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.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";
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)
*/
public EnsemblMap()
{
super();
}
/**
* Constructor given the target domain to fetch data from
*
* @param
*/
public EnsemblMap(String domain)
{
super(domain);
}
@Override
public String getDbName()
{
return DBRefSource.ENSEMBL;
}
@Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
return null; // not used
}
/**
* Constructs a URL of the format
* http://rest.ensembl.org/map/human/GRCh38/17:45051610..45109016:1/GRCh37?content-type=application/json
*
*
* @param species
* @param chromosome
* @param fromRef
* @param toRef
* @param startPos
* @param endPos
* @return
* @throws MalformedURLException
*/
protected URL getAssemblyMapUrl(String species, String chromosome, String fromRef,
String toRef, int startPos, int endPos)
throws MalformedURLException
{
/*
* start-end might be reverse strand - present forwards to the service
*/
boolean forward = startPos <= endPos;
int start = forward ? startPos : endPos;
int end = forward ? endPos : startPos;
String strand = forward ? "1" : "-1";
String url = String.format(
"%s/map/%s/%s/%s:%d..%d:%s/%s?content-type=application/json",
getDomain(), species, fromRef, chromosome, start, end, strand,
toRef);
return new URL(url);
}
@Override
protected boolean useGetRequest()
{
return true;
}
@Override
protected URL getUrl(List ids) throws MalformedURLException
{
return null; // not used
}
/**
* Calls the REST /map service to get the chromosomal coordinates (start/end)
* in 'toRef' that corresponding to the (start/end) queryRange in 'fromRef'
*
* @param species
* @param chromosome
* @param fromRef
* @param toRef
* @param queryRange
* @return
* @see http://rest.ensemblgenomes.org/documentation/info/assembly_map
*/
public int[] getAssemblyMapping(String species, String chromosome,
String fromRef, String toRef, int[] queryRange)
{
URL url = null;
try
{
url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0],
queryRange[1]);
return (parseAssemblyMappingResponse(url));
} catch (Throwable t)
{
System.out.println("Error calling " + url + ": " + t.getMessage());
return null;
}
}
/**
* Parses the JSON response from the /map/<species>/ REST service. The
* format is (with some fields omitted)
*
*
* {"mappings":
* [{
* "original": {"end":45109016,"start":45051610},
* "mapped" : {"end":43186384,"start":43128978}
* }] }
*
*
* @param br
* @return
*/
@SuppressWarnings("unchecked")
protected int[] parseAssemblyMappingResponse(URL url)
{
int[] result = null;
try
{
Iterator