org.molgenis.omx.observ

Class ObservableFeature

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservableFeature

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

@Entity
public class ObservableFeature
extends Characteristic

ObservableFeature: ObservableFeature defines anything that can be observed.

In other words, ObservableFeature are the questions asked, e.g. 'What is Height?', 'What is Systolic blood pressure?', or 'Has blue eyes?'.

Some questions may be repeated for multiple characteristics. For example 'What is [MarkerAllele] observed?' can be applied to all elements of a MarkerSet, and 'What is [medicin codes] uses' can be applied to a set of Medicine codes. This can be specified using the measuredCharacteristic field.

The identifier of ObservableFeature is globally unique. It is recommended that each ObservableFeature is named according to a well-defined ontology term or database accession. .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	DATATYPE
static String	DEFINITIONS
static String	DEFINITIONS_IDENTIFIER
static String	ID
static String	TEMPORAL
static String	UNIT
static String	UNIT_IDENTIFIER

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

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
ObservableFeature	create(Entity entity)
boolean	equals(Object obj)
static List<? extends ObservableFeature>	find(Database db, QueryRule... rules) Shorthand for db.find(ObservableFeature.class, org.molgenis.framework.db.QueryRule ...
static ObservableFeature	findById(Database db, Integer id)
static ObservableFeature	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
String	getDataType() Get the (Optional) Reference to the technical data type.
String	getDataType(Database db) Deprecated.
String	getDataTypeLabel() Get tha label for enum DataType.
List<ValueLabel>	getDataTypeOptions() DataType is enum.
List<Integer>	getDefinitions_Id()
List<String>	getDefinitions_Identifier() Get a pretty label for cross reference Definitions to OntologyTerm.Id.
List<OntologyTerm>	getDefinitions() Get the The concept that is being measured in a specific way..
List<OntologyTerm>	getDefinitions(Database db) Deprecated.
Collection<Protocol>	getFeaturesProtocolCollection()
Collection<Protocol>	getFeaturesProtocolCollection(Database db)
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of ObservableFeature.
String	getFields(String sep) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
Collection<Protocol>	getRequiredFeaturesProtocolCollection()
Collection<Protocol>	getRequiredFeaturesProtocolCollection(Database db)
Boolean	getTemporal() Get the Whether this feature is time dependent and can have different values when measured on different times (e.g.
Boolean	getTemporal(Database db) Deprecated.
Integer	getUnit_Id()
String	getUnit_Identifier() Get a pretty label Identifier for cross reference Unit to OntologyTerm.Id.
OntologyTerm	getUnit() Get the (Optional) Reference to the well-defined measurement unit used to observe this feature (if feature is that concrete).
OntologyTerm	getUnit(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends ObservableFeature>	query(Database db) Shorthand for db.query(ObservableFeature.class).
void	set(Entity entity, boolean strict)
void	setDataType(String dataType) Set the (Optional) Reference to the technical data type.
void	setDefinitions_Id(Integer... definitions)
void	setDefinitions_Id(List<Integer> definitions_id) Set foreign key for field definitions.
void	setDefinitions_Identifier(List<String> definitions_Identifier) Update the foreign key Definitions This sets definitions to null until next database transaction.
void	setDefinitions(List<OntologyTerm> definitions) Set the The concept that is being measured in a specific way..
void	setDefinitions(OntologyTerm... definitions)
void	setFeaturesProtocolCollection(Collection<Protocol> collection)
void	setRequiredFeaturesProtocolCollection(Collection<Protocol> collection)
void	setTemporal(Boolean temporal) Set the Whether this feature is time dependent and can have different values when measured on different times (e.g.
void	setUnit_Id(Integer unit_id) Set foreign key for field unit.
void	setUnit_Identifier(String unit_Identifier) Set a pretty label for cross reference Unit to OntologyTerm.Id.
void	setUnit(Integer unit_id)
void	setUnit(OntologyTerm unit) Set the (Optional) Reference to the well-defined measurement unit used to observe this feature (if feature is that concrete).
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

UNIT

public static final String UNIT

See Also:

Constant Field Values

UNIT_IDENTIFIER

public static final String UNIT_IDENTIFIER

See Also:

Constant Field Values

DEFINITIONS

public static final String DEFINITIONS

See Also:

Constant Field Values

DEFINITIONS_IDENTIFIER

public static final String DEFINITIONS_IDENTIFIER

See Also:

Constant Field Values

DATATYPE

public static final String DATATYPE

See Also:

Constant Field Values

TEMPORAL

public static final String TEMPORAL

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

ObservableFeature

public ObservableFeature()

ObservableFeature

public ObservableFeature(ObservableFeature copyMe)
                  throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(ObservableFeature.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

getUnit

public OntologyTerm getUnit()

Get the (Optional) Reference to the well-defined measurement unit used to observe this feature (if feature is that concrete). E.g. mmHg.

