1 package jalview.ext.ensembl;
3 import jalview.datamodel.Alignment;
4 import jalview.datamodel.AlignmentI;
5 import jalview.io.FeaturesFile;
6 import jalview.io.FileParse;
8 import java.io.IOException;
9 import java.net.MalformedURLException;
11 import java.util.ArrayList;
12 import java.util.List;
15 * A client for fetching and processing Ensembl feature data in GFF format by
16 * calling the overlap REST service
19 * @see http://rest.ensembl.org/documentation/info/overlap_id
21 class EnsemblFeatures extends EnsemblRestClient
24 * The default features to retrieve from Ensembl
25 * can override in getSequenceRecords parameter
27 private EnsemblFeatureType[] featuresWanted = { EnsemblFeatureType.cds,
28 EnsemblFeatureType.exon, EnsemblFeatureType.variation };
31 public String getDbName()
33 return "ENSEMBL (features)";
37 * Makes a query to the REST overlap endpoint for the given sequence
38 * identifier. This returns an 'alignment' consisting of one 'dummy sequence'
39 * (the genomic sequence for which overlap features are returned by the
40 * service). This sequence will have on it sequence features which are the
41 * real information of interest, such as CDS regions or sequence variations.
44 public AlignmentI getSequenceRecords(String query) throws IOException
46 // TODO: use a vararg String... for getSequenceRecords instead?
47 List<String> queries = new ArrayList<String>();
49 FileParse fp = getSequenceReader(queries);
50 FeaturesFile fr = new FeaturesFile(fp);
51 return new Alignment(fr.getSeqsAsArray());
55 * Returns a URL for the REST overlap endpoint
61 protected URL getUrl(List<String> ids) throws MalformedURLException
63 StringBuffer urlstring = new StringBuffer(128);
64 urlstring.append(ENSEMBL_REST).append("/overlap/id/")
67 // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
68 urlstring.append("?content-type=text/x-gff3");
71 * specify features to retrieve
72 * @see http://rest.ensembl.org/documentation/info/overlap_id
73 * could make the list a configurable entry in jalview.properties
75 for (EnsemblFeatureType feature : featuresWanted)
77 urlstring.append("&feature=").append(feature.name());
80 return new URL(urlstring.toString());
84 protected boolean useGetRequest()
90 * Returns the MIME type for GFF3. For GET requests the Content-type header
91 * describes the required encoding of the response.
94 protected String getRequestMimeType(boolean multipleIds)
100 * Returns the MIME type for GFF3.
103 protected String getResponseMimeType()
105 return "text/x-gff3";
109 * Overloaded method that allows a list of features to retrieve to be
115 * @throws IOException
117 protected AlignmentI getSequenceRecords(String accId,
118 EnsemblFeatureType[] features) throws IOException
120 featuresWanted = features;
121 return getSequenceRecords(accId);