org.molgenis.omx.xgap

Class Variant

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservationTarget

org.molgenis.omx.xgap.Variant

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Locus, Entity

@Entity
public class Variant
extends ObservationTarget
implements 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	CHROMOSOME_IDENTIFIER
static String	CM
static String	CODONCHANGE
static String	CONSEQUENCE
static String	DESCRIPTION
static String	DETAILSFORMUTATION
static String	EFFECTONSPLICING
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	TRACK_IDENTIFIER
static String	VARIANTLENGTH

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

__TYPE, IDENTIFIER, NAME

Constructor Summary

Constructors

Constructor and Description
Variant()
Variant(Variant copyMe) copy constructor

Method Summary

Methods

Modifier and Type	Method and Description
Variant	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Variant>	find(Database db, QueryRule... rules) Shorthand for db.find(Variant.class, org.molgenis.framework.db.QueryRule ...
static Variant	findById(Database db, Integer id)
static Variant	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
String	getAaNotation() Get the AaNotation.
String	getAaNotation(Database db) Deprecated.
Integer	getAaPosition() Get the AaPosition.
Integer	getAaPosition(Database db) Deprecated.
Long	getBpEnd() Get the numeric basepair postion (3') on the chromosome.
Long	getBpEnd(Database db) Deprecated.
Long	getBpStart() Get the numeric basepair postion (5') on the chromosome.
Long	getBpStart(Database db) Deprecated.
String	getCdnaNotation() Get the CdnaNotation.
String	getCdnaNotation(Database db) Deprecated.
Integer	getCdnaPosition() Get the CdnaPosition.
Integer	getCdnaPosition(Database db) Deprecated.
Integer	getChromosome_Id()
String	getChromosome_Identifier() Get a pretty label Identifier for cross reference Chromosome to Chromosome.Id.
Chromosome	getChromosome() Get the Reference to the chromosome this position belongs to..
Chromosome	getChromosome(Database db) Deprecated.
Double	getCM() Get the genetic map position in centi morgan (cM)..
Double	getCM(Database db) Deprecated.
String	getCodonchange() Get the Codonchange.
String	getCodonchange(Database db) Deprecated.
String	getConsequence() Get the Consequence.
String	getConsequence(Database db) Deprecated.
String	getDescription() Get the Description.
String	getDescription(Database db) Deprecated.
String	getDetailsForMutation() Get the DetailsForMutation.
String	getDetailsForMutation(Database db) Deprecated.
Boolean	getEffectOnSplicing() Get the EffectOnSplicing.
Boolean	getEffectOnSplicing(Database db) Deprecated.
String	getEvent() Get the Event.
String	getEvent(Database db) Deprecated.
String	getExon() Get the Exon.
String	getExon(Database db) Deprecated.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Variant.
String	getFields(String sep) Deprecated.
String	getGdnaNotation() Get the GdnaNotation.
String	getGdnaNotation(Database db) Deprecated.
String	getGene() Get the Gene.
String	getGene(Database db) Deprecated.
String	getIdField()
Integer	getIdMutation() Get the IdMutation.
Integer	getIdMutation(Database db) Deprecated.
Object	getIdValue()
String	getInheritance() Get the Inheritance.
String	getInheritance(Database db) Deprecated.
List<String>	getLabelFields()
Integer	getMutationPosition() Get the MutationPosition.
Integer	getMutationPosition(Database db) Deprecated.
String	getNtChange() Get the NtChange.
String	getNtChange(Database db) Deprecated.
String	getPathogenicity() Get the Pathogenicity.
String	getPathogenicity(Database db) Deprecated.
Boolean	getReportedSNP() Get the ReportedSNP.
Boolean	getReportedSNP(Database db) Deprecated.
String	getSeq() Get the The FASTA text representation of the sequence..
String	getSeq(Database db) Deprecated.
String	getSymbol() Get the todo.
String	getSymbol(Database db) Deprecated.
Integer	getTrack_Id()
String	getTrack_Identifier() Get a pretty label Identifier for cross reference Track to Track.Id.
Track	getTrack() Get the Track.
Track	getTrack(Database db) Deprecated.
String	getValues(String sep) Deprecated.
Integer	getVariantLength() Get the VariantLength.
Integer	getVariantLength(Database db) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Variant>	query(Database db) Shorthand for db.query(Variant.class).
void	set(Entity entity, boolean strict)
void	setAaNotation(String aaNotation) Set the AaNotation.
void	setAaPosition(Integer aaPosition) Set the AaPosition.
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 CdnaNotation.
void	setCdnaPosition(Integer cdnaPosition) Set the CdnaPosition.
void	setChromosome_Id(Integer chromosome_id) Set foreign key for field chromosome.
void	setChromosome_Identifier(String chromosome_Identifier) Set a pretty label for cross reference Chromosome to Chromosome.Id.
void	setChromosome(Chromosome chromosome) Set the Reference to the chromosome this position belongs to..
void	setChromosome(Integer chromosome_id)
void	setCM(Double cM) Set the genetic map position in centi morgan (cM)..
void	setCodonchange(String codonchange) Set the Codonchange.
void	setConsequence(String consequence) Set the Consequence.
void	setDescription(String description) Set the Description.
void	setDetailsForMutation(String detailsForMutation) Set the DetailsForMutation.
void	setEffectOnSplicing(Boolean effectOnSplicing) Set the EffectOnSplicing.
void	setEvent(String event) Set the Event.
void	setExon(String exon) Set the Exon.
void	setGdnaNotation(String gdnaNotation) Set the GdnaNotation.
void	setGene(String gene) Set the Gene.
void	setIdMutation(Integer idMutation) Set the IdMutation.
void	setInheritance(String inheritance) Set the Inheritance.
void	setMutationPosition(Integer mutationPosition) Set the MutationPosition.
void	setNtChange(String ntChange) Set the NtChange.
void	setPathogenicity(String pathogenicity) Set the Pathogenicity.
void	setReportedSNP(Boolean reportedSNP) Set the ReportedSNP.
void	setSeq(String seq) Set the The FASTA text representation of the sequence..
void	setSymbol(String symbol) Set the todo.
void	setTrack_Id(Integer track_id) Set foreign key for field track.
void	setTrack_Identifier(String track_Identifier) Set a pretty label for cross reference Track to Track.Id.
void	setTrack(Integer track_id)
void	setTrack(Track track) Set the Track.
void	setVariantLength(Integer variantLength) Set the VariantLength.
String	toString()
String	toString(boolean verbose)
void	validate()

