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 overlap data in GFF feature
19 * @see http://rest.ensembl.org/documentation/info/overlap_id
21 public class EnsemblOverlap extends EnsemblRestClient
24 * The default features to retrieve from Ensembl; can override in getSequenceRecords
26 private EnsemblFeatureType[] featuresWanted = { EnsemblFeatureType.cds,
27 EnsemblFeatureType.exon, EnsemblFeatureType.variation };
30 public String getDbName()
32 return "ENSEMBL (overlap)";
36 * Makes a query to the REST overlap endpoint for the given sequence
37 * identifier. This returns an 'alignment' consisting of one 'dummy sequence'
38 * (the genomic sequence for which overlap features are returned by the
39 * service). This sequence will have on it sequence features which are the
40 * real information of interest, such as CDS regions or sequence variations.
43 public AlignmentI getSequenceRecords(String query) throws IOException
45 long now = System.currentTimeMillis();
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 System.out.println(getClass().getName() + " took "
52 + (System.currentTimeMillis() - now) + "ms to fetch");
53 return new Alignment(fr.getSeqsAsArray());
57 * Returns a URL for the REST overlap endpoint
63 protected URL getUrl(List<String> ids) throws MalformedURLException
65 StringBuffer urlstring = new StringBuffer(128);
66 urlstring.append(ENSEMBL_REST).append("/overlap/id/")
69 // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
70 urlstring.append("?content-type=text/x-gff3");
73 * specify features to retrieve
74 * @see http://rest.ensembl.org/documentation/info/overlap_id
75 * could make the list a configurable entry in jalview.properties
77 for (EnsemblFeatureType feature : featuresWanted)
79 urlstring.append("&feature=").append(feature.name());
82 return new URL(urlstring.toString());
86 protected boolean useGetRequest()
92 * Returns the MIME type for GFF3. For GET requests the Content-type header
93 * describes the required encoding of the response.
96 protected String getRequestMimeType()
102 * Returns the MIME type for GFF3.
105 protected String getResponseMimeType()
107 return "text/x-gff3";
111 * Overloaded method that allows a list of features to retrieve to be
117 * @throws IOException
119 protected AlignmentI getSequenceRecords(String accId,
120 EnsemblFeatureType[] features) throws IOException
122 featuresWanted = features;
123 return getSequenceRecords(accId);