org.brapi.v2.model.geno

Class BrAPIAlleleMatrix

java.lang.Object

org.brapi.v2.model.geno.BrAPIAlleleMatrix

public class BrAPIAlleleMatrix
extends Object

AlleleMatrix

Constructor Summary

Constructors

Constructor and Description
BrAPIAlleleMatrix()

Method Summary

Modifier and Type	Method and Description
BrAPIAlleleMatrix	addCallSetDbIdsItem(String callSetDbIdsItem)
BrAPIAlleleMatrix	addDataMatricesItem(BrAPIAlleleMatrixDataMatrices dataMatricesItem)
BrAPIAlleleMatrix	addPaginationItem(BrAPIAlleleMatrixPagination paginationItem)
BrAPIAlleleMatrix	addVariantDbIdsItem(String variantDbIdsItem)
BrAPIAlleleMatrix	addVariantSetDbIdsItem(String variantSetDbIdsItem)
BrAPIAlleleMatrix	callSetDbIds(List<String> callSetDbIds)
BrAPIAlleleMatrix	dataMatrices(List<BrAPIAlleleMatrixDataMatrices> dataMatrices)
boolean	equals(Object o)
BrAPIAlleleMatrix	expandHomozygotes(Boolean expandHomozygotes)
List<String>	getCallSetDbIds() A list of unique identifiers for the CallSets contained in the matrix response.
List<BrAPIAlleleMatrixDataMatrices>	getDataMatrices() The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata.
List<BrAPIAlleleMatrixPagination>	getPagination() Pagination for the matrix
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 unique identifiers for the Variants contained in the matrix response.
List<String>	getVariantSetDbIds() A list of unique identifiers for the VariantSets contained in the matrix response.
int	hashCode()
Boolean	isExpandHomozygotes() Should homozygotes be expanded (true) or collapsed into a single occurrence (false)
BrAPIAlleleMatrix	pagination(List<BrAPIAlleleMatrixPagination> pagination)
BrAPIAlleleMatrix	sepPhased(String sepPhased)
BrAPIAlleleMatrix	sepUnphased(String sepUnphased)
void	setCallSetDbIds(List<String> callSetDbIds)
void	setDataMatrices(List<BrAPIAlleleMatrixDataMatrices> dataMatrices)
void	setExpandHomozygotes(Boolean expandHomozygotes)
void	setPagination(List<BrAPIAlleleMatrixPagination> pagination)
void	setSepPhased(String sepPhased)
void	setSepUnphased(String sepUnphased)
void	setUnknownString(String unknownString)
void	setVariantDbIds(List<String> variantDbIds)
void	setVariantSetDbIds(List<String> variantSetDbIds)
String	toString()
BrAPIAlleleMatrix	unknownString(String unknownString)
BrAPIAlleleMatrix	variantDbIds(List<String> variantDbIds)
BrAPIAlleleMatrix	variantSetDbIds(List<String> variantSetDbIds)

Methods inherited from class java.lang.Object

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

Constructor Detail

BrAPIAlleleMatrix

public BrAPIAlleleMatrix()

Method Detail

callSetDbIds

public BrAPIAlleleMatrix callSetDbIds(List<String> callSetDbIds)

addCallSetDbIdsItem

public BrAPIAlleleMatrix addCallSetDbIdsItem(String callSetDbIdsItem)

getCallSetDbIds

public List<String> getCallSetDbIds()

A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case.

Returns:

callSetDbIds

setCallSetDbIds

public void setCallSetDbIds(List<String> callSetDbIds)

dataMatrices

public BrAPIAlleleMatrix dataMatrices(List<BrAPIAlleleMatrixDataMatrices> dataMatrices)

addDataMatricesItem

public BrAPIAlleleMatrix addDataMatricesItem(BrAPIAlleleMatrixDataMatrices dataMatricesItem)

getDataMatrices

public List<BrAPIAlleleMatrixDataMatrices> getDataMatrices()

The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows.

Returns:

dataMatrices

setDataMatrices

public void setDataMatrices(List<BrAPIAlleleMatrixDataMatrices> dataMatrices)

expandHomozygotes

public BrAPIAlleleMatrix 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)

pagination

public BrAPIAlleleMatrix pagination(List<BrAPIAlleleMatrixPagination> pagination)

addPaginationItem

public BrAPIAlleleMatrix addPaginationItem(BrAPIAlleleMatrixPagination paginationItem)

getPagination

public List<BrAPIAlleleMatrixPagination> getPagination()

Pagination for the matrix

Returns:

pagination

setPagination

public void setPagination(List<BrAPIAlleleMatrixPagination> pagination)

sepPhased

public BrAPIAlleleMatrix 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 BrAPIAlleleMatrix 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 BrAPIAlleleMatrix 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 BrAPIAlleleMatrix variantDbIds(List<String> variantDbIds)

addVariantDbIdsItem

public BrAPIAlleleMatrix addVariantDbIdsItem(String variantDbIdsItem)

getVariantDbIds

public List<String> getVariantDbIds()

A list of unique identifiers for the Variants contained in the matrix response. This array should match the ordering for rows in the matrix.

Returns:

variantDbIds

setVariantDbIds

public void setVariantDbIds(List<String> variantDbIds)

variantSetDbIds

public BrAPIAlleleMatrix variantSetDbIds(List<String> variantSetDbIds)

addVariantSetDbIdsItem

public BrAPIAlleleMatrix addVariantSetDbIdsItem(String variantSetDbIdsItem)

getVariantSetDbIds

public List<String> getVariantSetDbIds()

A list of unique identifiers for the VariantSets contained in the matrix response. A VariantSet is a data set originating from a sequencing event. Often, users will only be interested in data from a single VariantSet, but in some cases a user might be interested in a matrix with data from multiple VariantSets.

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