Ontology). */ @Override protected boolean retainFeature(SequenceFeature sf, String accessionId) { if (isTranscript(sf.getType())) { return false; } return featureMayBelong(sf, accessionId); } /** * Answers true if the sequence feature type is 'exon' (or a subtype of exon * in the Sequence Ontology), and the Parent of the feature is the transcript * we are retrieving */ @Override protected boolean identifiesSequence(SequenceFeature sf, String accId) { if (SequenceOntologyFactory.getInstance().isA(sf.getType(), SequenceOntologyI.EXON)) { String parentFeature = (String) sf.getValue(PARENT); if (("transcript:" + accId).equals(parentFeature)) { return true; } } return false; } }