org.molgenis.omx.observ

Class Protocol

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.Protocol

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

@Entity
public class Protocol
extends Characteristic

Protocol: The Protocol class defines parameterizable descriptions of (analysis)methods. Examples of protocols are: Questionaires, SOPs, Assay platforms, Statistical analyses, etc. Each protocol has a unique identifier. Protocol has an association to OntologyTerm to represent the type of protocol. .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	FEATURES
static String	FEATURES_IDENTIFIER
static String	ID
static String	PROTOCOLTYPE
static String	PROTOCOLTYPE_IDENTIFIER
static String	REQUIREDFEATURES
static String	REQUIREDFEATURES_IDENTIFIER
static String	ROOT
static String	SUBPROTOCOLS
static String	SUBPROTOCOLS_IDENTIFIER

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

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
Protocol	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Protocol>	find(Database db, QueryRule... rules) Shorthand for db.find(Protocol.class, org.molgenis.framework.db.QueryRule ...
static Protocol	findById(Database db, Integer id)
static Protocol	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
List<Integer>	getFeatures_Id()
List<String>	getFeatures_Identifier() Get a pretty label for cross reference Features to ObservableFeature.Id.
List<ObservableFeature>	getFeatures() Get the parameters (in/out) that are used or produced by this protocol..
List<ObservableFeature>	getFeatures(Database db) Deprecated.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Protocol.
String	getFields(String sep) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
Integer	getProtocolType_Id()
String	getProtocolType_Identifier() Get a pretty label Identifier for cross reference ProtocolType to OntologyTerm.Id.
OntologyTerm	getProtocolType() Get the classification of protocol.
OntologyTerm	getProtocolType(Database db) Deprecated.
List<Integer>	getRequiredFeatures_Id()
List<String>	getRequiredFeatures_Identifier() Get a pretty label for cross reference RequiredFeatures to ObservableFeature.Id.
List<ObservableFeature>	getRequiredFeatures() Get the ...........
List<ObservableFeature>	getRequiredFeatures(Database db) Deprecated.
Boolean	getRoot() Get the Indicator whether this protocol defines a workflow (e.g is the first protocol of a workflow)..
Boolean	getRoot(Database db) Deprecated.
List<Integer>	getSubprotocols_Id()
List<String>	getSubprotocols_Identifier() Get a pretty label for cross reference Subprotocols to Protocol.Id.
List<Protocol>	getSubprotocols() Get the Subprotocols of this protocol.
List<Protocol>	getSubprotocols(Database db) Deprecated.
Collection<Protocol>	getSubprotocolsProtocolCollection()
Collection<Protocol>	getSubprotocolsProtocolCollection(Database db)
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Protocol>	query(Database db) Shorthand for db.query(Protocol.class).
void	set(Entity entity, boolean strict)
void	setFeatures_Id(Integer... features)
void	setFeatures_Id(List<Integer> features_id) Set foreign key for field features.
void	setFeatures_Identifier(List<String> features_Identifier) Update the foreign key Features This sets features to null until next database transaction.
void	setFeatures(List<ObservableFeature> features) Set the parameters (in/out) that are used or produced by this protocol..
void	setFeatures(ObservableFeature... features)
void	setProtocolType_Id(Integer protocolType_id) Set foreign key for field protocolType.
void	setProtocolType_Identifier(String protocolType_Identifier) Set a pretty label for cross reference ProtocolType to OntologyTerm.Id.
void	setProtocolType(Integer protocolType_id)
void	setProtocolType(OntologyTerm protocolType) Set the classification of protocol.
void	setRequiredFeatures_Id(Integer... requiredFeatures)
void	setRequiredFeatures_Id(List<Integer> requiredFeatures_id) Set foreign key for field requiredFeatures.
void	setRequiredFeatures_Identifier(List<String> requiredFeatures_Identifier) Update the foreign key RequiredFeatures This sets requiredFeatures to null until next database transaction.
void	setRequiredFeatures(List<ObservableFeature> requiredFeatures) Set the ...........
void	setRequiredFeatures(ObservableFeature... requiredFeatures)
void	setRoot(Boolean root) Set the Indicator whether this protocol defines a workflow (e.g is the first protocol of a workflow)..
void	setSubprotocols_Id(Integer... subprotocols)
void	setSubprotocols_Id(List<Integer> subprotocols_id) Set foreign key for field subprotocols.
void	setSubprotocols_Identifier(List<String> subprotocols_Identifier) Update the foreign key Subprotocols This sets subprotocols to null until next database transaction.
void	setSubprotocols(List<Protocol> subprotocols) Set the Subprotocols of this protocol.
void	setSubprotocols(Protocol... subprotocols)
void	setSubprotocolsProtocolCollection(Collection<Protocol> collection)
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

PROTOCOLTYPE

public static final String PROTOCOLTYPE

See Also:

Constant Field Values

PROTOCOLTYPE_IDENTIFIER

public static final String PROTOCOLTYPE_IDENTIFIER

See Also:

Constant Field Values

SUBPROTOCOLS

public static final String SUBPROTOCOLS

See Also:

Constant Field Values

SUBPROTOCOLS_IDENTIFIER

public static final String SUBPROTOCOLS_IDENTIFIER

See Also:

Constant Field Values

FEATURES

public static final String FEATURES

See Also:

Constant Field Values

FEATURES_IDENTIFIER

public static final String FEATURES_IDENTIFIER

See Also:

Constant Field Values

REQUIREDFEATURES

public static final String REQUIREDFEATURES

See Also:

Constant Field Values

REQUIREDFEATURES_IDENTIFIER

public static final String REQUIREDFEATURES_IDENTIFIER

See Also:

Constant Field Values

ROOT

public static final String ROOT

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

Constructor Detail

Protocol

public Protocol()

Protocol

public Protocol(Protocol copyMe)
         throws Exception

copy constructor

Throws:

Exception

Method Detail

query

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

Shorthand for db.query(Protocol.class).

find

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

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

Throws:

DatabaseException

findById

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

Throws:

DatabaseException

findByIdentifier

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

Throws:

DatabaseException

getProtocolType

public OntologyTerm getProtocolType()

Get the classification of protocol.

