org.molgenis.omx.xgap

Class Polymorphism

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservationTarget

org.molgenis.omx.xgap.Polymorphism

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

@Entity
public class Polymorphism
extends ObservationTarget

Polymorphism: The difference of a single base discovered between two sequenced individuals..

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	BASE
static String	ID
static String	VALUE

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

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
Polymorphism	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Polymorphism>	find(Database db, QueryRule... rules) Shorthand for db.find(Polymorphism.class, org.molgenis.framework.db.QueryRule ...
static Polymorphism	findById(Database db, Integer id)
static Polymorphism	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
String	getBase() Get the The affected DNA base.
String	getBase(Database db) Deprecated.
String	getBaseLabel() Get tha label for enum Base.
List<ValueLabel>	getBaseOptions() Base is enum.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Polymorphism.
String	getFields(String sep) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
Collection<SNP>	getPolymorphismSNPCollection()
Collection<SNP>	getPolymorphismSNPCollection(Database db)
String	getValue() Get the The strain/genotype for which this polymorphism was discovered.
String	getValue(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Polymorphism>	query(Database db) Shorthand for db.query(Polymorphism.class).
void	set(Entity entity, boolean strict)
void	setBase(String base) Set the The affected DNA base.
void	setPolymorphismSNPCollection(Collection<SNP> collection)
void	setValue(String value) Set the The strain/genotype for which this polymorphism was discovered.
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, 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

BASE

public static final String BASE

See Also:

Constant Field Values

VALUE

public static final String VALUE

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

Polymorphism

public Polymorphism()

Polymorphism

public Polymorphism(Polymorphism copyMe)
             throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(Polymorphism.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

getBase

public String getBase()

Get the The affected DNA base. Note that you can select the reference base here..

Returns:

base.

getBase

@Deprecated
public String getBase(Database db)

Deprecated.

setBase

public void setBase(String base)

Set the The affected DNA base. Note that you can select the reference base here..

Parameters:

base -

getBaseLabel

public String getBaseLabel()

Get tha label for enum Base.

getBaseOptions

public List<ValueLabel> getBaseOptions()

Base is enum. This method returns all available enum options.

getValue

public String getValue()

Get the The strain/genotype for which this polymorphism was discovered. E.g. 'N2' or 'CB4856'..

Returns:

value.

getValue

@Deprecated
public String getValue(Database db)

Deprecated.

setValue

public void setValue(String value)

Set the The strain/genotype for which this polymorphism was discovered. E.g. 'N2' or 'CB4856'..

Parameters:

value -

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 Polymorphism.

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 Polymorphism create(Entity entity)
                    throws Exception

Specified by:

create in interface Entity

Overrides:

create in class ObservationTarget

Throws:

Exception

getPolymorphismSNPCollection

public Collection<SNP> getPolymorphismSNPCollection()

getPolymorphismSNPCollection

public Collection<SNP> getPolymorphismSNPCollection(Database db)

setPolymorphismSNPCollection

public void setPolymorphismSNPCollection(Collection<SNP> collection)

equals

public boolean equals(Object obj)

Overrides:

equals in class ObservationTarget

hashCode

public int hashCode()

Overrides:

hashCode in class ObservationTarget