- 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) - 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
- 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.
- clear() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Sets the internal SBOL document used by the factory to a new SBOL document.
- clearAnnotations() - Method in class org.sbolstandard.core2.Identified
-
Removes all entries of this instance's list of annotations.
- clearCollections() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of collections owned by this SBOL document.
- clearCollections() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes all entries in the list of collections owned by the internal SBOL document of
the factory.
- clearComponentDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of component definitions owned by this SBOL document.
- clearComponentDefinitions() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes all entries in the list of component definitions
owned by the internal SBOL document of the factory.
- 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.
- 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.
- clearGenericTopLevels() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes all entries in the list of generic top-levels
owned by the internal SBOL document of the factory.
- 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.
- 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.
- clearModels() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes all entries in the list of models owned by the internal SBOL document
of thie factory.
- clearModuleDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all entries in the list of module definitions owned by this SBOL document.
- clearModuleDefinitions() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes all entries in the list of module definitions
owned by the internal SBOL document of the factory.
- 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.
- clearNamespaces() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes all non-required namespaces from the internal SBOL document of the factory.
- clearParticipations() - Method in class org.sbolstandard.core2.Interaction
-
Removes all entries of this interaction list of sequence annotations.
- clearRegistries() - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes all registries from this SBOL document.
- 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.
- 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.
- clearSequences() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes all entries in the list of sequences owned by the internal SBOL document of
the factory.
- clearWasDerivedFroms() - Method in class org.sbolstandard.core2.Identified
-
Removes all entries from the set of wasDerivedFrom 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).
- clone() - Method in class org.oboparser.obo.OBOIndividual
-
- clone() - Method in class org.oboparser.obo.OBOStanza
-
- clone(Class<? extends OBOStanza>) - Method in class org.oboparser.obo.OBOStanza
-
- clone() - Method in class org.oboparser.obo.OBOTerm
-
- clone() - Method in class org.oboparser.obo.OBOTypedef
-
- 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
- compareDocuments(String, SBOLDocument, String, SBOLDocument) - Static method in class org.sbolstandard.core2.SBOLValidate
-
Compares the given two SBOL documents and outputs the "standard" error output stream (System.err).
- 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).
- 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.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.
- 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.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.
- containsWasDerivedFrom(URI) - Method in class org.sbolstandard.core2.Identified
-
Checks if the given wasDerivedFrom URI is included in the set of wasDerivedFrom 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).
- 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, URI, 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.
- 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) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a collection first, and then adds to the factory's internal SBOL document's list of collections.
- createCollection(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a collection first, and then adds to the factory's internal SBOL document's list of collections.
- createCollection(String, String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a collection first, and then adds to factory's internal SBOL document's list of collections.
- 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.
- createComponentDefinition(String, Set<URI>) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a component definition, and then adds it to the factory's internal SBOL document's list of component definitions.
- createComponentDefinition(String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a component definition, and then adds it to the factory's internal SBOL document's list of component definitions.
- createComponentDefinition(String, String, Set<URI>) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a component definition, and then adds it to the factory's internal SBOL document's list of component definitions.
- createComponentDefinition(String, String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a component definition, and then adds it to the factory's internal SBOL document's list of component definitions.
- createComponentDefinition(String, String, String, Set<URI>) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a component definition, and then adds it to the factory's internal SBOL document's list of component definitions.
- createComponentDefinition(String, String, String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a component definition, and then adds it to the factory's internal 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.
- createCopy(SBOLDocument) - Static method in class org.sbolstandard.core2.SBOLFactory
-
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.
- createCopy(TopLevel) - Static method in class org.sbolstandard.core2.SBOLFactory
-
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.
- createCopy(TopLevel, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
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.
- createCopy(TopLevel, String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
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.
- createCopy(TopLevel, String, String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
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.
- 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.
- createGenericTopLevel(String, QName) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a generic top-level, and then adds it to the factory's internal SBOL document's list of generic top-levels.
- createGenericTopLevel(String, String, QName) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a generic top-level, and then adds it to the factory's internal SBOL document's list of generic top-levels.
- createGenericTopLevel(String, String, String, QName) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a generic top-level, and then adds it to the factory's internal SBOL document's list of generic top-levels.
- 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.
- 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.
- createModel(String, URI, URI, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a model, and then adds it to the factory's internal SBOL document's list of models.
- createModel(String, String, URI, URI, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a model, and then adds it to the factory's internal SBOL document's list of models.
- createModel(String, String, String, URI, URI, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a model, and then adds it to the factory's internal 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.
- createModuleDefinition(String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a module definition, and then adds it to the factory's internal SBOL document's list of module definitions.
- createModuleDefinition(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a module definition, and then adds it to the factory's internal SBOL document's list of module definitions.
- createModuleDefinition(String, String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a module definition, and then adds it to the factory's internal 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.
- 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(TopLevel) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates an identical copy of the given top-level and returns it in
a new SBOL document.
- 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.
- createSequence(String, String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a sequence with the given arguments, and then adds it to the factory's internal
SBOL document's list of sequences.
- createSequence(String, String, String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a sequence with the given arguments, and then adds it to the factory's internal
SBOL document's list of sequences.
- createSequence(String, String, String, String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Creates a sequence with the given arguments, and then adds it to the factory's internal
SBOL document's list of sequences.
- 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.
- Cut - Class in org.sbolstandard.core2
-
Represents the Cut extension of the SBOL Location class.
- GENBANK - Static variable in class org.sbolstandard.core2.SBOLDocument
-
Constant representing GenBank file format
- GENE - Static variable in class org.sbolstandard.core2.SequenceOntology
-
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript.
- GENERIC_TOP_LEVEL - Static variable in class org.sbolstandard.core2.TopLevel
-
The abbreviation for the GenericTopLevel type in URI
- GenericLocation - Class in org.sbolstandard.core2
-
Represents a GenericLocation extension object of the SBOL Location class.
- GenericTopLevel - Class in org.sbolstandard.core2
-
Represents a GenericTopLevel object in the SBOL data model.
- GENETIC_ENHANCEMENT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Genetic enhancement is said to have occurred when the phenotypic effect of an initial
mutation in a gene is made increasingly severe by a subsequent mutation
(
SBO:0000501).
- GENETIC_INTERACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable
by the simple additive effects of the individual gene pertubations alone (
SBO:0000343).
- GENETIC_PRODUCTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
A composite biochemical process through which a gene sequence is fully converted into
mature gene products (
SBO:0000589).
- GENETIC_SUPPRESSION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Genetic suppression is said to have occurred when the phenotypic effect of an initial
mutation in a gene is less severe, or entirely negated, by a subsequent mutation
(
SBO:0000500).
- GERANYLGERANYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Addition of a geranylgeranyl group
(CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2)
to a chemical entity
(
SBO:0000223).
- getAccess() - Method in class org.sbolstandard.core2.ComponentInstance
-
Returns the access property.
- getAnnotation(QName) - Method in class org.sbolstandard.core2.Identified
-
Returns the annotation matching the given QName.
- getAnnotations() - Method in class org.sbolstandard.core2.Annotation
-
Returns the list of Annotations of the nested value property.
- getAnnotations() - Method in class org.sbolstandard.core2.Identified
-
Returns the list of annotations owned by this instance.
- getAt() - Method in class org.sbolstandard.core2.Cut
-
Returns the at property of this Cut instance.
- getBackendUrl() - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Returns the URL for the SynBioHub instance.
- getBooleanValue() - Method in class org.sbolstandard.core2.Annotation
-
Returns a Boolean representation of the value property.
- getByWasDerivedFrom(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Retrieves a set of top-levels in this SBOL document whose wasDerivedFrom
field matches
the given one.
- getByWasDerivedFrom(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Retrieves a set of top-levels in the factory's internal SBOL document whose wasDerivedFrom field matches the given one.
- getCollection(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the collection matching the given display ID and version from this SBOL document's list of
collections.
- getCollection(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the collection matching the given identity URI from this
SBOL document's list of collections.
- getCollection(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the collection matching the given display ID and version from the factory's internal
SBOL document's list of collections.
- getCollection(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the collection matching the given identity URI from the factory's internal
SBOL document's list of collections.
- getCollections() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of Collection
instances owned by this SBOL document.
- getCollections() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the set of collections owned by the factory's internal SBOL document
- getComment() - Method in class org.oboparser.obo.OBOValue
-
- getComponent(String) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the component matching the given component's display ID.
- getComponent(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the instance matching the given component's identity URI.
- getComponent() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns the component this sequence annotation refers to.
- getComponentDefinition(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the component definition matching the given display ID and version from this SBOL document's list of
component definitions.
- getComponentDefinition(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the component definition matching the given identity URI from this
SBOL document's list of component definitions.
- getComponentDefinition(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the component definition matching the given display ID and version from
the factory's internal SBOL document's list of component definitions.
- getComponentDefinition(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the component definition matching the given identity URI from the factory's
internal SBOL document's list of component definitions.
- getComponentDefinition() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns the component definition for the component annotated by this sequence annotation.
- getComponentDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of component definitions owned by this SBOL document.
- getComponentDefinitions() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the set of component definitions owned by the factory's
internal SBOL document.
- getComponents() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the set of components owned by this component definition.
- getComponentURI() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns the component that this sequence annotation refers to.
- getCount(String) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Return the total number of objects of a specified type in the repository.
- getCriteria() - Method in class org.synbiohub.frontend.SearchQuery
-
Return the search criteria
- getDefaultSequenceEncoding() - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the default sequence encoding for FASTA conversion.
- getDefaultURIprefix() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the default URI prefix of this SBOL document.
- getDefaultURIprefix() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the default URI prefix of the factory's internal SBOL document.
- getDefinition() - Method in class org.sbolstandard.core2.ComponentInstance
-
Returns the component definition referenced by this component or functional component.
- getDefinition() - Method in class org.sbolstandard.core2.Module
-
Returns the module definition that this module refers to.
- getDefinitionURI() - Method in class org.sbolstandard.core2.ComponentInstance
-
Returns the reference component definition URI.
- getDefinitionURI() - Method in class org.sbolstandard.core2.Module
-
Returns the module definition URI that this module refers to.
- getDescendantNamesOf(String) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns the set of child names that are descendants of the given parent ID.
- getDescendantNamesOf(URI) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns the set of child names that are descendants of the given parent URI.
- getDescendantNamesOf(String) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the set of child names that are descendants of a given parent ID.
- getDescendantNamesOf(URI) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the set of child names that are descendants of a given parent URI.
- getDescendantNamesOf(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of child names that are descendants of a given parent ID.
- getDescendantNamesOf(URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of child names that are descendants of a given parent URI.
- getDescendantsOf(OBOStanza) - Method in class org.oboparser.obo.OBOOntology
-
- getDescendantsOf(String) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns a set of child IDs that are descendants of the given parent ID.
- getDescendantsOf(URI) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns a set of child IDs that are descendants of the given parent URI.
- getDescendantsOf(String) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the set of child IDs that are descendants of the given parent ID.
- getDescendantsOf(URI) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the set of child IDs that are descendants of the given parent URI.
- getDescendantsOf(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of child IDs that are descendants of the given parent ID.
- getDescendantsOf(URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of child IDs that are descendants of the given parent URI.
- getDescendantURIsOf(String) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns a set of child URIs that are descendants of the given parent ID.
- getDescendantURIsOf(URI) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns a set of child URIs that are descendants of the given parent URI.
- getDescendantURIsOf(String) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the set of child URIs that are descendants of the given parent ID.
- getDescendantURIsOf(URI) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the set of child URIs that are descendants of the given parent URI.
- getDescendantURIsOf(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of child URIs that are descendants of the given parent ID.
- getDescendantURIsOf(URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of child URIs that are descendants of the given parent URI.
- getDescription() - Method in class org.sbolstandard.core2.Identified
-
Returns the description property of this instance.
- getDescription() - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- getDirection() - Method in class org.sbolstandard.core2.FunctionalComponent
-
Returns the direction property of this functional component.
- getDisplayId() - Method in class org.sbolstandard.core2.Identified
-
Returns the display ID of this instance.
- getDisplayId() - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- getDocument() - Method in class org.sbolstandard.core2.TopLevel
-
Returns the SBOL document that hosts this top-level.
- getDoubleValue() - Method in class org.sbolstandard.core2.Annotation
-
Returns a Double representation of the value property.
- getElements() - Method in class org.sbolstandard.core2.Sequence
-
Returns the elements property of this sequence.
- getEncoding() - Method in class org.sbolstandard.core2.Sequence
-
Returns the encoding property of this sequence.
- getEnd() - Method in class org.sbolstandard.core2.Range
-
Returns the end position of this range.
- getErrors() - Static method in class org.sbolstandard.core2.SBOLReader
-
Returns the error list that is used to store SBOL validation exceptions.
- getErrors() - Static method in class org.sbolstandard.core2.SBOLValidate
-
Returns the error list used to store SBOL validation exceptions.
- getErrors() - Static method in class org.sbolstandard.core2.SBOLWriter
-
Returns the error list that is used to store SBOL conversion exceptions.
- getFramework() - Method in class org.sbolstandard.core2.Model
-
Returns the URI of the framework property of this Model object.
