org.sbolstandard.core2

Class ModuleDefinition

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.TopLevel

org.sbolstandard.core2.ModuleDefinition

public class ModuleDefinition
extends TopLevel

Represents a ModuleDefinition object in the SBOL data model.

Version:

2.1

Author:

Zhen Zhang, Nicholas Roehner, Chris Myers

Field Summary

Fields inherited from class org.sbolstandard.core2.TopLevel

ACTIVITY, AGENT, ANNOTATION, ATTACHMENT, COLLECTION, COMBINATORIAL_DERIVATION, COMPONENT_DEFINITION, EXPERIMENT, EXPERIMENTAL_DATA, GENERIC_TOP_LEVEL, IMPLEMENTATION, MODEL, MODULE_DEFINITION, PLAN, SEQUENCE

Method Summary

Modifier and Type	Method and Description
boolean	addModel(Model model) Adds the URI of the given model to this module definition's set of model URIs.
boolean	addModel(String modelId) Adds the URI of the model that has the given display ID to this module definition's set of model URIs.
boolean	addModel(String modelId, String version) Adds the URI of the model that has the given display ID and version to this module definition's set of model URIs.
boolean	addModel(URI modelURI) Adds the given model URI to this module definition's set of model URIs.
boolean	addRole(URI roleURI) Adds the given role URI to this module definition's set of role URIs.
void	clearFunctionalComponents() Removes all entries of this module definition's list of functional components.
void	clearInteractions() Removes all entries of this module definition's list of interactions.
void	clearModels() Removes all entries of this module definition's set of model URIs.
void	clearModules() Removes all entries of this module definition's list of modules.
void	clearRoles() Removes all entries of this module definition's set of role URIs.
boolean	containsModel(URI modelURI) Checks if the given model URI is included in this module definition's set of reference model URIs.
boolean	containsRole(URI roleURI) Checks if the given role URI is included in this module definition's set of role URIs.
FunctionalComponent	createFunctionalComponent(String displayId, AccessType access, String definitionId, DirectionType direction) Creates a child functional component for this module definition with the given arguments, and then adds to this module definition's list of functional components.
FunctionalComponent	createFunctionalComponent(String displayId, AccessType access, String definitionId, String version, DirectionType direction) Creates a child functional component for this module definition with the given arguments, and then adds to this module definition's list of functional components.
FunctionalComponent	createFunctionalComponent(String displayId, AccessType access, URI definitionURI, DirectionType direction) Creates a child functional component for this module definition with the given arguments, and then adds to this module definition's list of functional components.
Interaction	createInteraction(String displayId, Set<URI> types) Creates a child interaction for this module definition with the given arguments, and then adds to this module definition's list of interactions.
Interaction	createInteraction(String displayId, URI type) Creates a child interaction for this module definition with the given arguments, and then adds to this module definition's list of interactions.
Module	createModule(String displayId, String moduleDefinitionId) Creates a child module for this module definition with the given arguments, and then adds to this module definition's list of modules.
Module	createModule(String displayId, String moduleDefinitionId, String version) Creates a child module for this module definition with the given arguments, and then adds to this module definition's list of modules.
Module	createModule(String displayId, URI moduleDefinitionURI) Creates a child module for this module definition with the given arguments, and then adds to this module definition's list of modules.
boolean	equals(Object obj)
FunctionalComponent	getFunctionalComponent(String displayId) Returns the functional component matching the given display ID from this module definition's list of functional components.
FunctionalComponent	getFunctionalComponent(URI functionalComponentURI) Returns the functional component matching the given functional component identity URI from this module definition's list of functional components.
Set<FunctionalComponent>	getFunctionalComponents() Returns the set of functional components owned by this module definition.
Interaction	getInteraction(String displayId) Returns the interaction matching the given interaction's identity URI from the list of interactions.
Interaction	getInteraction(URI interactionURI) Returns the instance matching the given Interaction URI from the list of Interaction instances.
Set<Interaction>	getInteractions() Returns the set of interactions owned by this module definition.
Set<URI>	getModelIdentities() Returns the set of models identities referenced by this module definition.
Set<Model>	getModels() Returns the set of models referenced by this module definition.
Set<URI>	getModelURIs() Returns the set of model URIs referenced by this module definition.
Module	getModule(String displayId) Returns the module matching the given display ID from the list of modules.
Module	getModule(URI moduleURI) Returns the module matching the given identity URI from the list of modules.
Set<Module>	getModules() Returns the set of modules owned by this module definition.
Set<URI>	getRoles() Returns the set of role URIs owned by this module definition.
int	hashCode()
boolean	removeFunctionalComponent(FunctionalComponent functionalComponent) Removes the given functional component from this module definition's list of functional components.
boolean	removeInteraction(Interaction interaction) Removes the given interaction from the list of interactions.
boolean	removeModel(URI modelURI) Removes the given model URI from the set of model URIs owned by this module definition.
boolean	removeModule(Module module) Removes the given module from the list of modules.
boolean	removeRole(URI roleURI) Removes the given role from the set of roles.
void	setModels(Set<URI> models) Clears the existing set of model URIs first, then adds the given set of the model URIs to this module definition.
void	setRoles(Set<URI> roles) Clears the existing set of roles first, and then adds the given set of the roles this module definition.
String	toString()

