Package dev.pcvolkmer.mv64e.model

Class Snv

java.lang.Object

dev.pcvolkmer.mv64e.model.Snv

public class Snv
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	Snv.Builder

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	JSON_PROPERTY_ALLELIC_FREQUENCY
static java.lang.String	JSON_PROPERTY_ALT_ALLELE
static java.lang.String	JSON_PROPERTY_CHROMOSOME
static java.lang.String	JSON_PROPERTY_DNA_CHANGE
static java.lang.String	JSON_PROPERTY_EXON_ID
static java.lang.String	JSON_PROPERTY_EXTERNAL_IDS
static java.lang.String	JSON_PROPERTY_GENE
static java.lang.String	JSON_PROPERTY_ID
static java.lang.String	JSON_PROPERTY_INTERPRETATION
static java.lang.String	JSON_PROPERTY_LOCALIZATION
static java.lang.String	JSON_PROPERTY_PATIENT
static java.lang.String	JSON_PROPERTY_POSITION
static java.lang.String	JSON_PROPERTY_PROTEIN_CHANGE
static java.lang.String	JSON_PROPERTY_READ_DEPTH
static java.lang.String	JSON_PROPERTY_REF_ALLELE
static java.lang.String	JSON_PROPERTY_TRANSCRIPT_ID

Constructor Summary

Constructors

Constructor	Description
Snv()

Method Summary

Modifier and Type	Method	Description
Snv	addExternalIdsItem(VariantExternalId externalIdsItem)
Snv	addLocalizationItem(BaseVariantLocalizationCoding localizationItem)
Snv	allelicFrequency(java.math.BigDecimal allelicFrequency)
Snv	altAllele(java.lang.String altAllele)
static Snv.Builder	builder()
Snv	chromosome(Chromosome chromosome)
Snv	dnaChange(java.lang.String dnaChange)
boolean	equals(java.lang.Object o)
Snv	exonId(@Nullable java.lang.String exonId)
Snv	externalIds(@Nullable java.util.List<VariantExternalId> externalIds)
Snv	gene(Coding gene)
java.math.BigDecimal	getAllelicFrequency()
java.lang.String	getAltAllele()
Chromosome	getChromosome()
java.lang.String	getDnaChange()
@Nullable java.lang.String	getExonId()
@Nullable java.util.List<VariantExternalId>	getExternalIds()
Coding	getGene()
java.lang.String	getId()
@Nullable ClinVarCoding	getInterpretation()
@Nullable java.util.Set<BaseVariantLocalizationCoding>	getLocalization()
Reference	getPatient()
CnvEndRange	getPosition()
@Nullable java.lang.String	getProteinChange()
java.lang.Integer	getReadDepth()
java.lang.String	getRefAllele()
TranscriptId	getTranscriptId()
int	hashCode()
Snv	id(java.lang.String id)
Snv	interpretation(@Nullable ClinVarCoding interpretation)
Snv	localization(@Nullable java.util.Set<BaseVariantLocalizationCoding> localization)
Snv	patient(Reference patient)
Snv	position(CnvEndRange position)
Snv	proteinChange(@Nullable java.lang.String proteinChange)
Snv	readDepth(java.lang.Integer readDepth)
Snv	refAllele(java.lang.String refAllele)
void	setAllelicFrequency(java.math.BigDecimal allelicFrequency)
void	setAltAllele(java.lang.String altAllele)
void	setChromosome(Chromosome chromosome)
void	setDnaChange(java.lang.String dnaChange)
void	setExonId(@Nullable java.lang.String exonId)
void	setExternalIds(@Nullable java.util.List<VariantExternalId> externalIds)
void	setGene(Coding gene)
void	setId(java.lang.String id)
void	setInterpretation(@Nullable ClinVarCoding interpretation)
void	setLocalization(@Nullable java.util.Set<BaseVariantLocalizationCoding> localization)
void	setPatient(Reference patient)
void	setPosition(CnvEndRange position)
void	setProteinChange(@Nullable java.lang.String proteinChange)
void	setReadDepth(java.lang.Integer readDepth)
void	setRefAllele(java.lang.String refAllele)
void	setTranscriptId(TranscriptId transcriptId)
Snv.Builder	toBuilder()
java.lang.String	toString()
Snv	transcriptId(TranscriptId transcriptId)

Methods inherited from class java.lang.Object

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

Field Detail

JSON_PROPERTY_LOCALIZATION

public static final java.lang.String JSON_PROPERTY_LOCALIZATION

See Also:

Constant Field Values

JSON_PROPERTY_PROTEIN_CHANGE

public static final java.lang.String JSON_PROPERTY_PROTEIN_CHANGE

See Also:

Constant Field Values

JSON_PROPERTY_INTERPRETATION

public static final java.lang.String JSON_PROPERTY_INTERPRETATION

See Also:

Constant Field Values

JSON_PROPERTY_TRANSCRIPT_ID

public static final java.lang.String JSON_PROPERTY_TRANSCRIPT_ID

See Also:

Constant Field Values

JSON_PROPERTY_EXTERNAL_IDS

public static final java.lang.String JSON_PROPERTY_EXTERNAL_IDS

See Also:

