org.brapi.v2.model.geno

Class BrAPIVariantSet

java.lang.Object

org.brapi.v2.model.geno.BrAPIVariantSet

public class BrAPIVariantSet
extends Object

A VariantSet is a collection of variants and variant calls intended to be analyzed together.

Constructor Summary

Constructors

Constructor and Description
BrAPIVariantSet()

Method Summary

Modifier and Type	Method and Description
BrAPIVariantSet	addAnalysisItem(BrAPIAnalysis analysisItem)
BrAPIVariantSet	addAvailableFormatsItem(BrAPIVariantSetAvailableFormats availableFormatsItem)
BrAPIVariantSet	additionalInfo(com.google.gson.JsonObject additionalInfo)
BrAPIVariantSet	addMetadataFieldsItem(BrAPIVariantSetMetadataFields metadataFieldsItem)
BrAPIVariantSet	analysis(List<BrAPIAnalysis> analysis)
BrAPIVariantSet	availableFormats(List<BrAPIVariantSetAvailableFormats> availableFormats)
BrAPIVariantSet	callSetCount(Integer callSetCount)
boolean	equals(Object o)
BrAPIVariantSet	externalReferences(List<BrAPIExternalReference> externalReferences)
com.google.gson.JsonObject	getAdditionalInfo() Additional arbitrary info
@Valid List<BrAPIAnalysis>	getAnalysis() Set of Analysis descriptors for this VariantSet
@Valid List<BrAPIVariantSetAvailableFormats>	getAvailableFormats() When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats.
Integer	getCallSetCount() The number of CallSets included in this VariantSet
@Valid List<BrAPIExternalReference>	getExternalReferences() Get externalReferences
List<BrAPIVariantSetMetadataFields>	getMetadataFields() The 'metadataFields' array indicates which types of genotyping data and metadata are available in the VariantSet.
String	getReferenceSetDbId() The ID of the reference set that describes the sequences used by the variants in this set.
String	getStudyDbId() The ID of the dataset this variant set belongs to.
Integer	getVariantCount() The number of Variants included in this VariantSet
String	getVariantSetDbId() The variant set ID.
String	getVariantSetName() The variant set name.
int	hashCode()
BrAPIVariantSet	metadataFields(List<BrAPIVariantSetMetadataFields> metadataFields)
BrAPIVariantSet	putAdditionalInfoItem(String key, Object additionalInfoItem)
BrAPIVariantSet	referenceSetDbId(String referenceSetDbId)
void	setAdditionalInfo(com.google.gson.JsonObject additionalInfo)
void	setAnalysis(List<BrAPIAnalysis> analysis)
void	setAvailableFormats(List<BrAPIVariantSetAvailableFormats> availableFormats)
void	setCallSetCount(Integer callSetCount)
void	setExternalReferences(List<BrAPIExternalReference> externalReferences)
void	setMetadataFields(List<BrAPIVariantSetMetadataFields> metadataFields)
void	setReferenceSetDbId(String referenceSetDbId)
void	setStudyDbId(String studyDbId)
void	setVariantCount(Integer variantCount)
void	setVariantSetDbId(String variantSetDbId)
void	setVariantSetName(String variantSetName)
BrAPIVariantSet	studyDbId(String studyDbId)
String	toString()
BrAPIVariantSet	variantCount(Integer variantCount)
BrAPIVariantSet	variantSetDbId(String variantSetDbId)
BrAPIVariantSet	variantSetName(String variantSetName)

Methods inherited from class java.lang.Object

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

Constructor Detail

BrAPIVariantSet

public BrAPIVariantSet()

Method Detail

additionalInfo

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

putAdditionalInfoItem

public BrAPIVariantSet 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)

analysis

public BrAPIVariantSet analysis(List<BrAPIAnalysis> analysis)

addAnalysisItem

public BrAPIVariantSet addAnalysisItem(BrAPIAnalysis analysisItem)

getAnalysis

@Valid
public @Valid List<BrAPIAnalysis> getAnalysis()

Set of Analysis descriptors for this VariantSet

Returns:

analysis

setAnalysis

public void setAnalysis(List<BrAPIAnalysis> analysis)

availableFormats

public BrAPIVariantSet availableFormats(List<BrAPIVariantSetAvailableFormats> availableFormats)

addAvailableFormatsItem

public BrAPIVariantSet addAvailableFormatsItem(BrAPIVariantSetAvailableFormats availableFormatsItem)

getAvailableFormats

@Valid
public @Valid List<BrAPIVariantSetAvailableFormats> getAvailableFormats()

When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc) fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response.

Returns:

availableFormats

setAvailableFormats

public void setAvailableFormats(List<BrAPIVariantSetAvailableFormats> availableFormats)

callSetCount

public BrAPIVariantSet callSetCount(Integer callSetCount)

getCallSetCount

public Integer getCallSetCount()

The number of CallSets included in this VariantSet

Returns:

callSetCount

setCallSetCount

public void setCallSetCount(Integer callSetCount)

externalReferences

public BrAPIVariantSet externalReferences(List<BrAPIExternalReference> externalReferences)

getExternalReferences

@Valid
public @Valid List<BrAPIExternalReference> getExternalReferences()

Get externalReferences

Returns:

externalReferences

setExternalReferences

public void setExternalReferences(List<BrAPIExternalReference> externalReferences)

metadataFields

public BrAPIVariantSet metadataFields(List<BrAPIVariantSetMetadataFields> metadataFields)

addMetadataFieldsItem

public BrAPIVariantSet addMetadataFieldsItem(BrAPIVariantSetMetadataFields metadataFieldsItem)

getMetadataFields

public List<BrAPIVariantSetMetadataFields> getMetadataFields()

The 'metadataFields' array indicates which types of genotyping data and metadata are available in the VariantSet. <br> When possible, these field names and abbreviations should follow the VCF standard

Returns:

metadataFields

setMetadataFields

public void setMetadataFields(List<BrAPIVariantSetMetadataFields> metadataFields)

referenceSetDbId

public BrAPIVariantSet referenceSetDbId(String referenceSetDbId)

getReferenceSetDbId

public String getReferenceSetDbId()

The ID of the reference set that describes the sequences used by the variants in this set.

Returns:

referenceSetDbId

setReferenceSetDbId

public void setReferenceSetDbId(String referenceSetDbId)

studyDbId

public BrAPIVariantSet studyDbId(String studyDbId)

getStudyDbId

public String getStudyDbId()

The ID of the dataset this variant set belongs to.

Returns:

studyDbId

setStudyDbId

public void setStudyDbId(String studyDbId)

variantCount

public BrAPIVariantSet variantCount(Integer variantCount)

getVariantCount

public Integer getVariantCount()

The number of Variants included in this VariantSet

Returns:

variantCount

setVariantCount

public void setVariantCount(Integer variantCount)

variantSetDbId

public BrAPIVariantSet variantSetDbId(String variantSetDbId)

getVariantSetDbId

public String getVariantSetDbId()

The variant set ID.

Returns:

variantSetDbId

setVariantSetDbId

public void setVariantSetDbId(String variantSetDbId)

variantSetName

public BrAPIVariantSet variantSetName(String variantSetName)

getVariantSetName

public String getVariantSetName()

The variant set name.

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