Variant (molgenis-omx-das 1.1.0 API)

java.lang.Object
- org.molgenis.data.support.AbstractEntity
- - org.molgenis.omx.observ.Characteristic
  - - org.molgenis.omx.observ.ObservationTarget
    - - org.molgenis.omx.xgap.Variant

All Implemented Interfaces:

Serializable, Entity, Autoid, Identifiable, Locus
```
@Entity
public class Variant
extends ObservationTarget
implements Entity, Locus
```
Variant: A SNP is a special kind of Marker, but can also be seen as a phenotype to map against in some cases. A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in an individual..

Author:

MOLGENIS generator

See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`AANOTATION`
`static String`	`AAPOSITION`
`static String`	`BPEND`
`static String`	`BPSTART`
`static String`	`CDNANOTATION`
`static String`	`CDNAPOSITION`
`static String`	`CHROMOSOME`
`static String`	`CM`
`static String`	`CODONCHANGE`
`static String`	`CONSEQUENCE`
`static String`	`DETAILSFORMUTATION`
`static String`	`EFFECTONSPLICING`
`static String`	`ENTITY_NAME`
`static String`	`EVENT`
`static String`	`EXON`
`static String`	`GDNANOTATION`
`static String`	`GENE`
`static String`	`ID`
`static String`	`IDMUTATION`
`static String`	`INHERITANCE`
`static String`	`MUTATIONPOSITION`
`static String`	`NTCHANGE`
`static String`	`PATHOGENICITY`
`static String`	`REPORTEDSNP`
`static String`	`SEQ`
`static String`	`SYMBOL`
`static String`	`TRACK`
`static String`	`VARIANTLENGTH`

Fields inherited from class org.molgenis.omx.observ.Characteristic
__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors
Constructor and Description

Variant()

Constructors
Constructor and Description
`Variant()`

Method Summary

Methods
Modifier and Type	Method and Description
`boolean`	`equals(Object obj)`
`Object`	`get(String name)` Generic getter.
`String`	`getAaNotation()` Get the .
`Integer`	`getAaPosition()` Get the .
`Iterable<String>`	`getAttributeNames()`
`Long`	`getBpEnd()` Get the numeric basepair postion (3') on the chromosome.
`Long`	`getBpStart()` Get the numeric basepair postion (5') on the chromosome.
`String`	`getCdnaNotation()` Get the .
`Integer`	`getCdnaPosition()` Get the .
`Chromosome`	`getChromosome()` Get the Reference to the chromosome this position belongs to..
`Double`	`getCM()` Get the genetic map position in centi morgan (cM)..
`String`	`getCodonchange()` Get the .
`String`	`getConsequence()` Get the .
`String`	`getDetailsForMutation()` Get the .
`Boolean`	`getEffectOnSplicing()` Get the .
`EntityMetaData`	`getEntityMetaData()`
`String`	`getEntityName()`
`String`	`getEvent()` Get the .
`String`	`getExon()` Get the .
`String`	`getGdnaNotation()` Get the .
`String`	`getGene()` Get the .
`Integer`	`getIdMutation()` Get the .
`Integer`	`getIdValue()`
`String`	`getInheritance()` Get the .
`List<String>`	`getLabelAttributeNames()`
`Integer`	`getMutationPosition()` Get the .
`String`	`getNtChange()` Get the .
`String`	`getPathogenicity()` Get the .
`Boolean`	`getReportedSNP()` Get the .
`String`	`getSeq()` Get the The FASTA text representation of the sequence..
`String`	`getSymbol()` Get the todo.
`Track`	`getTrack()` Get the .
`Integer`	`getVariantLength()` Get the .
`int`	`hashCode()`
`void`	`set(Entity entity, boolean strict)`
`void`	`set(String attributeName, Object value)`
`void`	`setAaNotation(String aaNotation)` Set the .
`void`	`setAaPosition(Integer aaPosition)` Set the .
`void`	`setBpEnd(Long bpEnd)` Set the numeric basepair postion (3') on the chromosome.
`void`	`setBpStart(Long bpStart)` Set the numeric basepair postion (5') on the chromosome.
`void`	`setCdnaNotation(String cdnaNotation)` Set the .
`void`	`setCdnaPosition(Integer cdnaPosition)` Set the .
`void`	`setChromosome(Chromosome chromosome)` Set the Reference to the chromosome this position belongs to..
`void`	`setCM(Double cM)` Set the genetic map position in centi morgan (cM)..
`void`	`setCodonchange(String codonchange)` Set the .
`void`	`setConsequence(String consequence)` Set the .
`void`	`setDetailsForMutation(String detailsForMutation)` Set the .
`void`	`setEffectOnSplicing(Boolean effectOnSplicing)` Set the .
`void`	`setEvent(String event)` Set the .
`void`	`setExon(String exon)` Set the .
`void`	`setGdnaNotation(String gdnaNotation)` Set the .
`void`	`setGene(String gene)` Set the .
`void`	`setIdMutation(Integer idMutation)` Set the .
`void`	`setInheritance(String inheritance)` Set the .
`void`	`setMutationPosition(Integer mutationPosition)` Set the .
`void`	`setNtChange(String ntChange)` Set the .
`void`	`setPathogenicity(String pathogenicity)` Set the .
`void`	`setReportedSNP(Boolean reportedSNP)` Set the .
`void`	`setSeq(String seq)` Set the The FASTA text representation of the sequence..
`void`	`setSymbol(String symbol)` Set the todo.
`void`	`setTrack(Track track)` Set the .
`void`	`setVariantLength(Integer variantLength)` Set the .
`String`	`toString()`
`String`	`toString(boolean verbose)`

