| Package | Description |
|---|---|
| org.sbolstandard.core2 |
| Modifier and Type | Method and Description |
|---|---|
boolean |
TopLevel.addAttachment(Attachment attachment)
Adds the URI of the given Attachment instance to this top level's
set of attachment URIs.
|
boolean |
TopLevel.addAttachment(String displayId)
Constructs a compliant sequence URI using the given attachment display ID, and then adds this URI to
this top level's set of attachment URIs.
|
boolean |
TopLevel.addAttachment(String displayId,
String version)
Constructs a compliant attachment URI with the given display ID and version, and then adds this URI
to this top level's set of attachment URIs.
|
Cut |
Component.addCut(String displayId,
int at)
Creates a cut with the given arguments and then adds it to this component's
list of locations.
|
Cut |
SequenceAnnotation.addCut(String displayId,
int at)
Creates a cut with the given arguments and then adds it to this sequence annotation's
list of locations.
|
Cut |
Component.addCut(String displayId,
int at,
OrientationType orientation)
Creates a cut with the given arguments and then adds it to this component's
list of locations.
|
Cut |
SequenceAnnotation.addCut(String displayId,
int at,
OrientationType orientation)
Creates a cut with the given arguments and then adds it to this sequence annotation's
list of locations.
|
boolean |
Experiment.addExperimentalData(URI experimentalDataURI)
Adds the given experimentalData URI to this Experiment's
set of reference experimentalData URIs.
|
GenericLocation |
Component.addGenericLocation(String displayId)
Creates a generic location with the given arguments and then adds it to this component's
list of locations.
|
GenericLocation |
SequenceAnnotation.addGenericLocation(String displayId)
Creates a generic location with the given arguments and then adds it to this sequence annotation's
list of locations.
|
GenericLocation |
Component.addGenericLocation(String displayId,
OrientationType orientation)
Creates a generic location with the given arguments and then adds it to this component's
list of locations.
|
GenericLocation |
SequenceAnnotation.addGenericLocation(String displayId,
OrientationType orientation)
Creates a generic location with the given arguments and then adds it to this sequence annotation's
list of locations.
|
GenericLocation |
Component.addGenericSourceLocation(String displayId)
Creates a generic location with the given arguments and then adds it to this components's
list of source locations.
|
GenericLocation |
Component.addGenericSourceLocation(String displayId,
OrientationType orientation)
Creates a generic location with the given arguments and then adds it to this component's
list of source locations.
|
boolean |
Collection.addMember(URI memberURI)
Adds the given member URI to this Collection instance's
set of reference member URIs.
|
boolean |
ModuleDefinition.addModel(Model model)
Adds the URI of the given model to this module definition's
set of model URIs.
|
boolean |
ModuleDefinition.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 |
ModuleDefinition.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 |
ModuleDefinition.addModel(URI modelURI)
Adds the given model URI to this module definition's set of model URIs.
|
void |
SBOLDocument.addNamespace(QName qName)
Adds the given namespace QName to this SBOL document.
|
void |
SBOLDocument.addNamespace(URI nameSpaceURI,
String prefix)
Adds the given namespace URI and its prefix to this SBOL document.
|
Range |
Component.addRange(String displayId,
int start,
int end)
Creates a range with the given arguments and then adds it to this component's
list of locations.
|
Range |
SequenceAnnotation.addRange(String displayId,
int start,
int end)
Creates a range with the given arguments and then adds it to this sequence annotation's
list of locations.
|
Range |
Component.addRange(String displayId,
int start,
int end,
OrientationType orientation)
Creates a range with the given arguments and then adds it to this component's
list of locations.
|
Range |
SequenceAnnotation.addRange(String displayId,
int start,
int end,
OrientationType orientation)
Creates a range with the given arguments and then adds it to this sequence annotation's
list of locations.
|
boolean |
Component.addRole(URI roleURI)
Adds the given role URI to this component's set of role URIs.
|
boolean |
SequenceAnnotation.addRole(URI roleURI)
Adds the given role to this sequence annotation's set of roles.
|
boolean |
ComponentDefinition.addSequence(Sequence sequence)
Adds the URI of the given Sequence instance to this component definition's
set of sequence URIs.
|
boolean |
ComponentDefinition.addSequence(String displayId)
Constructs a compliant sequence URI using the given sequence display ID, and then adds this URI to
this component definition's set of sequence URIs.
|
boolean |
ComponentDefinition.addSequence(String displayId,
String version)
Constructs a compliant sequence URI with the given display ID and version, and then adds this URI
to this component definition's set of sequence URIs.
|
boolean |
ComponentDefinition.addSequence(URI sequenceURI)
Adds the given sequence URI to this component definition's set of sequence URIs.