- getFunctionalComponent(String) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the functional component matching the given display ID from
this module definition's list of functional components.
- getFunctionalComponent(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the functional component matching the given functional component identity URI from this
module definition's list of functional components.
- getFunctionalComponents() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the set of functional components owned by this
module definition.
- getGenericTopLevel(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the generic top-level matching the given display ID and version from this SBOL document's list of
generic top-levels.
- getGenericTopLevel(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the generic top-level matching the given display identity URI from this SBOL document's list of
generic top-levels.
- getGenericTopLevel(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the generic top-level matching the given display ID and version from
the factory's internal SBOL document's list of generic top-levels.
- getGenericTopLevel(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the generic top-level matching the given identity URI from
the factory's internal SBOL document's list of generic top-levels.
- getGenericTopLevels() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of generic top-levels owned by this SBOL document.
- getGenericTopLevels() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the set of generic topLevels owned by the factory's internal SBOL document.
- getId() - Method in class org.oboparser.obo.OBOStanza
-
- getId(URI) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns the extracted ID of the given stanza's URI.
- getId(String) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns the ID field of the stanza whose name field matches the given name.
- getId(URI) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the extracted ID of the given term's URI.
- getId(String) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the ID of the stanza whose name matches the given stanza name.
- getId(URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the extracted ID of the given term's URI.
- getId(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the ID of the stanza whose name matches the given stanza name.
- getIdentity() - Method in class org.sbolstandard.core2.Identified
-
Returns the identity URI of this instance.
- getImpliedNucleicAcidSequence() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Return the elements of a nucleic acid sequence implied by the hierarchically included components.
- getIntegerValue() - Method in class org.sbolstandard.core2.Annotation
-
Returns an Integer representation of the value property.
- getInteraction(String) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the interaction matching the given interaction's identity URI from the
list of interactions.
- getInteraction(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the instance matching the given Interaction URI from the list of
Interaction instances.
- getInteractions() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the set of interactions owned by this module definition.
- getKey() - Method in class org.synbiohub.frontend.SearchCriteria
-
Returns the search key
- getLanguage() - Method in class org.sbolstandard.core2.Model
-
Returns this model's language property.
- getLimit() - Method in class org.synbiohub.frontend.SearchQuery
-
Set the search limit
- getLocal() - Method in class org.sbolstandard.core2.MapsTo
-
Returns this mapsTo's local component instance.
- getLocalDefinition() - Method in class org.sbolstandard.core2.MapsTo
-
Retrieves referenced component definition by this mapsTo's local component instance.
- getLocalURI() - Method in class org.sbolstandard.core2.MapsTo
-
Returns this mapsTo's local component instance's URI.
- getLocation(String) - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns the location owned by this sequence annotation
that matches the given display ID.
- getLocation(URI) - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns the location owned by this sequence annotation
that matches the given identity URI.
- getLocations() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns the set of locations referenced by this sequence annotation.
- getMapsTo(String) - Method in class org.sbolstandard.core2.Component
-
Returns the mapsTo that matches the given display ID.
- getMapsTo(URI) - Method in class org.sbolstandard.core2.Component
-
Returns the mapsTo that matches the given URI.
- getMapsTo(String) - Method in class org.sbolstandard.core2.FunctionalComponent
-
Returns the mapsTo that matches the given display ID.
- getMapsTo(URI) - Method in class org.sbolstandard.core2.FunctionalComponent
-
Returns the mapsTo that matches the given URI.
- getMapsTo(String) - Method in class org.sbolstandard.core2.Module
-
Returns the mapsTo that matches the given display ID.
- getMapsTo(URI) - Method in class org.sbolstandard.core2.Module
-
Returns the MapsTo instance owned by this Module object that matches the given displayId
- getMapsTos() - Method in class org.sbolstandard.core2.Component
-
Returns the set of mapsTos owned by this instance.
- getMapsTos() - Method in class org.sbolstandard.core2.FunctionalComponent
-
Returns the set of mapsTos owned by this object.
- getMapsTos() - Method in class org.sbolstandard.core2.Module
-
Returns the set of MapsTo instances referenced by this Module object.
- getMatchingComponentDefinitionMetadata(String, Set<URI>, Set<URI>, Set<URI>, Integer, Integer) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Search the default store for ComponentDefinition instances matching a name and/or a set of roles
- getMembers() - Method in class org.sbolstandard.core2.Collection
-
Returns the set instances referenced by this Collection instance's members.
- getMemberURIs() - Method in class org.sbolstandard.core2.Collection
-
Returns the set of member URIs referenced by this Collection instance.
- getModel(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the model matching the given display ID and version from this SBOL document's list of
models.
- getModel(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the model matching the given identity URI from this
SBOL document's list of models.
- getModel(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the model matching the given display ID and version from
the factory's internal SBOL document's list of models.
- getModel(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the model matching the given identity URI from
the factory's internal SBOL document's list of models.
- getModels() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the set of models referenced by this module definition.
- getModels() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of models owned by this SBOL document.
- getModels() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the set of models owned by the factory's internal SBOL document.
- getModelURIs() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the set of model URIs referenced by this module definition.
- getModifiers() - Method in class org.oboparser.obo.OBOValue
-
- getModule(String) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the module matching the given display ID from the list of modules.
- getModule(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the module matching the given identity URI from the list of modules.
- getModuleDefinition(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the module definition matching the given display ID
and version from this SBOLDocument object's list of
module definitions.
- getModuleDefinition(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the module definition matching the given identity URI from this
SBOL document object's list of module definitions.
- getModuleDefinition(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the module definition matching the given display ID and version from the factory's internal SBOL document's
list of module definitions.
- getModuleDefinition(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the module definition matching the given identity URI from
the factory's internal SBOL document's list of module definitions.
- getModuleDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of module definitions owned by this SBOLDocument object.
- getModuleDefinitions() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the set of module definitions owned by the factory's internal SBOL document.
- getModules() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the set of modules owned by this module definition.
- getName() - Method in class org.oboparser.obo.OBOStanza
-
- getName() - Method in class org.oboparser.obo.OBOTerm
-
- getName(URI) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns the name field of the stanza that matches the ID for the given stanza URI.
- getName(String) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns the name field of the stanza matching the ID extracted from the given stanza URI.
- getName() - Method in class org.sbolstandard.core2.Identified
-
Returns the name property of this instance.
- getName(URI) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the name field of the stanza that matches the ID for the given term URI.
- getName(String) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the name field of the stanza that matches the ID referred by the given stanza URI.
- getName(URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the name field of the stanza that matches the ID for the given term URI.