Methods inherited from class org.sbolstandard.core2.TopLevel

addAttachment, addAttachment, addAttachment, clearAttachments, containsAttachment, getAttachments, getAttachmentURIs, removeAttachment, setAttachments

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

addRole

public boolean addRole(URI roleURI)

Adds the given role URI to this module definition's set of role URIs.

Parameters:

roleURI - the role URI to be added

Returns:

true if this set did not already contain the specified role; false otherwise

removeRole

public boolean removeRole(URI roleURI)

Removes the given role from the set of roles.

Parameters:

roleURI - the URI of the role to be removed

Returns:

true if the matching role was removed successfully, or false otherwise

setRoles

public void setRoles(Set<URI> roles)

Clears the existing set of roles first, and then adds the given set of the roles this module definition.

Parameters:

roles - the set of roles to be added

getRoles

public Set<URI> getRoles()

Returns the set of role URIs owned by this module definition.

Returns:

the set of role URIs owned by this module definition.

containsRole

public boolean containsRole(URI roleURI)

Checks if the given role URI is included in this module definition's set of role URIs.

Parameters:

roleURI - the given role URI to be checked

Returns:

true if this set contains the given role URI, or false otherwise

clearRoles

public void clearRoles()

Removes all entries of this module definition's set of role URIs. The set will be empty after this call returns.

createModule

public Module createModule(String displayId,
                           String moduleDefinitionId,
                           String version)
                    throws SBOLValidationException

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

This method creates a compliant module URI first. It starts with the associated SBOLDocument instance's URI prefix, followed by the the module's reference module definition display ID, and ends with the given version. It then calls createModule(String, URI) the given module's display ID, and the created reference module definition compliant URI.

Parameters:

displayId - the given display ID of the module to be created

moduleDefinitionId - the display ID of the module definition referenced by the module to be created

version - the given version for the module to be created

Returns:

the created module

Throws:

SBOLValidationException - if either of the following conditions is satisfied:

• either of the following SBOL validation rule violation occurred: 10204, 10206; or
• an SBOL validation rule violation occurred in createModule(String, URI).

createModule

public Module createModule(String displayId,
                           String moduleDefinitionId)
                    throws SBOLValidationException

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

This method calls createModule(String, String, String) with the given module display ID, the module's reference module definition display ID, and ends with the empty version string.

Parameters:

displayId - the display ID of the module to be created

moduleDefinitionId - the module definition referenced by the module to be created

Returns:

the created module

Throws:

SBOLValidationException - if an SBOL validation rule violation occurred in createModule(String, String, String)

createModule

public Module createModule(String displayId,
                           URI moduleDefinitionURI)
                    throws SBOLValidationException

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

This method creates a compliant Module URI with the default URI prefix for this SBOLDocument instance, the given display ID of the module to be created, and this module definition's version.

Parameters:

displayId - the display ID for the module to be created

moduleDefinitionURI - the identity URI of the module definition referenced by the module to be created

Returns:

the created module

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10804, 11702, 11703, 11704, 11705.

removeModule

public boolean removeModule(Module module)

Removes the given module from the list of modules.

Parameters:

module - the module to be removed

Returns:

true if the matching module was removed successfully, or false otherwise.

getModule

public Module getModule(String displayId)

Returns the module matching the given display ID from the list of modules.

Parameters:

displayId - the display ID of the module to be retrieved

Returns:

the matching module if present, or null otherwise

getModule

public Module getModule(URI moduleURI)

Returns the module matching the given identity URI from the list of modules.

Parameters:

moduleURI - the identity URI of the module to be retrieved

Returns:

the matching module if present, or null otherwise

getModules

public Set<Module> getModules()

Returns the set of modules owned by this module definition.

Returns:

the set of modules owned by this module definition

clearModules

public void clearModules()

Removes all entries of this module definition's list of modules. This set will be empty after this call returns.