|
Cut |
Component.addSourceCut(String displayId,
int at)
Creates a cut with the given arguments and then adds it to this component's
list of source locations.
|
Cut |
Component.addSourceCut(String displayId,
int at,
OrientationType orientation)
Creates a cut with the given arguments and then adds it to this component's
list of source locations.
|
Range |
Component.addSourceRange(String displayId,
int start,
int end)
Creates a range with the given arguments and then adds it to this component's
list of source locations.
|
Range |
Component.addSourceRange(String displayId,
int start,
int end,
OrientationType orientation)
Creates a range with the given arguments and then adds it to this component's
list of source locations.
|
boolean |
ComponentDefinition.addType(URI typeURI)
Adds the given type URI to this component definition's set of type URIs.
|
void |
VariableComponent.addVariant(String uriPrefix,
String displayId,
String version)
Adds the given variant to the list of variants.
|
void |
VariableComponent.addVariant(URI variant)
Adds the given variant URI to the list of variant URIs.
|
void |
VariableComponent.addVariantCollection(String uriPrefix,
String displayId,
String version)
Adds the given variant collection to the list of variant collections.
|
void |
VariableComponent.addVariantCollection(URI variantCollection)
Adds the given variant collection URI to the list of variant collection URIs.
|
void |
VariableComponent.addVariantDerivation(String uriPrefix,
String displayId,
String version)
Adds the given variant derivation to the list of variant derivations.
|
void |
VariableComponent.addVariantDerivation(URI variantDerivation)
Adds the given variant derivation URI to the list of variant derivations URIs.
|
boolean |
Identified.addWasDerivedFrom(URI wasDerivedFromURI)
Adds the given wasDerivedFrom URI to the set of wasDerivedFrom URIs.
|
boolean |
Identified.addWasGeneratedBy(URI wasGeneratedByURI)
Adds the given wasGeneratedBy URI to the set of wasGeneratedBy URIs.
|
boolean |
Activity.addWasInformedBy(Activity activity)
Adds the URI of the given Activity instance to this Activity's
set of wasInformdBy URIs.
|
boolean |
Activity.addWasInformedBy(String displayId)
Constructs a compliant activity URI using the given activity display ID, and then adds this URI to
this activity's set of wasInformedBy URIs.
|
boolean |
Activity.addWasInformedBy(String displayId,
String version)
Constructs a compliant activity URI with the given display ID and version, and then adds this URI
to this activity's set of wasInformedBy URIs.
|
boolean |
Activity.addWasInformedBy(URI activityURI)
Adds the given activity URI to this Activity's set of wasInformedBy URIs.
|
SBOLDocument |
SBOLDocument.changeURIPrefixVersion(String URIPrefix,
String version,
String defaultVersion)
Copy all objects to an a new SBOL Document and change the URI prefix/version
of each object
|
void |
CombinatorialDerivation.checkDescendantsURIcompliance() |
void |
SBOLDocument.clearActivitys()
Removes all entries in the list of activities owned by this SBOL document.
|
void |
SBOLDocument.clearAgents()
Removes all entries in the list of agents owned by this SBOL document.
|
void |
SBOLDocument.clearAttachments()
Removes all entries in the list of attachments owned by this SBOL document.
|
void |
SBOLDocument.clearCollections()
Removes all entries in the list of collections owned by this SBOL document.
|
void |
SBOLDocument.clearCombinatorialDerivations()
Removes all entries in the list of combinatorial derivations owned by this SBOL document.
|
void |
SBOLDocument.clearComponentDefinitions()
Removes all entries in the list of component definitions owned by this SBOL
document.
|
void |
ComponentDefinition.clearComponents()
Removes all entries of this component definition's list of components.
|
void |
SBOLDocument.clearExperimentalData()
Removes all entries in the list of experimentalData owned by this SBOL document.
|
void |
SBOLDocument.clearExperiments()
Removes all entries in the list of experiments owned by this SBOL document.
|
void |
ModuleDefinition.clearFunctionalComponents()
Removes all entries of this module definition's list of functional components.
|
void |
SBOLDocument.clearGenericTopLevels()
Removes all entries in the list of generic top-levels owned by this SBOL
document.
|
void |
SBOLDocument.clearImplementations()
Removes all entries in the list of implementations owned by this SBOL document.
|
void |
SBOLDocument.clearModels()
Removes all entries in the list of models owned by this SBOL document.
|
void |
SBOLDocument.clearModuleDefinitions()
Removes all entries in the list of module definitions owned by this SBOL
document.
|
void |
SBOLDocument.clearPlans()
Removes all entries in the list of plans owned by this SBOL document.
|
void |
SBOLDocument.clearSequences()
Removes all entries in the list of sequences owned by this SBOL document.
