- 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.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.
- 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 - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Connectedness between entities and/or interactions representing their relatedness or
influence
(
SBO:0000374).
- 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).
- removeActivity(Activity) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given activity from this SBOL document's list of activities.
- removeAgent(Agent) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given agent from this SBOL document's list of agents.
- removeAnnotation(Annotation) - Method in class org.sbolstandard.core2.Identified
-
Removes the given annotation from the list of annotations owned by this instance.
- removeAssociation(Association) - Method in class org.sbolstandard.core2.Activity
-
Removes the given association from the list of associations.
- removeAttachment(Attachment) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given attachment from this SBOL document's list of attachments.
- removeAttachment(URI) - Method in class org.sbolstandard.core2.TopLevel
-
Removes the given attachment from the list of attachments.
- removeCollection(Collection) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given collection from this SBOL document's list of collections.
- removeCombinatorialDerivation(CombinatorialDerivation) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given combinatorial derivation from this SBOL document's list of
combinatorial derivations.
- 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.
- removeExperiment(Experiment) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given experiment from this SBOL document's list of experiments.
- removeExperimentalData(URI) - Method in class org.sbolstandard.core2.Experiment
-
Removes the given experimentalData from this Experiment's set of experimentalData.
- removeExperimentalData(ExperimentalData) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given experimentalData from this SBOL document's list of experimentalData.
- 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.
- removeImplementation(Implementation) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given implementation from this SBOL document's list of
implementations.
- 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.Component
-
Removes the given location from the list of locations.
- 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.
- removeMeasure(Measure) - Method in class org.sbolstandard.core2.Measured
-
Removes the given measure from this measured object's list of measures.
- 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.
- 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.
- removeNamespace(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given namespace URI from this SBOL document's list of namespaces.
- removeParticipation(Participation) - Method in class org.sbolstandard.core2.Interaction
-
Removes the given participation from this interaction's list of participations.
- removePlan(Plan) - Method in class org.sbolstandard.core2.SBOLDocument
-
Removes the given plan from this SBOL document's list of plans.
- 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.Association
-
Removes the given role URI from the set of roles.
- 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.
- removeRole(URI) - Method in class org.sbolstandard.core2.Usage
-
Removes the given role URI from the 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.
- 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.
- removeSourceLocation(Location) - Method in class org.sbolstandard.core2.Component
-
Removes the given location from the list of source locations.
- removeTopLevel(TopLevel) - Method in class org.sbolstandard.core2.SBOLDocument
-
Method to remove a TopLevel object
- removeType(URI) - Method in class org.sbolstandard.core2.Activity
-
Removes the given type URI from the set of types.
- 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.
- removeType(URI) - Method in class org.sbolstandard.core2.Measure
-
Removes the given type URI from the set of types.
- removeUsages(Usage) - Method in class org.sbolstandard.core2.Activity
-
Removes the given usage from the list of usages.
- removeVariableComponent(VariableComponent) - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Removes the given variable component from the list of variable components.
- removeVariant(ComponentDefinition) - Method in class org.sbolstandard.core2.VariableComponent
-
Removes the given component definition from the list of variants.
- removeVariant(URI) - Method in class org.sbolstandard.core2.VariableComponent
-
Removes the component definition with the given URI from the list of
variants.
- removeVariantCollection(Collection) - Method in class org.sbolstandard.core2.VariableComponent
-
Removes the given collection from the list of variantCollections.
- removeVariantCollection(URI) - Method in class org.sbolstandard.core2.VariableComponent
-
Removes the collection with the given URI from the list of
variantCollections.
- removeVariantDerivation(CombinatorialDerivation) - Method in class org.sbolstandard.core2.VariableComponent
-
Removes the given combinatorial derivation from the list of variant
derivations.
- removeVariantDerivation(URI) - Method in class org.sbolstandard.core2.VariableComponent
-
Removes the combinatorial derivation with the given URI from the list of
variant derivations.
- removeWasDerivedFrom(URI) - Method in class org.sbolstandard.core2.Identified
-
Removes the given wasDerivedFrom URI from the set of wasDerivedFroms.
- removeWasGeneratedBy(URI) - Method in class org.sbolstandard.core2.Identified
-
Removes the given wasGeneratedBy URI from the set of wasGeneratedBys.
- 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.
- replaceSBOL(URI) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Remove SBOL TopLevel object from a SynBioHub instance using its URI,
but leave references to this object, since it is going to be replaced.
- 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:0000139)
- RNA - Static variable in class org.sbolstandard.core2.ComponentDefinition
-
Deprecated.
- 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.
- RNA_MOLECULE - Static variable in class org.sbolstandard.core2.ComponentDefinition
-
A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid.
- RNA_REGION - Static variable in class org.sbolstandard.core2.ComponentDefinition
-
A region on a RNA molecule.
- RoleIntegrationType - Enum in org.sbolstandard.core2
-
Represents the role integration relationship between roles specified in related objects.