- getName(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the name field of the stanza that matches the ID referred by the given stanza URI.
- getName() - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- getNamespace(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the QName matching the given namespace prefix from this
SBOL document's list of QNames.
- getNamespace(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the QName matching the given namespace URI from this
SBOL document's list of QNames.
- getNamespace(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the QName matching the given namespace URI from the factory's internal SBOL document's list of QNames.
- getNamespaces() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the list of namespaces owned by this SBOL document.
- getNamespaces() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the list of namespace bindings owned by the factory's internal SBOL document.
- getNestedIdentity() - Method in class org.sbolstandard.core2.Annotation
-
Returns the nested identity URI of the nested Annotation.
- getNestedQName() - Method in class org.sbolstandard.core2.Annotation
-
Returns the nested QName of the nested Annotation.
- getNumErrors() - Static method in class org.sbolstandard.core2.SBOLReader
-
Returns the number of errors in the error list.
- getNumErrors() - Static method in class org.sbolstandard.core2.SBOLValidate
-
Returns the number of errors in the error list.
- getNumErrors() - Static method in class org.sbolstandard.core2.SBOLWriter
-
Returns the number of errors in the error list.
- getObject() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the object component this sequence constraint refers to.
- getObjectDefinition() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the component definition that defines the object component of this sequence constraint.
- getObjectURI() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the object component's identity URI that this sequence constraint refers to.
- getOffset() - Method in class org.synbiohub.frontend.SearchQuery
-
Returns the search offset
- getOntology() - Method in class org.oboparser.obo.OBOParser
-
- getOrientation() - Method in class org.sbolstandard.core2.Location
-
Returns the orientation property of this location.
- getParticipant() - Method in class org.sbolstandard.core2.Participation
-
Returns the functional component this participation refers to.
- getParticipantDefinition() - Method in class org.sbolstandard.core2.Participation
-
Returns the component definition referenced by this participation's participant.
- getParticipantURI() - Method in class org.sbolstandard.core2.Participation
-
Returns the FunctionalComponent URI that this participation refers to.
- getParticipation(String) - Method in class org.sbolstandard.core2.Interaction
-
Returns the participation matching the given display ID from
this interaction's list of participations.
- getParticipation(URI) - Method in class org.sbolstandard.core2.Interaction
-
Returns the participation matching the given participation URI from this
interaction's list of participations.
- getParticipations() - Method in class org.sbolstandard.core2.Interaction
-
Returns the set of participations owned by this
interaction.
- getPersistentIdentity() - Method in class org.sbolstandard.core2.Identified
-
Returns the persistent identity URI of this instance.
- getPreciseLocations() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns the set of Range/Cut locations referenced by this sequence annotation.
- getQName() - Method in class org.sbolstandard.core2.Annotation
-
Returns the QName of this Annotation instance.
- getRawString() - Method in class org.oboparser.obo.OBOValue
-
- getRDFType() - Method in class org.sbolstandard.core2.GenericTopLevel
-
Returns the RDF type property of this GenericTopLevel instance.
- getRefinement() - Method in class org.sbolstandard.core2.MapsTo
-
Returns the refinement property of this mapsTo.
- getRegistries() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the list of registries used by this SBOL document.
- getRegistry(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the StackFrontend for the registry specified by its URL
- getRemote() - Method in class org.sbolstandard.core2.MapsTo
-
Returns this mapsTo's remote component instance.
- getRemoteDefinition() - Method in class org.sbolstandard.core2.MapsTo
-
Returns the remote component definition referenced by mapsTo.
- getRemoteURI() - Method in class org.sbolstandard.core2.MapsTo
-
Returns this mapsTo's remote URI.
- getRestriction() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the restriction property of this sequence constraint.
- getRestrictionURI() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the restriction property of this sequence constraint.
- getRoleIntegration() - Method in class org.sbolstandard.core2.Component
-
Returns the roleIntegration property of this object.
- getRoles() - Method in class org.sbolstandard.core2.Component
-
Returns the set of role URIs owned by this component.
- getRoles() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the set of role URIs owned by this component definition.
- getRoles() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the set of role URIs owned by this module definition.
- getRoles() - Method in class org.sbolstandard.core2.Participation
-
Returns the set of role URIs owned by this participation.
- getRoles() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns this sequence annotation's set of roles.
- getRootCollectionMetadata() - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Search the default store for Collections that are not members of any other Collections
- getRootComponentDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of root component definitions.
- getRootComponentDefinitions() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the set of root component definitions.
- getRootModuleDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of root module definitions.
- getSBOL(URI) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Retrieve SBOL TopLevel object from a SynBioHub instance using its URI.
- getSBOLVersion(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Takes in a given RDF file name and returns the SBOL version of the file.
- getSBOLVersion(File) - Static method in class org.sbolstandard.core2.SBOLReader
-
Takes in a given RDF file and returns its SBOL version.
- getSBOLVersion(InputStream) - Static method in class org.sbolstandard.core2.SBOLReader
-
Takes in a given RDF input stream and returns the SBOL version of the file.
- getSequence(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the sequence matching the given display ID
and version from this SBOL document's list of sequences.
- getSequence(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the sequence matching the given modelURI
from this
SBOL document's list of sequences.
- getSequence(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the sequence matching the given display ID and version from the factory's internal SBOL document's
list of sequences.
- getSequence(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the sequence matching the given identity URI from the factory's internal SBOL document's
list of sequences.
- getSequenceAnnotation(String) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the sequence annotation matching the given display ID.
- getSequenceAnnotation(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the instance matching the given SequenceAnnotation URI from the
list of sequence annotations.
- getSequenceAnnotation(Component) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the sequence annotation that references to the given component.
- getSequenceAnnotations() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the set of sequence annotations owned by this
component definition.
- getSequenceByEncoding(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the first sequence referenced by this component definition that matches the given sequence encoding.
- getSequenceConstraint(String) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the sequence constraint matching the given display ID.
- getSequenceConstraint(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the sequence constraint matching the given URI.
- getSequenceConstraints() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the set of sequence constraints owned by this
component definition.
- getSequences() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the set of sequences referenced by this component definition.
- getSequences() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of sequences owned by this SBOL document.
- getSequences() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the set of sequences owned by the factory's internal SBOL document.
- getSequenceURIs() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the set of sequence URIs referenced by this component definition.
- getSortedComponents() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns a sorted list of components owned by this component definition.
- getSortedLocations() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns a sorted list of locations owned by this sequence annotation.
- getSortedSequenceAnnotations() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns a sorted list of sequence annotations owned by this
component definition.
- getSource() - Method in class org.sbolstandard.core2.Model
-
Returns the this model's source property.