|
Activity |
SBOLDocument.createActivity(String displayId)
Creates an activity, and then adds it to this SBOL document's list of
activities.
|
Activity |
SBOLDocument.createActivity(String displayId,
String version)
Creates an activity, and then adds it to this SBOL document's list of
activities.
|
Activity |
SBOLDocument.createActivity(String URIprefix,
String displayId,
String version)
Creates an activity, and then adds it to this SBOL document's list of
activities.
|
Agent |
SBOLDocument.createAgent(String displayId)
Creates an agent, and then adds it to this SBOL document's list of agents.
|
Agent |
SBOLDocument.createAgent(String displayId,
String version)
Creates an agent, and then adds it to this SBOL document's list of agents.
|
Agent |
SBOLDocument.createAgent(String URIprefix,
String displayId,
String version)
Creates an agent, and then adds it to this SBOL document's list of agents.
|
Annotation |
Identified.createAnnotation(QName qName,
boolean literal)
Creates an annotation using the given arguments, and
then adds to the list of annotaions.
|
Annotation |
Identified.createAnnotation(QName qName,
double literal)
Creates an annotation using the given arguments,
then adds to this instance's list of annotations.
|
Annotation |
Identified.createAnnotation(QName qName,
int literal)
Creates an annotation using the given arguments,
then adds to this instance's list of annotations.
|
Annotation |
Annotation.createAnnotation(QName qName,
QName nestedQName,
String nestedId,
List<Annotation> annotations)
Creates an annotation with nested annotations using the given arguments, and then adds to this instance's list of annotations.
|
Annotation |
Identified.createAnnotation(QName qName,
QName nestedQName,
String nestedId,
List<Annotation> annotations)
Creates an annotation with nested annotations using the given arguments, and then adds to this instance's list of annotations.
|
Annotation |
Identified.createAnnotation(QName qName,
String literal)
Creates an annotation using the given arguments,
then adds to this instance's list of annotations.
|
Annotation |
Identified.createAnnotation(QName qName,
URI literal)
Creates an annotation using the given arguments,
then adds to this instance's list of annotations.
|
Association |
Activity.createAssociation(String displayId,
URI agent)
Creates a child association for this activity with the given arguments,
and then adds to this activity's list of associations.
|
Attachment |
SBOLDocument.createAttachment(String URIprefix,
String displayId,
String version,
URI source)
Creates an attachment, and then adds it to this SBOL document's list of attachments.
|
Attachment |
SBOLDocument.createAttachment(String displayId,
String version,
URI source)
Creates an attachment, and then adds it to this SBOL document's list of attachments.
|
Attachment |
SBOLDocument.createAttachment(String displayId,
URI source)
Creates an attachment, and then adds it to this SBOL document's list of attachments.
|
Collection |
SBOLDocument.createCollection(String displayId)
Creates a collection first, and then adds to this SBOL document's list of
collections.
|
Collection |
SBOLDocument.createCollection(String displayId,
String version)
Creates a collection first, and then adds to this SBOL document's list of
collections.
|
Collection |
SBOLDocument.createCollection(String URIprefix,
String displayId,
String version)
Creates a collection first, and then adds to this SBOL document's list of
collections.
|
CombinatorialDerivation |
SBOLDocument.createCombinatorialDerivation(String displayId,
String version,
String templateDisplayId,
String templateVersion)
Creates a combinatorial derivation, and then adds it to this SBOL document's
list of combinatorial derivations.
|
CombinatorialDerivation |
SBOLDocument.createCombinatorialDerivation(String URIprefix,
String displayId,
String version,
URI template)
Creates a combinatorial derivation, and then adds it to this SBOL document's
list of combinatorial derivations.
|
CombinatorialDerivation |
SBOLDocument.createCombinatorialDerivation(String displayId,
String version,
URI template)
Creates a combinatorial derivation, and then adds it to this SBOL document's
list of combinatorial derivations.
|
CombinatorialDerivation |
SBOLDocument.createCombinatorialDerivation(String displayId,
URI template)
Creates a combinatorial derivation, and then adds it to this SBOL document's
list of combinatorial derivations.
|
Component |
ComponentDefinition.createComponent(String displayId,
AccessType access,
String definitionId)
Creates a child component for this component definition with the given arguments,
and then adds it to this component definition's list of components.
|
Component |
ComponentDefinition.createComponent(String displayId,
AccessType access,
String definitionId,
String version)
Creates a child component for this component definition with the given arguments,
and then adds it to this component definition's list of components.
|
Component |
ComponentDefinition.createComponent(String displayId,
AccessType access,
URI definitionURI)
Creates a child component for this component definition with the given arguments,
and then adds to this component definition's list of components.
