org.brapi.v2.model.geno

Class BrAPIReferenceSet

java.lang.Object

org.brapi.v2.model.geno.BrAPIReferenceSet

public class BrAPIReferenceSet
extends Object

A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data.

Constructor Summary

Constructors

Constructor and Description
BrAPIReferenceSet()

Method Summary

Modifier and Type	Method and Description
BrAPIReferenceSet	additionalInfo(com.google.gson.JsonObject additionalInfo)
BrAPIReferenceSet	addSourceAccessionsItem(String sourceAccessionsItem)
BrAPIReferenceSet	addSourceGermplasmItem(BrAPIReferenceSetSourceGermplasm sourceGermplasmItem)
BrAPIReferenceSet	assemblyPUI(String assemblyPUI)
BrAPIReferenceSet	commonCropName(String commonCropName)
BrAPIReferenceSet	description(String description)
boolean	equals(Object o)
BrAPIReferenceSet	externalReferences(List<BrAPIExternalReference> externalReferences)
com.google.gson.JsonObject	getAdditionalInfo() Additional arbitrary info
String	getAssemblyPUI() The remaining information is about the source of the sequences Public id of this reference set, such as `GRCH_37`.
String	getCommonCropName() Common name for the crop
String	getDescription() Optional free text description of this reference set.
@Valid List<BrAPIExternalReference>	getExternalReferences() Get externalReferences
String	getMd5checksum() Order-independent MD5 checksum which identifies this `ReferenceSet`.
String	getReferenceSetDbId() The reference set ID.
String	getReferenceSetName() The reference set name.
List<String>	getSourceAccessions() All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g.
List<BrAPIReferenceSetSourceGermplasm>	getSourceGermplasm() All known corresponding Germplasm
String	getSourceURI() Specifies a FASTA format file/string.
@Valid BrAPIOntologyTerm	getSpecies() Get species
int	hashCode()
BrAPIReferenceSet	isDerived(Boolean isDerived)
Boolean	isIsDerived() A reference set may be derived from a source if it contains additional sequences, or some of the sequences within it are derived (see the definition of `isDerived` in `Reference`).
BrAPIReferenceSet	md5checksum(String md5checksum)
BrAPIReferenceSet	putAdditionalInfoItem(String key, Object additionalInfoItem)
BrAPIReferenceSet	referenceSetDbId(String referenceSetDbId)
BrAPIReferenceSet	referenceSetName(String referenceSetName)
void	setAdditionalInfo(com.google.gson.JsonObject additionalInfo)
void	setAssemblyPUI(String assemblyPUI)
void	setCommonCropName(String commonCropName)
void	setDescription(String description)
void	setExternalReferences(List<BrAPIExternalReference> externalReferences)
void	setIsDerived(Boolean isDerived)
void	setMd5checksum(String md5checksum)
void	setReferenceSetDbId(String referenceSetDbId)
void	setReferenceSetName(String referenceSetName)
void	setSourceAccessions(List<String> sourceAccessions)
void	setSourceGermplasm(List<BrAPIReferenceSetSourceGermplasm> sourceGermplasm)
void	setSourceURI(String sourceURI)
void	setSpecies(BrAPIOntologyTerm species)
BrAPIReferenceSet	sourceAccessions(List<String> sourceAccessions)
BrAPIReferenceSet	sourceGermplasm(List<BrAPIReferenceSetSourceGermplasm> sourceGermplasm)
BrAPIReferenceSet	sourceURI(String sourceURI)
BrAPIReferenceSet	species(BrAPIOntologyTerm species)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

BrAPIReferenceSet

public BrAPIReferenceSet()

Method Detail

additionalInfo

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

putAdditionalInfoItem

public BrAPIReferenceSet 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)

assemblyPUI

public BrAPIReferenceSet assemblyPUI(String assemblyPUI)

getAssemblyPUI

public String getAssemblyPUI()

The remaining information is about the source of the sequences Public id of this reference set, such as `GRCH_37`.

