org.molgenis.omx.xgap

Class SNP

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservationTarget

org.molgenis.omx.xgap.Marker

org.molgenis.omx.xgap.SNP

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Locus, Entity

@Entity
public class SNP
extends Marker

SNP: 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	ID
static String	POLYMORPHISM
static String	POLYMORPHISM_IDENTIFIER
static String	STATUS

Fields inherited from class org.molgenis.omx.xgap.Marker

BPEND, BPSTART, CHROMOSOME, CHROMOSOME_IDENTIFIER, CM, REPORTSFOR, REPORTSFOR_IDENTIFIER, SEQ, SYMBOL

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

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
SNP	create(Entity entity)
boolean	equals(Object obj)
static List<? extends SNP>	find(Database db, QueryRule... rules) Shorthand for db.find(SNP.class, org.molgenis.framework.db.QueryRule ...
static SNP	findById(Database db, Integer id)
static SNP	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of SNP.
String	getFields(String sep) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
List<Integer>	getPolymorphism_Id()
List<String>	getPolymorphism_Identifier() Get a pretty label for cross reference Polymorphism to Polymorphism.Id.
List<Polymorphism>	getPolymorphism() Get the The polymorphism that belongs to this SNP..
List<Polymorphism>	getPolymorphism(Database db) Deprecated.
String	getStatus() Get the The status of this SNP, eg 'confirmed'..
String	getStatus(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends SNP>	query(Database db) Shorthand for db.query(SNP.class).
void	set(Entity entity, boolean strict)
void	setPolymorphism_Id(Integer... polymorphism)
void	setPolymorphism_Id(List<Integer> polymorphism_id) Set foreign key for field polymorphism.
void	setPolymorphism_Identifier(List<String> polymorphism_Identifier) Update the foreign key Polymorphism This sets polymorphism to null until next database transaction.
void	setPolymorphism(List<Polymorphism> polymorphism) Set the The polymorphism that belongs to this SNP..
void	setPolymorphism(Polymorphism... polymorphism)
void	setStatus(String status) Set the The status of this SNP, eg 'confirmed'..
String	toString()
String	toString(boolean verbose)
void	validate()

Methods inherited from class org.molgenis.omx.xgap.Marker

getBpEnd, getBpEnd, getBpStart, getBpStart, getChromosome_Id, getChromosome_Identifier, getChromosome, getChromosome, getCM, getCM, getReportsFor_Id, getReportsFor_Identifier, getReportsFor, getReportsFor, getReportsForMarkerCollection, getReportsForMarkerCollection, getSeq, getSeq, getSymbol, getSymbol, setBpEnd, setBpStart, setChromosome_Id, setChromosome_Identifier, setChromosome, setChromosome, setCM, setReportsFor_Id, setReportsFor_Id, setReportsFor_Identifier, setReportsFor, setReportsFor, setReportsForMarkerCollection, setSeq, setSymbol

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

get__Type, get__Type, get__TypeLabel, get__TypeOptions, getDescription, getDescription, getId, getIdentifier, getIdentifier, getName, getName, getValueMrefValueCollection, getValueMrefValueCollection, set__Type, setDescription, 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

STATUS

public static final String STATUS

See Also:

Constant Field Values

POLYMORPHISM

public static final String POLYMORPHISM

See Also:

Constant Field Values

POLYMORPHISM_IDENTIFIER

public static final String POLYMORPHISM_IDENTIFIER

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

SNP

public SNP()

SNP

public SNP(SNP copyMe)
    throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(SNP.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

getStatus

public String getStatus()

Get the The status of this SNP, eg 'confirmed'..

Returns:

status.

getStatus

@Deprecated
public String getStatus(Database db)

Deprecated.

setStatus

public void setStatus(String status)

Set the The status of this SNP, eg 'confirmed'..

Parameters:

status -

getPolymorphism

public List<Polymorphism> getPolymorphism()

Get the The polymorphism that belongs to this SNP..

Returns:

polymorphism.

getPolymorphism

@Deprecated
public List<Polymorphism> getPolymorphism(Database db)

Deprecated.

setPolymorphism

public void setPolymorphism(List<Polymorphism> polymorphism)

Set the The polymorphism that belongs to this SNP..

Parameters:

polymorphism -

setPolymorphism_Id

public void setPolymorphism_Id(Integer... polymorphism)

setPolymorphism

public void setPolymorphism(Polymorphism... polymorphism)

setPolymorphism_Id

public void setPolymorphism_Id(List<Integer> polymorphism_id)

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

getPolymorphism_Id

public List<Integer> getPolymorphism_Id()

getPolymorphism_Identifier

public List<String> getPolymorphism_Identifier()

Get a pretty label for cross reference Polymorphism to Polymorphism.Id.

setPolymorphism_Identifier

public void setPolymorphism_Identifier(List<String> polymorphism_Identifier)

Update the foreign key Polymorphism This sets polymorphism to null until next database transaction.

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 Marker

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Overrides:

validate in class Marker

Throws:

DatabaseException

set

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

Specified by:

set in interface Entity

Overrides:

set in class Marker

Throws:

Exception

toString

public String toString()

Overrides:

toString in class Marker

toString

public String toString(boolean verbose)

Overrides:

toString in class Marker

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of SNP.

Specified by:

getFields in interface Entity

Overrides:

getFields in class Marker

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

Overrides:

getFields in class Marker

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

Overrides:

getIdField in class Marker

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

Overrides:

getLabelFields in class Marker

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

Overrides:

getFields in class Marker

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

Overrides:

getIdValue in class Marker

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

Overrides:

getXrefIdFieldName in class Marker

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class Marker

create

public SNP create(Entity entity)
           throws Exception

Specified by:

create in interface Entity

Overrides:

create in class Marker

Throws:

Exception

equals

public boolean equals(Object obj)

Overrides:

equals in class Marker

hashCode

public int hashCode()

Overrides:

hashCode in class Marker