|
ComponentDefinition |
SBOLDocument.createComponentDefinition(String displayId,
Set<URI> types)
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
|
ComponentDefinition |
SBOLDocument.createComponentDefinition(String displayId,
String version,
Set<URI> types)
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
|
ComponentDefinition |
SBOLDocument.createComponentDefinition(String URIprefix,
String displayId,
String version,
Set<URI> types)
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
|
ComponentDefinition |
SBOLDocument.createComponentDefinition(String URIprefix,
String displayId,
String version,
URI type)
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
|
ComponentDefinition |
SBOLDocument.createComponentDefinition(String displayId,
String version,
URI type)
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
|
ComponentDefinition |
SBOLDocument.createComponentDefinition(String displayId,
URI type)
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
|
void |
SBOLDocument.createCopy(SBOLDocument document)
Creates an identical copy of each top-level element of a document, and then
adds the created top-level to the corresponding list of top-levels in this
SBOL document.
|
TopLevel |
SBOLDocument.createCopy(TopLevel topLevel)
Creates an identical copy of the given top-level, and then adds the created
top-level to the corresponding list of top-levels in this SBOL document.
|
TopLevel |
SBOLDocument.createCopy(TopLevel topLevel,
String displayId)
Creates a copy of the given top-level with the given display ID, and then
adds the created top-level to the corresponding list of top-levels in this
SBOL document.
|
TopLevel |
SBOLDocument.createCopy(TopLevel topLevel,
String displayId,
String version)
Creates a copy of the given top-level with the given display ID and version,
and then adds the created top-level to the corresponding list of top-levels
in this SBOL document.
|
TopLevel |
SBOLDocument.createCopy(TopLevel topLevel,
String URIprefix,
String displayId,
String version)
Creates a copy of the given top-level with the given URI prefix, display ID
and version, and then adds the created top-level to the corresponding list of
top-levels in this SBOL document.
|
Experiment |
SBOLDocument.createExperiment(String displayId)
Creates a experiment first, and then adds to this SBOL document's list of
experiments.
|
Experiment |
SBOLDocument.createExperiment(String displayId,
String version)
Creates a experiment first, and then adds to this SBOL document's list of
experiments.
|
Experiment |
SBOLDocument.createExperiment(String URIprefix,
String displayId,
String version)
Creates a experiment first, and then adds to this SBOL document's list of
experiments.
|
ExperimentalData |
SBOLDocument.createExperimentalData(String displayId)
Creates a experimentalData first, and then adds to this SBOL document's list of
experimentalDatas.
|
ExperimentalData |
SBOLDocument.createExperimentalData(String displayId,
String version)
Creates a experimentalData first, and then adds to this SBOL document's list of
experimentalDatas.
|
ExperimentalData |
SBOLDocument.createExperimentalData(String URIprefix,
String displayId,
String version)
Creates a experimentalData first, and then adds to this SBOL document's list of
experimentalDatas.
|
FunctionalComponent |
ModuleDefinition.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 |
ModuleDefinition.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 |
ModuleDefinition.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.
|
GenericTopLevel |
SBOLDocument.createGenericTopLevel(String displayId,
QName rdfType)
Creates a generic top-level, and then adds it to this SBOL document's list of
generic top-levels.
|
GenericTopLevel |
SBOLDocument.createGenericTopLevel(String displayId,
String version,
QName rdfType)
Creates a generic top-level, and then adds it to this SBOL document's list of
generic top-levels.
|
GenericTopLevel |
SBOLDocument.createGenericTopLevel(String URIprefix,
String displayId,
String version,
QName rdfType)
Creates a generic top-level, and then adds it to this SBOL document's list of
generic top-levels.
|
Implementation |
SBOLDocument.createImplementation(String displayId)
Creates an implementation, and then adds it to this SBOL document's
list of implementations.
|
Implementation |
SBOLDocument.createImplementation(String displayId,
String version)
Creates an implementation, and then adds it to this SBOL document's
list of implementations.
|
Implementation |
SBOLDocument.createImplementation(String URIprefix,
String displayId,
String version)
Creates an implementation, and then adds it to this SBOL document's
list of implementations.
|
Interaction |
ModuleDefinition.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 |
ModuleDefinition.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.
|
MapsTo |
Component.createMapsTo(String displayId,
RefinementType refinement,
String localId,
String remoteId)
Creates a child mapsTo for this component with the given arguments, and then adds it to its list of mapsTos.
|
MapsTo |
Module.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 |
FunctionalComponent.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 |
Component.createMapsTo(String displayId,
RefinementType refinement,
URI local,
URI remote)
Creates a child mapsTo for this component with the given arguments,
and then adds it to its list of mapsTos.