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

get__Type, get__Type, get__TypeLabel, get__TypeOptions, getId, getIdentifier, getIdentifier, getName, getName, getValueMrefValueCollection, getValueMrefValueCollection, set__Type, setId, setIdentifier, setName, setValueMrefValueCollection

Methods inherited from class org.molgenis.util.AbstractEntity

getLabelValue, getValues, isObjectRepresentation, isReadonly, set, set, setReadonly, setValuesFromString, string2date

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.molgenis.util.Entity

getLabelValue, getValues, isReadonly, set, set, setReadonly

Field Detail

CHROMOSOME

public static final String CHROMOSOME

See Also:

Constant Field Values

CHROMOSOME_IDENTIFIER

public static final String CHROMOSOME_IDENTIFIER

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

DESCRIPTION

public static final String DESCRIPTION

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

TRACK_IDENTIFIER

public static final String TRACK_IDENTIFIER

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

Variant

public Variant()

Variant

public Variant(Variant copyMe)
        throws Exception

copy constructor

Throws:

Exception

Method Detail

query

public static Query<? extends Variant> query(Database db)

Shorthand for db.query(Variant.class).

find

public static List<? extends Variant> find(Database db,
                           QueryRule... rules)
                                    throws DatabaseException

Shorthand for db.find(Variant.class, org.molgenis.framework.db.QueryRule ... rules).

Throws:

DatabaseException

findById

public static Variant findById(Database db,
               Integer id)
                        throws DatabaseException

Throws:

DatabaseException

findByIdentifier

public static Variant findByIdentifier(Database db,
                       String identifier)
                                throws DatabaseException

Throws:

DatabaseException

getChromosome

public Chromosome getChromosome()

Get the Reference to the chromosome this position belongs to..

Specified by:

getChromosome in interface Locus

Returns:

chromosome.

getChromosome

@Deprecated
public Chromosome getChromosome(Database db)

Deprecated.

setChromosome

public void setChromosome(Chromosome chromosome)

Set the Reference to the chromosome this position belongs to..

Specified by:

setChromosome in interface Locus

Parameters:

chromosome -

setChromosome_Id

public void setChromosome_Id(Integer chromosome_id)

Set foreign key for field chromosome. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

Specified by:

setChromosome_Id in interface Locus

setChromosome

public void setChromosome(Integer chromosome_id)

getChromosome_Id

public Integer getChromosome_Id()

Specified by:

getChromosome_Id in interface Locus

getChromosome_Identifier

public String getChromosome_Identifier()

Get a pretty label Identifier for cross reference Chromosome to Chromosome.Id.