- getStanza(String) - Method in class org.oboparser.obo.OBOOntology
-
- getStanzas() - Method in class org.oboparser.obo.OBOOntology
-
- getStart() - Method in class org.sbolstandard.core2.Range
-
Returns the start position of this range.
- getStringValue() - Method in class org.sbolstandard.core2.Annotation
-
Returns a string representation of the value property.
- getSubCollectionMetadata(URI) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Search the default store for Collections that are members of the specified Collection
- getSubject() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the subject component this sequence constraint refers to.
- getSubjectDefinition() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the component definition that defines the subject component of this sequence constraint.
- getSubjectURI() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the subject component's identity URI that this sequence constraint refers to.
- getTopLevel(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the top-level matching the given identity URI from this
SBOL document's lists of top-levels.
- getTopLevel(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the top-level matching the given identity URI from the factory's internal SBOL document's
list of top-levels.
- getTopLevels() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of all top-levels owned by this SBOL document.
- getTopLevels() - Static method in class org.sbolstandard.core2.SBOLFactory
-
Returns the set of top-levels owned by the factory's internal SBOL document.
- getType() - Method in class org.oboparser.obo.OBOStanza
-
- getTypes() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the set of type URIs owned by this component definition.
- getTypes() - Method in class org.sbolstandard.core2.Interaction
-
Returns the set of type URIs owned by this Interaction object.
- getUri() - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- getURIbyId(String) - Method in class org.sbolstandard.core2.EDAMOntology
-
Creates a new URI from the EDAM Ontology namespace with the given ID.
- getURIbyId(String) - Method in class org.sbolstandard.core2.SequenceOntology
-
Creates a URI by appending the given stanza ID to the end of the
Sequence Ontology (SO) namespace,i.e.
- getURIbyId(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Creates a URI by appending the given stanza ID to the end of the
Systems Biology Ontology (SBO) namespace,i.e.
- getURIbyName(String) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns the URI, i.e.
- getURIbyName(String) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns the URI that is composed of the Sequence Ontology (SO) namespace, i.e.
- getURIbyName(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the URI that is composed of the Systems Biology Ontology (SBO) namespace, "http://identifiers.org/biomodels.sbo/",
followed by the ID of an SBO term, of the stanza whose name matches the given name.
- getURIValue() - Method in class org.sbolstandard.core2.Annotation
-
Returns a URI representation of the value property.
- getValue() - Method in class org.oboparser.obo.OBOValue
-
- getValue() - Method in class org.synbiohub.frontend.SearchCriteria
-
Return the search value
- getVersion() - Method in class org.sbolstandard.core2.Identified
-
Returns this instance's version.
- getVersion() - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- getWasDerivedFrom() - Method in class org.sbolstandard.core2.Identified
-
Deprecated.
- getWasDerivedFroms() - Method in class org.sbolstandard.core2.Identified
-
Returns the set of wasDerivedFrom URIs.
- GLYCOSYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Addition of a saccharide group to a chemical entity
(
SBO:0000217).
- Range - Class in org.sbolstandard.core2
-
Represents a Range extension object of the SBOL Location class.
- RDF - Static variable in class org.sbolstandard.core2.SBOLDocument
-
Constant representing RDF file format
- RDFV1 - Static variable in class org.sbolstandard.core2.SBOLDocument
-
Constant representing the format of an SBOL version 1.1 output file as being RDF format
- REACTANT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Substance consumed by a chemical reaction (
SBO:0000010).
- read(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Takes in a given RDF file name and adds the data read to this SBOLDocument.
- read(File) - Method in class org.sbolstandard.core2.SBOLDocument
-
Takes in a given RDF file and adds the data read to this SBOL document.
- read(InputStream) - Method in class org.sbolstandard.core2.SBOLDocument
-
Takes in a given RDF input stream and adds the data read to this SBOL document.
- read(String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Takes in a given RDF file name and add the data read to the factory's internal SBOL document.
- read(File) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Takes in a given RDF file and adds the data read to the factory's internal SBOL document.
- read(InputStream) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Takes in a given RDF input stream and add the data read to the factory's internal SBOL document.
- read(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Takes in the given RDF filename and converts the file to an SBOLDocument.
- read(File) - Static method in class org.sbolstandard.core2.SBOLReader
-
Parses the given RDF file and stores its contents in an SBOLDocument object.
- read(InputStream) - Static method in class org.sbolstandard.core2.SBOLReader
-
Takes in a given RDF InputStream and converts the file to an SBOLDocument.
- read(InputStream, String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Takes in a given InputStream and fileType, and convert the file to an SBOLDocument.
- REDOX_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Chemical process in which atoms have their oxidation number (oxidation state) changed
(
SBO:0000200).
- REDUCTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Chemical process in which a molecular entity gain electrons
(
SBO:0000202).
- RefinementType - Enum in org.sbolstandard.core2
-
Represents the refinement relationship between a MapsTo instance's local and remote components.
- relationship(String) - Method in class org.oboparser.obo.OBOTerm
-
- RELATIONSHIP - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Connectedness between entities and/or interactions representing their relatedness or
influence
(
SBO:0000374).
- relationships() - Method in class org.oboparser.obo.OBOTerm
-
- REMOVAL_OF_A_CHEMICAL_GROUP - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Covalent reaction that results in the removal of a chemical group from a molecule
(
SBO:0000211).
- removeAnnotation(Annotation) - Method in class org.sbolstandard.core2.Identified
-
Removes the given annotation from the list of annotations owned by this instance.
- removeCollection(Collection) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given collection from this SBOL document's list of collections.
- removeCollection(Collection) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes the given collection from the factory's internal SBOL document's list of collections.
- removeComponent(Component) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes the given component from the list of components.
- removeComponentDefinition(ComponentDefinition) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given component definition from this SBOL document's list of component definitions.
- removeComponentDefinition(ComponentDefinition) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes the given component definition from the factory's internal SBOL document's list of component definitions.
- removeFunctionalComponent(FunctionalComponent) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Removes the given functional component from this module definition's list of
functional components.
- removeGenericTopLevel(GenericTopLevel) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given generic top-level from this SBOL document's list of generic top-levels.
- removeGenericTopLevel(GenericTopLevel) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes the given generic top-level from the factory's internal SBOL document's list of generic top-levels.
- removeInteraction(Interaction) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Removes the given interaction from the list of interactions.
- removeLocation(Location) - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Removes the given location from the list of locations.
- removeMapsTo(MapsTo) - Method in class org.sbolstandard.core2.Component
-
Removes the given mapsTo from the list of
mapsTos.
- removeMapsTo(MapsTo) - Method in class org.sbolstandard.core2.FunctionalComponent
-
Removes the given mapsTo.
