org.molgenis.omx.xgap

Class Chromosome

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservationTarget

org.molgenis.omx.xgap.Chromosome

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

@Entity
public class Chromosome
extends ObservationTarget

Chromosome: .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	BPLENGTH
static String	ID
static String	ISAUTOSOMAL
static String	ORDERNR
static String	SPECIES
static String	SPECIES_IDENTIFIER

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

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
Chromosome	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Chromosome>	find(Database db, QueryRule... rules) Shorthand for db.find(Chromosome.class, org.molgenis.framework.db.QueryRule ...
static Chromosome	findById(Database db, Integer id)
static Chromosome	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
Integer	getBpLength() Get the Lenght of the chromsome in base pairs..
Integer	getBpLength(Database db) Deprecated.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Chromosome.
String	getFields(String sep) Deprecated.
String	getIdField()
Object	getIdValue()
Boolean	getIsAutosomal() Get the Is 'yes' when number of chromosomes is equal in male and female individuals, i.e., if not a sex chromosome..
Boolean	getIsAutosomal(Database db) Deprecated.
List<String>	getLabelFields()
Integer	getOrderNr() Get the orderNr.
Integer	getOrderNr(Database db) Deprecated.
Integer	getSpecies_Id()
String	getSpecies_Identifier() Get a pretty label Identifier for cross reference Species to OntologyTerm.Id.
OntologyTerm	getSpecies() Get the Reference to the species this chromosome belongs to..
OntologyTerm	getSpecies(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Chromosome>	query(Database db) Shorthand for db.query(Chromosome.class).
void	set(Entity entity, boolean strict)
void	setBpLength(Integer bpLength) Set the Lenght of the chromsome in base pairs..
void	setIsAutosomal(Boolean isAutosomal) Set the Is 'yes' when number of chromosomes is equal in male and female individuals, i.e., if not a sex chromosome..
void	setOrderNr(Integer orderNr) Set the orderNr.
void	setSpecies_Id(Integer species_id) Set foreign key for field species.
void	setSpecies_Identifier(String species_Identifier) Set a pretty label for cross reference Species to OntologyTerm.Id.
void	setSpecies(Integer species_id)
void	setSpecies(OntologyTerm species) Set the Reference to the species this chromosome belongs to..
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

ORDERNR

public static final String ORDERNR

See Also:

Constant Field Values

ISAUTOSOMAL

public static final String ISAUTOSOMAL

See Also:

Constant Field Values

BPLENGTH

public static final String BPLENGTH

See Also:

Constant Field Values

SPECIES

public static final String SPECIES

See Also:

Constant Field Values

SPECIES_IDENTIFIER

public static final String SPECIES_IDENTIFIER

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

Chromosome

public Chromosome()

Chromosome

public Chromosome(Chromosome copyMe)
           throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(Chromosome.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

getOrderNr

public Integer getOrderNr()

Get the orderNr.

Returns:

orderNr.

getOrderNr

@Deprecated
public Integer getOrderNr(Database db)

Deprecated.

setOrderNr

public void setOrderNr(Integer orderNr)

Set the orderNr.

Parameters:

orderNr -

getIsAutosomal

public Boolean getIsAutosomal()

Get the Is 'yes' when number of chromosomes is equal in male and female individuals, i.e., if not a sex chromosome..

Returns:

isAutosomal.

getIsAutosomal

@Deprecated
public Boolean getIsAutosomal(Database db)

Deprecated.

setIsAutosomal

public void setIsAutosomal(Boolean isAutosomal)

Set the Is 'yes' when number of chromosomes is equal in male and female individuals, i.e., if not a sex chromosome..

Parameters:

isAutosomal -

getBpLength

public Integer getBpLength()

Get the Lenght of the chromsome in base pairs..

Returns:

bpLength.

getBpLength

@Deprecated
public Integer getBpLength(Database db)

Deprecated.

setBpLength

public void setBpLength(Integer bpLength)

Set the Lenght of the chromsome in base pairs..

Parameters:

bpLength -

getSpecies

public OntologyTerm getSpecies()

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

Returns:

species.

getSpecies

@Deprecated
public OntologyTerm getSpecies(Database db)

Deprecated.

setSpecies

public void setSpecies(OntologyTerm species)

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

Parameters:

species -

setSpecies_Id

public void setSpecies_Id(Integer species_id)

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

setSpecies

public void setSpecies(Integer species_id)

getSpecies_Id

public Integer getSpecies_Id()

getSpecies_Identifier

public String getSpecies_Identifier()

Get a pretty label Identifier for cross reference Species to OntologyTerm.Id.

setSpecies_Identifier

public void setSpecies_Identifier(String species_Identifier)

Set a pretty label for cross reference Species to OntologyTerm.Id. Implies setSpecies(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 Chromosome.

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 Chromosome 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