public class ModuleDefinition extends TopLevel
ACTIVITY, AGENT, ANNOTATION, ATTACHMENT, COLLECTION, COMBINATORIAL_DERIVATION, COMPONENT_DEFINITION, EXPERIMENT, EXPERIMENTAL_DATA, GENERIC_TOP_LEVEL, IMPLEMENTATION, MODEL, MODULE_DEFINITION, PLAN, SEQUENCE
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() |
addAttachment, addAttachment, addAttachment, clearAttachments, containsAttachment, getAttachments, getAttachmentURIs, removeAttachment, setAttachments
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
public boolean addRole(URI roleURI)
roleURI
- the role URI to be addedtrue
if this set did not already contain the specified role; false
otherwisepublic boolean removeRole(URI roleURI)
roleURI
- the URI of the role to be removedtrue
if the matching role was removed successfully,
or false
otherwisepublic void setRoles(Set<URI> roles)
roles
- the set of roles to be addedpublic Set<URI> getRoles()
public boolean containsRole(URI roleURI)
roleURI
- the given role URI to be checkedtrue
if this set contains the given role URI, or false
otherwisepublic void clearRoles()
public Module createModule(String displayId, String moduleDefinitionId, String version) throws SBOLValidationException
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.
displayId
- the given display ID of the module to be createdmoduleDefinitionId
- the display ID of the module definition referenced by the module to be createdversion
- the given version for the module to be createdSBOLValidationException
- if either of the following conditions is satisfied:
createModule(String, URI)
.public Module createModule(String displayId, String moduleDefinitionId) throws SBOLValidationException
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.
displayId
- the display ID of the module to be createdmoduleDefinitionId
- the module definition referenced by the module to be createdSBOLValidationException
- if an SBOL validation rule violation occurred in createModule(String, String, String)
public Module createModule(String displayId, URI moduleDefinitionURI) throws SBOLValidationException
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.
displayId
- the display ID for the module to be createdmoduleDefinitionURI
- the identity URI of the module definition referenced by the module to be createdSBOLValidationException
- if any of the following SBOL validation rules was violated:
10201, 10202, 10204, 10206, 10804, 11702, 11703, 11704, 11705.public boolean removeModule(Module module)
module
- the module to be removedtrue
if the matching module was removed successfully, or false
otherwise.public Module getModule(String displayId)
displayId
- the display ID of the module to be retrievednull
otherwisepublic Module getModule(URI moduleURI)
moduleURI
- the identity URI of the module to be retrievednull
otherwisepublic Set<Module> getModules()
public void clearModules()
This method calls removeModule(Module)
to iteratively remove each module.
public Interaction createInteraction(String displayId, Set<URI> types) throws SBOLValidationException
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.
displayId
- The displayId identifier for this interactiontypes
- The set of types to be added to the InteractionSBOLValidationException
- if any of the following SBOL validation rules was violated:
10201, 10202, 10204, 10206, 11902, 12003.public Interaction createInteraction(String displayId, URI type) throws SBOLValidationException
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.
displayId
- the display ID of the interaction to be createdtype
- the type to be added to the interaction to be createdSBOLValidationException
- if any of the following SBOL validation rules was violated:
10201, 10202, 10204, 10206, 11902, 12003.public boolean removeInteraction(Interaction interaction)
interaction
- the interaction to be removedtrue
if the matching interaction was removed successfully, or false
otherwisepublic Interaction getInteraction(String displayId)
displayId
- the display ID of the interaction to be retrievednull
otherwisepublic Interaction getInteraction(URI interactionURI)
interactionURI
- The referenced URI for the interactionnull
otherwise.public Set<Interaction> getInteractions()
public void clearInteractions()
This method calls removeInteraction(Interaction)
to iteratively remove each interaction.
public FunctionalComponent createFunctionalComponent(String displayId, AccessType access, String definitionId, String version, DirectionType direction) throws SBOLValidationException
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.
