org.sbolstandard.core2

Class FunctionalComponent

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.Measured

org.sbolstandard.core2.ComponentInstance

org.sbolstandard.core2.FunctionalComponent

public class FunctionalComponent
extends ComponentInstance

Represents a FunctionalComponent object in the SBOL data model.

Version:

2.1

Author:

Zhen Zhang, Nicholas Roehner, Chris Myers

Method Summary

Modifier and Type	Method and Description
void	clearMapsTos() Removes all entries of this object's list of mapsTos.
MapsTo	createMapsTo(String displayId, RefinementType refinement, String localId, String remoteId) Creates a child MapsTo instance for this module with the given arguments, and then adds to this module's list of mapsTos.
MapsTo	createMapsTo(String displayId, RefinementType refinement, URI local, URI remote) Creates a child mapsTo for this functional component with the given arguments, and then adds it to this functional compoennt's list of mapsTos.
boolean	equals(Object obj)
DirectionType	getDirection() Returns the direction property of this functional component.
MapsTo	getMapsTo(String displayId) Returns the mapsTo that matches the given display ID.
MapsTo	getMapsTo(URI mapsToURI) Returns the mapsTo that matches the given URI.
Set<MapsTo>	getMapsTos() Returns the set of mapsTos owned by this object.
int	hashCode()
boolean	removeMapsTo(MapsTo mapsTo) Removes the given mapsTo.
void	setDefinition(URI definition) Sets the definition property to the given one.
void	setDirection(DirectionType direction) Sets the direction property of this functional component to the given one.
String	toString()

Methods inherited from class org.sbolstandard.core2.ComponentInstance

getAccess, getDefinition, getDefinitionIdentity, getDefinitionURI, setAccess

Methods inherited from class org.sbolstandard.core2.Measured

clearMeasures, createMeasure, getMeasure, getMeasure, getMeasures, removeMeasure

Methods inherited from class org.sbolstandard.core2.Identified

addWasDerivedFrom, addWasGeneratedBy, clearAnnotations, clearWasDerivedFroms, clearWasGeneratedBys, containsWasDerivedFrom, containsWasGeneratedBy, createAnnotation, createAnnotation, createAnnotation, createAnnotation, createAnnotation, createAnnotation, getAnnotation, getAnnotations, getDescription, getDisplayId, getIdentity, getName, getPersistentIdentity, getVersion, getWasDerivedFrom, getWasDerivedFroms, getWasGeneratedBys, hasAnnotations, isSetDescription, isSetDisplayId, isSetName, isSetPersistentIdentity, isSetVersion, isSetWasDerivedFrom, removeAnnotation, removeWasDerivedFrom, removeWasGeneratedBy, setDescription, setName, setWasDerivedFrom, setWasDerivedFroms, setWasGeneratedBys, unsetDescription, unsetName, unsetWasDerivedFrom

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Method Detail

getDirection

public DirectionType getDirection()

Returns the direction property of this functional component.

Returns:

the direction property of this functional component

setDirection

public void setDirection(DirectionType direction)
                  throws SBOLValidationException

Sets the direction property of this functional component to the given one.

Parameters:

direction - The direction for the FunctionalComponent

Throws:

SBOLValidationException - if the following SBOL validation rule violation occurred: 11802.

setDefinition

public void setDefinition(URI definition)
                   throws SBOLValidationException

Sets the definition property to the given one.

Overrides:

setDefinition in class ComponentInstance

Parameters:

definition - the given definition URI to set to

Throws:

SBOLValidationException - if either of the following SBOL validation rules was violated: 10604.

hashCode

public int hashCode()

Overrides:

hashCode in class ComponentInstance

equals

public boolean equals(Object obj)

Overrides:

equals in class ComponentInstance

createMapsTo

public MapsTo createMapsTo(String displayId,
                           RefinementType refinement,
                           String localId,
                           String remoteId)
                    throws SBOLValidationException

Creates a child MapsTo instance for this module with the given arguments, and then adds to this module's list of mapsTos.

This method creates compliant local and remote URIs first. The compliant local URI is created with this module's persistent identity URI, followed by the given local component's display ID, followed by this module's version. The compliant remote URI is created following the same pattern. It then calls createMapsTo(String, RefinementType, URI, URI) to create a MapsTo instance.

This method automatically creates a local functional component if all of the following conditions are satisfied:

• the associated SBOLDocument instance for this module is not null;
• if default functional components should be automatically created when not present for the associated SBOLDocument instance, i.e., SBOLDocument.isCreateDefaults() returns true;
• if this module's parent module definition exists; and
• if this module's parent module definition does not already have a functional component with the created compliant local functional component URI.

Parameters:

displayId - the display ID of the mapsTo to be created

refinement - the relationship between the local and remote functional components

localId - the display ID of the local functional component

remoteId - the display ID of the remote functional component

Returns:

the created mapsTo

Throws:

SBOLValidationException - if any of the following conditions is satisfied:

• if either of the following SBOL validation rules was violated: 10204, 10206;
• an SBOL validation rule violation occurred in ModuleDefinition.createFunctionalComponent(String, AccessType, String, String, DirectionType); or
• an SBOL validation rule violation occurred in createMapsTo(String, RefinementType, URI, URI).

createMapsTo

public MapsTo createMapsTo(String displayId,
                           RefinementType refinement,
                           URI local,
                           URI remote)
                    throws SBOLValidationException

Creates a child mapsTo for this functional component with the given arguments, and then adds it to this functional compoennt's list of mapsTos.

The compliant mapsTo URI is created with this functional component's persistent identity URI, followed by the given mapsTo's display ID, followed by this functional component's version.

Parameters:

displayId - the display ID of the mapsTo to be created

refinement - the refinement property of the mapsTo to be created

local - the URI of the referenced local component instance

remote - the URI of the referenced remote component instance

Returns:

the created mapsTo

Throws:

SBOLValidationException - if any of the following SBOL validation rule was violated: 10201, 10202, 10204, 10206, 10802, 10803, 10804, 10805, 10807, 10808, 10809, 10811.

removeMapsTo

public boolean removeMapsTo(MapsTo mapsTo)

Removes the given mapsTo.

Parameters:

mapsTo - The mapsTo to be removed

Returns:

true if the matching mapsTo was removed successfully, false otherwise.

getMapsTo

public MapsTo getMapsTo(String displayId)

Returns the mapsTo that matches the given display ID.

Parameters:

displayId - the display ID of the mapsTo to be retrieved

Returns:

the mapsTo that matches the given display ID, or null otherwise

getMapsTo

public MapsTo getMapsTo(URI mapsToURI)

Returns the mapsTo that matches the given URI.

Parameters:

mapsToURI - the URI for the mapsTo to be retrieved

Returns:

the matching mapsTo, or null otherwise

getMapsTos

public Set<MapsTo> getMapsTos()

Returns the set of mapsTos owned by this object.

Returns:

the set of mapsTos owned by this object.

clearMapsTos

public void clearMapsTos()

Removes all entries of this object's list of mapsTos. The list will be empty after this call returns.

toString

public String toString()

Overrides:

toString in class ComponentInstance