Package | Description |
---|---|
org.sbolstandard.core2 |
Modifier and Type | Method and Description |
---|---|
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 |
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.
|
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 |
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.
|
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.
|
static void |
SBOLFactory.addNamespace(QName qName)
Adds the given namespace QName to the internal SBOL document used by the factory.
|
void |
SBOLDocument.addNamespace(QName qName)
Adds the given namespace QName to this SBOL document.
|
static void |
SBOLFactory.addNamespace(URI namespaceURI,
String prefix)
Adds the given namespace URI and its prefix to the internal SBOL document used by the factory.
|
void |
SBOLDocument.addNamespace(URI nameSpaceURI,
String prefix)
Adds the given namespace URI and its prefix to this SBOL document.
|
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 |
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 |
SequenceAnnotation.addRole(URI roleURI)
Adds the given role to this sequence annotation's set of roles.
|
boolean |
Component.addRole(URI roleURI)
Adds the given role URI to this component's set of role URIs.
|
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.
|
boolean |
ComponentDefinition.addType(URI typeURI)
Adds the given type URI to this component definition's set of type URIs.
|
SBOLDocument |
SBOLDocument.changeURIPrefixVersion(String URIPrefix,
String version)
Copy all objects to an a new SBOL Document and change the URI prefix/version of each object
|
static void |
SBOLFactory.clearCollections()
Removes all entries in the list of collections owned by the internal SBOL document of
the factory.
|
void |
SBOLDocument.clearCollections()
Removes all entries in the list of collections owned by this SBOL document.
|
static void |
SBOLFactory.clearComponentDefinitions()
Removes all entries in the list of component definitions
owned by the internal SBOL document of the factory.
|
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 |
ModuleDefinition.clearFunctionalComponents()
Removes all entries of this module definition's list of functional components.
|
static void |
SBOLFactory.clearGenericTopLevels()
Removes all entries in the list of generic top-levels
owned by the internal SBOL document of the factory.
|
void |
SBOLDocument.clearGenericTopLevels()
Removes all entries in the list of generic top-levels
owned by this SBOL document.
|
static void |
SBOLFactory.clearModels()
Removes all entries in the list of models owned by the internal SBOL document
of thie factory.
|
void |
SBOLDocument.clearModels()
Removes all entries in the list of models owned by this SBOL document.
|
static void |
SBOLFactory.clearModuleDefinitions()
Removes all entries in the list of module definitions
owned by the internal SBOL document of the factory.
|
void |
SBOLDocument.clearModuleDefinitions()
Removes all entries in the list of module definitions owned by this SBOL document.
|
static void |
SBOLFactory.clearSequences()
Removes all entries in the list of sequences owned by the internal SBOL document of
the factory.
|
void |
SBOLDocument.clearSequences()
Removes all entries in the list of sequences owned by this SBOL document.
|
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 |
Identified.createAnnotation(QName qName,
QName nestedQName,
URI nestedURI,
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.
|
static Collection |
SBOLFactory.createCollection(String displayId)
Creates a collection first, and then adds to the factory's internal SBOL document's list of collections.
|
Collection |
SBOLDocument.createCollection(String displayId)
Creates a collection first, and then adds to this SBOL document's list of collections.
|
static Collection |
SBOLFactory.createCollection(String displayId,
String version)
Creates a collection first, and then adds to the factory's internal 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.
|
static Collection |
SBOLFactory.createCollection(String URIprefix,
String displayId,
String version)
Creates a collection first, and then adds to factory's internal 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.
|
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.
|
static ComponentDefinition |
SBOLFactory.createComponentDefinition(String displayId,
Set<URI> types)
Creates a component definition, and then adds it to the factory's internal SBOL document's list of component definitions.
|
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.
|
static ComponentDefinition |
SBOLFactory.createComponentDefinition(String displayId,
String version,
Set<URI> types)
Creates a component definition, and then adds it to the factory's internal 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.
|
static ComponentDefinition |
SBOLFactory.createComponentDefinition(String URIprefix,
String displayId,
String version,
Set<URI> types)
Creates a component definition, and then adds it to the factory's internal 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.
|
static ComponentDefinition |
SBOLFactory.createComponentDefinition(String URIprefix,
String displayId,
String version,
URI type)
Creates a component definition, and then adds it to the factory's internal 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.
|
static ComponentDefinition |
SBOLFactory.createComponentDefinition(String displayId,
String version,
URI type)
Creates a component definition, and then adds it to the factory's internal 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.
|
static ComponentDefinition |
SBOLFactory.createComponentDefinition(String displayId,
URI type)
Creates a component definition, and then adds it to the factory's internal 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.
|
static void |
SBOLFactory.createCopy(SBOLDocument document)
Creates an identical copy of each top-level element of the given SBOL document, and then adds the created top-level to the corresponding
list of top-levels in the factory's internal SBOL document.
|
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.
|
static TopLevel |
SBOLFactory.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 the factory's internal 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.
|
static TopLevel |
SBOLFactory.createCopy(TopLevel topLevel,
String displayId)
Creates an identical copy of the given top-level, and then adds the created top-level to the
corresponding list of top-levels in the factory's internal 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.