|
MapsTo |
Module.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.
|
MapsTo |
FunctionalComponent.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.
|
Measure |
Measured.createMeasure(String displayId,
Double numericalValue,
URI unit)
Creates a child measure for this measured object with the given arguments,
and then adds to this measured object's list of measures.
|
Model |
SBOLDocument.createModel(String URIprefix,
String displayId,
String version,
URI source,
URI language,
URI framework)
Creates a model, and then adds it to this SBOL document's list of models.
|
Model |
SBOLDocument.createModel(String displayId,
String version,
URI source,
URI language,
URI framework)
Creates a model, and then adds it to this SBOL document's list of models.
|
Model |
SBOLDocument.createModel(String displayId,
URI source,
URI language,
URI framework)
Creates a model, and then adds it to this SBOL document's list of models.
|
Module |
ModuleDefinition.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 |
ModuleDefinition.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 |
ModuleDefinition.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.
|
ModuleDefinition |
SBOLDocument.createModuleDefinition(String displayId)
Creates a module definition, and then adds it to this SBOL document's list of
module definitions.
|
ModuleDefinition |
SBOLDocument.createModuleDefinition(String displayId,
String version)
Creates a module definition, and then adds it to this SBOL document's list of
module definitions.
|
ModuleDefinition |
SBOLDocument.createModuleDefinition(String URIprefix,
String displayId,
String version)
Creates a module definition with the given arguments, and then adds it to
this SBOL document's list of module definitions.
|
Participation |
Interaction.createParticipation(String displayId,
String participantId,
Set<URI> roles)
Creates a child participation for this interaction with the given arguments, and then adds to this interaction's
list of participations.
|
Participation |
Interaction.createParticipation(String displayId,
String participantId,
URI role)
Creates a child participation for this interaction with the given arguments,
and then adds to this interaction's list of participations.
|
Participation |
Interaction.createParticipation(String displayId,
URI participant,
Set<URI> roles)
Creates a child participation for this interaction with the given arguments,
and then adds to this interaction's list of participations.
|
Participation |
Interaction.createParticipation(String displayId,
URI participant,
URI role)
Creates a child participation for this interaction with the given arguments, and then adds to its list of participations.
|
Plan |
SBOLDocument.createPlan(String displayId)
Creates an plan, and then adds it to this SBOL document's list of plans.
|
Plan |
SBOLDocument.createPlan(String displayId,
String version)
Creates an plan, and then adds it to this SBOL document's list of plans.
|
Plan |
SBOLDocument.createPlan(String URIprefix,
String displayId,
String version)
Creates an plan, and then adds it to this SBOL document's list of plans.
|
void |
SBOLDocument.createRecursiveCopy(SBOLDocument document,
TopLevel topLevel) |
SBOLDocument |
SBOLDocument.createRecursiveCopy(TopLevel topLevel)
Creates an identical copy of the given top-level and returns it in a new
SBOLDocument.
|
Sequence |
SBOLDocument.createSequence(String URIprefix,
String displayId,
String version,
String elements,
URI encoding)
Creates a Sequence instance with the given arguments, and then adds it to
this SBOLDocument object's list of Sequence instances.
|
Sequence |
SBOLDocument.createSequence(String displayId,
String version,
String elements,
URI encoding)
Creates a Sequence instance with this SBOL document's
defaultURIprefix and the given arguments, and then adds it to this
SBOL document's list of Sequence instances. |
Sequence |
SBOLDocument.createSequence(String displayId,
String elements,
URI encoding)
Creates a Sequence instance with this SBOL document's
defaultURIprefix, the given arguments, and an empty version string,
and then adds it to this SBOL document's list of Sequence instances. |
SequenceAnnotation |
ComponentDefinition.createSequenceAnnotation(String displayId,
String locationId)
Creates a child sequence annotation for this component definition with the given arguments,
and then adds to this component definition's list of sequence annotations.
|
SequenceAnnotation |
ComponentDefinition.createSequenceAnnotation(String displayId,
String locationId,
int at)
Creates a child sequence annotation for this component definition with the given arguments,
and then adds to its list of sequence annotations.
|
SequenceAnnotation |
ComponentDefinition.createSequenceAnnotation(String displayId,
String locationId,
int start,
int end)
Creates a child sequence annotation for this component definition with the given arguments, and then adds to this ComponentDefinition's
list of sequence annotations.
|
SequenceAnnotation |
ComponentDefinition.createSequenceAnnotation(String displayId,
String locationId,
int start,
int end,
OrientationType orientation)
Creates a child sequence annotation for this ComponentDefinition
instance with the given arguments, and then adds to this ComponentDefinition's
list of sequence annotations.
