org.sbolstandard.core2

Class Module

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.Measured

org.sbolstandard.core2.Module

public class Module
extends Measured

Represents a Module 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 module's list of mapsTos.
MapsTo	createMapsTo(String displayId, RefinementType refinement, String localId, String remoteId) Creates a child mapsTo for this module with the given arguments, and then adds it to its list of mapsTos.
MapsTo	createMapsTo(String displayId, RefinementType refinement, URI local, URI remote) Creates a child mapsTo for this module with the given arguments, and then adds it to its list of mapsTos.
boolean	equals(Object obj)
ModuleDefinition	getDefinition() Returns the module definition that this module refers to.
URI	getDefinitionIdentity() Returns the module definition identity that this module refers to.
URI	getDefinitionURI() Returns the module definition URI that this module refers to.
MapsTo	getMapsTo(String displayId) Returns the mapsTo that matches the given display ID.
MapsTo	getMapsTo(URI referenceURI) Returns the MapsTo instance owned by this Module object that matches the given referenceURI
Set<MapsTo>	getMapsTos() Returns the set of MapsTo instances referenced by this Module object.
int	hashCode()
boolean	removeMapsTo(MapsTo mapsTo) Removes the given mapsTo from the list of mapsTos owned by this module.
void	setDefinition(URI definitionURI) Sets the reference definition URI to this module.
String	toString()

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

getDefinitionURI

public URI getDefinitionURI()

Returns the module definition URI that this module refers to.

Returns:

the module definition URI that this module refers to

getDefinitionIdentity

public URI getDefinitionIdentity()

Returns the module definition identity that this module refers to.

Returns:

the the module definition identity that this module refers to

getDefinition

public ModuleDefinition getDefinition()

Returns the module definition that this module refers to.

Returns:

the the module definition that this module refers to

setDefinition

public void setDefinition(URI definitionURI)
                   throws SBOLValidationException

Sets the reference definition URI to this module.

This method creates a compliant local and a compliant remote URIs. They are created with this Module object's persistent ID, the given localId or remoteId, and this Module object's version. It then calls createMapsTo(String, RefinementType, URI, URI) to create a MapsTo instance.

Parameters:

definitionURI - The definition URI for this Module.

Throws:

SBOLValidationException - if either of the following SBOL validation rule was violated: 11702, 11703, 11704, 11705.

createMapsTo

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

Creates a child mapsTo for this module with the given arguments, and then adds it to its 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 module'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) with the given mapsTo's display ID, its refinement type, and the created compliant local and remote functional components' URIs.

This method calls ModuleDefinition.createFunctionalComponent(String, AccessType, String, String, DirectionType) to automatically create a local functional component with the given display ID of referenced local component definition, AccessType.PUBLIC, an empty version string, and DirectionType.INOUT, 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 in the associated SBOLDocument instance, i.e., SBOLDocument.isCreateDefaults() returns true;
• if this module's parent ModuleDefinition instance exists; and
• if this module's parent ModuleDefinition instance does not already have a functional component with the created compliant local URI.

This automatically created created functional component has the same display ID as its referenced component definition.

Parameters:

displayId - the display ID of the mapsTo to be created

refinement - the relationship between the local and remote 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 condition is satisfied:

• if either of the following SBOL validation rules was violated: 10204, 10206;
• an SBOL validation exception occurred in ModuleDefinition.createFunctionalComponent(String, AccessType, String, String, DirectionType); or
• an SBOL validation exception 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 module with the given arguments, and then adds it to its list of mapsTos.

This method creates a compliant URI for the mapsTo to be created. It starts with this module's persistent identity, followed by the mapsTo's display ID, and ends with this module's version.

Parameters:

displayId - the display ID of the mapsTo to be created

refinement - the relationship between the local and remote components

local - the identity URI of the local functional component

remote - the identity URI of the remote functional component

Returns:

the created mapsTo

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10802, 10803, 10804, 10805, 10807, 10808, 10809, 10811, 11609.

removeMapsTo

public boolean removeMapsTo(MapsTo mapsTo)

Removes the given mapsTo from the list of mapsTos owned by this module.

Parameters:

mapsTo - the mapsTo to be removed

Returns:

true if the matching mapsTo is removed successfully, false otherwise

getMapsTo

public MapsTo getMapsTo(String displayId)

Returns the mapsTo that matches the given display ID.

This method first creates a compliant URI for the mapsTo to be retrieved. It starts with this module's persistent identity, followed by the given display ID, and ends with this module's version.

Parameters:

displayId - the display ID of the mapsTo to be retrieved

Returns:

the matching mapsTo

getMapsTo

public MapsTo getMapsTo(URI referenceURI)

Returns the MapsTo instance owned by this Module object that matches the given referenceURI

Parameters:

referenceURI - The MapsTo URI object

Returns:

the matching MapsTo instance URI

getMapsTos

public Set<MapsTo> getMapsTos()

Returns the set of MapsTo instances referenced by this Module object.

Returns:

the set of MapsTo instances referenced by this Module object.

clearMapsTos

public void clearMapsTos()

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

This method calls removeMapsTo(MapsTo) iteratively to remove each mapsTo at a time.

hashCode

public int hashCode()

Overrides:

hashCode in class Measured

equals

public boolean equals(Object obj)

Overrides:

equals in class Measured

toString

public String toString()

Overrides:

toString in class Measured