Package ubic.gemma.rest.util.args

Class TaxonArgService

java.lang.Object

ubic.gemma.rest.util.args.AbstractEntityArgService<ubic.gemma.model.genome.Taxon,ubic.gemma.persistence.service.genome.taxon.TaxonService>

ubic.gemma.rest.util.args.TaxonArgService

All Implemented Interfaces:

EntityArgService<ubic.gemma.model.genome.Taxon,ubic.gemma.persistence.service.genome.taxon.TaxonService>

@Service
public class TaxonArgService
extends AbstractEntityArgService<ubic.gemma.model.genome.Taxon,ubic.gemma.persistence.service.genome.taxon.TaxonService>

Field Summary

Fields inherited from class ubic.gemma.rest.util.args.AbstractEntityArgService

service

Constructor Summary

Constructors

Constructor	Description
TaxonArgService(ubic.gemma.persistence.service.genome.taxon.TaxonService service, ubic.gemma.persistence.service.genome.ChromosomeService chromosomeService, ubic.gemma.persistence.service.genome.gene.GeneService geneService)

Method Summary

Modifier and Type	Method	Description
protected Map<String,List<String>>	getArgsByPropertyName(AbstractEntityArrayArg<ubic.gemma.model.genome.Taxon,ubic.gemma.persistence.service.genome.taxon.TaxonService> entitiesArg)	Given a AbstractEntityArrayArg, construct a mapping of properties it refers to values those properties are allowed to take in a filter.
<A> ubic.gemma.persistence.util.Filters	getFilters(AbstractEntityArg<A,ubic.gemma.model.genome.Taxon,ubic.gemma.persistence.service.genome.taxon.TaxonService> entityArg)	Translate the provided entity argument into a Filters.
List<ubic.gemma.model.genome.gene.GeneValueObject>	getGenesOnChromosome(TaxonArg<?> arg, String chromosomeName, String strand, long start, int size)	Lists Genes overlapping a location on a specific chromosome on a taxon that this TaxonArg represents.

Methods inherited from class ubic.gemma.rest.util.args.AbstractEntityArgService

checkEntity, entityArgValueOf, getElementClass, getEntities, getEntities, getEntity, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getFilters, getFilters, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

TaxonArgService

@Autowired
public TaxonArgService(ubic.gemma.persistence.service.genome.taxon.TaxonService service,
 ubic.gemma.persistence.service.genome.ChromosomeService chromosomeService,
 ubic.gemma.persistence.service.genome.gene.GeneService geneService)

Method Details

getFilters

public <A> ubic.gemma.persistence.util.Filters getFilters(AbstractEntityArg<A,ubic.gemma.model.genome.Taxon,ubic.gemma.persistence.service.genome.taxon.TaxonService> entityArg)
                                                   throws javax.ws.rs.BadRequestException

Description copied from interface: EntityArgService

Translate the provided entity argument into a Filters.

This will generate clause in the form of property = value.

Specified by:

getFilters in interface EntityArgService<ubic.gemma.model.genome.Taxon,ubic.gemma.persistence.service.genome.taxon.TaxonService>

Overrides:

getFilters in class AbstractEntityArgService<ubic.gemma.model.genome.Taxon,ubic.gemma.persistence.service.genome.taxon.TaxonService>

Throws:

javax.ws.rs.BadRequestException - if the argument is malformed

getArgsByPropertyName

protected Map<String,List<String>> getArgsByPropertyName(AbstractEntityArrayArg<ubic.gemma.model.genome.Taxon,ubic.gemma.persistence.service.genome.taxon.TaxonService> entitiesArg)

Description copied from class: AbstractEntityArgService

Given a AbstractEntityArrayArg, construct a mapping of properties it refers to values those properties are allowed to take in a filter.

Overrides:

getArgsByPropertyName in class AbstractEntityArgService<ubic.gemma.model.genome.Taxon,ubic.gemma.persistence.service.genome.taxon.TaxonService>

getGenesOnChromosome

public List<ubic.gemma.model.genome.gene.GeneValueObject> getGenesOnChromosome(TaxonArg<?> arg,
 String chromosomeName,
 @Nullable
 String strand,
 long start,
 int size)
                                                                        throws javax.ws.rs.NotFoundException

Lists Genes overlapping a location on a specific chromosome on a taxon that this TaxonArg represents.

Parameters:

chromosomeName - name of the chromosome to look on

strand - the strand that the gene has to have which is either '+' or '-', or null to ignore

start - the start nucleotide denoting the location to look for genes at.

size - the size (in nucleotides) of the location from the 'start' nucleotide.

Returns:

collection of Gene VOs overlapping the location defined by the 'start' and 'size' parameters.

Throws:

javax.ws.rs.NotFoundException - if the taxon cannot retrieved