Methods inherited from class org.molgenis.omx.observ.Characteristic
get__Type, get__TypeLabel, get__TypeOptions, getDescription, getId, getIdentifier, getName, getValueMrefValueCollection, set__Type, setDescription, setId, setIdentifier, setName, setValueMrefValueCollection

Methods inherited from class org.molgenis.data.support.AbstractEntity
getBoolean, getDate, getDouble, getEntities, getEntity, getInt, getIntList, getLabelValue, getList, getLong, getString, getTimestamp, getUtilDate, isObjectRepresentation, set, setValuesFromString

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.molgenis.data.Entity
getBoolean, getDate, getDouble, getEntities, getEntity, getInt, getIntList, getLabelValue, getList, getLong, getString, getTimestamp, getUtilDate, set

- Field Detail
  - ENTITY_NAME
```
public static final String ENTITY_NAME
```
    See Also:
    Constant Field Values
  - CHROMOSOME
```
public static final String CHROMOSOME
```
    See Also:
    Constant Field Values
  - CM
```
public static final String CM
```
    See Also:
    Constant Field Values
  - BPSTART
```
public static final String BPSTART
```
    See Also:
    Constant Field Values
  - BPEND
```
public static final String BPEND
```
    See Also:
    Constant Field Values
  - SEQ
```
public static final String SEQ
```
    See Also:
    Constant Field Values
  - SYMBOL
```
public static final String SYMBOL
```
    See Also:
    Constant Field Values
  - MUTATIONPOSITION
```
public static final String MUTATIONPOSITION
```
    See Also:
    Constant Field Values
  - CDNAPOSITION
```
public static final String CDNAPOSITION
```
    See Also:
    Constant Field Values
  - AAPOSITION
```
public static final String AAPOSITION
```
    See Also:
    Constant Field Values
  - VARIANTLENGTH
```
public static final String VARIANTLENGTH
```
    See Also:
    Constant Field Values
  - EVENT
```
public static final String EVENT
```
    See Also:
    Constant Field Values
  - NTCHANGE
```
public static final String NTCHANGE
```
    See Also:
    Constant Field Values
  - CODONCHANGE
```
public static final String CODONCHANGE
```
    See Also:
    Constant Field Values
  - CDNANOTATION
```
public static final String CDNANOTATION
```
    See Also:
    Constant Field Values
  - GDNANOTATION
```
public static final String GDNANOTATION
```
    See Also:
    Constant Field Values
  - AANOTATION
```
public static final String AANOTATION
```
    See Also:
    Constant Field Values
  - EXON
```
public static final String EXON
```
    See Also:
    Constant Field Values
  - CONSEQUENCE
```
public static final String CONSEQUENCE
```
    See Also:
    Constant Field Values
  - INHERITANCE
```
public static final String INHERITANCE
```
    See Also:
    Constant Field Values
  - REPORTEDSNP
```
public static final String REPORTEDSNP
```
    See Also:
    Constant Field Values
  - EFFECTONSPLICING
```
public static final String EFFECTONSPLICING
```
    See Also:
    Constant Field Values
  - PATHOGENICITY
```
public static final String PATHOGENICITY
```
    See Also:
    Constant Field Values
  - GENE
```
public static final String GENE
```
    See Also:
    Constant Field Values
  - IDMUTATION
```
public static final String IDMUTATION
```
    See Also:
    Constant Field Values
  - DETAILSFORMUTATION
```
public static final String DETAILSFORMUTATION
```
    See Also:
    Constant Field Values
  - TRACK
```
public static final String TRACK
```
    See Also:
    Constant Field Values
  - ID
```
public static final String ID
```
    See Also:
    Constant Field Values
- Constructor Detail
  - Variant
```
public Variant()
```
- Method Detail
  - getEntityName
```
public String getEntityName()
```
    Overrides:
    