- removeMapsTo(MapsTo) - Method in class org.sbolstandard.core2.Module
-
Removes the given mapsTo from the list of mapsTos owned by this module.
- removeMember(URI) - Method in class org.sbolstandard.core2.Collection
-
Removes the given member from this Collection instance's set of members.
- removeModel(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Removes the given model URI from the set of model URIs owned by this module definition.
- removeModel(Model) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given model from this SBOL document's list of models.
- removeModel(Model) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes the given model from the factory's internal SBOL document's list of models.
- removeModule(Module) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Removes the given module from the list of modules.
- removeModuleDefinition(ModuleDefinition) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given module definition from this SBOL document's list of module definitions.
- removeModuleDefinition(ModuleDefinition) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes the given module definition from this SBOL document's list of module definitions.
- removeNamespace(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given namespace URI from this SBOL document's list of namespaces.
- removeNamespace(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes the given namespace URI from the factory's internal SBOL document.
- removeParticipation(Participation) - Method in class org.sbolstandard.core2.Interaction
-
Removes the given participation from this interaction's list of participations.
- removeRegistry(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given registry id from this SBOL document's list of registries.
- removeRegistryParts(SBOLDocument) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Remove all parts from this registry from a given SBOL document
- removeRole(URI) - Method in class org.sbolstandard.core2.Component
-
Removes the given role URI from the set of roles.
- removeRole(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes the given role URI from the set of roles.
- removeRole(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Removes the given role from the set of roles.
- removeRole(URI) - Method in class org.sbolstandard.core2.Participation
-
Removes the given role from the set of roles.
- removeRole(URI) - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Removes the given role from this sequence annotation's set of roles.
- removeSBOL(URI) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Remove SBOL TopLevel object from a SynBioHub instance using its URI.
- removeSequence(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes the given sequence URI from the set of sequence URIs.
- removeSequence(Sequence) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given sequence from this SBOL document's list of sequences.
- removeSequence(Sequence) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Removes the given sequence from the factory's internal SBOL document's list of sequences.
- removeSequenceAnnotation(SequenceAnnotation) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes the given sequence annotation from the list of sequence annotations.
- removeSequenceConstraint(SequenceConstraint) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes the given sequence constraint from the list of sequence constraints.
- removeTopLevel(TopLevel) - Method in class org.sbolstandard.core2.SBOLDocument
-
Method to remove a TopLevel object
- removeType(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Removes the given type URI from the set of types.
- removeType(URI) - Method in class org.sbolstandard.core2.Interaction
-
Removes the given type URI from this interation's the set of type URIs.
- removeWasDerivedFrom(URI) - Method in class org.sbolstandard.core2.Identified
-
Removes the given wasDerivedFrom URI from the set of wasDerivedFroms.
- rename(TopLevel, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Renames the given top-level's display ID with the given one.
- rename(TopLevel, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Renames the given top-level's display ID and version with the given ones.
- rename(TopLevel, String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Renames the given top-level's URI prefix, display ID, and version with the given ones.
- RESTRICTION_ENZYME_RECOGNITION_SITE - Static variable in class org.sbolstandard.core2.SequenceOntology
-
Represents a region of a DNA molecule which is a nucleotide region (usually a palindrome) that is recognized by a
restriction enzyme (
SO:0001687).
- RestrictionType - Enum in org.sbolstandard.core2
-
Represents the relationship between a sequence constraint's subject and object components.
- reverseComplement(String, URI) - Static method in class org.sbolstandard.core2.Sequence
-
Perform the reverse complement of a sequence encoded using IUPAC_DNA
- RIBOSOME_ENTRY_SITE - Static variable in class org.sbolstandard.core2.SequenceOntology
-
Region in mRNA where ribosome assembles (
SO:0000193)
- RNA - Static variable in class org.sbolstandard.core2.ComponentDefinition
-
A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid
(
RNA).
- RNA - Static variable in class org.sbolstandard.core2.SequenceOntology
-
An attribute describing a sequence consisting of nucleobases bound to a repeating
unit made of a D-ribose ring connected to a phosphate backbone.
- RoleIntegrationType - Enum in org.sbolstandard.core2
-
Represents the role integration relationship between roles specified in related objects.
- SBML - Static variable in class org.sbolstandard.core2.EDAMOntology
-
Systems Biology Markup Language (SBML), the standard XML format for models of biological
processes such as for example metabolism, cell signaling, and gene regulation
(
SBML).
- SBOLConversionException - Exception in org.sbolstandard.core2
-
Signals that an exception related to conversion between SBOL and other file formats has occurred.
- SBOLDocument - Class in org.sbolstandard.core2
-
Represents the SBOL document where all top-level instances can be created and manipulated.
- SBOLDocument() - Constructor for class org.sbolstandard.core2.SBOLDocument
-
Creates a new SBOLDocument instance with one empty list for the namespaces and one for each top-level instance,
and then adds the following namespaces: Sbol2Terms.sbol2
, Sbol1Terms.rdf
, Sbol2Terms.dc
,
and Sbol2Terms.prov
.
- SBOLFactory - Class in org.sbolstandard.core2
-
This is a helper class that avoids the need for the user to explicitly create an SBOLDocument instance,
and allows the user to directly create and manipulate top-level instances.
- SBOLFactory() - Constructor for class org.sbolstandard.core2.SBOLFactory
-
- SBOLReader - Class in org.sbolstandard.core2
-
Provides methods to read input SBOL files.
- SBOLReader() - Constructor for class org.sbolstandard.core2.SBOLReader
-
- SBOLValidate - Class in org.sbolstandard.core2
-
Provides functionality for validating SBOL data models.
- SBOLValidate() - Constructor for class org.sbolstandard.core2.SBOLValidate
-
- SBOLValidationException - Exception in org.sbolstandard.core2
-
Signals that an SBOL validation rule violation has occurred.
- SBOLVERSION1 - Static variable in class org.sbolstandard.core2.SBOLReader
-
Constant representing SBOL version 1.1
- SBOLVERSION2 - Static variable in class org.sbolstandard.core2.SBOLReader
-
Constant representing SBOL version 2.0
- SBOLWriter - Class in org.sbolstandard.core2
-
Provides methods to output SBOL files in XML/RDF format.
- SBOLWriter() - Constructor for class org.sbolstandard.core2.SBOLWriter
-
- search(SearchQuery) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Search this SynBioHub instance for objects matching a search query
- SearchCriteria - Class in org.synbiohub.frontend
-
Class for search criteria
- SearchCriteria() - Constructor for class org.synbiohub.frontend.SearchCriteria
-
- SearchQuery - Class in org.synbiohub.frontend
-
Class for search queries
- SearchQuery() - Constructor for class org.synbiohub.frontend.SearchQuery
-
- Sequence - Class in org.sbolstandard.core2
-
Represents a Sequence object in the SBOL data model.
