* @return
* @throws MalformedURLException
*/
- protected URL getAssemblyMapUrl(String species, String chromosome, String fromRef,
- String toRef, int startPos, int endPos)
+ protected URL getAssemblyMapUrl(String species, String chromosome,
+ String fromRef, String toRef, int startPos, int endPos)
throws MalformedURLException
{
/*
URL url = null;
try
{
- url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0],
- queryRange[1]);
+ url = getAssemblyMapUrl(species, chromosome, fromRef, toRef,
+ queryRange[0], queryRange[1]);
return (parseAssemblyMappingResponse(url));
} catch (Throwable t)
{
try
{
- Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1,
+ MODE_ITERATOR, MAPPINGS);
if (rvals == null)
{
return null;
URL getIdMapUrl(String domain, String accession, int start, int end,
String cdsOrCdna) throws MalformedURLException
{
- String url = String
- .format("%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json",
- domain, cdsOrCdna, accession, start, end);
+ String url = String.format(
+ "%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json",
+ domain, cdsOrCdna, accession, start, end);
return new URL(url);
}
* @return
*/
@SuppressWarnings("unchecked")
-GeneLociI parseIdMappingResponse(URL url, String accession,
- String domain)
+ GeneLociI parseIdMappingResponse(URL url, String accession, String domain)
{
try
{
- Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1,
+ MODE_ITERATOR, MAPPINGS);
if (rvals == null)
{
return null;
while (rvals.hasNext())
{
Map<String, Object> val = (Map<String, Object>) rvals.next();
- Map<String, Object> original = (Map<String, Object>) val.get("original");
+ Map<String, Object> original = (Map<String, Object>) val
+ .get("original");
fromEnd = Integer.parseInt(original.get("end").toString());
Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
String ass = mapped.get("assembly_name").toString();
if (assembly != null && !assembly.equals(ass))
{
- System.err
- .println("EnsemblMap found multiple assemblies - can't resolve");
+ 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");
+ System.err.println(
+ "EnsemblMap found multiple chromosomes - can't resolve");
return null;
}
chromosome = chr;
.getSpecies(accession);
final String as = assembly;
final String chr = chromosome;
- List<int[]> fromRange = Collections.singletonList(new int[] { 1,
- fromEnd });
+ List<int[]> fromRange = Collections
+ .singletonList(new int[]
+ { 1, fromEnd });
Mapping mapping = new Mapping(new MapList(fromRange, regions, 1, 1));
return new GeneLocus(species == null ? "" : species, as, chr,
mapping);