    getEntityName in class ObservationTarget
  - getChromosome
```
public Chromosome getChromosome()
```
    Get the Reference to the chromosome this position belongs to..
    
    Specified by:
    
    getChromosome in interface Locus
    
    Returns:
    chromosome.
  - setChromosome
```
public void setChromosome(Chromosome chromosome)
```
    Set the Reference to the chromosome this position belongs to..
    
    Specified by:
    
    setChromosome in interface Locus
    
    Parameters:
    chromosome -
  - getCM
```
public Double getCM()
```
    Get the genetic map position in centi morgan (cM)..
    
    Specified by:
    
    getCM in interface Locus
    
    Returns:
    cM.
  - setCM
```
public void setCM(Double cM)
```
    Set the genetic map position in centi morgan (cM)..
    
    Specified by:
    
    setCM in interface Locus
    
    Parameters:
    cM -
  - getBpStart
```
public Long getBpStart()
```
    Get the numeric basepair postion (5') on the chromosome.
    
    Specified by:
    
    getBpStart in interface Locus
    
    Returns:
    bpStart.
  - setBpStart
```
public void setBpStart(Long bpStart)
```
    Set the numeric basepair postion (5') on the chromosome.
    
    Specified by:
    
    setBpStart in interface Locus
    
    Parameters:
    bpStart -
  - getBpEnd
```
public Long getBpEnd()
```
    Get the numeric basepair postion (3') on the chromosome.
    
    Specified by:
    
    getBpEnd in interface Locus
    
    Returns:
    bpEnd.
  - setBpEnd
```
public void setBpEnd(Long bpEnd)
```
    Set the numeric basepair postion (3') on the chromosome.
    
    Specified by:
    
    setBpEnd in interface Locus
    
    Parameters:
    bpEnd -
  - getSeq
```
public String getSeq()
```
    Get the The FASTA text representation of the sequence..
    
    Specified by:
    
    getSeq in interface Locus
    
    Returns:
    seq.
  - setSeq
```
public void setSeq(String seq)
```
    Set the The FASTA text representation of the sequence..
    
    Specified by:
    
    setSeq in interface Locus
    
    Parameters:
    seq -
  - getSymbol
```
public String getSymbol()
```
    Get the todo.
    
    Specified by:
    
    getSymbol in interface Locus
    
    Returns:
    symbol.
  - setSymbol
```
public void setSymbol(String symbol)
```
    Set the todo.
    
    Specified by:
    
    setSymbol in interface Locus
    
    Parameters:
    symbol -
  - getMutationPosition
```
public Integer getMutationPosition()
```
    Get the .
    
