- CATALYSIS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Modification of the velocity of a reaction by lowering the energy of the transition state
(
SBO:0000172).
- CATALYST - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Substance that accelerates the velocity of a chemical reaction without itself being
consumed or transformed (
SBO:0000013).
- CATALYTIC_ACTIVATOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
An essential activator that affects the apparent value of the catalytic constant
(
SBO:0000534).
- CDS - Static variable in class org.sbolstandard.core2.SequenceOntology
-
A contiguous sequence which begins with, and includes, a start codon, and ends with, and includes, a stop codon
(
SO:0000316).
- CELLML - Static variable in class org.sbolstandard.core2.EDAMOntology
-
CellML, the format for mathematical models of biological and other networks
(
CELLML).
- changeURIPrefixVersion(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Copy all objects to an a new SBOL Document and change the URI prefix/version
of each object
- checkDescendantsURIcompliance() - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
- CIRCULAR - Static variable in class org.sbolstandard.core2.SequenceOntology
-
A quality of a nucleotide polymer that has no terminal nucleotide residues.
- CIS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Positional relationship between entities on the same strand (e.g.
- clearActivitys() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of activities owned by this SBOL document.
- clearAgents() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of agents owned by this SBOL document.
- clearAnnotations() - Method in class org.sbolstandard.core2.Identified
-
Removes all entries of this instance's list of annotations.
- clearAssociations() - Method in class org.sbolstandard.core2.Activity
-
Removes all entries of this activity's list of associations.
- clearAttachments() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of attachments owned by this SBOL document.
- clearAttachments() - Method in class org.sbolstandard.core2.TopLevel
-
Removes all entries of this top level's list of attachments.
- clearCollections() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of collections owned by this SBOL document.
- clearCombinatorialDerivations() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of combinatorial derivations owned by this SBOL document.
- clearComponentDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of component definitions owned by this SBOL
document.
- clearComponents() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes all entries of this component definition's list of components.
- clearErrors() - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the error list that is used to store SBOL validation exceptions
during reading to empty.
- clearErrors() - Static method in class org.sbolstandard.core2.SBOLValidate
-
Empties the error list that is used to store SBOL validation exceptions.
- clearErrors() - Static method in class org.sbolstandard.core2.SBOLWriter
-
Sets the error list that is used to store SBOL conversion exceptions
during reading to empty.
- clearExperimentalData() - Method in class org.sbolstandard.core2.Experiment
-
Removes all entries of this Experiment's set of reference
experimentalData URIs.
- clearExperimentalData() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of experimentalData owned by this SBOL document.
- clearExperiments() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of experiments owned by this SBOL document.
- clearFunctionalComponents() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Removes all entries of this module definition's list of functional components.
- clearGenericTopLevels() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of generic top-levels owned by this SBOL
document.
- clearImplementations() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of implementations owned by this SBOL document.
- clearInteractions() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Removes all entries of this module definition's list of interactions.
- clearMapsTos() - Method in class org.sbolstandard.core2.Component
-
Removes all entries the list of mapsTos.
- clearMapsTos() - Method in class org.sbolstandard.core2.FunctionalComponent
-
Removes all entries of this object's list of
mapsTos.
- clearMapsTos() - Method in class org.sbolstandard.core2.Module
-
Removes all entries of this module's list of mapsTos.
- clearMeasures() - Method in class org.sbolstandard.core2.Measured
-
Removes all entries of this measured object list of measures.
- clearMembers() - Method in class org.sbolstandard.core2.Collection
-
Removes all entries of this Collection instance's set of reference
member URIs.
- clearModels() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Removes all entries of this module definition's set of model URIs.
- clearModels() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of models owned by this SBOL document.
- clearModuleDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of module definitions owned by this SBOL
document.
- clearModules() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Removes all entries of this module definition's list of modules.
- clearNamespaces() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all non-required namespaces from this SBOL document.
- clearParticipations() - Method in class org.sbolstandard.core2.Interaction
-
Removes all entries of this interaction list of participations.
