org.brapi.v2.model.geno

Class BrAPICall

java.lang.Object

org.brapi.v2.model.geno.BrAPICall

public class BrAPICall
extends Object

A `Call` represents the determination of genotype with respect to a particular `Variant`. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345.

Constructor Summary

Constructors

Constructor and Description
BrAPICall()

Method Summary

Modifier and Type	Method and Description
BrAPICall	addGenotypeLikelihoodItem(Double genotypeLikelihoodItem)
BrAPICall	addGenotypeMetadataItem(BrAPICallGenotypeMetadata genotypeMetadataItem)
BrAPICall	additionalInfo(com.google.gson.JsonObject additionalInfo)
BrAPICall	callSetDbId(String callSetDbId)
BrAPICall	callSetName(String callSetName)
boolean	equals(Object o)
BrAPICall	genotype(BrAPIListValue genotype)
BrAPICall	genotypeLikelihood(List<Double> genotypeLikelihood)
BrAPICall	genotypeMetadata(List<BrAPICallGenotypeMetadata> genotypeMetadata)
BrAPICall	genotypeValue(String genotypeValue)
com.google.gson.JsonObject	getAdditionalInfo() Additional arbitrary info
String	getCallSetDbId() The ID of the call set this variant call belongs to.
String	getCallSetName() The name of the call set this variant call belongs to.
@Valid BrAPIListValue	getGenotype() Get genotype
List<Double>	getGenotypeLikelihood() The genotype likelihood for this variant call.
List<BrAPICallGenotypeMetadata>	getGenotypeMetadata() Genotype Metadata are additional layers of metadata associated with each genotype.
String	getGenotypeValue()
String	getPhaseSet() If this field is populated, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls on the same contig which have the same phase set string.
String	getVariantDbId() The ID of the variant this call belongs to.
String	getVariantName() The name of the variant this call belongs to.
String	getVariantSetDbId() The unique identifier for a VariantSet
String	getVariantSetName() The human readable name for a VariantSet
int	hashCode()
BrAPICall	phaseSet(String phaseSet)
BrAPICall	putAdditionalInfoItem(String key, Object additionalInfoItem)
void	setAdditionalInfo(com.google.gson.JsonObject additionalInfo)
void	setCallSetDbId(String callSetDbId)
void	setCallSetName(String callSetName)
void	setGenotype(BrAPIListValue genotype)
void	setGenotypeLikelihood(List<Double> genotypeLikelihood)
void	setGenotypeMetadata(List<BrAPICallGenotypeMetadata> genotypeMetadata)
void	setGenotypeValue(String genotypeValue)
void	setPhaseSet(String phaseSet)
void	setVariantDbId(String variantDbId)
void	setVariantName(String variantName)
void	setVariantSetDbId(String variantSetDbId)
void	setVariantSetName(String variantSetName)
String	toString()
BrAPICall	variantDbId(String variantDbId)
BrAPICall	variantName(String variantName)
BrAPICall	variantSetDbId(String variantSetDbId)
BrAPICall	variantSetName(String variantSetName)

Methods inherited from class java.lang.Object

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

Constructor Detail

BrAPICall

public BrAPICall()

Method Detail

additionalInfo

public BrAPICall additionalInfo(com.google.gson.JsonObject additionalInfo)

putAdditionalInfoItem

public BrAPICall putAdditionalInfoItem(String key,
                                       Object additionalInfoItem)

getAdditionalInfo

public com.google.gson.JsonObject getAdditionalInfo()

Additional arbitrary info

Returns:

additionalInfo

setAdditionalInfo

public void setAdditionalInfo(com.google.gson.JsonObject additionalInfo)

callSetDbId

public BrAPICall callSetDbId(String callSetDbId)

getCallSetDbId

public String getCallSetDbId()

The ID of the call set this variant call belongs to. If this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same.

Returns:

callSetDbId

setCallSetDbId

public void setCallSetDbId(String callSetDbId)

callSetName

public BrAPICall callSetName(String callSetName)

getCallSetName

public String getCallSetName()

The name of the call set this variant call belongs to. If this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same.

Returns:

callSetName

setCallSetName

public void setCallSetName(String callSetName)

genotype

public BrAPICall genotype(BrAPIListValue genotype)

getGenotype

@Valid
public @Valid BrAPIListValue getGenotype()

Get genotype

Returns:

genotype

setGenotype

public void setGenotype(BrAPIListValue genotype)

genotypeMetadata

public BrAPICall genotypeMetadata(List<BrAPICallGenotypeMetadata> genotypeMetadata)

addGenotypeMetadataItem

public BrAPICall addGenotypeMetadataItem(BrAPICallGenotypeMetadata genotypeMetadataItem)

getGenotypeMetadata

public List<BrAPICallGenotypeMetadata> getGenotypeMetadata()

Genotype Metadata are additional layers of metadata associated with each genotype.

Returns:

genotypeMetadata

setGenotypeMetadata

public void setGenotypeMetadata(List<BrAPICallGenotypeMetadata> genotypeMetadata)

genotypeValue

public BrAPICall genotypeValue(String genotypeValue)

getGenotypeValue

public String getGenotypeValue()

setGenotypeValue

public void setGenotypeValue(String genotypeValue)

genotypeLikelihood

public BrAPICall genotypeLikelihood(List<Double> genotypeLikelihood)

addGenotypeLikelihoodItem

public BrAPICall addGenotypeLikelihoodItem(Double genotypeLikelihoodItem)

getGenotypeLikelihood

public List<Double> getGenotypeLikelihood()

The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec.

Returns:

genotypeLikelihood

setGenotypeLikelihood

public void setGenotypeLikelihood(List<Double> genotypeLikelihood)

phaseSet

public BrAPICall phaseSet(String phaseSet)

getPhaseSet

public String getPhaseSet()

If this field is populated, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls on the same contig which have the same phase set string.

Returns:

phaseSet

setPhaseSet

public void setPhaseSet(String phaseSet)

variantDbId

public BrAPICall variantDbId(String variantDbId)

getVariantDbId

public String getVariantDbId()

The ID of the variant this call belongs to.

Returns:

variantDbId

setVariantDbId

public void setVariantDbId(String variantDbId)

variantName

public BrAPICall variantName(String variantName)

getVariantName

public String getVariantName()

The name of the variant this call belongs to.

Returns:

variantName

setVariantName

public void setVariantName(String variantName)

variantSetDbId

public BrAPICall variantSetDbId(String variantSetDbId)

getVariantSetDbId

public String getVariantSetDbId()

The unique identifier for a VariantSet

Returns:

variantSetDbId

setVariantSetDbId

public void setVariantSetDbId(String variantSetDbId)

variantSetName

public BrAPICall variantSetName(String variantSetName)

getVariantSetName

public String getVariantSetName()

The human readable name for a VariantSet

Returns:

variantSetName

setVariantSetName

public void setVariantSetName(String variantSetName)

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