    Returns:
    mutationPosition.
  - setMutationPosition
```
public void setMutationPosition(Integer mutationPosition)
```
    Set the .
    
    Parameters:
    mutationPosition -
  - getCdnaPosition
```
public Integer getCdnaPosition()
```
    Get the .
    
    Returns:
    cdnaPosition.
  - setCdnaPosition
```
public void setCdnaPosition(Integer cdnaPosition)
```
    Set the .
    
    Parameters:
    cdnaPosition -
  - getAaPosition
```
public Integer getAaPosition()
```
    Get the .
    
    Returns:
    aaPosition.
  - setAaPosition
```
public void setAaPosition(Integer aaPosition)
```
    Set the .
    
    Parameters:
    aaPosition -
  - getVariantLength
```
public Integer getVariantLength()
```
    Get the .
    
    Returns:
    variantLength.
  - setVariantLength
```
public void setVariantLength(Integer variantLength)
```
    Set the .
    
    Parameters:
    variantLength -
  - getEvent
```
public String getEvent()
```
    Get the .
    
    Returns:
    event.
  - setEvent
```
public void setEvent(String event)
```
    Set the .
    
    Parameters:
    event -
  - getNtChange
```
public String getNtChange()
```
    Get the .
    
    Returns:
    ntChange.
  - setNtChange
```
public void setNtChange(String ntChange)
```
    Set the .
    
    Parameters:
    ntChange -
  - getCodonchange
```
public String getCodonchange()
```
    Get the .
    
    Returns:
    codonchange.
  - setCodonchange
```
public void setCodonchange(String codonchange)
```
    Set the .
    
    Parameters:
    codonchange -
  - getCdnaNotation
```
public String getCdnaNotation()
```
    Get the .
    
    Returns:
    cdnaNotation.
  - setCdnaNotation
```
public void setCdnaNotation(String cdnaNotation)
```
    Set the .
    
    Parameters:
    cdnaNotation -
  - getGdnaNotation
```
public String getGdnaNotation()
```
    Get the .
    
    Returns:
    gdnaNotation.
  - setGdnaNotation
```
public void setGdnaNotation(String gdnaNotation)
```
    Set the .
    
    Parameters:
    gdnaNotation -
  - getAaNotation
```
public String getAaNotation()
```
    Get the .
    
    Returns:
    aaNotation.
  - setAaNotation
```
public void setAaNotation(String aaNotation)
```
    Set the .
    
    Parameters:
    aaNotation -
  - getExon
```
public String getExon()
```
    Get the .
    
    Returns:
    exon.
  - setExon
```
public void setExon(String exon)
```
    Set the .
    
    Parameters:
    exon -
  - getConsequence
```
public String getConsequence()
```
    Get the .
    
    Returns:
    consequence.
  - setConsequence
```
public void setConsequence(String consequence)
```
    Set the .
    
    Parameters:
    consequence -
  - getInheritance
```
public String getInheritance()
```
    Get the .
    
    Returns:
    inheritance.
  - setInheritance
```
public void setInheritance(String inheritance)
```
    Set the .
    
    Parameters:
    inheritance -
  - getReportedSNP
```
public Boolean getReportedSNP()
```
    Get the .
    
    Returns:
    reportedSNP.
  - setReportedSNP
```
public void setReportedSNP(Boolean reportedSNP)
```
    Set the .
    
    Parameters:
    reportedSNP -
  - getEffectOnSplicing
```
public Boolean getEffectOnSplicing()
```
    Get the .
    
    Returns:
    effectOnSplicing.
  - setEffectOnSplicing
```
public void setEffectOnSplicing(Boolean effectOnSplicing)
```
    Set the .
    
    Parameters:
    effectOnSplicing -
  - getPathogenicity
```
public String getPathogenicity()
```
    Get the .
    
    Returns:
    pathogenicity.
  - setPathogenicity
```
public void setPathogenicity(String pathogenicity)
```
    Set the .
    
    Parameters:
    pathogenicity -
  - getGene
```
public String getGene()
```
    Get the .
    