- SEQUENCE - Static variable in class org.sbolstandard.core2.TopLevel
-
The abbreviation for the Sequence type in URI
- SEQUENCE_FEATURE - Static variable in class org.sbolstandard.core2.SequenceOntology
-
Any extent of continuous biological sequence.
- SequenceAnnotation - Class in org.sbolstandard.core2
-
Represents a SequenceAnnotation object in the SBOL data model.
- SequenceConstraint - Class in org.sbolstandard.core2
-
Represents a SequenceConstraint object in the SBOL data model.
- SequenceOntology - Class in org.sbolstandard.core2
-
This class provides methods for accessing
Sequence Ontology (SO) terms
and querying about their relationships.
- SequenceOntology() - Constructor for class org.sbolstandard.core2.SequenceOntology
-
Construct an SO ontology and reads the OBO definition file, if it has not been read in before.
- setAccess(AccessType) - Method in class org.sbolstandard.core2.ComponentInstance
-
Sets the access property to the given one.
- setAnnotations(List<Annotation>) - Method in class org.sbolstandard.core2.Annotation
-
Sets the list of Annotations of the nested value property.
- setAt(int) - Method in class org.sbolstandard.core2.Cut
-
Sets the at property of this Cut instance to the given one.
- setBooleanValue(boolean) - Method in class org.sbolstandard.core2.Annotation
-
Sets the boolean representation of the value property.
- setComplete(boolean) - Method in class org.sbolstandard.core2.SBOLDocument
-
Sets the complete flag to the given value.
- setComplete(boolean) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Sets the complete flag to the given value.
- setCompliant(boolean) - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the compliant flag to the given value.
- setComponent(String) - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Sets this sequence annotation's reference component (its identity URI) to the one matching
the given display ID.
- setComponent(URI) - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Sets the reference component's identity URI to the given URI.
- setCreateDefaults(boolean) - Method in class org.sbolstandard.core2.SBOLDocument
-
Sets the createDefaults flag to the given value.
- setCreateDefaults(boolean) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Sets the createDefaults flag to the given value.
- setCriteria(ArrayList<SearchCriteria>) - Method in class org.synbiohub.frontend.SearchQuery
-
Set the search criteria
- setDefaultSequenceEncoding(URI) - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the defaultsequenceEndocding flag to the given value.
- setDefaultURIprefix(String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Sets the default URI prefix of this SBOL document to the given one.
- setDefaultURIprefix(String) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Sets the default URI prefix to the given one.
- setDefinition(URI) - Method in class org.sbolstandard.core2.Component
-
Sets the definition property to the given one.
- setDefinition(URI) - Method in class org.sbolstandard.core2.ComponentInstance
-
Sets the definition property to the given one.
- setDefinition(URI) - Method in class org.sbolstandard.core2.FunctionalComponent
-
Sets the definition property to the given one.
- setDefinition(URI) - Method in class org.sbolstandard.core2.Module
-
Sets the reference definition URI to this module.
- setDescription(String) - Method in class org.sbolstandard.core2.Identified
-
Sets the description property for this instance.
- setDescription(String) - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- setDirection(DirectionType) - Method in class org.sbolstandard.core2.FunctionalComponent
-
Sets the direction property of this functional component to the given one.
- setDisplayId(String) - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- setDoubleValue(double) - Method in class org.sbolstandard.core2.Annotation
-
Sets the double representation of the value property.
- setDropObjectsWithDuplicateURIs(boolean) - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the value of the dropObjectsWithDuplicateURIs flag.
- setElements(String) - Method in class org.sbolstandard.core2.Sequence
-
Sets the elements property to the given argument.
- setEncoding(URI) - Method in class org.sbolstandard.core2.Sequence
-
Sets the encoding property to the given argument.
- setEnd(int) - Method in class org.sbolstandard.core2.Range
-
Sets the end position of this range.
- setFramework(URI) - Method in class org.sbolstandard.core2.Model
-
Sets the framework property to the given one.
- setIntegerValue(int) - Method in class org.sbolstandard.core2.Annotation
-
Sets the integer representation of the value property.
- setKeepGoing(boolean) - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the value for the keepGoing flag to the given boolean value.
- setKeepGoing(boolean) - Static method in class org.sbolstandard.core2.SBOLWriter
-
Sets the value for the keepGoing flag to the given boolean value.
- setKey(String) - Method in class org.synbiohub.frontend.SearchCriteria
-
Set the search key
- setLanguage(URI) - Method in class org.sbolstandard.core2.Model
-
Sets the language property to the given one.
- setLimit(Integer) - Method in class org.synbiohub.frontend.SearchQuery
-
Set the search limit
- setLocal(URI) - Method in class org.sbolstandard.core2.MapsTo
-
Sets the local property of this mapsTo to the given one.
- setMembers(Set<URI>) - Method in class org.sbolstandard.core2.Collection
-
Clears the existing set of members of this Collection instance first, then adds the given
set of the member references to it.
- setModels(Set<URI>) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Clears the existing set of model URIs first, then adds the given
set of the model URIs to this module definition.
- setName(String) - Method in class org.sbolstandard.core2.Identified
-
Sets the name property for this instance.
- setName(String) - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- setNestedIdentity(URI) - Method in class org.sbolstandard.core2.Annotation
-
Sets the nested URI for this annotation.
- setNestedQName(QName) - Method in class org.sbolstandard.core2.Annotation
-
Sets the nested QName for this annotation.
- setObject(URI) - Method in class org.sbolstandard.core2.SequenceConstraint
-
Sets the reference object component's identity URI to the given one.
- setOffset(Integer) - Method in class org.synbiohub.frontend.SearchQuery
-
Set the search offset
- setOrientation(OrientationType) - Method in class org.sbolstandard.core2.Location
-
Sets the orientation property of this location to the given one.
- setParticipant(URI) - Method in class org.sbolstandard.core2.Participation
-
Sets the participant property of this object to the given one.
- setQName(QName) - Method in class org.sbolstandard.core2.Annotation
-
Sets the QName of this annotation.
- setRDFType(QName) - Method in class org.sbolstandard.core2.GenericTopLevel
-
Set the RDF type property of this GenericTopLevel instance to the specified one.
- setRefinement(RefinementType) - Method in class org.sbolstandard.core2.MapsTo
-
Sets the refinement property of this mapsTo to the given one.
- setRemote(URI) - Method in class org.sbolstandard.core2.MapsTo
-
Sets the remote property of this mapsTo to the given one.