|
SequenceAnnotation |
ComponentDefinition.createSequenceAnnotation(String displayId,
String locationId,
int at,
OrientationType orientation)
Creates a child sequence annotation for this component definition with the given arguments,
and then adds to its list of sequence annotations.
|
SequenceAnnotation |
ComponentDefinition.createSequenceAnnotation(String displayId,
String locationId,
OrientationType orientation)
Creates a child sequence annotation for this component definition with the given arguments,
and then adds to this component definition's list of sequence annotations.
|
SequenceConstraint |
ComponentDefinition.createSequenceConstraint(String displayId,
RestrictionType restriction,
String subjectId,
String objectId)
Creates a child sequence constraint for this component definition with the given arguments,
and then adds to this component definition's list of sequence constraints.
|
SequenceConstraint |
ComponentDefinition.createSequenceConstraint(String displayId,
RestrictionType restriction,
URI subjectURI,
URI objectURI)
Creates a child sequence constraint for this component definition
with the given arguments, and then adds to this component definition's
list of sequence constraints.
|
Usage |
Activity.createUsage(String displayId,
URI entity)
Creates a child usage for this activity with the given arguments,
and then adds to this activity's list of usages.
|
VariableComponent |
CombinatorialDerivation.createVariableComponent(String displayId,
OperatorType operator,
String variableId)
Creates a child variable component for this combinatorial derivation with the
given arguments, and then adds to this combinatorial derivation's list of
variable components.
|
VariableComponent |
CombinatorialDerivation.createVariableComponent(String displayId,
OperatorType operator,
URI variable)
Creates a child variable component for this combinatorial derivation with the
given arguments, and then adds to this combinatorial derivation's list of
variable components.
|
CombinatorialDerivation |
SBOLDocument.getCombinatorialDerivation(String displayId,
String version)
Returns the combinatorial derivation matching the given display ID and
version from this SBOL document's list of combinatorial derivations.
|
Implementation |
SBOLDocument.getImplementation(String displayId,
String version)
Returns the implementation matching the given display ID and
version from this SBOL document's list of implementations.
|
static String |
SBOLReader.getSBOLVersion(File file)
Takes in a given RDF file and returns its SBOL version.
|
static String |
SBOLReader.getSBOLVersion(InputStream in)
Takes in a given RDF input stream and returns the SBOL version of the file.
|
static String |
SBOLReader.getSBOLVersion(String fileName)
Takes in a given RDF file name and returns the SBOL version of the file.
|
List<Component> |
ComponentDefinition.getSortedComponents()
Returns a sorted list of components owned by this component definition.
|
void |
SBOLDocument.read(File file)
Takes in a given RDF file and adds the data read to this SBOL document.
|
static SBOLDocument |
SBOLReader.read(File file)
Parses the given RDF file and stores its contents in an SBOLDocument object.
|
void |
SBOLDocument.read(InputStream in)
Takes in a given RDF input stream and adds the data read to this SBOL
document.
|
static SBOLDocument |
SBOLReader.read(InputStream in)
Takes in a given RDF InputStream and converts the file to an SBOLDocument.
|
void |
SBOLDocument.read(String fileName)
Takes in a given RDF file name and adds the data read to this SBOLDocument.
|
static SBOLDocument |
SBOLReader.read(String fileName)
Takes in the given RDF filename and converts the file to an SBOLDocument.
|
boolean |
SBOLDocument.removeActivity(Activity activity)
Removes the given activity from this SBOL document's list of activities.
|
boolean |
SBOLDocument.removeAgent(Agent agent)
Removes the given agent from this SBOL document's list of agents.
|
boolean |
SBOLDocument.removeAttachment(Attachment attachment)
Removes the given attachment from this SBOL document's list of attachments.
|
boolean |
SBOLDocument.removeCollection(Collection collection)
Removes the given collection from this SBOL document's list of collections.
|
boolean |
SBOLDocument.removeCombinatorialDerivation(CombinatorialDerivation combinatorialDerivation)
Removes the given combinatorial derivation from this SBOL document's list of
combinatorial derivations.
|
boolean |
ComponentDefinition.removeComponent(Component component)
Removes the given component from the list of components.
|
boolean |
SBOLDocument.removeComponentDefinition(ComponentDefinition componentDefinition)
Removes the given component definition from this SBOL document's list of
component definitions.
|
boolean |
SBOLDocument.removeExperiment(Experiment experiment)
Removes the given experiment from this SBOL document's list of experiments.
|
boolean |
SBOLDocument.removeExperimentalData(ExperimentalData experimentalDatum)
Removes the given experimentalData from this SBOL document's list of experimentalData.
