org.brapi.v2.model.geno.request

Class BrAPIVariantsSearchRequest

java.lang.Object

org.brapi.v2.model.BrAPISearchRequestParametersPaging

org.brapi.v2.model.BrAPISearchRequestParametersTokenPaging

org.brapi.v2.model.geno.request.BrAPIVariantsSearchRequest

public class BrAPIVariantsSearchRequest
extends BrAPISearchRequestParametersTokenPaging

VariantsSearchRequest

Constructor Summary

Constructors

Constructor and Description
BrAPIVariantsSearchRequest()

Method Summary

Modifier and Type	Method and Description
BrAPIVariantsSearchRequest	addCallSetDbIdsItem(String callSetDbIdsItem)
BrAPIVariantsSearchRequest	addCommonCropNamesItem(String commonCropNamesItem)
BrAPIVariantsSearchRequest	addExternalReferenceIdsItem(String externalReferenceIdsItem)
BrAPIVariantsSearchRequest	addExternalReferenceIDsItem(String externalReferenceIDsItem)
BrAPIVariantsSearchRequest	addExternalReferenceSourcesItem(String externalReferenceSourcesItem)
BrAPIVariantsSearchRequest	addProgramDbIdsItem(String programDbIdsItem)
BrAPIVariantsSearchRequest	addProgramNamesItem(String programNamesItem)
BrAPIVariantsSearchRequest	addReferenceDbIdsItem(String referenceDbIdsItem)
BrAPIVariantsSearchRequest	addReferenceSetDbIdsItem(String referenceSetDbIdsItem)
BrAPIVariantsSearchRequest	addStudyDbIdsItem(String studyDbIdsItem)
BrAPIVariantsSearchRequest	addStudyNamesItem(String studyNamesItem)
BrAPIVariantsSearchRequest	addTrialDbIdsItem(String trialDbIdsItem)
BrAPIVariantsSearchRequest	addTrialNamesItem(String trialNamesItem)
BrAPIVariantsSearchRequest	addVariantDbIdsItem(String variantDbIdsItem)
BrAPIVariantsSearchRequest	addVariantSetDbIdsItem(String variantSetDbIdsItem)
BrAPIVariantsSearchRequest	callSetDbIds(List<String> callSetDbIds)
BrAPIVariantsSearchRequest	commonCropNames(List<String> commonCropNames)
BrAPIVariantsSearchRequest	end(Integer end)
boolean	equals(Object o)
BrAPIVariantsSearchRequest	externalReferenceIds(List<String> externalReferenceIds)
BrAPIVariantsSearchRequest	externalReferenceIDs(List<String> externalReferenceIDs)
BrAPIVariantsSearchRequest	externalReferenceSources(List<String> externalReferenceSources)
List<String>	getCallSetDbIds()
List<String>	getCommonCropNames() The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched.
Integer	getEnd() The end of the window (0-based, exclusive) for which overlapping variants should be returned.
List<String>	getExternalReferenceIds() List of external reference IDs.
List<String>	getExternalReferenceIDs() **Deprecated in v2.1** Please use `externalReferenceIds`.
List<String>	getExternalReferenceSources() List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)
List<String>	getProgramDbIds() A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies.
List<String>	getProgramNames() Use this parameter to only return results associated with the given program names.
String	getReferenceDbId() Only return variants on this reference.
List<String>	getReferenceDbIds() The unique identifier representing a genotype `Reference`
List<String>	getReferenceSetDbIds() The unique identifier representing a genotype `ReferenceSet`
Integer	getStart() The beginning of the window (0-based, inclusive) for which overlapping variants should be returned.
List<String>	getStudyDbIds() List of study identifiers to search for
List<String>	getStudyNames() List of study names to filter search results
List<String>	getTrialDbIds() The ID which uniquely identifies a trial to search for
List<String>	getTrialNames() The human readable name of a trial to search for
List<String>	getVariantDbIds()
List<String>	getVariantSetDbIds()
int	hashCode()
BrAPIVariantsSearchRequest	programDbIds(List<String> programDbIds)
BrAPIVariantsSearchRequest	programNames(List<String> programNames)
BrAPIVariantsSearchRequest	referenceDbId(String referenceDbId)
BrAPIVariantsSearchRequest	referenceDbIds(List<String> referenceDbIds)
BrAPIVariantsSearchRequest	referenceSetDbIds(List<String> referenceSetDbIds)
void	setCallSetDbIds(List<String> callSetDbIds)
void	setCommonCropNames(List<String> commonCropNames)
void	setEnd(Integer end)
void	setExternalReferenceIds(List<String> externalReferenceIds)
void	setExternalReferenceIDs(List<String> externalReferenceIDs)
void	setExternalReferenceSources(List<String> externalReferenceSources)
void	setProgramDbIds(List<String> programDbIds)
void	setProgramNames(List<String> programNames)
void	setReferenceDbId(String referenceDbId)
void	setReferenceDbIds(List<String> referenceDbIds)
void	setReferenceSetDbIds(List<String> referenceSetDbIds)
void	setStart(Integer start)
void	setStudyDbIds(List<String> studyDbIds)
void	setStudyNames(List<String> studyNames)
void	setTrialDbIds(List<String> trialDbIds)
void	setTrialNames(List<String> trialNames)
void	setVariantDbIds(List<String> variantDbIds)
void	setVariantSetDbIds(List<String> variantSetDbIds)
BrAPIVariantsSearchRequest	start(Integer start)
BrAPIVariantsSearchRequest	studyDbIds(List<String> studyDbIds)
BrAPIVariantsSearchRequest	studyNames(List<String> studyNames)
String	toString()
BrAPIVariantsSearchRequest	trialDbIds(List<String> trialDbIds)
BrAPIVariantsSearchRequest	trialNames(List<String> trialNames)
BrAPIVariantsSearchRequest	variantDbIds(List<String> variantDbIds)
BrAPIVariantsSearchRequest	variantSetDbIds(List<String> variantSetDbIds)