Returns:

unit.

getUnit

@Deprecated
public OntologyTerm getUnit(Database db)

Deprecated.

setUnit

public void setUnit(OntologyTerm unit)

Set the (Optional) Reference to the well-defined measurement unit used to observe this feature (if feature is that concrete). E.g. mmHg.

Parameters:

unit -

setUnit_Id

public void setUnit_Id(Integer unit_id)

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

setUnit

public void setUnit(Integer unit_id)

getUnit_Id

public Integer getUnit_Id()

getUnit_Identifier

public String getUnit_Identifier()

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

setUnit_Identifier

public void setUnit_Identifier(String unit_Identifier)

Set a pretty label for cross reference Unit to OntologyTerm.Id. Implies setUnit(null) until save

getDefinitions

public List<OntologyTerm> getDefinitions()

Get the The concept that is being measured in a specific way..

Returns:

definitions.

getDefinitions

@Deprecated
public List<OntologyTerm> getDefinitions(Database db)

Deprecated.

setDefinitions

public void setDefinitions(List<OntologyTerm> definitions)

Set the The concept that is being measured in a specific way..

Parameters:

definitions -

setDefinitions_Id

public void setDefinitions_Id(Integer... definitions)

setDefinitions

public void setDefinitions(OntologyTerm... definitions)

setDefinitions_Id

public void setDefinitions_Id(List<Integer> definitions_id)

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

getDefinitions_Id

public List<Integer> getDefinitions_Id()

getDefinitions_Identifier

public List<String> getDefinitions_Identifier()

Get a pretty label for cross reference Definitions to OntologyTerm.Id.

setDefinitions_Identifier

public void setDefinitions_Identifier(List<String> definitions_Identifier)

Update the foreign key Definitions This sets definitions to null until next database transaction.

getDataType

public String getDataType()

Get the (Optional) Reference to the technical data type. E.g. 'int'.

Returns:

dataType.

getDataType

@Deprecated
public String getDataType(Database db)

Deprecated.

setDataType

public void setDataType(String dataType)

Set the (Optional) Reference to the technical data type. E.g. 'int'.

Parameters:

dataType -

getDataTypeLabel

public String getDataTypeLabel()

Get tha label for enum DataType.

getDataTypeOptions

public List<ValueLabel> getDataTypeOptions()

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

getTemporal

public Boolean getTemporal()

Get the Whether this feature is time dependent and can have different values when measured on different times (e.g. weight, temporal=true) or generally only measured once (e.g. birth date, temporal=false).

Returns:

temporal.

getTemporal

@Deprecated
public Boolean getTemporal(Database db)

Deprecated.

setTemporal

public void setTemporal(Boolean temporal)

Set the Whether this feature is time dependent and can have different values when measured on different times (e.g. weight, temporal=true) or generally only measured once (e.g. birth date, temporal=false).

Parameters:

temporal -

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 ObservableFeature.

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 ObservableFeature create(Entity entity)
                         throws Exception

Specified by:

create in interface Entity

Overrides:

create in class Characteristic

Throws:

Exception

getFeaturesProtocolCollection

public Collection<Protocol> getFeaturesProtocolCollection()

getFeaturesProtocolCollection

public Collection<Protocol> getFeaturesProtocolCollection(Database db)

setFeaturesProtocolCollection

public void setFeaturesProtocolCollection(Collection<Protocol> collection)

getRequiredFeaturesProtocolCollection

public Collection<Protocol> getRequiredFeaturesProtocolCollection()

getRequiredFeaturesProtocolCollection

public Collection<Protocol> getRequiredFeaturesProtocolCollection(Database db)

setRequiredFeaturesProtocolCollection

public void setRequiredFeaturesProtocolCollection(Collection<Protocol> collection)

equals

public boolean equals(Object obj)

Overrides:

equals in class Characteristic

hashCode

public int hashCode()

Overrides:

hashCode in class Characteristic