org.brapi.v2.model.geno.request

Class BrAPIAlleleMatrixSearchRequest

java.lang.Object

org.brapi.v2.model.geno.request.BrAPIAlleleMatrixSearchRequest

public class BrAPIAlleleMatrixSearchRequest
extends Object

AlleleMatrixSearchRequest

Constructor Summary

Constructors

Constructor and Description
BrAPIAlleleMatrixSearchRequest()

Method Summary

Modifier and Type	Method and Description
BrAPIAlleleMatrixSearchRequest	addCallSetDbIdsItem(String callSetDbIdsItem)
BrAPIAlleleMatrixSearchRequest	addDataMatrixAbbreviationsItem(String dataMatrixAbbreviationsItem)
BrAPIAlleleMatrixSearchRequest	addDataMatrixNamesItem(String dataMatrixNamesItem)
BrAPIAlleleMatrixSearchRequest	addGermplasmDbIdsItem(String germplasmDbIdsItem)
BrAPIAlleleMatrixSearchRequest	addGermplasmNamesItem(String germplasmNamesItem)
BrAPIAlleleMatrixSearchRequest	addGermplasmPUIsItem(String germplasmPUIsItem)
BrAPIAlleleMatrixSearchRequest	addPaginationItem(BrAPIAlleleMatrixSearchRequestPagination paginationItem)
BrAPIAlleleMatrixSearchRequest	addPositionRangesItem(String positionRangesItem)
BrAPIAlleleMatrixSearchRequest	addSampleDbIdsItem(String sampleDbIdsItem)
BrAPIAlleleMatrixSearchRequest	addVariantDbIdsItem(String variantDbIdsItem)
BrAPIAlleleMatrixSearchRequest	addVariantSetDbIdsItem(String variantSetDbIdsItem)
BrAPIAlleleMatrixSearchRequest	callSetDbIds(List<String> callSetDbIds)
BrAPIAlleleMatrixSearchRequest	dataMatrixAbbreviations(List<String> dataMatrixAbbreviations)
BrAPIAlleleMatrixSearchRequest	dataMatrixNames(List<String> dataMatrixNames)
boolean	equals(Object o)
BrAPIAlleleMatrixSearchRequest	expandHomozygotes(Boolean expandHomozygotes)
BrAPIAlleleMatrixSearchRequest	germplasmDbIds(List<String> germplasmDbIds)
BrAPIAlleleMatrixSearchRequest	germplasmNames(List<String> germplasmNames)
BrAPIAlleleMatrixSearchRequest	germplasmPUIs(List<String> germplasmPUIs)
List<String>	getCallSetDbIds() A list of IDs which uniquely identify `CallSets` within the given database server
List<String>	getDataMatrixAbbreviations() `dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc).
List<String>	getDataMatrixNames() `dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc).
List<String>	getGermplasmDbIds() A list of IDs which uniquely identify `Germplasm` within the given database server
List<String>	getGermplasmNames() A list of human readable `Germplasm` names
List<String>	getGermplasmPUIs() A list of premenant unique identifiers associated with `Germplasm`
List<BrAPIAlleleMatrixSearchRequestPagination>	getPagination() Pagination for the matrix
List<String>	getPositionRanges() The postion range to search <br/> Uses the format \"<chrom>:<start>-<end>\" where <chrom> is the chromosome name, <start> is the starting position of the range, and <end> is the ending position of the range
List<String>	getSampleDbIds() A list of IDs which uniquely identify `Samples` within the given database server
String	getSepPhased() The string used as a separator for phased allele calls.
String	getSepUnphased() The string used as a separator for unphased allele calls.
String	getUnknownString() The string used as a representation for missing data.
List<String>	getVariantDbIds() A list of IDs which uniquely identify `Variants` within the given database server
List<String>	getVariantSetDbIds() A list of IDs which uniquely identify `VariantSets` within the given database server
int	hashCode()
Boolean	isExpandHomozygotes() Should homozygotes be expanded (true) or collapsed into a single occurrence (false)
Boolean	isPreview() Default Value = false <br/> If 'preview' is set to true, then the server should only return the lists of 'callSetDbIds', 'variantDbIds', and 'variantSetDbIds'.
BrAPIAlleleMatrixSearchRequest	pagination(List<BrAPIAlleleMatrixSearchRequestPagination> pagination)
BrAPIAlleleMatrixSearchRequest	positionRanges(List<String> positionRanges)
BrAPIAlleleMatrixSearchRequest	preview(Boolean preview)
BrAPIAlleleMatrixSearchRequest	sampleDbIds(List<String> sampleDbIds)
BrAPIAlleleMatrixSearchRequest	sepPhased(String sepPhased)
BrAPIAlleleMatrixSearchRequest	sepUnphased(String sepUnphased)
void	setCallSetDbIds(List<String> callSetDbIds)
void	setDataMatrixAbbreviations(List<String> dataMatrixAbbreviations)
void	setDataMatrixNames(List<String> dataMatrixNames)
void	setExpandHomozygotes(Boolean expandHomozygotes)
void	setGermplasmDbIds(List<String> germplasmDbIds)
void	setGermplasmNames(List<String> germplasmNames)
void	setGermplasmPUIs(List<String> germplasmPUIs)
void	setPagination(List<BrAPIAlleleMatrixSearchRequestPagination> pagination)
void	setPositionRanges(List<String> positionRanges)
void	setPreview(Boolean preview)
void	setSampleDbIds(List<String> sampleDbIds)
void	setSepPhased(String sepPhased)
void	setSepUnphased(String sepUnphased)
void	setUnknownString(String unknownString)
void	setVariantDbIds(List<String> variantDbIds)
void	setVariantSetDbIds(List<String> variantSetDbIds)
String	toString()
BrAPIAlleleMatrixSearchRequest	unknownString(String unknownString)
BrAPIAlleleMatrixSearchRequest	variantDbIds(List<String> variantDbIds)
BrAPIAlleleMatrixSearchRequest	variantSetDbIds(List<String> variantSetDbIds)

