org.molgenis.omx.observ.target

Class Species

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.target.OntologyTerm

org.molgenis.omx.observ.target.Species

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

@Entity
public class Species
extends OntologyTerm

Species: Ontology terms for species. E.g. Arabidopsis thaliana. DISCUSSION: should we avoid subclasses of OntologyTerm and instead make a 'tag' filter on terms so we can make pulldowns context dependent (e.g. to only show particular subqueries of ontologies). .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	ID

Fields inherited from class org.molgenis.omx.observ.target.OntologyTerm

DEFINITION, ONTOLOGY, ONTOLOGY_IDENTIFIER, TERMACCESSION

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

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
Species	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Species>	find(Database db, QueryRule... rules) Shorthand for db.find(Species.class, org.molgenis.framework.db.QueryRule ...
static Species	findById(Database db, Integer id)
static Species	findByIdentifier(Database db, String identifier)
static Species	findByOntologyTermAccession(Database db, Integer ontology, String termAccession)
Object	get(String name) Generic getter.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Species.
String	getFields(String sep) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Species>	query(Database db) Shorthand for db.query(Species.class).
void	set(Entity entity, boolean strict)
String	toString()
String	toString(boolean verbose)
void	validate()

Methods inherited from class org.molgenis.omx.observ.target.OntologyTerm

getDefinition, getDefinition, getDefinitionsObservableFeatureCollection, getDefinitionsObservableFeatureCollection, getOntology_Id, getOntology_Identifier, getOntology, getOntology, getTermAccession, getTermAccession, setDefinition, setDefinitionsObservableFeatureCollection, setOntology_Id, setOntology_Identifier, setOntology, setOntology, setTermAccession

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

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

Species

public Species()

Species

public Species(Species copyMe)
        throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(Species.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

findByOntologyTermAccession

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

Throws:

DatabaseException

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 OntologyTerm

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Overrides:

validate in class OntologyTerm

Throws:

DatabaseException

set

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

Specified by:

set in interface Entity

Overrides:

set in class OntologyTerm

Throws:

Exception

toString

public String toString()

Overrides:

toString in class OntologyTerm

toString

public String toString(boolean verbose)

Overrides:

toString in class OntologyTerm

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of Species.

Specified by:

getFields in interface Entity

Overrides:

getFields in class OntologyTerm

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

Overrides:

getFields in class OntologyTerm

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

Overrides:

getIdField in class OntologyTerm

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

Overrides:

getLabelFields in class OntologyTerm

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

Overrides:

getFields in class OntologyTerm

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

Overrides:

getIdValue in class OntologyTerm

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

Overrides:

getXrefIdFieldName in class OntologyTerm

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class OntologyTerm

create

public Species create(Entity entity)
               throws Exception

Specified by:

create in interface Entity

Overrides:

create in class OntologyTerm

Throws:

Exception

equals

public boolean equals(Object obj)

Overrides:

equals in class OntologyTerm

hashCode

public int hashCode()

Overrides:

hashCode in class OntologyTerm