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A

ABSOLUTE_INHIBITION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Control that precludes the execution of a process (SBO:0000407).
ABSOLUTE_STIMULATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Control that always triggers the controlled process (SBO:0000411).
AccessType - Enum in org.sbolstandard.core2
Represents all access types for a ComponentInstance object.
ACETYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Addition of an acetyl group (-COCH3) to a chemical entity (SBO:0000215).
ACID_BASE_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Chemical reaction where a proton is given by a compound, the acid, to another one, the base (Brønsted-Lowry definition) (SBO:0000208).
add(OBOOntology) - Method in class org.oboparser.obo.OBOOntology
 
add(OBOStanza) - Method in class org.oboparser.obo.OBOStanza
 
addCriteria(SearchCriteria) - Method in class org.synbiohub.frontend.SearchQuery
Add a search criterion
addCut(String, int) - Method in class org.sbolstandard.core2.SequenceAnnotation
Creates a cut with the given arguments and then adds it to this sequence annotation's list of locations.
addCut(String, int, OrientationType) - Method in class org.sbolstandard.core2.SequenceAnnotation
Creates a cut with the given arguments and then adds it to this sequence annotation's list of locations.
addGenericLocation(String) - Method in class org.sbolstandard.core2.SequenceAnnotation
Creates a generic location with the given arguments and then adds it to this sequence annotation's list of locations.
addGenericLocation(String, OrientationType) - Method in class org.sbolstandard.core2.SequenceAnnotation
Creates a generic location with the given arguments and then adds it to this sequence annotation's list of locations.
ADDITION_OF_A_CHEMICAL_GROUP - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Covalent reaction that results in the addition of a chemical group on a molecule (SBO:0000210).
addMember(URI) - Method in class org.sbolstandard.core2.Collection
Adds the given member URI to this Collection instance's set of reference member URIs.
addModel(Model) - Method in class org.sbolstandard.core2.ModuleDefinition
Adds the URI of the given model to this module definition's set of model URIs.
addModel(String, String) - Method in class org.sbolstandard.core2.ModuleDefinition
Adds the URI of the model that has the given display ID and version to this module definition's set of model URIs.
addModel(String) - Method in class org.sbolstandard.core2.ModuleDefinition
Adds the URI of the model that has the given display ID to this module definition's set of model URIs.
addModel(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
Adds the given model URI to this module definition's set of model URIs.
addNamespace(URI, String) - Method in class org.sbolstandard.core2.SBOLDocument
Adds the given namespace URI and its prefix to this SBOL document.
addNamespace(QName) - Method in class org.sbolstandard.core2.SBOLDocument
Adds the given namespace QName to this SBOL document.
addNamespace(URI, String) - Static method in class org.sbolstandard.core2.SBOLFactory
Adds the given namespace URI and its prefix to the internal SBOL document used by the factory.
addNamespace(QName) - Static method in class org.sbolstandard.core2.SBOLFactory
Adds the given namespace QName to the internal SBOL document used by the factory.
addOBOStanza(OBOStanza) - Method in class org.oboparser.obo.OBOOntology
 
addRange(String, int, int) - Method in class org.sbolstandard.core2.SequenceAnnotation
Creates a range with the given arguments and then adds it to this sequence annotation's list of locations.
addRange(String, int, int, OrientationType) - Method in class org.sbolstandard.core2.SequenceAnnotation
Creates a range with the given arguments and then adds it to this sequence annotation's list of locations.
addRegistry(String) - Method in class org.sbolstandard.core2.SBOLDocument
Adds the given registry to this SBOL document.
addRegistry(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
Adds the given registry to this SBOL document.
addRole(URI) - Method in class org.sbolstandard.core2.Component
Adds the given role URI to this component's set of role URIs.
addRole(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
Adds the given role URI to this component definition's set of role URIs.
addRole(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
Adds the given role URI to this module definition's set of role URIs.
addRole(URI) - Method in class org.sbolstandard.core2.Participation
Adds the given role to this participation's set of roles.
addRole(URI) - Method in class org.sbolstandard.core2.SequenceAnnotation
Adds the given role to this sequence annotation's set of roles.
addSequence(Sequence) - Method in class org.sbolstandard.core2.ComponentDefinition
Adds the URI of the given Sequence instance to this component definition's set of sequence URIs.
addSequence(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
Adds the given sequence URI to this component definition's set of sequence URIs.
addSequence(String, String) - Method in class org.sbolstandard.core2.ComponentDefinition
Constructs a compliant sequence URI with the given display ID and version, and then adds this URI to this component definition's set of sequence URIs.
addSequence(String) - Method in class org.sbolstandard.core2.ComponentDefinition
Constructs a compliant sequence URI using the given sequence display ID, and then adds this URI to this component definition's set of sequence URIs.
addType(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
Adds the given type URI to this component definition's set of type URIs.
addType(URI) - Method in class org.sbolstandard.core2.Interaction
Adds the given type URI to this interaction's set of type URIs.
addValue(String, OBOValue) - Method in class org.oboparser.obo.OBOStanza
 