Methods inherited from class java.lang.Object

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

Constructor Detail

BrAPIAlleleMatrixSearchRequest

public BrAPIAlleleMatrixSearchRequest()

Method Detail

callSetDbIds

public BrAPIAlleleMatrixSearchRequest callSetDbIds(List<String> callSetDbIds)

addCallSetDbIdsItem

public BrAPIAlleleMatrixSearchRequest addCallSetDbIdsItem(String callSetDbIdsItem)

getCallSetDbIds

public List<String> getCallSetDbIds()

A list of IDs which uniquely identify `CallSets` within the given database server

Returns:

callSetDbIds

setCallSetDbIds

public void setCallSetDbIds(List<String> callSetDbIds)

dataMatrixAbbreviations

public BrAPIAlleleMatrixSearchRequest dataMatrixAbbreviations(List<String> dataMatrixAbbreviations)

addDataMatrixAbbreviationsItem

public BrAPIAlleleMatrixSearchRequest addDataMatrixAbbreviationsItem(String dataMatrixAbbreviationsItem)

getDataMatrixAbbreviations

public List<String> getDataMatrixAbbreviations()

`dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.

Returns:

dataMatrixAbbreviations

setDataMatrixAbbreviations

public void setDataMatrixAbbreviations(List<String> dataMatrixAbbreviations)

dataMatrixNames

public BrAPIAlleleMatrixSearchRequest dataMatrixNames(List<String> dataMatrixNames)

addDataMatrixNamesItem

public BrAPIAlleleMatrixSearchRequest addDataMatrixNamesItem(String dataMatrixNamesItem)

getDataMatrixNames

public List<String> getDataMatrixNames()

`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.

Returns:

dataMatrixNames

setDataMatrixNames

public void setDataMatrixNames(List<String> dataMatrixNames)

expandHomozygotes

public BrAPIAlleleMatrixSearchRequest expandHomozygotes(Boolean expandHomozygotes)

isExpandHomozygotes

public Boolean isExpandHomozygotes()

Should homozygotes be expanded (true) or collapsed into a single occurrence (false)

Returns:

expandHomozygotes

setExpandHomozygotes

public void setExpandHomozygotes(Boolean expandHomozygotes)

germplasmDbIds

public BrAPIAlleleMatrixSearchRequest germplasmDbIds(List<String> germplasmDbIds)

addGermplasmDbIdsItem

public BrAPIAlleleMatrixSearchRequest addGermplasmDbIdsItem(String germplasmDbIdsItem)

getGermplasmDbIds

public List<String> getGermplasmDbIds()

A list of IDs which uniquely identify `Germplasm` within the given database server

Returns:

germplasmDbIds

setGermplasmDbIds

public void setGermplasmDbIds(List<String> germplasmDbIds)

germplasmNames

public BrAPIAlleleMatrixSearchRequest germplasmNames(List<String> germplasmNames)

addGermplasmNamesItem

public BrAPIAlleleMatrixSearchRequest addGermplasmNamesItem(String germplasmNamesItem)

getGermplasmNames

public List<String> getGermplasmNames()

