org.molgenis.omx.observ.target

Class OntologyTerm

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.target.OntologyTerm

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

Direct Known Subclasses:

Accession, PersonRole, Species

@Entity
public class OntologyTerm
extends Characteristic

OntologyTerm: OntologyTerm defines a single entry (term) from an ontology or a controlled vocabulary (defined by Ontology). The identifier is the ontology term is unique. E.g. 'NCI:Antigen Gene'. Other data entities can reference to this OntologyTerm to harmonize naming of concepts. If no suitable ontology term exists then one can define new terms locally (in which case there is no formal accession for the term limiting its use for cross-Investigation queries). .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFINITION
static String	ID
static String	ONTOLOGY
static String	ONTOLOGY_IDENTIFIER
static String	TERMACCESSION

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

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
OntologyTerm	create(Entity entity)
boolean	equals(Object obj)
static List<? extends OntologyTerm>	find(Database db, QueryRule... rules) Shorthand for db.find(OntologyTerm.class, org.molgenis.framework.db.QueryRule ...
static OntologyTerm	findById(Database db, Integer id)
static OntologyTerm	findByIdentifier(Database db, String identifier)
static OntologyTerm	findByOntologyTermAccession(Database db, Integer ontology, String termAccession)
Object	get(String name) Generic getter.
String	getDefinition() Get the (Optional) The definition of the term..
String	getDefinition(Database db) Deprecated.
Collection<ObservableFeature>	getDefinitionsObservableFeatureCollection()
Collection<ObservableFeature>	getDefinitionsObservableFeatureCollection(Database db)
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of OntologyTerm.
String	getFields(String sep) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
Integer	getOntology_Id()
String	getOntology_Identifier() Get a pretty label Identifier for cross reference Ontology to Ontology.Id.
Ontology	getOntology() Get the (Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from..
Ontology	getOntology(Database db) Deprecated.
String	getTermAccession() Get the (Optional) The accession number assigned to the ontology term in its source ontology.
String	getTermAccession(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends OntologyTerm>	query(Database db) Shorthand for db.query(OntologyTerm.class).
void	set(Entity entity, boolean strict)
void	setDefinition(String definition) Set the (Optional) The definition of the term..
void	setDefinitionsObservableFeatureCollection(Collection<ObservableFeature> collection)
void	setOntology_Id(Integer ontology_id) Set foreign key for field ontology.
void	setOntology_Identifier(String ontology_Identifier) Set a pretty label for cross reference Ontology to Ontology.Id.
void	setOntology(Integer ontology_id)
void	setOntology(Ontology ontology) Set the (Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from..
void	setTermAccession(String termAccession) Set the (Optional) The accession number assigned to the ontology term in its source ontology.
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

ONTOLOGY

public static final String ONTOLOGY

See Also:

Constant Field Values

ONTOLOGY_IDENTIFIER

public static final String ONTOLOGY_IDENTIFIER

See Also:

Constant Field Values

TERMACCESSION

public static final String TERMACCESSION

See Also:

Constant Field Values

DEFINITION

public static final String DEFINITION

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

OntologyTerm

public OntologyTerm()

OntologyTerm

public OntologyTerm(OntologyTerm copyMe)
             throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(OntologyTerm.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

findByOntologyTermAccession

public static OntologyTerm findByOntologyTermAccession(Database db,
                                       Integer ontology,
                                       String termAccession)
                                                throws DatabaseException

Throws:

DatabaseException

getOntology

public Ontology getOntology()

Get the (Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from..

Returns:

ontology.

getOntology

@Deprecated
public Ontology getOntology(Database db)

Deprecated.

setOntology

public void setOntology(Ontology ontology)

Set the (Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from..

Parameters:

ontology -

setOntology_Id

public void setOntology_Id(Integer ontology_id)

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

setOntology

public void setOntology(Integer ontology_id)

getOntology_Id

public Integer getOntology_Id()

getOntology_Identifier

public String getOntology_Identifier()

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

setOntology_Identifier

public void setOntology_Identifier(String ontology_Identifier)

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

getTermAccession

public String getTermAccession()

Get the (Optional) The accession number assigned to the ontology term in its source ontology. If empty it is assumed to be a locally defined term..

Returns:

termAccession.

getTermAccession

@Deprecated
public String getTermAccession(Database db)

Deprecated.

setTermAccession

public void setTermAccession(String termAccession)

Set the (Optional) The accession number assigned to the ontology term in its source ontology. If empty it is assumed to be a locally defined term..

Parameters:

termAccession -

getDefinition

public String getDefinition()

Get the (Optional) The definition of the term..

Returns:

definition.

getDefinition

@Deprecated
public String getDefinition(Database db)

Deprecated.

setDefinition

public void setDefinition(String definition)

Set the (Optional) The definition of the term..

Parameters:

definition -

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 Characteristic

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Overrides:

validate in class Characteristic

Throws:

DatabaseException

set

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

Specified by:

set in interface Entity

Overrides:

set in class Characteristic

Throws:

Exception

toString

public String toString()

Overrides:

toString in class Characteristic

toString

public String toString(boolean verbose)

Overrides:

toString in class Characteristic

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of OntologyTerm.

Specified by:

getFields in interface Entity

Overrides:

getFields in class Characteristic

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

Overrides:

getFields in class Characteristic

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

Overrides:

getIdField in class Characteristic

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

Overrides:

getLabelFields in class Characteristic

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

Overrides:

getFields in class Characteristic

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

Overrides:

getIdValue in class Characteristic

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

Overrides:

getXrefIdFieldName in class Characteristic

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class Characteristic

create

public OntologyTerm create(Entity entity)
                    throws Exception

Specified by:

create in interface Entity

Overrides:

create in class Characteristic

Throws:

Exception

getDefinitionsObservableFeatureCollection

public Collection<ObservableFeature> getDefinitionsObservableFeatureCollection()

getDefinitionsObservableFeatureCollection

public Collection<ObservableFeature> getDefinitionsObservableFeatureCollection(Database db)

setDefinitionsObservableFeatureCollection

public void setDefinitionsObservableFeatureCollection(Collection<ObservableFeature> collection)

equals

public boolean equals(Object obj)

Overrides:

equals in class Characteristic

hashCode

public int hashCode()

Overrides:

hashCode in class Characteristic