org.molgenis.omx.observ

Class Characteristic

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

Direct Known Subclasses:

Category, DataSet, Institute, ObservableFeature, ObservationTarget, OntologyTerm, Person, Protocol

@Entity
public class Characteristic
extends AbstractEntity
implements Identifiable

Characteristic: Characteristics are yes-no statements about things in the world. These can be used as part of an observation, as parameter of ObservableFeature ('measuredCharacteristic'). For example: 'What is allele of [Marker]', here the [Marker] is a characteristic. Also, Characteristics can be used as target of observation. Typical examples are 'Individual' or 'Panel'. But also 'Marker' can be an Target when asked the question 'QTL p-value for [phenotype]': here both target and feature are characteristic, for example 'leave count' (phenotype characteristic) and 'PVV4' (marker characteristic). .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	__TYPE
static String	DESCRIPTION
static String	ID
static String	IDENTIFIER
static String	NAME

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
Characteristic	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Characteristic>	find(Database db, QueryRule... rules) Shorthand for db.find(Characteristic.class, org.molgenis.framework.db.QueryRule ...
static Characteristic	findById(Database db, Integer id)
static Characteristic	findByIdentifier(Database db, String identifier)
String	get__Type() Get the Subtypes have to be set to allow searching.
String	get__Type(Database db) Deprecated.
String	get__TypeLabel() Get tha label for enum __Type.
List<ValueLabel>	get__TypeOptions() __Type is enum.
Object	get(String name) Generic getter.
String	getDescription() Get the (Optional) Rudimentary meta data about the observable feature.
String	getDescription(Database db) Deprecated.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Characteristic.
String	getFields(String sep) Deprecated.
Integer	getId() Get the automatically generated internal id, only for internal use..
String	getIdentifier() Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
String	getIdentifier(Database db) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
String	getName() Get the human readible name, not necessary unique..
String	getName(Database db) Deprecated.
Collection<MrefValue>	getValueMrefValueCollection()
Collection<MrefValue>	getValueMrefValueCollection(Database db)
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Characteristic>	query(Database db) Shorthand for db.query(Characteristic.class).
void	set__Type(String __Type) Set the Subtypes have to be set to allow searching.
void	set(Entity entity, boolean strict)
void	setDescription(String description) Set the (Optional) Rudimentary meta data about the observable feature.
void	setId(Integer id) Set the automatically generated internal id, only for internal use..
void	setIdentifier(String identifier) Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
void	setName(String name) Set the human readible name, not necessary unique..
void	setValueMrefValueCollection(Collection<MrefValue> collection)
String	toString()
String	toString(boolean verbose)
void	validate()

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

ID

public static final String ID

See Also:

Constant Field Values

IDENTIFIER

public static final String IDENTIFIER

See Also:

Constant Field Values

NAME

public static final String NAME

See Also:

Constant Field Values

__TYPE

public static final String __TYPE

See Also:

Constant Field Values

DESCRIPTION

public static final String DESCRIPTION

See Also:

Constant Field Values

Constructor Detail

Characteristic

public Characteristic()

Characteristic

public Characteristic(Characteristic copyMe)
               throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(Characteristic.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

getId

public Integer getId()

Get the automatically generated internal id, only for internal use..

Specified by:

getId in interface Autoid

Returns:

id.

setId

public void setId(Integer id)

Set the automatically generated internal id, only for internal use..

Specified by:

setId in interface Autoid

Parameters:

id -

getIdentifier

public String getIdentifier()

Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234.

Specified by:

getIdentifier in interface Identifiable

Returns:

identifier.

getIdentifier

@Deprecated
public String getIdentifier(Database db)

Deprecated.

setIdentifier

public void setIdentifier(String identifier)

Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234.

Specified by:

setIdentifier in interface Identifiable

Parameters:

identifier -

getName

public String getName()

Get the human readible name, not necessary unique..

Specified by:

getName in interface Identifiable

Returns:

name.

getName

@Deprecated
public String getName(Database db)

Deprecated.

setName

public void setName(String name)

Set the human readible name, not necessary unique..

Specified by:

setName in interface Identifiable

Parameters:

name -

get__Type

public String get__Type()

Get the Subtypes have to be set to allow searching.

Overrides:

get__Type in class AbstractEntity

Returns:

__Type.

get__Type

@Deprecated
public String get__Type(Database db)

Deprecated.

set__Type

public void set__Type(String __Type)

Set the Subtypes have to be set to allow searching.

Overrides:

set__Type in class AbstractEntity

Parameters:

__Type -

get__TypeLabel

public String get__TypeLabel()

Get tha label for enum __Type.

Overrides:

get__TypeLabel in class AbstractEntity

get__TypeOptions

public List<ValueLabel> get__TypeOptions()

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

Overrides:

get__TypeOptions in class AbstractEntity

getDescription

public String getDescription()

Get the (Optional) Rudimentary meta data about the observable feature. Use of ontology terms references to establish unambigious descriptions is recommended.

Returns:

description.

getDescription

@Deprecated
public String getDescription(Database db)

Deprecated.

setDescription

public void setDescription(String description)

Set the (Optional) Rudimentary meta data about the observable feature. Use of ontology terms references to establish unambigious descriptions is recommended.

Parameters:

description -

get

public Object get(String name)

Generic getter. Get the property by using the name.

Specified by:

get in interface Entity

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Throws:

DatabaseException

set

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

Specified by:

set in interface Entity

Throws:

Exception

toString

public String toString()

Overrides:

toString in class Object

toString

public String toString(boolean verbose)

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of Characteristic.

Specified by:

getFields in interface Entity

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class AbstractEntity

create

public Characteristic create(Entity entity)
                      throws Exception

Specified by:

create in interface Entity

Throws:

Exception

getValueMrefValueCollection

public Collection<MrefValue> getValueMrefValueCollection()

getValueMrefValueCollection

public Collection<MrefValue> getValueMrefValueCollection(Database db)

setValueMrefValueCollection

public void setValueMrefValueCollection(Collection<MrefValue> collection)

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object