Specified by:

getChromosome_Identifier in interface Locus

setChromosome_Identifier

public void setChromosome_Identifier(String chromosome_Identifier)

Set a pretty label for cross reference Chromosome to Chromosome.Id. Implies setChromosome(null) until save

Specified by:

setChromosome_Identifier in interface Locus

getCM

public Double getCM()

Get the genetic map position in centi morgan (cM)..

Specified by:

getCM in interface Locus

Returns:

cM.

getCM

@Deprecated
public Double getCM(Database db)

Deprecated.

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.

getBpStart

@Deprecated
public Long getBpStart(Database db)

Deprecated.

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.

getBpEnd

@Deprecated
public Long getBpEnd(Database db)

Deprecated.

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.

getSeq

@Deprecated
public String getSeq(Database db)

Deprecated.

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.

getSymbol

@Deprecated
public String getSymbol(Database db)

Deprecated.

setSymbol

public void setSymbol(String symbol)

Set the todo.

Specified by:

setSymbol in interface Locus

Parameters:

symbol -

getMutationPosition

public Integer getMutationPosition()

Get the MutationPosition.

Returns:

mutationPosition.

getMutationPosition

@Deprecated
public Integer getMutationPosition(Database db)

Deprecated.

setMutationPosition

public void setMutationPosition(Integer mutationPosition)

Set the MutationPosition.

Parameters:

mutationPosition -

getCdnaPosition

public Integer getCdnaPosition()

Get the CdnaPosition.

Returns:

cdnaPosition.

getCdnaPosition

@Deprecated
public Integer getCdnaPosition(Database db)

Deprecated.

setCdnaPosition

public void setCdnaPosition(Integer cdnaPosition)

Set the CdnaPosition.

Parameters:

cdnaPosition -

getAaPosition

public Integer getAaPosition()

Get the AaPosition.

Returns:

aaPosition.

getAaPosition

@Deprecated
public Integer getAaPosition(Database db)

Deprecated.

setAaPosition

public void setAaPosition(Integer aaPosition)

Set the AaPosition.

Parameters:

aaPosition -

getVariantLength

public Integer getVariantLength()

Get the VariantLength.

Returns:

variantLength.

getVariantLength

@Deprecated
public Integer getVariantLength(Database db)

Deprecated.

setVariantLength

public void setVariantLength(Integer variantLength)

Set the VariantLength.

Parameters:

variantLength -

getEvent

public String getEvent()

Get the Event.

Returns:

event.

getEvent

@Deprecated
public String getEvent(Database db)

Deprecated.

setEvent

public void setEvent(String event)

Set the Event.

Parameters:

event -

getDescription

public String getDescription()

Get the Description.

Overrides:

getDescription in class Characteristic

Returns:

description.

getDescription

@Deprecated
public String getDescription(Database db)

Deprecated.

Overrides:

getDescription in class Characteristic

setDescription

public void setDescription(String description)

Set the Description.

Overrides:

setDescription in class Characteristic

Parameters:

description -

getNtChange

public String getNtChange()

Get the NtChange.

Returns:

ntChange.

getNtChange

@Deprecated
public String getNtChange(Database db)

Deprecated.

setNtChange

public void setNtChange(String ntChange)

Set the NtChange.

Parameters:

ntChange -

getCodonchange

public String getCodonchange()

Get the Codonchange.

Returns:

codonchange.

getCodonchange

@Deprecated
public String getCodonchange(Database db)

Deprecated.

setCodonchange

public void setCodonchange(String codonchange)

Set the Codonchange.

Parameters:

codonchange -

getCdnaNotation

public String getCdnaNotation()

Get the CdnaNotation.

Returns:

cdnaNotation.

getCdnaNotation

@Deprecated
public String getCdnaNotation(Database db)

Deprecated.

setCdnaNotation

public void setCdnaNotation(String cdnaNotation)

Set the CdnaNotation.

Parameters:

cdnaNotation -

getGdnaNotation

public String getGdnaNotation()

Get the GdnaNotation.

Returns:

gdnaNotation.

getGdnaNotation

@Deprecated
public String getGdnaNotation(Database db)

Deprecated.

setGdnaNotation

public void setGdnaNotation(String gdnaNotation)

Set the GdnaNotation.

Parameters:

gdnaNotation -

getAaNotation

public String getAaNotation()

Get the AaNotation.

Returns:

aaNotation.

getAaNotation

@Deprecated
public String getAaNotation(Database db)

Deprecated.

setAaNotation

public void setAaNotation(String aaNotation)

Set the AaNotation.

Parameters:

aaNotation -

getExon

public String getExon()

Get the Exon.

Returns:

exon.

getExon

@Deprecated
public String getExon(Database db)

Deprecated.

setExon

public void setExon(String exon)

Set the Exon.