- clearPlans() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of plans owned by this SBOL document.
- clearRegistries() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all registries from this SBOL document.
- clearRoles() - Method in class org.sbolstandard.core2.Association
-
Removes all entries of this associations's set of role URIs.
- clearRoles() - Method in class org.sbolstandard.core2.Component
-
Removes all entries of this component's set of role URIs.
- clearRoles() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes all entries of this component definition's set of role URIs.
- clearRoles() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Removes all entries of this module definition's set of role URIs.
- clearRoles() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Removes all entries of this sequence annotation's set of roles.
- clearRoles() - Method in class org.sbolstandard.core2.Usage
-
Removes all entries of this usage's set of role URIs.
- clearSequenceAnnotations() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes all entries of this component definition's list of sequence annotations.
- clearSequenceConstraints() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes all entries of this component definition's list of sequence constraints.
- clearSequences() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes all entries of this component definition's set of reference
sequence URIs.
- clearSequences() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of sequences owned by this SBOL document.
- clearTypes() - Method in class org.sbolstandard.core2.Measure
-
Removes all entries of this measure's set of type URIs.
- clearUsages() - Method in class org.sbolstandard.core2.Activity
-
Removes all entries of this activity's list of usages.
- clearVariableComponents() - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Removes all entries of this combinatorial derivation's list of variable
components.
- clearVariantCollections() - Method in class org.sbolstandard.core2.VariableComponent
-
removes all entries of this variable component's set of variant collection
URIs.
- clearVariantDerivations() - Method in class org.sbolstandard.core2.VariableComponent
-
removes all entries of this variable component's set of variant derivation
URIs.
- clearVariants() - Method in class org.sbolstandard.core2.VariableComponent
-
removes all entries of this variable component's set of variant URIs.
- clearWasDerivedFroms() - Method in class org.sbolstandard.core2.Identified
-
Removes all entries from the set of wasDerivedFrom URIs.
- clearWasGeneratedBys() - Method in class org.sbolstandard.core2.Identified
-
Removes all entries from the set of wasGeneratedBy URIs.
- clearWasInformedBys() - Method in class org.sbolstandard.core2.Activity
-
Removes all entries of this activity's set of reference
wasInformedBy URIs.
- CLEAVAGE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Rupture of a covalent bond resulting in the conversion of one physical entity into
several physical entities
(
SBO:0000178).
- Collection - Class in org.sbolstandard.core2
-
Represents an Collection object in the SBOL data model.
- COLLECTION - Static variable in class org.sbolstandard.core2.TopLevel
-
The abbreviation for the Collection type in URI
- COMBINATORIAL_DERIVATION - Static variable in class org.sbolstandard.core2.TopLevel
-
The abbreviation for the CombinatorialDerivation type in URI
- CombinatorialDerivation - Class in org.sbolstandard.core2
-
Represents a CombinatorialDerivation object in the SBOL data model.
- compareDocuments(String, SBOLDocument, String, SBOLDocument) - Static method in class org.sbolstandard.core2.SBOLValidate
-
Compares the given two SBOL documents and outputs the difference into the
list of errors.
- compareTo(Annotation) - Method in class org.sbolstandard.core2.Annotation
-
- compareTo(Location) - Method in class org.sbolstandard.core2.Cut
-
- compareTo(Location) - Method in class org.sbolstandard.core2.GenericLocation
-
- compareTo(Location) - Method in class org.sbolstandard.core2.Range
-
- compareTo(SequenceAnnotation) - Method in class org.sbolstandard.core2.SequenceAnnotation
-
- COMPETITIVE_INHIBITOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Substance that decreases the probability of a chemical reaction, without itself being
consumed or transformed by the reaction, by stericaly hindering the interaction between
reactants
(
SBO:0000206).
- COMPLEX - Static variable in class org.sbolstandard.core2.ComponentDefinition
-
A physical entity whose structure is comprised of other physical entities bound to each other covalently or non-covalently,
at least one of which is a macromolecule (e.g.
