org.molgenis.omx.observ.target

Class Panel

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.ObservationTarget

org.molgenis.omx.observ.target.Panel

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

@Entity
public class Panel
extends ObservationTarget

Panel: The Panel class defines groups of individuals based on cohort design, case/controls, families, etc. For instance: 'LifeLines cohort', 'middle aged man', 'recombinant mouse inbred Line dba x b6' or 'Smith family'. A Panel can act as a single ObservationTarget. For example: average height (Measurement) in the LifeLines cohort (Panel) is 174cm (ObservedValue). The Panel class maps to XGAP:Strain and PaGE:Panel classes. In METABASE this is assumed there is one panel per study. .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	ID
static String	INDIVIDUALS
static String	INDIVIDUALS_IDENTIFIER
static String	NUMBEROFINDIVIDUALS
static String	PANELTYPE
static String	PANELTYPE_IDENTIFIER
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
Panel()
Panel(Panel copyMe) copy constructor

Method Summary

Methods

Modifier and Type	Method and Description
Panel	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Panel>	find(Database db, QueryRule... rules) Shorthand for db.find(Panel.class, org.molgenis.framework.db.QueryRule ...
static Panel	findById(Database db, Integer id)
static Panel	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Panel.
String	getFields(String sep) Deprecated.
String	getIdField()
Object	getIdValue()
List<Integer>	getIndividuals_Id()
List<String>	getIndividuals_Identifier() Get a pretty label for cross reference Individuals to Individual.Id.
List<Individual>	getIndividuals() Get the The list of individuals in this panel.
List<Individual>	getIndividuals(Database db) Deprecated.
List<String>	getLabelFields()
Integer	getNumberOfIndividuals() Get the NumberOfIndividuals.
Integer	getNumberOfIndividuals(Database db) Deprecated.
Integer	getPanelType_Id()
String	getPanelType_Identifier() Get a pretty label Identifier for cross reference PanelType to OntologyTerm.Id.
OntologyTerm	getPanelType() Get the Indicate the type of Panel (example: Sample panel, AssayedPanel, Natural=wild type, Parental=parents of a cross, F1=First generation of cross, RCC=Recombinant congenic, CSS=chromosome substitution).
OntologyTerm	getPanelType(Database db) Deprecated.
Integer	getSpecies_Id()
String	getSpecies_Identifier() Get a pretty label Identifier for cross reference Species to Species.Id.
Species	getSpecies() Get the The species this panel is an instance of/part of/extracted from..
Species	getSpecies(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Panel>	query(Database db) Shorthand for db.query(Panel.class).
void	set(Entity entity, boolean strict)
void	setIndividuals_Id(Integer... individuals)
void	setIndividuals_Id(List<Integer> individuals_id) Set foreign key for field individuals.
void	setIndividuals_Identifier(List<String> individuals_Identifier) Update the foreign key Individuals This sets individuals to null until next database transaction.
void	setIndividuals(Individual... individuals)
void	setIndividuals(List<Individual> individuals) Set the The list of individuals in this panel.
void	setNumberOfIndividuals(Integer numberOfIndividuals) Set the NumberOfIndividuals.
void	setPanelType_Id(Integer panelType_id) Set foreign key for field panelType.
void	setPanelType_Identifier(String panelType_Identifier) Set a pretty label for cross reference PanelType to OntologyTerm.Id.
void	setPanelType(Integer panelType_id)
void	setPanelType(OntologyTerm panelType) Set the Indicate the type of Panel (example: Sample panel, AssayedPanel, Natural=wild type, Parental=parents of a cross, F1=First generation of cross, RCC=Recombinant congenic, CSS=chromosome substitution).
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 Species.Id.
void	setSpecies(Integer species_id)
void	setSpecies(Species species) Set the The species this panel is an instance of/part of/extracted from..
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

PANELTYPE

public static final String PANELTYPE

See Also:

Constant Field Values

PANELTYPE_IDENTIFIER

public static final String PANELTYPE_IDENTIFIER

See Also:

Constant Field Values

NUMBEROFINDIVIDUALS

public static final String NUMBEROFINDIVIDUALS

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

INDIVIDUALS

public static final String INDIVIDUALS

See Also:

Constant Field Values

INDIVIDUALS_IDENTIFIER

public static final String INDIVIDUALS_IDENTIFIER

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

Panel

public Panel()

Panel

public Panel(Panel copyMe)
      throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(Panel.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

getPanelType

public OntologyTerm getPanelType()

Get the Indicate the type of Panel (example: Sample panel, AssayedPanel, Natural=wild type, Parental=parents of a cross, F1=First generation of cross, RCC=Recombinant congenic, CSS=chromosome substitution).

Returns:

panelType.

getPanelType

@Deprecated
public OntologyTerm getPanelType(Database db)

Deprecated.

setPanelType

public void setPanelType(OntologyTerm panelType)

Set the Indicate the type of Panel (example: Sample panel, AssayedPanel, Natural=wild type, Parental=parents of a cross, F1=First generation of cross, RCC=Recombinant congenic, CSS=chromosome substitution).

Parameters:

panelType -

setPanelType_Id

public void setPanelType_Id(Integer panelType_id)

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

setPanelType

public void setPanelType(Integer panelType_id)

getPanelType_Id

public Integer getPanelType_Id()

getPanelType_Identifier

public String getPanelType_Identifier()

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

setPanelType_Identifier

public void setPanelType_Identifier(String panelType_Identifier)

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

getNumberOfIndividuals

public Integer getNumberOfIndividuals()

Get the NumberOfIndividuals.

Returns:

numberOfIndividuals.

getNumberOfIndividuals

@Deprecated
public Integer getNumberOfIndividuals(Database db)

Deprecated.

setNumberOfIndividuals

public void setNumberOfIndividuals(Integer numberOfIndividuals)

Set the NumberOfIndividuals.

Parameters:

numberOfIndividuals -

getSpecies

public Species getSpecies()

Get the The species this panel is an instance of/part of/extracted from..

Returns:

species.

getSpecies

@Deprecated
public Species getSpecies(Database db)

Deprecated.

setSpecies

public void setSpecies(Species species)

Set the The species this panel is an instance of/part of/extracted from..

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 Species.Id.

setSpecies_Identifier

public void setSpecies_Identifier(String species_Identifier)

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

getIndividuals

public List<Individual> getIndividuals()

Get the The list of individuals in this panel.

Returns:

individuals.

getIndividuals

@Deprecated
public List<Individual> getIndividuals(Database db)

Deprecated.

setIndividuals

public void setIndividuals(List<Individual> individuals)

Set the The list of individuals in this panel.

Parameters:

individuals -

setIndividuals_Id

public void setIndividuals_Id(Integer... individuals)

setIndividuals

public void setIndividuals(Individual... individuals)

setIndividuals_Id

public void setIndividuals_Id(List<Integer> individuals_id)

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

getIndividuals_Id

public List<Integer> getIndividuals_Id()

getIndividuals_Identifier

public List<String> getIndividuals_Identifier()

Get a pretty label for cross reference Individuals to Individual.Id.

setIndividuals_Identifier

public void setIndividuals_Identifier(List<String> individuals_Identifier)

Update the foreign key Individuals This sets individuals to null until next database transaction.

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 Panel.

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 Panel 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