Methods inherited from class org.brapi.v2.model.BrAPISearchRequestParametersTokenPaging

getPageToken, pageSize, pageToken, setPageToken

Methods inherited from class org.brapi.v2.model.BrAPISearchRequestParametersPaging

getPage, getPageSize, page, setPage, setPageSize

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

BrAPIVariantsSearchRequest

public BrAPIVariantsSearchRequest()

Method Detail

callSetDbIds

public BrAPIVariantsSearchRequest callSetDbIds(List<String> callSetDbIds)

addCallSetDbIdsItem

public BrAPIVariantsSearchRequest addCallSetDbIdsItem(String callSetDbIdsItem)

getCallSetDbIds

public List<String> getCallSetDbIds()

setCallSetDbIds

public void setCallSetDbIds(List<String> callSetDbIds)

commonCropNames

public BrAPIVariantsSearchRequest commonCropNames(List<String> commonCropNames)

addCommonCropNamesItem

public BrAPIVariantsSearchRequest addCommonCropNamesItem(String commonCropNamesItem)

getCommonCropNames

public List<String> getCommonCropNames()

The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. Use this parameter to only return results associated with the given crops. Use `GET /commoncropnames` to find the list of available crops on a server.

Returns:

commonCropNames

setCommonCropNames

public void setCommonCropNames(List<String> commonCropNames)

end

public BrAPIVariantsSearchRequest end(Integer end)

getEnd

public Integer getEnd()

The end of the window (0-based, exclusive) for which overlapping variants should be returned.

Returns:

end

setEnd

public void setEnd(Integer end)

externalReferenceIDs

public BrAPIVariantsSearchRequest externalReferenceIDs(List<String> externalReferenceIDs)

addExternalReferenceIDsItem

public BrAPIVariantsSearchRequest addExternalReferenceIDsItem(String externalReferenceIDsItem)

getExternalReferenceIDs

public List<String> getExternalReferenceIDs()

**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 <br>List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)

Returns:

externalReferenceIDs

setExternalReferenceIDs

public void setExternalReferenceIDs(List<String> externalReferenceIDs)

externalReferenceIds

public BrAPIVariantsSearchRequest externalReferenceIds(List<String> externalReferenceIds)

addExternalReferenceIdsItem

public BrAPIVariantsSearchRequest addExternalReferenceIdsItem(String externalReferenceIdsItem)

getExternalReferenceIds

public List<String> getExternalReferenceIds()

List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)

Returns:

externalReferenceIds

setExternalReferenceIds

public void setExternalReferenceIds(List<String> externalReferenceIds)

externalReferenceSources

public BrAPIVariantsSearchRequest externalReferenceSources(List<String> externalReferenceSources)

addExternalReferenceSourcesItem

public BrAPIVariantsSearchRequest addExternalReferenceSourcesItem(String externalReferenceSourcesItem)

getExternalReferenceSources

public List<String> getExternalReferenceSources()

List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)

Returns:

externalReferenceSources

setExternalReferenceSources

public void setExternalReferenceSources(List<String> externalReferenceSources)

programDbIds

public BrAPIVariantsSearchRequest programDbIds(List<String> programDbIds)

addProgramDbIdsItem

public BrAPIVariantsSearchRequest addProgramDbIdsItem(String programDbIdsItem)

getProgramDbIds

public List<String> getProgramDbIds()

A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. Use this parameter to only return results associated with the given programs. Use `GET /programs` to find the list of available programs on a server.