- Component - Class in org.sbolstandard.core2
-
Represents a Component object in the SBOL data model.
- COMPONENT_DEFINITION - Static variable in class org.sbolstandard.core2.TopLevel
-
The abbreviation for the ComponentDefinition type in URI
- ComponentDefinition - Class in org.sbolstandard.core2
-
Represents a ComponentDefinition object in the SBOL data model.
- ComponentInstance - Class in org.sbolstandard.core2
-
Represents a ComponentInstance object in the SBOL data model.
- COMPOSITE_BIOCHEMICAL_PROCESS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Process that involves the participation of chemical or biological entities and is
composed of several elementary steps or reactions
(
SBO:0000205).
- CONFORMATIONAL_TRANSITION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Biochemical reaction that does not result in the modification of covalent bonds of
reactants, but rather modifies the conformation of some reactants, that is the relative
position of their atoms in space (
SBO:0000181).
- CONSUMPTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Decrease in amount of a material or conceptual entity
(
SBO:0000394).
- CONTAINMENT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
An entity that is a subset of another entity or object
(
SBO:0000469).
- containsAttachment(URI) - Method in class org.sbolstandard.core2.TopLevel
-
Checks if the given attachment URI is included in this top level's
set of attachment URIs.
- containsExperimentalData(URI) - Method in class org.sbolstandard.core2.Experiment
-
Checks if the given URI is included in this Experiment
instance's set of experimentalData URIs.
- containsMember(URI) - Method in class org.sbolstandard.core2.Collection
-
Checks if the given URI is included in this Collection
instance's set of member URIs.
- containsModel(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Checks if the given model URI is included in this module definition's set of reference model URIs.
- containsRole(URI) - Method in class org.sbolstandard.core2.Association
-
Checks if the given role URI is included in this association's set of role URIs.
- containsRole(URI) - Method in class org.sbolstandard.core2.Component
-
Checks if the given role URI is included in this component's set of role URIs.
- containsRole(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Checks if the given role URI is included in this component definition's set of role URIs.
- containsRole(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Checks if the given role URI is included in this module definition's set of role URIs.
- containsRole(URI) - Method in class org.sbolstandard.core2.Participation
-
Checks if the given role is included in this participation's set of roles.
- containsRole(URI) - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Checks if the given role is included in this sequence annotation's set of roles.
- containsRole(URI) - Method in class org.sbolstandard.core2.Usage
-
Checks if the given role URI is included in this usage's set of role URIs.
- containsSequence(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Checks if the given sequence URI is included in this component definition's
set of sequence URIs.
- containsType(URI) - Method in class org.sbolstandard.core2.Activity
-
Checks if the given type URI is included in this activity's
set of type URIs.
- containsType(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Checks if the given type URI is included in this component definition's
set of type URIs.
- containsType(URI) - Method in class org.sbolstandard.core2.Interaction
-
Checks if the given type URI is included in this interaction's set of type URIs.
- containsType(URI) - Method in class org.sbolstandard.core2.Measure
-
Checks if the given type URI is included in this measure's set of type URIs.
- containsWasDerivedFrom(URI) - Method in class org.sbolstandard.core2.Identified
-
Checks if the given wasDerivedFrom URI is included in the set of wasDerivedFrom URIs.
- containsWasGeneratedBy(URI) - Method in class org.sbolstandard.core2.Identified
-
Checks if the given wasGeneratedBy URI is included in the set of wasGeneratedBy URIs.
- CONTINUOUS_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Modelling approach where the quantities of participants are considered continuous,
and represented by real values (
SBO:0000062).
- CONTROL - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Modification of the execution of an event or a process
(
SBO:0000168).
- CONVERSION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Biochemical reaction that results in the modification of some covalent bonds (
SBO:0000182).
- createActivity(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an activity, and then adds it to this SBOL document's list of
activities.