|
static TopLevel |
SBOLFactory.createCopy(TopLevel topLevel,
String displayId,
String version)
Creates an identical copy of the given top-level, and then adds the created top-level to the
corresponding list of top-levels in the factory's internal 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.
|
static TopLevel |
SBOLFactory.createCopy(TopLevel topLevel,
String URIprefix,
String displayId,
String version)
Creates an identical copy of the given top-level, and then adds the created top-level to the
corresponding list of top-levels in the factory's internal 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.
|
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.
|
static GenericTopLevel |
SBOLFactory.createGenericTopLevel(String displayId,
QName rdfType)
Creates a generic top-level, and then adds it to the factory's internal SBOL document's list of generic top-levels.
|
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.
|
static GenericTopLevel |
SBOLFactory.createGenericTopLevel(String displayId,
String version,
QName rdfType)
Creates a generic top-level, and then adds it to the factory's internal 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.
|
static GenericTopLevel |
SBOLFactory.createGenericTopLevel(String URIprefix,
String displayId,
String version,
QName rdfType)
Creates a generic top-level, and then adds it to the factory's internal 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.
|
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 |
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,
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,
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.
|
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.
|
static Model |
SBOLFactory.createModel(String URIprefix,
String displayId,
String version,
URI source,
URI language,
URI framework)
Creates a model, and then adds it to the factory's internal SBOL document's list of models.
|
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.
|
static Model |
SBOLFactory.createModel(String displayId,
String version,
URI source,
URI language,
URI framework)
Creates a model, and then adds it to the factory's internal 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.
|
static Model |
SBOLFactory.createModel(String displayId,
URI source,
URI language,
URI framework)
Creates a model, and then adds it to the factory's internal 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.
|
static ModuleDefinition |
SBOLFactory.createModuleDefinition(String displayId)
Creates a module definition, and then adds it to the factory's internal SBOL document's list of module definitions.
|
ModuleDefinition |
SBOLDocument.createModuleDefinition(String displayId)
Creates a module definition, and then adds it to this SBOL document's list of module definitions.
|
static ModuleDefinition |
SBOLFactory.createModuleDefinition(String displayId,
String version)
Creates a module definition, and then adds it to the factory's internal 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.
|
static ModuleDefinition |
SBOLFactory.createModuleDefinition(String URIprefix,
String displayId,
String version)
Creates a module definition, and then adds it to the factory's internal 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.
|
static SBOLDocument |
SBOLFactory.createRecursiveCopy(TopLevel topLevel)
Creates an identical copy of the given top-level and returns it in
a new SBOL document.
|
SBOLDocument |
SBOLDocument.createRecursiveCopy(TopLevel topLevel)
Creates an identical copy of the given top-level and returns it in
a new SBOLDocument.
|
static Sequence |
SBOLFactory.createSequence(String URIprefix,
String displayId,
String version,
String elements,
URI encoding)
Creates a sequence with the given arguments, and then adds it to the factory's internal
SBOL document's list of sequences.
|
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.
|
static Sequence |
SBOLFactory.createSequence(String displayId,
String version,
String elements,
URI encoding)
Creates a sequence with the given arguments, and then adds it to the factory's internal
SBOL document's list of sequences.
|
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. |
static Sequence |
SBOLFactory.createSequence(String displayId,
String elements,
URI encoding)
Creates a sequence with the given arguments, and then adds it to the factory's internal
SBOL document's list of sequences.
|
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.
|
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.
|
static SBOLDocument |
SBOLReader.read(File file)
Parses the given RDF file and stores its contents in an SBOLDocument object.
|
static void |
SBOLFactory.read(File file)
Takes in a given RDF file and adds the data read to the factory's internal SBOL document.
|
void |
SBOLDocument.read(File file)
Takes in a given RDF file 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.
|
static void |
SBOLFactory.read(InputStream in)
Takes in a given RDF input stream and add the data read to the factory's internal SBOL document.
|
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,
String fileType)
Takes in a given InputStream and fileType, and convert the file to an SBOLDocument.
|
static SBOLDocument |
SBOLReader.read(String fileName)
Takes in the given RDF filename and converts the file to an SBOLDocument.
|
static void |
SBOLFactory.read(String fileName)
Takes in a given RDF file name and add the data read to the factory's internal SBOL document.
|
void |
SBOLDocument.read(String fileName)
Takes in a given RDF file name and adds the data read to this SBOLDocument.
|
static boolean |
SBOLFactory.removeCollection(Collection collection)
Removes the given collection from the factory's internal SBOL document's list of collections.
|
boolean |
SBOLDocument.removeCollection(Collection collection)
Removes the given collection from this SBOL document's list of collections.
|
boolean |
ComponentDefinition.removeComponent(Component component)
Removes the given component from the list of components.
|
static boolean |
SBOLFactory.removeComponentDefinition(ComponentDefinition componentDefinition)
Removes the given component definition from the factory's internal SBOL document's list of component definitions.