Constant Field Values

JSON_PROPERTY_CHROMOSOME

public static final java.lang.String JSON_PROPERTY_CHROMOSOME

See Also:

Constant Field Values

JSON_PROPERTY_ID

public static final java.lang.String JSON_PROPERTY_ID

See Also:

Constant Field Values

JSON_PROPERTY_ALT_ALLELE

public static final java.lang.String JSON_PROPERTY_ALT_ALLELE

See Also:

Constant Field Values

JSON_PROPERTY_POSITION

public static final java.lang.String JSON_PROPERTY_POSITION

See Also:

Constant Field Values

JSON_PROPERTY_GENE

public static final java.lang.String JSON_PROPERTY_GENE

See Also:

Constant Field Values

JSON_PROPERTY_EXON_ID

public static final java.lang.String JSON_PROPERTY_EXON_ID

See Also:

Constant Field Values

JSON_PROPERTY_DNA_CHANGE

public static final java.lang.String JSON_PROPERTY_DNA_CHANGE

See Also:

Constant Field Values

JSON_PROPERTY_PATIENT

public static final java.lang.String JSON_PROPERTY_PATIENT

See Also:

Constant Field Values

JSON_PROPERTY_REF_ALLELE

public static final java.lang.String JSON_PROPERTY_REF_ALLELE

See Also:

Constant Field Values

JSON_PROPERTY_READ_DEPTH

public static final java.lang.String JSON_PROPERTY_READ_DEPTH

See Also:

Constant Field Values

JSON_PROPERTY_ALLELIC_FREQUENCY

public static final java.lang.String JSON_PROPERTY_ALLELIC_FREQUENCY

See Also:

Constant Field Values

Constructor Detail

Snv

public Snv()

Method Detail

localization

public Snv localization(@Nullable java.util.Set<BaseVariantLocalizationCoding> localization)

addLocalizationItem

public Snv addLocalizationItem(BaseVariantLocalizationCoding localizationItem)

getLocalization

public @Nullable java.util.Set<BaseVariantLocalizationCoding> getLocalization()

setLocalization

public void setLocalization(@Nullable java.util.Set<BaseVariantLocalizationCoding> localization)

proteinChange

public Snv proteinChange(@Nullable java.lang.String proteinChange)

getProteinChange

public @Nullable java.lang.String getProteinChange()

setProteinChange

public void setProteinChange(@Nullable java.lang.String proteinChange)

interpretation

public Snv interpretation(@Nullable ClinVarCoding interpretation)

getInterpretation

public @Nullable ClinVarCoding getInterpretation()

setInterpretation

public void setInterpretation(@Nullable ClinVarCoding interpretation)

transcriptId

public Snv transcriptId(TranscriptId transcriptId)

getTranscriptId

public TranscriptId getTranscriptId()

setTranscriptId

public void setTranscriptId(TranscriptId transcriptId)

externalIds

public Snv externalIds(@Nullable java.util.List<VariantExternalId> externalIds)

addExternalIdsItem

public Snv addExternalIdsItem(VariantExternalId externalIdsItem)

getExternalIds

public @Nullable java.util.List<VariantExternalId> getExternalIds()

setExternalIds

public void setExternalIds(@Nullable java.util.List<VariantExternalId> externalIds)

chromosome

public Snv chromosome(Chromosome chromosome)

getChromosome

public Chromosome getChromosome()

setChromosome

public void setChromosome(Chromosome chromosome)

id

public Snv id(java.lang.String id)

getId

public java.lang.String getId()

setId

public void setId(java.lang.String id)

altAllele

public Snv altAllele(java.lang.String altAllele)

getAltAllele

public java.lang.String getAltAllele()

setAltAllele

public void setAltAllele(java.lang.String altAllele)

position

public Snv position(CnvEndRange position)

getPosition

public CnvEndRange getPosition()

setPosition

public void setPosition(CnvEndRange position)

gene

public Snv gene(Coding gene)

getGene

public Coding getGene()

setGene

public void setGene(Coding gene)

exonId

public Snv exonId(@Nullable java.lang.String exonId)

getExonId

public @Nullable java.lang.String getExonId()

setExonId

public void setExonId(@Nullable java.lang.String exonId)

dnaChange

public Snv dnaChange(java.lang.String dnaChange)

getDnaChange

public java.lang.String getDnaChange()

setDnaChange

public void setDnaChange(java.lang.String dnaChange)

patient

public Snv patient(Reference patient)

getPatient

public Reference getPatient()

setPatient

public void setPatient(Reference patient)

refAllele

public Snv refAllele(java.lang.String refAllele)

getRefAllele

public java.lang.String getRefAllele()

setRefAllele

public void setRefAllele(java.lang.String refAllele)

readDepth

public Snv readDepth(java.lang.Integer readDepth)

getReadDepth

public java.lang.Integer getReadDepth()

setReadDepth

public void setReadDepth(java.lang.Integer readDepth)

allelicFrequency

public Snv allelicFrequency(java.math.BigDecimal allelicFrequency)

getAllelicFrequency

public java.math.BigDecimal getAllelicFrequency()

setAllelicFrequency

public void setAllelicFrequency(java.math.BigDecimal allelicFrequency)

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

builder

public static Snv.Builder builder()

toBuilder

public Snv.Builder toBuilder()