Package org.intermine.bio.webservice

Class GenomicRegionSearchListInput.GenomicRegionSearchInfo

java.lang.Object

org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

Enclosing class:

GenomicRegionSearchListInput

public class GenomicRegionSearchListInput.GenomicRegionSearchInfo
extends java.lang.Object

Constructor Summary

Constructors

Constructor	Description
GenomicRegionSearchInfo()

Method Summary

Modifier and Type	Method	Description
GenomicRegionSearchConstraint	asSearchConstraint()
int	getExtension()
java.util.Set<org.intermine.metadata.ClassDescriptor>	getFeatureCds()	Returns an unmodifiable set of the classdescriptors corresponding to the feature types in this query.
java.util.Set<java.lang.Class<?>>	getFeatureClasses()
java.util.Set<java.lang.String>	getFeatureTypes()
java.util.List<GenomicRegion>	getGenomicRegions()
java.util.Set<java.lang.String>	getInvalidSpans()
java.lang.String	getOrganism()
java.util.List<java.lang.String>	getRegions()
boolean	getStrandSpecific()
boolean	isInterbase()
void	setExtension(int extension)
void	setFeatureTypes(java.util.Collection<java.lang.String> featureTypes)	Set the feature types for this request.
void	setInterbase(boolean isInterbase)
void	setOrganism(java.lang.String organism)
void	setRegions(java.util.List<java.lang.String> regions)
void	setStrandSpecific(boolean strandSpecific)

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomicRegionSearchInfo

public GenomicRegionSearchInfo()

Method Detail

getInvalidSpans

public java.util.Set<java.lang.String> getInvalidSpans()

Returns:

set of invalid spans

getOrganism

public java.lang.String getOrganism()

Returns:

organism

setOrganism

public void setOrganism(java.lang.String organism)

Parameters:

organism - organism

getStrandSpecific

public boolean getStrandSpecific()

Returns:

strandSpecific

setStrandSpecific

public void setStrandSpecific(boolean strandSpecific)

Parameters:

strandSpecific - Whether or not this search specifies a strand

getFeatureTypes

public java.util.Set<java.lang.String> getFeatureTypes()

Returns:

featuretypes

setFeatureTypes

public void setFeatureTypes(java.util.Collection<java.lang.String> featureTypes)

Set the feature types for this request. Immediately parses the class names to ClassDescriptors and fails as soon as possible.

Parameters:

featureTypes - A collection of feature type names.

Throws:

org.intermine.webservice.server.exceptions.BadRequestException - if the feature types are not mappable to classes, and if those classes are not Sequence Features.

getFeatureCds

public java.util.Set<org.intermine.metadata.ClassDescriptor> getFeatureCds()

Returns an unmodifiable set of the classdescriptors corresponding to the feature types in this query.

Returns:

feature class descriptors

getFeatureClasses

public java.util.Set<java.lang.Class<?>> getFeatureClasses()

Returns:

an unmodifiable set of the classes that the Class-Descriptors in this query represent.

getRegions

public java.util.List<java.lang.String> getRegions()

Returns:

regions

setRegions

public void setRegions(java.util.List<java.lang.String> regions)

Parameters:

regions - regions

getGenomicRegions

public java.util.List<GenomicRegion> getGenomicRegions()

Returns:

list of valid regions

getExtension

public int getExtension()

Returns:

extension

setExtension

public void setExtension(int extension)

Parameters:

extension - extension

isInterbase

public boolean isInterbase()

Returns:

true if interbase

setInterbase

public void setInterbase(boolean isInterbase)

Parameters:

isInterbase - true if interbase

asSearchConstraint

public GenomicRegionSearchConstraint asSearchConstraint()

Returns:

region search constraint