Returns:

protocolType.

getProtocolType

@Deprecated
public OntologyTerm getProtocolType(Database db)

Deprecated.

setProtocolType

public void setProtocolType(OntologyTerm protocolType)

Set the classification of protocol.

Parameters:

protocolType -

setProtocolType_Id

public void setProtocolType_Id(Integer protocolType_id)

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

setProtocolType

public void setProtocolType(Integer protocolType_id)

getProtocolType_Id

public Integer getProtocolType_Id()

getProtocolType_Identifier

public String getProtocolType_Identifier()

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

setProtocolType_Identifier

public void setProtocolType_Identifier(String protocolType_Identifier)

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

getSubprotocols

public List<Protocol> getSubprotocols()

Get the Subprotocols of this protocol.

Returns:

subprotocols.

getSubprotocols

@Deprecated
public List<Protocol> getSubprotocols(Database db)

Deprecated.

setSubprotocols

public void setSubprotocols(List<Protocol> subprotocols)

Set the Subprotocols of this protocol.

Parameters:

subprotocols -

setSubprotocols_Id

public void setSubprotocols_Id(Integer... subprotocols)

setSubprotocols

public void setSubprotocols(Protocol... subprotocols)

setSubprotocols_Id

public void setSubprotocols_Id(List<Integer> subprotocols_id)

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

getSubprotocols_Id

public List<Integer> getSubprotocols_Id()

getSubprotocols_Identifier

public List<String> getSubprotocols_Identifier()

Get a pretty label for cross reference Subprotocols to Protocol.Id.

setSubprotocols_Identifier

public void setSubprotocols_Identifier(List<String> subprotocols_Identifier)

Update the foreign key Subprotocols This sets subprotocols to null until next database transaction.

getFeatures

public List<ObservableFeature> getFeatures()

Get the parameters (in/out) that are used or produced by this protocol..

Returns:

features.

getFeatures

@Deprecated
public List<ObservableFeature> getFeatures(Database db)

Deprecated.

setFeatures

public void setFeatures(List<ObservableFeature> features)

Set the parameters (in/out) that are used or produced by this protocol..

Parameters:

features -

setFeatures_Id

public void setFeatures_Id(Integer... features)

setFeatures

public void setFeatures(ObservableFeature... features)

setFeatures_Id

public void setFeatures_Id(List<Integer> features_id)

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

getFeatures_Id

public List<Integer> getFeatures_Id()

getFeatures_Identifier

public List<String> getFeatures_Identifier()

Get a pretty label for cross reference Features to ObservableFeature.Id.

setFeatures_Identifier

public void setFeatures_Identifier(List<String> features_Identifier)

Update the foreign key Features This sets features to null until next database transaction.

getRequiredFeatures

public List<ObservableFeature> getRequiredFeatures()

Get the ...........

Returns:

requiredFeatures.

getRequiredFeatures

@Deprecated
public List<ObservableFeature> getRequiredFeatures(Database db)

Deprecated.

setRequiredFeatures

public void setRequiredFeatures(List<ObservableFeature> requiredFeatures)

Set the ...........

Parameters:

requiredFeatures -

setRequiredFeatures_Id

public void setRequiredFeatures_Id(Integer... requiredFeatures)

setRequiredFeatures

public void setRequiredFeatures(ObservableFeature... requiredFeatures)

setRequiredFeatures_Id

public void setRequiredFeatures_Id(List<Integer> requiredFeatures_id)

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

getRequiredFeatures_Id

public List<Integer> getRequiredFeatures_Id()

getRequiredFeatures_Identifier

public List<String> getRequiredFeatures_Identifier()

Get a pretty label for cross reference RequiredFeatures to ObservableFeature.Id.

setRequiredFeatures_Identifier

public void setRequiredFeatures_Identifier(List<String> requiredFeatures_Identifier)

Update the foreign key RequiredFeatures This sets requiredFeatures to null until next database transaction.

getRoot

public Boolean getRoot()

Get the Indicator whether this protocol defines a workflow (e.g is the first protocol of a workflow)..

Returns:

root.

getRoot

@Deprecated
public Boolean getRoot(Database db)

Deprecated.

setRoot

public void setRoot(Boolean root)

Set the Indicator whether this protocol defines a workflow (e.g is the first protocol of a workflow)..

Parameters:

root -

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 Protocol.

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 Protocol create(Entity entity)
                throws Exception

Specified by:

create in interface Entity

Overrides:

create in class Characteristic

Throws:

Exception

getSubprotocolsProtocolCollection

public Collection<Protocol> getSubprotocolsProtocolCollection()

getSubprotocolsProtocolCollection

public Collection<Protocol> getSubprotocolsProtocolCollection(Database db)

setSubprotocolsProtocolCollection

public void setSubprotocolsProtocolCollection(Collection<Protocol> collection)

equals

public boolean equals(Object obj)

Overrides:

equals in class Characteristic

hashCode

public int hashCode()

Overrides:

hashCode in class Characteristic