Returns:

assemblyPUI

setAssemblyPUI

public void setAssemblyPUI(String assemblyPUI)

commonCropName

public BrAPIReferenceSet commonCropName(String commonCropName)

getCommonCropName

public String getCommonCropName()

Common name for the crop

Returns:

commonCropName

setCommonCropName

public void setCommonCropName(String commonCropName)

description

public BrAPIReferenceSet description(String description)

getDescription

public String getDescription()

Optional free text description of this reference set.

Returns:

description

setDescription

public void setDescription(String description)

externalReferences

public BrAPIReferenceSet externalReferences(List<BrAPIExternalReference> externalReferences)

getExternalReferences

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

Get externalReferences

Returns:

externalReferences

setExternalReferences

public void setExternalReferences(List<BrAPIExternalReference> externalReferences)

isDerived

public BrAPIReferenceSet isDerived(Boolean isDerived)

isIsDerived

public Boolean isIsDerived()

A reference set may be derived from a source if it contains additional sequences, or some of the sequences within it are derived (see the definition of `isDerived` in `Reference`).

Returns:

isDerived

setIsDerived

public void setIsDerived(Boolean isDerived)

md5checksum

public BrAPIReferenceSet md5checksum(String md5checksum)

getMd5checksum

public String getMd5checksum()

Order-independent MD5 checksum which identifies this `ReferenceSet`. To compute this checksum, make a list of `Reference.md5checksum` for all `Reference` s in this set. Then sort that list, and take the MD5 hash of all the strings concatenated together. Express the hash as a lower-case hexadecimal string.

Returns:

md5checksum

setMd5checksum

public void setMd5checksum(String md5checksum)

referenceSetDbId

public BrAPIReferenceSet referenceSetDbId(String referenceSetDbId)

getReferenceSetDbId

public String getReferenceSetDbId()

The reference set ID. Unique in the repository.

Returns:

referenceSetDbId

setReferenceSetDbId

public void setReferenceSetDbId(String referenceSetDbId)

referenceSetName

public BrAPIReferenceSet referenceSetName(String referenceSetName)

getReferenceSetName

public String getReferenceSetName()

The reference set name.

Returns:

referenceSetName

setReferenceSetName

public void setReferenceSetName(String referenceSetName)

sourceAccessions

public BrAPIReferenceSet sourceAccessions(List<String> sourceAccessions)

addSourceAccessionsItem

public BrAPIReferenceSet addSourceAccessionsItem(String sourceAccessionsItem)

getSourceAccessions

public List<String> getSourceAccessions()

All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`.

Returns:

sourceAccessions

setSourceAccessions

public void setSourceAccessions(List<String> sourceAccessions)

sourceGermplasm

public BrAPIReferenceSet sourceGermplasm(List<BrAPIReferenceSetSourceGermplasm> sourceGermplasm)

addSourceGermplasmItem

public BrAPIReferenceSet addSourceGermplasmItem(BrAPIReferenceSetSourceGermplasm sourceGermplasmItem)

getSourceGermplasm

public List<BrAPIReferenceSetSourceGermplasm> getSourceGermplasm()

All known corresponding Germplasm

Returns:

sourceGermplasm

setSourceGermplasm

public void setSourceGermplasm(List<BrAPIReferenceSetSourceGermplasm> sourceGermplasm)

sourceURI

public BrAPIReferenceSet sourceURI(String sourceURI)

getSourceURI

public String getSourceURI()

Specifies a FASTA format file/string.

Returns:

sourceURI

setSourceURI

public void setSourceURI(String sourceURI)

species

public BrAPIReferenceSet species(BrAPIOntologyTerm species)

getSpecies

@Valid
public @Valid BrAPIOntologyTerm getSpecies()

Get species

Returns:

species

setSpecies

public void setSpecies(BrAPIOntologyTerm species)

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