- createActivity(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an activity, and then adds it to this SBOL document's list of
activities.
- createActivity(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an activity, and then adds it to this SBOL document's list of
activities.
- createAgent(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an agent, and then adds it to this SBOL document's list of agents.
- createAgent(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an agent, and then adds it to this SBOL document's list of agents.
- createAgent(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an agent, and then adds it to this SBOL document's list of agents.
- createAnnotation(QName, QName, String, List<Annotation>) - Method in class org.sbolstandard.core2.Annotation
-
Creates an annotation with nested annotations using the given arguments, and then adds to this instance's list of annotations.
- createAnnotation(QName, String) - Method in class org.sbolstandard.core2.Identified
-
Creates an annotation using the given arguments,
then adds to this instance's list of annotations.
- createAnnotation(QName, double) - Method in class org.sbolstandard.core2.Identified
-
Creates an annotation using the given arguments,
then adds to this instance's list of annotations.
- createAnnotation(QName, int) - Method in class org.sbolstandard.core2.Identified
-
Creates an annotation using the given arguments,
then adds to this instance's list of annotations.
- createAnnotation(QName, boolean) - Method in class org.sbolstandard.core2.Identified
-
Creates an annotation using the given arguments, and
then adds to the list of annotaions.
- createAnnotation(QName, URI) - Method in class org.sbolstandard.core2.Identified
-
Creates an annotation using the given arguments,
then adds to this instance's list of annotations.
- createAnnotation(QName, QName, String, List<Annotation>) - Method in class org.sbolstandard.core2.Identified
-
Creates an annotation with nested annotations using the given arguments, and then adds to this instance's list of annotations.
- createAssociation(String, URI) - Method in class org.sbolstandard.core2.Activity
-
Creates a child association for this activity with the given arguments,
and then adds to this activity's list of associations.
- createAttachment(String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an attachment, and then adds it to this SBOL document's list of attachments.
- createAttachment(String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an attachment, and then adds it to this SBOL document's list of attachments.
- createAttachment(String, String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an attachment, and then adds it to this SBOL document's list of attachments.
- createCollection(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a collection first, and then adds to this SBOL document's list of
collections.
- createCollection(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a collection first, and then adds to this SBOL document's list of
collections.
- createCollection(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a collection first, and then adds to this SBOL document's list of
collections.
- createCollection(String, String, String, String, String, boolean) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Create a new private collection on SynBioHub
- createCollection(String, String, String, String, String, boolean, SBOLDocument) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Create a new private collection on SynBioHub and add the contents of the
SBOL document to this collection
- createCollection(String, String, String, String, String, boolean, String) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Create a new private collection on SynBioHub and add the contents of the file to this collection
- createCollection(String, String, String, String, String, boolean, File) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Create a new private collection on SynBioHub and add the contents of the file to this collection
- createCollection(String, String, String, String, String, boolean, InputStream) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Create a new private collection on SynBioHub and add the contents of the file to this collection
- createCombinatorialDerivation(String, String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a combinatorial derivation, and then adds it to this SBOL document's
list of combinatorial derivations.
- createCombinatorialDerivation(String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a combinatorial derivation, and then adds it to this SBOL document's
list of combinatorial derivations.
- createCombinatorialDerivation(String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a combinatorial derivation, and then adds it to this SBOL document's
list of combinatorial derivations.
- createCombinatorialDerivation(String, String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a combinatorial derivation, and then adds it to this SBOL document's
list of combinatorial derivations.
- createComponent(String, AccessType, String, String) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Creates a child component for this component definition with the given arguments,
and then adds it to this component definition's list of components.
- createComponent(String, AccessType, String) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Creates a child component for this component definition with the given arguments,
and then adds it to this component definition's list of components.
- createComponent(String, AccessType, URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Creates a child component for this component definition with the given arguments,
and then adds to this component definition's list of components.