displayId
- the display ID of the functional component to be createdaccess
- the access property of the functional component to be createddefinitionId
- the display ID of the component definition referenced by the functional component to be createdversion
- the version of the functional component to be createddirection
- the direction property of the functional component to be createdSBOLValidationException
- if either of the following condition is satisfied:
createFunctionalComponent(String, AccessType, URI, DirectionType)
public FunctionalComponent createFunctionalComponent(String displayId, AccessType access, String definitionId, DirectionType direction) throws SBOLValidationException
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.
displayId
- the display ID of the functional component to be createdaccess
- the access type of the functional component to be createddefinitionId
- the display ID of the component definition referenced by the functional component to be createddirection
- the direction type of the functional component to be createdSBOLValidationException
- if an SBOL validation rule violation occurred in createFunctionalComponent(String, AccessType, String, String, DirectionType)
.public FunctionalComponent createFunctionalComponent(String displayId, AccessType access, URI definitionURI, DirectionType direction) throws SBOLValidationException
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.
displayId
- the display ID of the functional component to be createdaccess
- the access property of the functional component to be createddefinitionURI
- the identity URI of the component definition referenced by the functional component to be createddirection
- the direction property of the functional component to be createdSBOLValidationException
- if any of the following SBOL validation rules was violated:
10201, 10202, 10204, 10206, 10602, 10604, 10607, 11802, 10804.public boolean removeFunctionalComponent(FunctionalComponent functionalComponent) throws SBOLValidationException
functionalComponent
- The FunctionalComponent to be removedtrue
if the matching functional component was removed successfully,
or false
otherwiseSBOLValidationException
- if any of the following SBOL validation rules was violated:
10804, 10806, 12003.public FunctionalComponent getFunctionalComponent(String displayId)
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.
displayId
- the display ID of the functional component to be retrievednull
otherwisepublic FunctionalComponent getFunctionalComponent(URI functionalComponentURI)
functionalComponentURI
- The URI of the functional component to be retrievednull
otherwisepublic Set<FunctionalComponent> getFunctionalComponents()
public void clearFunctionalComponents() throws SBOLValidationException
SBOLValidationException
- if an SBOL validation rule violation occurred in removeFunctionalComponent(FunctionalComponent)
.public boolean addModel(Model model) throws SBOLValidationException
This method calls addModel(URI)
with this model's URI.
model
- the given model to this moduleDefinitiontrue
if this set did not already contain the given model, false
otherwiseSBOLValidationException
- if either of the following condition is satisfied:
addModel(URI)
.public boolean addModel(String modelId, String version) throws SBOLValidationException
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.
modelId
- the given model display IDversion
- the given versiontrue
if this set did not already contain the model with the given model's display ID
and version, or false
otherwise.SBOLValidationException
- if an SBOL validation violation occurred in addModel(URI)
.public boolean addModel(String modelId) throws SBOLValidationException
This method then calls addModel(String, String)
with the given model display ID
and an empty string version.
modelId
- the given model display IDtrue
if this set did not already contain the model, false
otherwiseSBOLValidationException
- if an SBOL validation rule violation occurred in addModel(String, String)
.public boolean addModel(URI modelURI) throws SBOLValidationException
modelURI
- the given model URI to be addedtrue
if this set did not already contain the given model URI, or false
otherwiseSBOLValidationException
- if the following SBOL validation rule was violated: 11608.public boolean removeModel(URI modelURI)
modelURI
- the given Model URI instance to this ModuleDefinitiontrue
if the matching Model reference is removed successfully,
or false
otherwisepublic void setModels(Set<URI> models) throws SBOLValidationException
models
- the given set of URIs of modelsSBOLValidationException
- if an SBOL validation rule violation occurred in addModel(URI)
.public Set<URI> getModelURIs()
public Set<URI> getModelIdentities()
public Set<Model> getModels()
public boolean containsModel(URI modelURI)
modelURI
- the given model URI to be checkedtrue
if this set contains the given URI, or false
otherwisepublic void clearModels()
public String toString()
toString
in class Identified