Returns:

programDbIds

setProgramDbIds

public void setProgramDbIds(List<String> programDbIds)

programNames

public BrAPIVariantsSearchRequest programNames(List<String> programNames)

addProgramNamesItem

public BrAPIVariantsSearchRequest addProgramNamesItem(String programNamesItem)

getProgramNames

public List<String> getProgramNames()

Use this parameter to only return results associated with the given program names. Program names are not required to be unique. Use `GET /programs` to find the list of available programs on a server.

Returns:

programNames

setProgramNames

public void setProgramNames(List<String> programNames)

referenceDbId

public BrAPIVariantsSearchRequest referenceDbId(String referenceDbId)

getReferenceDbId

public String getReferenceDbId()

Only return variants on this reference.

Returns:

referenceDbId

setReferenceDbId

public void setReferenceDbId(String referenceDbId)

referenceDbIds

public BrAPIVariantsSearchRequest referenceDbIds(List<String> referenceDbIds)

addReferenceDbIdsItem

public BrAPIVariantsSearchRequest addReferenceDbIdsItem(String referenceDbIdsItem)

getReferenceDbIds

public List<String> getReferenceDbIds()

The unique identifier representing a genotype `Reference`

Returns:

referenceDbIds

setReferenceDbIds

public void setReferenceDbIds(List<String> referenceDbIds)

referenceSetDbIds

public BrAPIVariantsSearchRequest referenceSetDbIds(List<String> referenceSetDbIds)

addReferenceSetDbIdsItem

public BrAPIVariantsSearchRequest addReferenceSetDbIdsItem(String referenceSetDbIdsItem)

getReferenceSetDbIds

public List<String> getReferenceSetDbIds()

The unique identifier representing a genotype `ReferenceSet`

Returns:

referenceSetDbIds

setReferenceSetDbIds

public void setReferenceSetDbIds(List<String> referenceSetDbIds)

start

public BrAPIVariantsSearchRequest start(Integer start)

getStart

public Integer getStart()

The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).

Returns:

start

setStart

public void setStart(Integer start)

studyDbIds

public BrAPIVariantsSearchRequest studyDbIds(List<String> studyDbIds)

addStudyDbIdsItem

public BrAPIVariantsSearchRequest addStudyDbIdsItem(String studyDbIdsItem)

getStudyDbIds

public List<String> getStudyDbIds()

List of study identifiers to search for

Returns:

studyDbIds

setStudyDbIds

public void setStudyDbIds(List<String> studyDbIds)

studyNames

public BrAPIVariantsSearchRequest studyNames(List<String> studyNames)

addStudyNamesItem

public BrAPIVariantsSearchRequest addStudyNamesItem(String studyNamesItem)

getStudyNames

public List<String> getStudyNames()

List of study names to filter search results

Returns:

studyNames

setStudyNames

public void setStudyNames(List<String> studyNames)

trialDbIds

public BrAPIVariantsSearchRequest trialDbIds(List<String> trialDbIds)

addTrialDbIdsItem

public BrAPIVariantsSearchRequest addTrialDbIdsItem(String trialDbIdsItem)

getTrialDbIds

public List<String> getTrialDbIds()

The ID which uniquely identifies a trial to search for

Returns:

trialDbIds

setTrialDbIds

public void setTrialDbIds(List<String> trialDbIds)

trialNames

public BrAPIVariantsSearchRequest trialNames(List<String> trialNames)

addTrialNamesItem

public BrAPIVariantsSearchRequest addTrialNamesItem(String trialNamesItem)

getTrialNames

public List<String> getTrialNames()

The human readable name of a trial to search for

Returns:

trialNames

setTrialNames

public void setTrialNames(List<String> trialNames)

variantSetDbIds

public BrAPIVariantsSearchRequest variantSetDbIds(List<String> variantSetDbIds)

addVariantSetDbIdsItem

public BrAPIVariantsSearchRequest addVariantSetDbIdsItem(String variantSetDbIdsItem)

getVariantSetDbIds

public List<String> getVariantSetDbIds()

setVariantSetDbIds

public void setVariantSetDbIds(List<String> variantSetDbIds)

variantDbIds

public BrAPIVariantsSearchRequest variantDbIds(List<String> variantDbIds)

addVariantDbIdsItem

public BrAPIVariantsSearchRequest addVariantDbIdsItem(String variantDbIdsItem)

getVariantDbIds

public List<String> getVariantDbIds()

setVariantDbIds

public void setVariantDbIds(List<String> variantDbIds)

equals

public boolean equals(Object o)

Overrides:

equals in class BrAPISearchRequestParametersTokenPaging

hashCode

public int hashCode()

Overrides:

hashCode in class BrAPISearchRequestParametersTokenPaging

toString

public String toString()

Overrides:

toString in class BrAPISearchRequestParametersTokenPaging