- setRestriction(RestrictionType) - Method in class org.sbolstandard.core2.SequenceConstraint
-
Sets the restriction property to the given one.
- setRestriction(URI) - Method in class org.sbolstandard.core2.SequenceConstraint
-
Sets the reference subject component's identity URI to the given one.
- setRoleIntegration(RoleIntegrationType) - Method in class org.sbolstandard.core2.Component
-
Sets the roleIntegration property of this object to the given one.
- setRoles(Set<URI>) - Method in class org.sbolstandard.core2.Component
-
Clears the existing set of roles first, and then adds the given
set of the roles to this component.
- setRoles(Set<URI>) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Clears the existing set of roles first, and then adds the given
set of the roles to this component definition.
- setRoles(Set<URI>) - Method in class org.sbolstandard.core2.ModuleDefinition
-
Clears the existing set of roles first, and then adds the given
set of the roles this module definition.
- setRoles(Set<URI>) - Method in class org.sbolstandard.core2.Participation
-
Clears the existing set of roles first, and then adds the given
set of the roles to this participation.
- setRoles(Set<URI>) - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Clears the existing set of roles first, and then adds the given
set of the roles to this sequence annotation.
- setSBOLDocument(SBOLDocument) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Sets the internal SBOL document used by the factory to the given one.
- setSequences(Set<URI>) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Clears the existing set of sequences first, and then adds the given
set of the sequences to this component definition.
- setSource(URI) - Method in class org.sbolstandard.core2.Model
-
Sets the source property to the given one.
- setStart(int) - Method in class org.sbolstandard.core2.Range
-
Sets the start position of this range.
- setStringValue(String) - Method in class org.sbolstandard.core2.Annotation
-
Sets the string representation of the value property.
- setSubject(URI) - Method in class org.sbolstandard.core2.SequenceConstraint
-
Sets the reference subject Component URI to the given subjectURI
.
- setTypes(Set<URI>) - Method in class org.sbolstandard.core2.ComponentDefinition
-
Clears the existing set of types first, then adds the given
set of the types to this component definition.
- setTypes(Set<URI>) - Method in class org.sbolstandard.core2.Interaction
-
Clears the existing set of type URIs first, then adds the given
set of the type URIs to this interaction.
- setTypesInURI(boolean) - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the value for the typesInURI flag.
- setTypesInURIs(boolean) - Method in class org.sbolstandard.core2.SBOLDocument
-
Sets the typesInURIs flag to the given value.
- setTypesInURIs(boolean) - Static method in class org.sbolstandard.core2.SBOLFactory
-
Sets the typesInURIs flag to the given value.
- setUri(String) - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- setURIPrefix(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the specified authority as the prefix.
- setURIValue(URI) - Method in class org.sbolstandard.core2.Annotation
-
Sets the string representation of the value property.
- setValue(String) - Method in class org.synbiohub.frontend.SearchCriteria
-
Set the search value
- setVersion(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the SBOL version for this reader.
- setVersion(String) - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- setWasDerivedFrom(URI) - Method in class org.sbolstandard.core2.Identified
-
Deprecated.
- setWasDerivedFroms(Set<URI>) - Method in class org.sbolstandard.core2.Identified
-
Clears the existing set of wasDerivedFroms first, and then adds the given
set of the wasDerivedFroms.
- SGRNA - Static variable in class org.sbolstandard.core2.SequenceOntology
-
A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the
CRISPR/cas mutagenesis method.
- SIDE_PRODUCT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
A substance that is produced in a chemical reaction but is not itself the primary
product or focus of that reaction (
SBO:0000603).
- SIDE_SUBSTRATE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
A substance that is consumed in a chemical reaction but is not itself the primary
substrate or focus of that reaction (
SBO:0000604).
- SILENCER - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
A silencer is a modifier which acts in a manner that completely prevents an event or
process from occurring (
SBO:0000597).
- SINGLE - Static variable in class org.sbolstandard.core2.SequenceOntology
-
A stand attribute that it indicates it is composed of a single strand.
- SMALL_MOLECULE - Static variable in class org.sbolstandard.core2.ComponentDefinition
-
- SMILES - Static variable in class org.sbolstandard.core2.Sequence
-
SMILES was originally developed as a proprietary specification by Daylight Chemical
Information Systems Since the introduction of SMILES in the late 1980’s, it has become
widely accepted as a defacto standard for exchange of molecular structures
(
SMILES).
- SPATIAL_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:0000292).
- SPATIAL_DISCRETE_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Modelling approach where the quantities of participants are considered discrete, and represented
by integer values (
SBO:0000294).
- SPECIFIC_ACTIVATOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
An essential activator that affects the apparent value of the specificity constant (
SBO:0000533).
- STATE_VARIABLE_ASSIGNMENT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Assignment of a state or a value to a state variable, characteristic or property, of a
biological entity
(
SBO:0000464).
- STIMULATED - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Conceptual or material entity that is the object of a stimulation process, and is
acted upon by a stimulator (
SBO:0000643).
- STIMULATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Positive modulation of the execution of a process
(
SBO:0000170).
- STIMULATOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Substance that accelerates the velocity of a chemical reaction without itself being
consumed or transformed
(
SBO:0000459).
- STRAND_ATTRIBUTE - Static variable in class org.sbolstandard.core2.SequenceOntology
-
Attributes added to describe the different kinds of replicon.
- submit(String, String, String, String, String, String, String, SBOLDocument) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Submit to the SynBioHub.
- SUBSTRATE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Molecule which is acted upon by an enzyme (
SBO:0000015).
- SULFATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Addition of a sulfate group (SO4--) to a chemical entity
(
SBO:0000220).
- SynBioHubException - Exception in org.synbiohub.frontend
-
Thrown when the SynBioHub returns an error code.
- SynBioHubFrontend - Class in org.synbiohub.frontend
-
Provides a Java API to SynBioHub instances.
- SynBioHubFrontend(String, String) - Constructor for class org.synbiohub.frontend.SynBioHubFrontend
-
Creates an instance of the SynBioHub API.
- SynBioHubFrontend(String) - Constructor for class org.synbiohub.frontend.SynBioHubFrontend
-
Creates an instance of the SynBioHub API.
- SYNTHETIC_LETHALITY - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Synthetic lethality is said to have occurred where gene mutations, each of which map to
a separate locus, fail to complement in an offspring to correct a phenotype, as would be
expected
(
SBO:0000502).
- SystemsBiologyOntology - Class in org.sbolstandard.core2
-
- SystemsBiologyOntology() - Constructor for class org.sbolstandard.core2.SystemsBiologyOntology
-
Construct an SBO ontology object and read the OBO definition file, if it has not been constructed.