- createComponentDefinition(String, Set<URI>) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
- createComponentDefinition(String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
- createComponentDefinition(String, String, Set<URI>) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
- createComponentDefinition(String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
- createComponentDefinition(String, String, String, Set<URI>) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
- createComponentDefinition(String, String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a component definition, and then adds it to this SBOL document's list
of component definitions.
- createCopy(SBOLDocument) - Method in class org.sbolstandard.core2.SBOLDocument
-
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.
- createCopy(TopLevel) - Method in class org.sbolstandard.core2.SBOLDocument
-
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.
- createCopy(TopLevel, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
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.
- createCopy(TopLevel, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
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.
- createCopy(TopLevel, String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
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.
- createExperiment(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a experiment first, and then adds to this SBOL document's list of
experiments.
- createExperiment(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a experiment first, and then adds to this SBOL document's list of
experiments.
- createExperiment(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a experiment first, and then adds to this SBOL document's list of
experiments.
- createExperimentalData(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a experimentalData first, and then adds to this SBOL document's list of
experimentalDatas.
- createExperimentalData(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a experimentalData first, and then adds to this SBOL document's list of
experimentalDatas.
- createExperimentalData(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a experimentalData first, and then adds to this SBOL document's list of
experimentalDatas.
- createFunctionalComponent(String, AccessType, String, String, DirectionType) - Method in class org.sbolstandard.core2.ModuleDefinition
-
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.
- createFunctionalComponent(String, AccessType, String, DirectionType) - Method in class org.sbolstandard.core2.ModuleDefinition
-
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.
- createFunctionalComponent(String, AccessType, URI, DirectionType) - Method in class org.sbolstandard.core2.ModuleDefinition
-
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.
- createGenericTopLevel(String, QName) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a generic top-level, and then adds it to this SBOL document's list of
generic top-levels.
- createGenericTopLevel(String, String, QName) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a generic top-level, and then adds it to this SBOL document's list of
generic top-levels.
- createGenericTopLevel(String, String, String, QName) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a generic top-level, and then adds it to this SBOL document's list of
generic top-levels.
- createImplementation(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an implementation, and then adds it to this SBOL document's
list of implementations.
- createImplementation(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an implementation, and then adds it to this SBOL document's
list of implementations.
- createImplementation(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an implementation, and then adds it to this SBOL document's
list of implementations.
- createInteraction(String, Set<URI>) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Creates a child interaction for this module definition with
the given arguments, and then adds to this module definition's list of interactions.
- createInteraction(String, URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Creates a child interaction for this module definition with
the given arguments, and then adds to this module definition's list of interactions.
- createMapsTo(String, RefinementType, String, String) - Method in class org.sbolstandard.core2.Component
-
Creates a child mapsTo for this component with the given arguments, and then adds it to its list of mapsTos.
- createMapsTo(String, RefinementType, URI, URI) - Method in class org.sbolstandard.core2.Component
-
Creates a child mapsTo for this component with the given arguments,
and then adds it to its list of mapsTos.
- createMapsTo(String, RefinementType, String, String) - Method in class org.sbolstandard.core2.FunctionalComponent
-
Creates a child MapsTo instance for this module with the given arguments, and then adds to this module's list of mapsTos.
- createMapsTo(String, RefinementType, URI, URI) - Method in class org.sbolstandard.core2.FunctionalComponent
-
Creates a child mapsTo for this functional component with the given arguments,
and then adds it to this functional compoennt's list of mapsTos.
- createMapsTo(String, RefinementType, String, String) - Method in class org.sbolstandard.core2.Module
-
Creates a child mapsTo for this module with the given arguments, and then adds it to its list of mapsTos.
- createMapsTo(String, RefinementType, URI, URI) - Method in class org.sbolstandard.core2.Module
-
Creates a child mapsTo for this module with the given arguments, and then adds it to its list of mapsTos.
- createMeasure(String, Double, URI) - Method in class org.sbolstandard.core2.Measured
-
Creates a child measure for this measured object with the given arguments,
and then adds to this measured object's list of measures.
