X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblMap.java;h=add71b3b7935ba6cafb84e42c5371bc73ef7c3d0;hb=8e7cf85a7f61f425e808cac53ead7bc27e402242;hp=c94528ec395d43a1945502cc761bdfe87208ba26;hpb=da31d3e5aebfcdbb1ae7084bbc75bbc3539ee2e6;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java index c94528e..add71b3 100644 --- a/src/jalview/ext/ensembl/EnsemblMap.java +++ b/src/jalview/ext/ensembl/EnsemblMap.java @@ -2,17 +2,20 @@ package jalview.ext.ensembl; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefSource; +import jalview.datamodel.GeneLociI; +import jalview.util.JSONUtils; +import jalview.util.MapList; import java.io.BufferedReader; import java.io.IOException; import java.net.MalformedURLException; import java.net.URL; +import java.util.ArrayList; +import java.util.Collections; import java.util.Iterator; import java.util.List; +import java.util.Map; -import org.json.simple.JSONArray; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; public class EnsemblMap extends EnsemblRestClient @@ -21,6 +24,10 @@ public class EnsemblMap extends EnsemblRestClient private static final String MAPPINGS = "mappings"; + private static final String CDS = "cds"; + + private static final String CDNA = "cdna"; + /** * Default constructor (to use rest.ensembl.org) */ @@ -111,30 +118,15 @@ public class EnsemblMap extends EnsemblRestClient String fromRef, String toRef, int[] queryRange) { URL url = null; - BufferedReader br = null; - try { url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0], queryRange[1]); - br = getHttpResponse(url, null); - return (parseAssemblyMappingResponse(br)); + return (parseAssemblyMappingResponse(url)); } catch (Throwable t) { System.out.println("Error calling " + url + ": " + t.getMessage()); return null; - } finally - { - if (br != null) - { - try - { - br.close(); - } catch (IOException e) - { - // ignore - } - } } } @@ -153,22 +145,21 @@ public class EnsemblMap extends EnsemblRestClient * @param br * @return */ - protected int[] parseAssemblyMappingResponse(BufferedReader br) + @SuppressWarnings("unchecked") + protected int[] parseAssemblyMappingResponse(URL url) { int[] result = null; - JSONParser jp = new JSONParser(); try { - JSONObject parsed = (JSONObject) jp.parse(br); - JSONArray mappings = (JSONArray) parsed.get(MAPPINGS); - - Iterator rvals = mappings.iterator(); + Iterator rvals = (Iterator) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS); + if (rvals == null) + return null; while (rvals.hasNext()) { // todo check for "mapped" - JSONObject val = (JSONObject) rvals.next(); - JSONObject mapped = (JSONObject) val.get(MAPPED); + Map val = (Map) rvals.next(); + Map mapped = (Map) val.get(MAPPED); int start = Integer.parseInt(mapped.get("start").toString()); int end = Integer.parseInt(mapped.get("end").toString()); String strand = mapped.get("strand").toString(); @@ -189,6 +180,62 @@ public class EnsemblMap extends EnsemblRestClient } /** + * Calls the REST /map/cds/id service, and returns a DBRefEntry holding the + * returned chromosomal coordinates, or returns null if the call fails + * + * @param division + * e.g. Ensembl, EnsemblMetazoa + * @param accession + * e.g. ENST00000592782, Y55B1AR.1.1 + * @param start + * @param end + * @return + */ + public GeneLociI getCdsMapping(String division, String accession, + int start, int end) + { + return getIdMapping(division, accession, start, end, CDS); + } + + /** + * Calls the REST /map/cdna/id service, and returns a DBRefEntry holding the + * returned chromosomal coordinates, or returns null if the call fails + * + * @param division + * e.g. Ensembl, EnsemblMetazoa + * @param accession + * e.g. ENST00000592782, Y55B1AR.1.1 + * @param start + * @param end + * @return + */ + public GeneLociI getCdnaMapping(String division, String accession, + int start, int end) + { + return getIdMapping(division, accession, start, end, CDNA); + } + + GeneLociI getIdMapping(String division, String accession, int start, + int end, String cdsOrCdna) + { + URL url = null; + try + { + String domain = new EnsemblInfo().getDomain(division); + if (domain != null) + { + url = getIdMapUrl(domain, accession, start, end, cdsOrCdna); + return (parseIdMappingResponse(url, accession, domain)); + } + return null; + } catch (Throwable t) + { + System.out.println("Error calling " + url + ": " + t.getMessage()); + return null; + } + } + + /** * Constructs a URL to the /map/cds/ or /map/cdna/ REST service. The * REST call is to either ensembl or ensemblgenomes, as determined from the * division, e.g. Ensembl or EnsemblProtists. @@ -210,4 +257,121 @@ public class EnsemblMap extends EnsemblRestClient return new URL(url); } + /** + * Parses the JSON response from the /map/cds/ or /map/cdna REST service. The + * format is + * + * 
+   * {"mappings":
+   *   [
+   *    {"assembly_name":"TAIR10","end":2501311,"seq_region_name":"1","gap":0,
+   *     "strand":-1,"coord_system":"chromosome","rank":0,"start":2501114},
+   *    {"assembly_name":"TAIR10","end":2500815,"seq_region_name":"1","gap":0,
+   *     "strand":-1,"coord_system":"chromosome","rank":0,"start":2500714}
+   *   ]
+   * }
+   *
+ * + * @param br + * @param accession + * @param domain + * @return + */ + @SuppressWarnings("unchecked") +GeneLociI parseIdMappingResponse(URL url, String accession, + String domain) + { + + try + { + Iterator rvals = (Iterator) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS); + if (rvals == null) + return null; + String assembly = null; + String chromosome = null; + int fromEnd = 0; + List regions = new ArrayList<>(); + + while (rvals.hasNext()) + { + Map val = (Map) rvals.next(); + Map original = (Map) val.get("original"); + fromEnd = Integer.parseInt(original.get("end").toString()); + + Map mapped = (Map) val.get(MAPPED); + int start = Integer.parseInt(mapped.get("start").toString()); + int end = Integer.parseInt(mapped.get("end").toString()); + String ass = mapped.get("assembly_name").toString(); + if (assembly != null && !assembly.equals(ass)) + { + System.err + .println("EnsemblMap found multiple assemblies - can't resolve"); + return null; + } + assembly = ass; + String chr = mapped.get("seq_region_name").toString(); + if (chromosome != null && !chromosome.equals(chr)) + { + System.err + .println("EnsemblMap found multiple chromosomes - can't resolve"); + return null; + } + chromosome = chr; + String strand = mapped.get("strand").toString(); + if ("-1".equals(strand)) + { + regions.add(new int[] { end, start }); + } + else + { + regions.add(new int[] { start, end }); + } + } + + /* + * processed all mapped regions on chromosome, assemble the result, + * having first fetched the species id for the accession + */ + final String species = new EnsemblLookup(domain) + .getSpecies(accession); + final String as = assembly; + final String chr = chromosome; + List fromRange = Collections.singletonList(new int[] { 1, + fromEnd }); + final MapList map = new MapList(fromRange, regions, 1, 1); + return new GeneLociI() + { + + @Override + public String getSpeciesId() + { + return species == null ? "" : species; + } + + @Override + public String getAssemblyId() + { + return as; + } + + @Override + public String getChromosomeId() + { + return chr; + } + + @Override + public MapList getMap() + { + return map; + } + }; + } catch (IOException | ParseException | NumberFormatException e) + { + // ignore + } + + return null; + } + }