|
boolean |
ModuleDefinition.removeFunctionalComponent(FunctionalComponent functionalComponent)
Removes the given functional component from this module definition's list of
functional components.
|
boolean |
SBOLDocument.removeGenericTopLevel(GenericTopLevel genericTopLevel)
Removes the given generic top-level from this SBOL document's list of generic
top-levels.
|
boolean |
SBOLDocument.removeImplementation(Implementation implementation)
Removes the given implementation from this SBOL document's list of
implementations.
|
boolean |
SequenceAnnotation.removeLocation(Location location)
Removes the given location from the list of locations.
|
boolean |
SBOLDocument.removeModel(Model model)
Removes the given model from this SBOL document's list of models.
|
boolean |
SBOLDocument.removeModuleDefinition(ModuleDefinition moduleDefinition)
Removes the given module definition from this SBOL document's list of module
definitions.
|
boolean |
SBOLDocument.removePlan(Plan plan)
Removes the given plan from this SBOL document's list of plans.
|
boolean |
Participation.removeRole(URI roleURI)
Removes the given role from the set of roles.
|
boolean |
SBOLDocument.removeSequence(Sequence sequence)
Removes the given sequence from this SBOL document's list of sequences.
|
void |
SBOLDocument.removeTopLevel(TopLevel topLevel)
Method to remove a TopLevel object
|
boolean |
ComponentDefinition.removeType(URI typeURI)
Removes the given type URI from the set of types.
|
boolean |
Interaction.removeType(URI typeURI)
Removes the given type URI from this interation's the set of type URIs.
|
TopLevel |
SBOLDocument.rename(TopLevel topLevel,
String displayId)
Renames the given top-level's display ID with the given one.
|
TopLevel |
SBOLDocument.rename(TopLevel topLevel,
String displayId,
String version)
Renames the given top-level's display ID and version with the given ones.
|
TopLevel |
SBOLDocument.rename(TopLevel topLevel,
String URIprefix,
String displayId,
String version)
Renames the given top-level's URI prefix, display ID, and version with the
given ones.
|
void |
ComponentInstance.setAccess(AccessType access)
Sets the access property to the given one.
|
void |
Association.setAgent(URI agent) |
void |
Annotation.setAnnotations(List<Annotation> annotations)
Sets the list of Annotations of the nested value property.
|
void |
Cut.setAt(int at)
Sets the at property of this Cut instance to the given one.
|
void |
TopLevel.setAttachments(Set<URI> attachments)
Clears the existing set of attachments first, and then adds the given set of
the attachments to this top level.
|
void |
Implementation.setBuilt(TopLevel built)
Sets the the built property to the given one.
|
void |
Implementation.setBuilt(URI builtURI)
Sets the URI of the built property to the given one.
|
void |
SequenceAnnotation.setComponent(String displayId)
Sets this sequence annotation's reference component (its identity URI) to the one matching
the given display ID.
|
void |
SequenceAnnotation.setComponent(URI componentURI)
Sets the reference component's identity URI to the given URI.
|
void |
ComponentInstance.setDefinition(URI definition)
Sets the definition property to the given one.
|
void |
Component.setDefinition(URI definition)
Sets the definition property to the given one.
|
void |
Module.setDefinition(URI definitionURI)
Sets the reference definition URI to this module.
|
void |
FunctionalComponent.setDefinition(URI definition)
Sets the definition property to the given one.
|
void |
FunctionalComponent.setDirection(DirectionType direction)
Sets the direction property of this functional component to the given one.
|
void |
Sequence.setElements(String elements)
Sets the elements property to the given argument.
|
void |
Sequence.setEncoding(URI encoding)
Sets the encoding property to the given argument.
|
void |
Range.setEnd(int value)
Sets the end position of this range.
|
void |
Usage.setEntity(URI entity) |
void |
Experiment.setExperimentalData(Set<URI> experimentalData)
Clears the existing set of experimentalData of this Experiment instance first, then adds the given
set of the experimentalData references to it.
|
void |
Model.setFramework(URI framework)
Sets the framework property to the given one.
|
void |
Model.setLanguage(URI language)
Sets the language property to the given one.
|
void |
MapsTo.setLocal(URI local)
Sets the local property of this mapsTo to the given one.
|
void |
Collection.setMembers(Set<URI> members)
Clears the existing set of members of this Collection instance first, then adds the given
set of the member references to it.
|
void |
ModuleDefinition.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 |
Annotation.setNestedIdentity(URI uri)
Sets the nested URI for this annotation.
|
void |
Annotation.setNestedQName(QName qName)
Sets the nested QName for this annotation.
|
void |
Measure.setNumericalValue(Double hasNumericalValue) |
void |
SequenceConstraint.setObject(URI objectURI)
Sets the reference object component's identity URI to the given one.
