X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblMap.java;h=e9cc9e15fb11f4d7fe09b72714cba36e47c33815;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=ae36749738b870b245f98289d761797be8bcc342;hpb=4b1c969e87feaefd4fb9c49ba3d6b828b3ce1a9c;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java index ae36749..e9cc9e1 100644 --- a/src/jalview/ext/ensembl/EnsemblMap.java +++ b/src/jalview/ext/ensembl/EnsemblMap.java @@ -3,6 +3,8 @@ package jalview.ext.ensembl; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefSource; import jalview.datamodel.GeneLociI; +import jalview.datamodel.GeneLocus; +import jalview.datamodel.Mapping; import jalview.util.MapList; import java.io.IOException; @@ -16,6 +18,18 @@ import java.util.Map; import org.json.simple.parser.ParseException; +/** + * A client for the Ensembl REST service /map endpoint, to convert from + * coordinates of one genome assembly to another. + *
+ * Note that species and assembly identifiers passed to this class must be valid
+ * in Ensembl. They are not case sensitive.
+ *
+ * @author gmcarstairs
+ * @see https://rest.ensembl.org/documentation/info/assembly_map
+ * @see https://rest.ensembl.org/info/assembly/human?content-type=text/xml
+ * @see https://rest.ensembl.org/info/species?content-type=text/xml
+ */
public class EnsemblMap extends EnsemblRestClient
{
private static final String MAPPED = "mapped";
@@ -340,34 +354,9 @@ GeneLociI parseIdMappingResponse(URL url, String accession,
final String chr = chromosome;
List