This method calls removeModule(Module) to iteratively remove each module.

createInteraction

public Interaction createInteraction(String displayId,
                                     Set<URI> types)
                              throws SBOLValidationException

Creates a child interaction for this module definition with the given arguments, and then adds to this module definition's list of interactions.

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

Parameters:

displayId - The displayId identifier for this interaction

types - The set of types to be added to the Interaction

Returns:

the created Interaction instance

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 11902, 12003.

createInteraction

public Interaction createInteraction(String displayId,
                                     URI type)
                              throws SBOLValidationException

Creates a child interaction for this module definition with the given arguments, and then adds to this module definition's list of interactions.

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

Parameters:

displayId - the display ID of the interaction to be created

type - the type to be added to the interaction to be created

Returns:

the created interaction

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 11902, 12003.

removeInteraction

public boolean removeInteraction(Interaction interaction)

Removes the given interaction from the list of interactions.

Parameters:

interaction - the interaction to be removed

Returns:

true if the matching interaction was removed successfully, or false otherwise

getInteraction

public Interaction getInteraction(String displayId)

Returns the interaction matching the given interaction's identity URI from the list of interactions.

Parameters:

displayId - the display ID of the interaction to be retrieved

Returns:

the matching interaction if present, or null otherwise

getInteraction

public Interaction getInteraction(URI interactionURI)

Returns the instance matching the given Interaction URI from the list of Interaction instances.

Parameters:

interactionURI - The referenced URI for the interaction

Returns:

the matching instance if present, null otherwise.

getInteractions

public Set<Interaction> getInteractions()

Returns the set of interactions owned by this module definition.

Returns:

the set of interactions owned by this module definition

clearInteractions

public void clearInteractions()

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

This method calls removeInteraction(Interaction) to iteratively remove each interaction.

createFunctionalComponent

public FunctionalComponent createFunctionalComponent(String displayId,
                                                     AccessType access,
                                                     String definitionId,
                                                     String version,
                                                     DirectionType direction)
                                              throws SBOLValidationException

Creates a child functional component for this module definition with the given arguments, and then adds to this module definition's list of functional components.

This method first creates a compliant component definition URI that is referenced by the functional component to be created. This compliant URI is created with the associated SBOLDocument instance's URI prefix, followed by the given functional component's component definition's display ID, and ends with the given version.

This method calls createFunctionalComponent(String, AccessType, URI, DirectionType) with the given functional component's display ID, access type, the created functional component's component definition's URI, and the given direction.

Parameters:

displayId - the display ID of the functional component to be created

access - the access property of the functional component to be created

definitionId - the display ID of the component definition referenced by the functional component to be created

version - the version of the functional component to be created

direction - the direction property of the functional component to be created

Returns:

the created functional component

Throws:

SBOLValidationException - if either of the following condition is satisfied:

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

createFunctionalComponent

public FunctionalComponent createFunctionalComponent(String displayId,
                                                     AccessType access,
                                                     String definitionId,
                                                     DirectionType direction)
                                              throws SBOLValidationException

Creates a child functional component for this module definition with the given arguments, and then adds to this module definition's list of functional components.

This method calls createFunctionalComponent(String, AccessType, String, String, DirectionType) with the given functional component's display ID, access type, the functional component's component definition's display ID, an empty version string, and the given direction.

Parameters:

displayId - the display ID of the functional component to be created

access - the access type of the functional component to be created

definitionId - the display ID of the component definition referenced by the functional component to be created

direction - the direction type of the functional component to be created

Returns:

the created functional component

Throws:

SBOLValidationException - if an SBOL validation rule violation occurred in createFunctionalComponent(String, AccessType, String, String, DirectionType).

createFunctionalComponent

public FunctionalComponent createFunctionalComponent(String displayId,
                                                     AccessType access,
                                                     URI definitionURI,
                                                     DirectionType direction)
                                              throws SBOLValidationException

Creates a child functional component for this module definition with the given arguments, and then adds to this module definition's list of functional components.

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

Parameters:

displayId - the display ID of the functional component to be created

access - the access property of the functional component to be created

definitionURI - the identity URI of the component definition referenced by the functional component to be created

direction - the direction property of the functional component to be created

Returns:

the created functional component

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10602, 10604, 10607, 11802, 10804.

removeFunctionalComponent

public boolean removeFunctionalComponent(FunctionalComponent functionalComponent)
                                  throws SBOLValidationException

Removes the given functional component from this module definition's list of functional components.

