org.brapi.v2.model.geno

Class BrAPIAlleleMatrixDataMatrices

java.lang.Object

org.brapi.v2.model.geno.BrAPIAlleleMatrixDataMatrices

public class BrAPIAlleleMatrixDataMatrices
extends Object

This is a single data matrix. It could be the allele matrix or an additional layer of metadata associated with each genotype value.

Constructor Summary

Constructors

Constructor and Description
BrAPIAlleleMatrixDataMatrices()

Method Summary

Modifier and Type	Method and Description
BrAPIAlleleMatrixDataMatrices	addDataMatrixItem(List<String> dataMatrixItem)
BrAPIAlleleMatrixDataMatrices	dataMatrix(List<List<String>> dataMatrix)
BrAPIAlleleMatrixDataMatrices	dataMatrixAbbreviation(String dataMatrixAbbreviation)
BrAPIAlleleMatrixDataMatrices	dataMatrixName(String dataMatrixName)
BrAPIAlleleMatrixDataMatrices	dataType(BrAPIDataTypeEnum dataType)
boolean	equals(Object o)
List<List<String>>	getDataMatrix() The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value.
String	getDataMatrixAbbreviation() The abbreviated code of the field represented in this data matrix.
String	getDataMatrixName() The name of the field represented in this data matrix.
BrAPIDataTypeEnum	getDataType() The type of field represented in this data matrix.
int	hashCode()
void	setDataMatrix(List<List<String>> dataMatrix)
void	setDataMatrixAbbreviation(String dataMatrixAbbreviation)
void	setDataMatrixName(String dataMatrixName)
void	setDataType(BrAPIDataTypeEnum dataType)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

BrAPIAlleleMatrixDataMatrices

public BrAPIAlleleMatrixDataMatrices()

Method Detail

dataMatrix

public BrAPIAlleleMatrixDataMatrices dataMatrix(List<List<String>> dataMatrix)

addDataMatrixItem

public BrAPIAlleleMatrixDataMatrices addDataMatrixItem(List<String> dataMatrixItem)

getDataMatrix

public List<List<String>> getDataMatrix()

The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows.

Returns:

dataMatrix

setDataMatrix

public void setDataMatrix(List<List<String>> dataMatrix)

dataMatrixAbbreviation

public BrAPIAlleleMatrixDataMatrices dataMatrixAbbreviation(String dataMatrixAbbreviation)

getDataMatrixAbbreviation

public String getDataMatrixAbbreviation()

The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word \"GT\" is reserved for the allele matrix. Examples of other metadata matrices include: \"GQ\", \"RD\", and \"HQ\" <br> This maps to a FORMAT field in the VCF file standard.

Returns:

dataMatrixAbbreviation

setDataMatrixAbbreviation

public void setDataMatrixAbbreviation(String dataMatrixAbbreviation)

dataMatrixName

public BrAPIAlleleMatrixDataMatrices dataMatrixName(String dataMatrixName)

getDataMatrixName

public String getDataMatrixName()

The name of the field represented in this data matrix. The key word \"Genotype\" is reserved for the allele matrix. Examples of other metadata matrices include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\" <br> This maps to a FORMAT field in the VCF file standard.

Returns:

dataMatrixName

setDataMatrixName

public void setDataMatrixName(String dataMatrixName)

dataType

public BrAPIAlleleMatrixDataMatrices dataType(BrAPIDataTypeEnum dataType)

getDataType

public BrAPIDataTypeEnum getDataType()

The type of field represented in this data matrix. This is intended to help parse the data out of JSON.

Returns:

dataType

setDataType

public void setDataType(BrAPIDataTypeEnum dataType)

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