package jalview.ext.ensembl; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; import java.util.ArrayList; import java.util.List; /** * A client for direct fetching of CDS sequences from Ensembl (i.e. that part of * the genomic sequence that is translated to protein) * * TODO: not currently used as CDS sequences are computed from CDS features on * transcripts - delete this class? * * @author gmcarstairs * */ public class EnsemblCds extends EnsemblSeqProxy { /* * fetch cds features on genomic sequence (to identify the CDS regions) * and exon and variation features (to retain for display) */ private static final EnsemblFeatureType[] FEATURES_TO_FETCH = { EnsemblFeatureType.cds, EnsemblFeatureType.exon, EnsemblFeatureType.variation }; /** * Default constructor (to use rest.ensembl.org) */ public EnsemblCds() { super(); } /** * Constructor given the target domain to fetch data from * * @param d */ public EnsemblCds(String d) { super(d); } @Override public String getDbName() { return "ENSEMBL (CDS)"; } @Override protected EnsemblSeqType getSourceEnsemblType() { return EnsemblSeqType.CDS; } @Override protected EnsemblFeatureType[] getFeaturesToFetch() { return FEATURES_TO_FETCH; } /** * Answers true unless the feature type is 'CDS' (or a sub-type of CDS in the * Sequence Ontology). CDS features are only retrieved in order to identify * the cds sequence range, and are redundant information on the cds sequence * itself. */ @Override protected boolean retainFeature(SequenceFeature sf, String accessionId) { if (SequenceOntologyFactory.getInstance().isA(sf.getType(), SequenceOntologyI.CDS)) { return false; } return featureMayBelong(sf, accessionId); } /** * Answers true if the sequence feature type is 'CDS' (or a subtype of CDS 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.CDS)) { String parentFeature = (String) sf.getValue(PARENT); if (("transcript:" + accId).equals(parentFeature)) { return true; } } return false; } /** * Overrides this method to trivially return a range which is the whole of the * nucleotide sequence. This is both faster than scanning for CDS features, * and also means we don't need to keep CDS features on CDS sequence (where * they are redundant information). */ protected List getCdsRanges(SequenceI dnaSeq) { int len = dnaSeq.getLength(); List ranges = new ArrayList(); ranges.add(new int[] { 1, len }); return ranges; } }