Parameters:

functionalComponent - The FunctionalComponent to be removed

Returns:

true if the matching functional component was removed successfully, or false otherwise

Throws:

SBOLValidationException - if any of the following SBOL validation rules was violated: 10804, 10806, 12003.

getFunctionalComponent

public FunctionalComponent getFunctionalComponent(String displayId)

Returns the functional component matching the given display ID from this module definition's list of functional components.

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

Parameters:

displayId - the display ID of the functional component to be retrieved

Returns:

the matching functional component if present, or null otherwise

getFunctionalComponent

public FunctionalComponent getFunctionalComponent(URI functionalComponentURI)

Returns the functional component matching the given functional component identity URI from this module definition's list of functional components.

Parameters:

functionalComponentURI - The URI of the functional component to be retrieved

Returns:

the matching functional component if present, or null otherwise

getFunctionalComponents

public Set<FunctionalComponent> getFunctionalComponents()

Returns the set of functional components owned by this module definition.

Returns:

the set of functional components owned by this module definition

clearFunctionalComponents

public void clearFunctionalComponents()
                               throws SBOLValidationException

Removes all entries of this module definition's list of functional components. The list will be empty after this call returns.

Throws:

SBOLValidationException - if an SBOL validation rule violation occurred in removeFunctionalComponent(FunctionalComponent).

addModel

public boolean addModel(Model model)
                 throws SBOLValidationException

Adds the URI of the given model to this module definition's set of model URIs.

This method calls addModel(URI) with this model's URI.

Parameters:

model - the given model to this moduleDefinition

Returns:

true if this set did not already contain the given model, false otherwise

Throws:

SBOLValidationException - if either of the following condition is satisfied:

• the following SBOL validation rule was violated: 11608; or
• an SBOL validation rule violation occurred in addModel(URI).

addModel

public boolean addModel(String modelId,
                        String version)
                 throws SBOLValidationException

Adds the URI of the model that has the given display ID and version to this module definition's set of model URIs.

This method creates a compliant model URI first. It starts with this module definition's persistent identity, followed by the given model display ID, and ends with the given version. This method then calls addModel(URI) with the created model URI.

Parameters:

modelId - the given model display ID

version - the given version

Returns:

true if this set did not already contain the model with the given model's display ID and version, or false otherwise.

Throws:

SBOLValidationException - if an SBOL validation violation occurred in addModel(URI).

addModel

public boolean addModel(String modelId)
                 throws SBOLValidationException

Adds the URI of the model that has the given display ID to this module definition's set of model URIs.

This method then calls addModel(String, String) with the given model display ID and an empty string version.

Parameters:

modelId - the given model display ID

Returns:

true if this set did not already contain the model, false otherwise

Throws:

SBOLValidationException - if an SBOL validation rule violation occurred in addModel(String, String).

addModel

public boolean addModel(URI modelURI)
                 throws SBOLValidationException

Adds the given model URI to this module definition's set of model URIs.

Parameters:

modelURI - the given model URI to be added

Returns:

true if this set did not already contain the given model URI, or false otherwise

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 11608.

removeModel

public boolean removeModel(URI modelURI)

Removes the given model URI from the set of model URIs owned by this module definition.

Parameters:

modelURI - the given Model URI instance to this ModuleDefinition

Returns:

true if the matching Model reference is removed successfully, or false otherwise

setModels

public void setModels(Set<URI> models)
               throws SBOLValidationException

Clears the existing set of model URIs first, then adds the given set of the model URIs to this module definition.

Parameters:

models - the given set of URIs of models

Throws:

SBOLValidationException - if an SBOL validation rule violation occurred in addModel(URI).

getModelURIs

public Set<URI> getModelURIs()

Returns the set of model URIs referenced by this module definition.

Returns:

the set of model URIs referenced by this module definition.

getModelIdentities

public Set<URI> getModelIdentities()

Returns the set of models identities referenced by this module definition.

Returns:

the set of models identities referenced by this module definition

getModels

public Set<Model> getModels()

Returns the set of models referenced by this module definition.

Returns:

the set of models referenced by this module definition

containsModel

public boolean containsModel(URI modelURI)

Checks if the given model URI is included in this module definition's set of reference model URIs.

Parameters:

modelURI - the given model URI to be checked

Returns:

true if this set contains the given URI, or false otherwise

clearModels

public void clearModels()

Removes all entries of this module definition's set of model URIs. The set will be empty after this call returns.

hashCode

public int hashCode()

Overrides:

hashCode in class TopLevel

equals

public boolean equals(Object obj)

Overrides:

equals in class TopLevel

toString

public String toString()

Overrides:

toString in class Identified