    Returns:
    gene.
  - setGene
```
public void setGene(String gene)
```
    Set the .
    
    Parameters:
    gene -
  - getIdMutation
```
public Integer getIdMutation()
```
    Get the .
    
    Returns:
    idMutation.
  - setIdMutation
```
public void setIdMutation(Integer idMutation)
```
    Set the .
    
    Parameters:
    idMutation -
  - getDetailsForMutation
```
public String getDetailsForMutation()
```
    Get the .
    
    Returns:
    detailsForMutation.
  - setDetailsForMutation
```
public void setDetailsForMutation(String detailsForMutation)
```
    Set the .
    
    Parameters:
    detailsForMutation -
  - getTrack
```
public Track getTrack()
```
    Get the .
    
    Returns:
    track.
  - setTrack
```
public void setTrack(Track track)
```
    Set the .
    
    Parameters:
    track -
  - get
```
public Object get(String name)
```
    Generic getter. Get the property by using the name.
    
    Specified by:
    
    get in interface Entity
    
    Overrides:
    
    get in class ObservationTarget
  - set
```
public void set(Entity entity,
       boolean strict)
```
    Specified by:
    
    set in interface Entity
    
    Overrides:
    
    set in class ObservationTarget
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class ObservationTarget
  - toString
```
public String toString(boolean verbose)
```
    Overrides:
    
    toString in class ObservationTarget
  - getIdValue
```
public Integer getIdValue()
```
    Specified by:
    
    getIdValue in interface Entity
    
    Overrides:
    
    getIdValue in class ObservationTarget
  - getAttributeNames
```
public Iterable<String> getAttributeNames()
```
    Specified by:
    
    getAttributeNames in interface Entity
    
    Overrides:
    
    getAttributeNames in class ObservationTarget
  - getLabelAttributeNames
```
public List<String> getLabelAttributeNames()
```
    Specified by:
    
    getLabelAttributeNames in interface Entity
    
    Overrides:
    
    getLabelAttributeNames in class ObservationTarget
  - set
```
public void set(String attributeName,
       Object value)
```
    Specified by:
    
    set in interface Entity
    
    Overrides:
    
    set in class ObservationTarget
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class ObservationTarget
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class ObservationTarget
  - getEntityMetaData
```
public EntityMetaData getEntityMetaData()
```
    Specified by:
    
    getEntityMetaData in interface Entity
    
    Overrides:
    
    getEntityMetaData in class ObservationTarget

Class Variant

Field Summary

Fields inherited from class org.molgenis.omx.observ.Characteristic

Constructor Summary

Method Summary

Methods inherited from class org.molgenis.omx.observ.Characteristic

Methods inherited from class org.molgenis.data.support.AbstractEntity

Methods inherited from class java.lang.Object

Methods inherited from interface org.molgenis.data.Entity

Field Detail

ENTITY_NAME

CHROMOSOME

CM

BPSTART

BPEND

SEQ

SYMBOL

MUTATIONPOSITION

CDNAPOSITION

AAPOSITION

VARIANTLENGTH

EVENT

NTCHANGE

CODONCHANGE

CDNANOTATION

GDNANOTATION

AANOTATION

EXON

CONSEQUENCE

INHERITANCE

REPORTEDSNP

EFFECTONSPLICING

PATHOGENICITY

GENE

IDMUTATION

DETAILSFORMUTATION

TRACK

ID

Constructor Detail

Variant

Method Detail

getEntityName

getChromosome

setChromosome

getCM

setCM

getBpStart

setBpStart

getBpEnd

setBpEnd

getSeq

setSeq

getSymbol

setSymbol

getMutationPosition

setMutationPosition

getCdnaPosition

setCdnaPosition

getAaPosition

setAaPosition

getVariantLength

setVariantLength

getEvent

setEvent

getNtChange

setNtChange

getCodonchange

setCodonchange

getCdnaNotation

setCdnaNotation

getGdnaNotation

setGdnaNotation

getAaNotation

setAaNotation

getExon

setExon

getConsequence

setConsequence

getInheritance

setInheritance