A list of human readable `Germplasm` names

Returns:

germplasmNames

setGermplasmNames

public void setGermplasmNames(List<String> germplasmNames)

germplasmPUIs

public BrAPIAlleleMatrixSearchRequest germplasmPUIs(List<String> germplasmPUIs)

addGermplasmPUIsItem

public BrAPIAlleleMatrixSearchRequest addGermplasmPUIsItem(String germplasmPUIsItem)

getGermplasmPUIs

public List<String> getGermplasmPUIs()

A list of premenant unique identifiers associated with `Germplasm`

Returns:

germplasmPUIs

setGermplasmPUIs

public void setGermplasmPUIs(List<String> germplasmPUIs)

pagination

public BrAPIAlleleMatrixSearchRequest pagination(List<BrAPIAlleleMatrixSearchRequestPagination> pagination)

addPaginationItem

public BrAPIAlleleMatrixSearchRequest addPaginationItem(BrAPIAlleleMatrixSearchRequestPagination paginationItem)

getPagination

public List<BrAPIAlleleMatrixSearchRequestPagination> getPagination()

Pagination for the matrix

Returns:

pagination

setPagination

public void setPagination(List<BrAPIAlleleMatrixSearchRequestPagination> pagination)

positionRanges

public BrAPIAlleleMatrixSearchRequest positionRanges(List<String> positionRanges)

addPositionRangesItem

public BrAPIAlleleMatrixSearchRequest addPositionRangesItem(String positionRangesItem)

getPositionRanges

public List<String> getPositionRanges()

The postion range to search <br/> Uses the format \"<chrom>:<start>-<end>\" where <chrom> is the chromosome name, <start> is the starting position of the range, and <end> is the ending position of the range

Returns:

positionRanges

setPositionRanges

public void setPositionRanges(List<String> positionRanges)

preview

public BrAPIAlleleMatrixSearchRequest preview(Boolean preview)

isPreview

public Boolean isPreview()

Default Value = false <br/> If 'preview' is set to true, then the server should only return the lists of 'callSetDbIds', 'variantDbIds', and 'variantSetDbIds'. The server should not return any matrix data. This is intended to be a preview and give the client a sense of how large the matrix returned will be <br/> If 'preview' is set to false or not set (default), then the server should return all the matrix data as requested.

Returns:

preview

setPreview

public void setPreview(Boolean preview)

sampleDbIds

public BrAPIAlleleMatrixSearchRequest sampleDbIds(List<String> sampleDbIds)

addSampleDbIdsItem

public BrAPIAlleleMatrixSearchRequest addSampleDbIdsItem(String sampleDbIdsItem)

getSampleDbIds

public List<String> getSampleDbIds()

A list of IDs which uniquely identify `Samples` within the given database server

Returns:

sampleDbIds

setSampleDbIds

public void setSampleDbIds(List<String> sampleDbIds)

sepPhased

public BrAPIAlleleMatrixSearchRequest sepPhased(String sepPhased)

getSepPhased

public String getSepPhased()

The string used as a separator for phased allele calls.

Returns:

sepPhased

setSepPhased

public void setSepPhased(String sepPhased)

sepUnphased

public BrAPIAlleleMatrixSearchRequest sepUnphased(String sepUnphased)

getSepUnphased

public String getSepUnphased()

The string used as a separator for unphased allele calls.

Returns:

sepUnphased

setSepUnphased

public void setSepUnphased(String sepUnphased)

unknownString

public BrAPIAlleleMatrixSearchRequest unknownString(String unknownString)

getUnknownString

public String getUnknownString()

The string used as a representation for missing data.

Returns:

unknownString

setUnknownString

public void setUnknownString(String unknownString)

variantDbIds

public BrAPIAlleleMatrixSearchRequest variantDbIds(List<String> variantDbIds)

addVariantDbIdsItem

public BrAPIAlleleMatrixSearchRequest addVariantDbIdsItem(String variantDbIdsItem)

getVariantDbIds

public List<String> getVariantDbIds()

A list of IDs which uniquely identify `Variants` within the given database server

Returns:

variantDbIds

setVariantDbIds

public void setVariantDbIds(List<String> variantDbIds)

variantSetDbIds

public BrAPIAlleleMatrixSearchRequest variantSetDbIds(List<String> variantSetDbIds)

addVariantSetDbIdsItem

public BrAPIAlleleMatrixSearchRequest addVariantSetDbIdsItem(String variantSetDbIdsItem)

getVariantSetDbIds

public List<String> getVariantSetDbIds()

A list of IDs which uniquely identify `VariantSets` within the given database server

Returns:

variantSetDbIds

setVariantSetDbIds

public void setVariantSetDbIds(List<String> variantSetDbIds)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object