- createModel(String, URI, URI, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a model, and then adds it to this SBOL document's list of models.
- createModel(String, String, URI, URI, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a model, and then adds it to this SBOL document's list of models.
- createModel(String, String, String, URI, URI, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a model, and then adds it to this SBOL document's list of models.
- createModule(String, String, String) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Creates a child module for this module definition with the
given arguments, and then adds to this module definition's list of modules.
- createModule(String, String) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Creates a child module for this module definition with the
given arguments, and then adds to this module definition's list of modules.
- createModule(String, URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Creates a child module for this module definition with the
given arguments, and then adds to this module definition's list of modules.
- createModuleDefinition(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a module definition, and then adds it to this SBOL document's list of
module definitions.
- createModuleDefinition(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a module definition, and then adds it to this SBOL document's list of
module definitions.
- createModuleDefinition(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a module definition with the given arguments, and then adds it to
this SBOL document's list of module definitions.
- createParticipation(String, String, URI) - Method in class org.sbolstandard.core2.Interaction
-
Creates a child participation for this interaction with the given arguments,
and then adds to this interaction's list of participations.
- createParticipation(String, String, Set<URI>) - Method in class org.sbolstandard.core2.Interaction
-
Creates a child participation for this interaction with the given arguments, and then adds to this interaction's
list of participations.
- createParticipation(String, URI, URI) - Method in class org.sbolstandard.core2.Interaction
-
Creates a child participation for this interaction with the given arguments, and then adds to its list of participations.
- createParticipation(String, URI, Set<URI>) - Method in class org.sbolstandard.core2.Interaction
-
Creates a child participation for this interaction with the given arguments,
and then adds to this interaction's list of participations.
- createPlan(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an plan, and then adds it to this SBOL document's list of plans.
- createPlan(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an plan, and then adds it to this SBOL document's list of plans.
- createPlan(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an plan, and then adds it to this SBOL document's list of plans.
- createRecursiveCopy(TopLevel) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates an identical copy of the given top-level and returns it in a new
SBOLDocument.
- createRecursiveCopy(SBOLDocument, TopLevel) - Method in class org.sbolstandard.core2.SBOLDocument
-
- createSequence(String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
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.
- createSequence(String, String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
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.
- createSequence(String, String, String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Creates a Sequence instance with the given arguments, and then adds it to
this SBOLDocument object's list of Sequence instances.
- createSequenceAnnotation(String, String) - Method in class org.sbolstandard.core2.ComponentDefinition
-
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.
- createSequenceAnnotation(String, String, OrientationType) - Method in class org.sbolstandard.core2.ComponentDefinition
-
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.
- createSequenceAnnotation(String, String, int) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Creates a child sequence annotation for this component definition with the given arguments,
and then adds to its list of sequence annotations.
- createSequenceAnnotation(String, String, int, OrientationType) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Creates a child sequence annotation for this component definition with the given arguments,
and then adds to its list of sequence annotations.
- createSequenceAnnotation(String, String, int, int) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Creates a child sequence annotation for this component definition with the given arguments, and then adds to this ComponentDefinition's
list of sequence annotations.
- createSequenceAnnotation(String, String, int, int, OrientationType) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Creates a child sequence annotation for this ComponentDefinition
instance with the given arguments, and then adds to this ComponentDefinition's
list of sequence annotations.
- createSequenceConstraint(String, RestrictionType, String, String) - Method in class org.sbolstandard.core2.ComponentDefinition
-
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.
- createSequenceConstraint(String, RestrictionType, URI, URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
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.
- createUsage(String, URI) - Method in class org.sbolstandard.core2.Activity
-
Creates a child usage for this activity with the given arguments,
and then adds to this activity's list of usages.
- createVariableComponent(String, OperatorType, URI) - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
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.
- createVariableComponent(String, OperatorType, String) - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
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.
- Cut - Class in org.sbolstandard.core2
-
Represents the Cut extension of the SBOL Location class.