Parameters:

exon -

getConsequence

public String getConsequence()

Get the Consequence.

Returns:

consequence.

getConsequence

@Deprecated
public String getConsequence(Database db)

Deprecated.

setConsequence

public void setConsequence(String consequence)

Set the Consequence.

Parameters:

consequence -

getInheritance

public String getInheritance()

Get the Inheritance.

Returns:

inheritance.

getInheritance

@Deprecated
public String getInheritance(Database db)

Deprecated.

setInheritance

public void setInheritance(String inheritance)

Set the Inheritance.

Parameters:

inheritance -

getReportedSNP

public Boolean getReportedSNP()

Get the ReportedSNP.

Returns:

reportedSNP.

getReportedSNP

@Deprecated
public Boolean getReportedSNP(Database db)

Deprecated.

setReportedSNP

public void setReportedSNP(Boolean reportedSNP)

Set the ReportedSNP.

Parameters:

reportedSNP -

getEffectOnSplicing

public Boolean getEffectOnSplicing()

Get the EffectOnSplicing.

Returns:

effectOnSplicing.

getEffectOnSplicing

@Deprecated
public Boolean getEffectOnSplicing(Database db)

Deprecated.

setEffectOnSplicing

public void setEffectOnSplicing(Boolean effectOnSplicing)

Set the EffectOnSplicing.

Parameters:

effectOnSplicing -

getPathogenicity

public String getPathogenicity()

Get the Pathogenicity.

Returns:

pathogenicity.

getPathogenicity

@Deprecated
public String getPathogenicity(Database db)

Deprecated.

setPathogenicity

public void setPathogenicity(String pathogenicity)

Set the Pathogenicity.

Parameters:

pathogenicity -

getGene

public String getGene()

Get the Gene.

Returns:

gene.

getGene

@Deprecated
public String getGene(Database db)

Deprecated.

setGene

public void setGene(String gene)

Set the Gene.

Parameters:

gene -

getIdMutation

public Integer getIdMutation()

Get the IdMutation.

Returns:

idMutation.

getIdMutation

@Deprecated
public Integer getIdMutation(Database db)

Deprecated.

setIdMutation

public void setIdMutation(Integer idMutation)

Set the IdMutation.

Parameters:

idMutation -

getDetailsForMutation

public String getDetailsForMutation()

Get the DetailsForMutation.

Returns:

detailsForMutation.

getDetailsForMutation

@Deprecated
public String getDetailsForMutation(Database db)

Deprecated.

setDetailsForMutation

public void setDetailsForMutation(String detailsForMutation)

Set the DetailsForMutation.

Parameters:

detailsForMutation -

getTrack

public Track getTrack()

Get the Track.

Returns:

track.

getTrack

@Deprecated
public Track getTrack(Database db)

Deprecated.

setTrack

public void setTrack(Track track)

Set the Track.

Parameters:

track -

setTrack_Id

public void setTrack_Id(Integer track_id)

Set foreign key for field track. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

setTrack

public void setTrack(Integer track_id)

getTrack_Id

public Integer getTrack_Id()

getTrack_Identifier

public String getTrack_Identifier()

Get a pretty label Identifier for cross reference Track to Track.Id.

setTrack_Identifier

public void setTrack_Identifier(String track_Identifier)

Set a pretty label for cross reference Track to Track.Id. Implies setTrack(null) until save

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

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Overrides:

validate in class ObservationTarget

Throws:

DatabaseException

set

public void set(Entity entity,
       boolean strict)
         throws Exception

Specified by:

set in interface Entity

Overrides:

set in class ObservationTarget

Throws:

Exception

toString

public String toString()

Overrides:

toString in class ObservationTarget

toString

public String toString(boolean verbose)

Overrides:

toString in class ObservationTarget

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of Variant.

Specified by:

getFields in interface Entity

Overrides:

getFields in class ObservationTarget

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

Overrides:

getFields in class ObservationTarget

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

Overrides:

getIdField in class ObservationTarget

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

Overrides:

getLabelFields in class ObservationTarget

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

Overrides:

getFields in class ObservationTarget

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

Overrides:

getIdValue in class ObservationTarget

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

Overrides:

getXrefIdFieldName in class ObservationTarget

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class ObservationTarget

create

public Variant create(Entity entity)
               throws Exception

Specified by:

create in interface Entity

Overrides:

create in class ObservationTarget

Throws:

Exception

equals

public boolean equals(Object obj)

Overrides:

equals in class ObservationTarget

hashCode

public int hashCode()

Overrides:

hashCode in class ObservationTarget