|
void |
VariableComponent.setOperator(OperatorType operator)
Sets the operator property to the given one.
|
void |
Participation.setParticipant(URI participant)
Sets the participant property of this object to the given one.
|
void |
Association.setPlan(URI plan) |
void |
Annotation.setQName(QName qName)
Sets the QName of this annotation.
|
void |
GenericTopLevel.setRDFType(QName rdfType)
Set the RDF type property of this GenericTopLevel instance to the specified one.
|
void |
MapsTo.setRemote(URI remote)
Sets the remote property of this mapsTo to the given one.
|
void |
SequenceConstraint.setRestriction(RestrictionType restriction)
Sets the restriction property to the given one.
|
void |
SequenceConstraint.setRestriction(URI restrictionURI)
Sets the reference subject component's identity URI to the given one.
|
void |
Component.setRoleIntegration(RoleIntegrationType roleIntegration)
Sets the roleIntegration property of this object to the given one.
|
void |
Component.setRoles(Set<URI> roles)
Clears the existing set of roles first, and then adds the given
set of the roles to this component.
|
void |
SequenceAnnotation.setRoles(Set<URI> roles)
Clears the existing set of roles first, and then adds the given
set of the roles to this sequence annotation.
|
void |
Participation.setRoles(Set<URI> roles)
Clears the existing set of roles first, and then adds the given
set of the roles to this participation.
|
void |
Location.setSequence(URI sequence)
Sets the sequence property to the given one.
|
void |
ComponentDefinition.setSequences(Set<URI> sequences)
Clears the existing set of sequences first, and then adds the given
set of the sequences to this component definition.
|
void |
Model.setSource(URI source)
Sets the source property to the given one.
|
void |
Attachment.setSource(URI source)
Sets the source property to the given one.
|
void |
Range.setStart(int value)
Sets the start position of this range.
|
void |
CombinatorialDerivation.setStrategy(StrategyType strategy)
Sets the strategy property to the given one.
|
void |
Annotation.setStringValue(String literal)
Sets the string representation of the value property.
|
void |
SequenceConstraint.setSubject(URI subjectURI)
Sets the reference subject Component URI to the given
subjectURI. |
void |
CombinatorialDerivation.setTemplate(URI template)
Sets the template property to the given one.
|
void |
ComponentDefinition.setTypes(Set<URI> types)
Clears the existing set of types first, then adds the given
set of the types to this component definition.
|
void |
Interaction.setTypes(Set<URI> types)
Clears the existing set of type URIs first, then adds the given
set of the type URIs to this interaction.
|
void |
Measure.setUnit(URI hasUnit) |
void |
Annotation.setURIValue(URI literal)
Sets the string representation of the value property.
|
void |
VariableComponent.setVariable(URI variable)
Sets the variable property to the given one.
|
void |
CombinatorialDerivation.setVariableComponents(Set<VariableComponent> variableComponents)
Clears the existing set of variable components first, and then adds the given
set of the variable components to this combinatorial derivation.
|
void |
VariableComponent.setVariantCollections(Set<URI> variantCollections)
Clears the existing set of variant collections first, and then adds the given
set of the variant collections to this variable component.
|
void |
VariableComponent.setVariantDerivations(Set<URI> variantDerivations)
Clears the existing set of variant derivations first, and then adds the given
set of the variant derivations to this variable component.
|
void |
VariableComponent.setVariants(Set<URI> variants)
Clears the existing set of variants first, and then adds the given
set of the variants to this variable component.
|
void |
Identified.setWasDerivedFrom(URI wasDerivedFrom)
Deprecated.
|
void |
Identified.setWasDerivedFroms(Set<URI> wasDerivedFroms)
Clears the existing set of wasDerivedFroms first, and then adds the given
set of the wasDerivedFroms.
|
void |
Identified.setWasGeneratedBys(Set<URI> wasGeneratedBys)
Clears the existing set of wasGeneratedBys first, and then adds the given
set of the wasGeneratedBys.
|
void |
Activity.setWasInformedBys(Set<URI> wasInformedBys) |
void |
Component.unsetRoleIntegration()
Sets the roleIntegration property of this object to
null. |
| Constructor and Description |
|---|
Annotation(QName qName,
boolean literal)
Constructs an annotation using the given qName and the boolean type literal.
|
Annotation(QName qName,
double literal)
Constructs an annotation using the given qName and the double type literal.
|
Annotation(QName qName,
int literal)
Constructs an annotation using the given qName and the integer type literal.
|
Annotation(QName qName,
String literal)
Constructs an annotation using the given qName and the string type literal.
|
Annotation(QName qName,
URI literal)
Constructs an annotation using the given qName and the
URI type literal. |