|
boolean |
SBOLDocument.removeComponentDefinition(ComponentDefinition componentDefinition)
Removes the given component definition from this SBOL document's list of component definitions.
|
boolean |
ModuleDefinition.removeFunctionalComponent(FunctionalComponent functionalComponent)
Removes the given functional component from this module definition's list of
functional components.
|
static boolean |
SBOLFactory.removeGenericTopLevel(GenericTopLevel genericTopLevel)
Removes the given generic top-level from the factory's internal SBOL document's list of generic top-levels.
|
boolean |
SBOLDocument.removeGenericTopLevel(GenericTopLevel genericTopLevel)
Removes the given generic top-level from this SBOL document's list of generic top-levels.
|
boolean |
SequenceAnnotation.removeLocation(Location location)
Removes the given location from the list of locations.
|
static boolean |
SBOLFactory.removeModel(Model model)
Removes the given model from the factory's internal SBOL document's list of models.
|
boolean |
SBOLDocument.removeModel(Model model)
Removes the given model from this SBOL document's list of models.
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static boolean |
SBOLFactory.removeModuleDefinition(ModuleDefinition moduleDefinition)
Removes the given module definition from this SBOL document's list of module definitions.
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boolean |
SBOLDocument.removeModuleDefinition(ModuleDefinition moduleDefinition)
Removes the given module definition from this SBOL document's list of module definitions.
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boolean |
Participation.removeRole(URI roleURI)
Removes the given role from the set of roles.
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static boolean |
SBOLFactory.removeSequence(Sequence sequence)
Removes the given sequence from the factory's internal SBOL document's list of sequences.
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boolean |
SBOLDocument.removeSequence(Sequence sequence)
Removes the given sequence from this SBOL document's list of sequences.
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void |
SBOLDocument.removeTopLevel(TopLevel topLevel)
Method to remove a TopLevel object
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boolean |
Interaction.removeType(URI typeURI)
Removes the given type URI from this interation's the set of type URIs.
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boolean |
ComponentDefinition.removeType(URI typeURI)
Removes the given type URI from the set of types.
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TopLevel |
SBOLDocument.rename(TopLevel topLevel,
String displayId)
Renames the given top-level's display ID with the given one.
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TopLevel |
SBOLDocument.rename(TopLevel topLevel,
String displayId,
String version)
Renames the given top-level's display ID and version with the given ones.
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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.
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void |
ComponentInstance.setAccess(AccessType access)
Sets the access property to the given one.
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void |
Cut.setAt(int at)
Sets the at property of this Cut instance to the given one.
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void |
SequenceAnnotation.setComponent(String displayId)
Sets this sequence annotation's reference component (its identity URI) to the one matching
the given display ID.
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void |
SequenceAnnotation.setComponent(URI componentURI)
Sets the reference component's identity URI to the given URI.
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void |
Module.setDefinition(URI definitionURI)
Sets the reference definition URI to this module.
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void |
FunctionalComponent.setDefinition(URI definition)
Sets the definition property to the given one.
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void |
ComponentInstance.setDefinition(URI definition)
Sets the definition property to the given one.
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void |
Component.setDefinition(URI definition)
Sets the definition property to the given one.
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void |
FunctionalComponent.setDirection(DirectionType direction)
Sets the direction property of this functional component to the given one.
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void |
Sequence.setElements(String elements)
Sets the elements property to the given argument.
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void |
Sequence.setEncoding(URI encoding)
Sets the encoding property to the given argument.
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void |
Range.setEnd(int value)
Sets the end position of this range.
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void |
Model.setFramework(URI framework)
Sets the framework property to the given one.
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void |
Model.setLanguage(URI language)
Sets the language property to the given one.
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void |
MapsTo.setLocal(URI local)
Sets the local property of this mapsTo to the given one.
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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.
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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.
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void |
SequenceConstraint.setObject(URI objectURI)
Sets the reference object component's identity URI to the given one.
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void |
Participation.setParticipant(URI participant)
Sets the participant property of this object to the given one.
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void |
GenericTopLevel.setRDFType(QName rdfType)
Set the RDF type property of this GenericTopLevel instance to the specified one.
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void |
MapsTo.setRemote(URI remote)
Sets the remote property of this mapsTo to the given one.
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void |
SequenceConstraint.setRestriction(RestrictionType restriction)
Sets the restriction property to the given one.
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void |
SequenceConstraint.setRestriction(URI restrictionURI)
Sets the reference subject component's identity URI to the given one.
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void |
Component.setRoleIntegration(RoleIntegrationType roleIntegration)
Sets the roleIntegration property of this object to the given one.
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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.
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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.
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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.
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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.
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void |
Model.setSource(URI source)
Sets the source property to the given one.
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void |
Range.setStart(int value)
Sets the start position of this range.
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void |
SequenceConstraint.setSubject(URI subjectURI)
Sets the reference subject Component URI to the given
subjectURI . |
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.
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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.
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void |
Identified.setWasDerivedFrom(URI wasDerivedFrom)
Deprecated.
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void |
Component.unsetRoleIntegration()
Sets the roleIntegration property of this object to
null . |
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