package jalview.ext.ensembl; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.io.FeaturesFile; import jalview.io.FileParse; import java.io.IOException; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.List; /** * A client for fetching and processing Ensembl feature data in GFF format by * calling the overlap REST service * * @author gmcarstairs * @see http://rest.ensembl.org/documentation/info/overlap_id */ class EnsemblFeatures extends EnsemblRestClient { /* * The default features to retrieve from Ensembl * can override in getSequenceRecords parameter */ private EnsemblFeatureType[] featuresWanted = { EnsemblFeatureType.cds, EnsemblFeatureType.exon, EnsemblFeatureType.variation }; /** * Default constructor (to use rest.ensembl.org) */ public EnsemblFeatures() { super(); } /** * Constructor given the target domain to fetch data from * * @param d */ public EnsemblFeatures(String d) { super(d); } @Override public String getDbName() { return "ENSEMBL (features)"; } /** * Makes a query to the REST overlap endpoint for the given sequence * identifier. This returns an 'alignment' consisting of one 'dummy sequence' * (the genomic sequence for which overlap features are returned by the * service). This sequence will have on it sequence features which are the * real information of interest, such as CDS regions or sequence variations. */ @Override public AlignmentI getSequenceRecords(String query) throws IOException { // TODO: use a vararg String... for getSequenceRecords instead? List queries = new ArrayList(); queries.add(query); FileParse fp = getSequenceReader(queries); FeaturesFile fr = new FeaturesFile(fp); return new Alignment(fr.getSeqsAsArray()); } /** * Returns a URL for the REST overlap endpoint * * @param ids * @return */ @Override protected URL getUrl(List ids) throws MalformedURLException { StringBuffer urlstring = new StringBuffer(128); urlstring.append(getDomain()).append("/overlap/id/") .append(ids.get(0)); // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats urlstring.append("?content-type=text/x-gff3"); /* * specify features to retrieve * @see http://rest.ensembl.org/documentation/info/overlap_id * could make the list a configurable entry in jalview.properties */ for (EnsemblFeatureType feature : featuresWanted) { urlstring.append("&feature=").append(feature.name()); } return new URL(urlstring.toString()); } @Override protected boolean useGetRequest() { return true; } /** * Returns the MIME type for GFF3. For GET requests the Content-type header * describes the required encoding of the response. */ @Override protected String getRequestMimeType(boolean multipleIds) { return "text/x-gff3"; } /** * Returns the MIME type for GFF3. */ @Override protected String getResponseMimeType() { return "text/x-gff3"; } /** * Overloaded method that allows a list of features to retrieve to be * specified * * @param accId * @param features * @return * @throws IOException */ protected AlignmentI getSequenceRecords(String accId, EnsemblFeatureType[] features) throws IOException { featuresWanted = features; return getSequenceRecords(accId); } }