addValue(String, OBOValue) - Method in class org.oboparser.obo.OBOTerm
 
addWasDerivedFrom(URI) - Method in class org.sbolstandard.core2.Identified
Adds the given wasDerivedFrom URI to the set of wasDerivedFrom URIs.
ALLOSTERIC_CONTROL - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Regulation of the influence of a reaction participant by binding an effector to a binding site of the participant different of the site of the participant conveying the influence (SBO:0000239).
AND - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
All the preceding events or participating entities are necessary to perform the control (SBO:0000173).
Annotation - Class in org.sbolstandard.core2
Represents an Annotation object in the cSBOL data model.
Annotation(QName, String) - Constructor for class org.sbolstandard.core2.Annotation
Constructs an annotation using the given qName and the string type literal.
Annotation(QName, int) - Constructor for class org.sbolstandard.core2.Annotation
Constructs an annotation using the given qName and the integer type literal.
Annotation(QName, double) - Constructor for class org.sbolstandard.core2.Annotation
Constructs an annotation using the given qName and the double type literal.
Annotation(QName, boolean) - Constructor for class org.sbolstandard.core2.Annotation
Constructs an annotation using the given qName and the boolean type literal.
Annotation(QName, URI) - Constructor for class org.sbolstandard.core2.Annotation
Constructs an annotation using the given qName and the URI type literal.
Annotation(QName, QName, URI, List<Annotation>) - Constructor for class org.sbolstandard.core2.Annotation
Constructs a nested annotation using the given qName, nested qName, nested URI, and list of annotations.

B

BINDING_ACTIVATOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
An essential activator that affects the apparent value of the Michaelis constant(s) (SBO:0000535).
BIOCHEMICAL_OR_TRANSPORT_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants (SBO:0000167).
BIOCHEMICAL_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants.
BIOLOGICAL_ACTIVITY - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
The potential action that a biological entity has on other entities (SBO:0000412).
BIOLOGICAL_EFFECT_OF_A_PERTURBATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Biochemical networks can be affected by external influences (SBO:0000357).
BIOPAX - Static variable in class org.sbolstandard.core2.EDAMOntology
BioPAX is an exchange format for pathway data, with its data model defined in OWL (BIOPAX).
BOOLEAN_LOGICAL_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Equationally defined algebraic framework usually interpreted as a two-valued logic using the basic Boolean operations (conjunction, disjunction and negation), together with the constants '0' and '1' denoting false and true values, respectively (SBO:0000547).

C

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.

D

DEAMINATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Removal of an amine group from a molecule, often under the addition of water (SBO:0000401).
DECARBONYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Removal of a carbonyl group (-C-O-) from a molecule, usually as carbon monoxide (SBO:0000400).
DECARBOXYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A process in which a carboxyl group (COOH) is removed from a molecule as carbon dioxide (SBO:0000399).
DEGRADATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Complete disappearance of a physical entity (SBO:0000179).
DEPHOSPHORYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Removal of a phosphate group (-H2PO4) from a chemical entity (SBO:0000330).
DEPROTONATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Removal of a proton (hydrogen ion H+) from a chemical entity (SBO:0000213).
DirectionType - Enum in org.sbolstandard.core2
Represents all direction types for a FunctionalComponent object.
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:0000063).
DISSOCIATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Transformation of a non-covalent complex that results in the formation of several independent biochemical entities (SBO:0000180).
DNA - Static variable in class org.sbolstandard.core2.ComponentDefinition
A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid (DNA).
DNA - Static variable in class org.sbolstandard.core2.SequenceOntology
An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.
DNA_REPLICATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Process in which a DNA duplex is transformed into two identical DNA duplexes (SBO:0000204).
DOUBLE - Static variable in class org.sbolstandard.core2.SequenceOntology
A stand attribute that it indicates it is composed of a double strand.
DUAL_ACTIVITY_MODIFIER - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A modifier that can exhibit either inhibitory or stimulatory effects on a process depending on the context in which it occurs (SBO:0000595).

E

EDAMOntology - Class in org.sbolstandard.core2
This class provides methods for accessing EMBRACE Data and Methods (EDAM) terms and querying about their relationships.
EDAMOntology() - Constructor for class org.sbolstandard.core2.EDAMOntology
Construct an EDAM ontology object and read the OBO definition file, if necessary.
EFFECTOR - Static variable in class org.sbolstandard.core2.ComponentDefinition
A small molecule which increases (activator) or decreases (inhibitor) the activity of an (allosteric) enzyme by binding to the enzyme at the regulatory site (which is different from the substrate-binding catalytic site) (Effector).
ENCAPSULATING_PROCESS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
An aggregation of interactions and entities into a single process (SBO:0000395).
ENGINEERED_GENE - Static variable in class org.sbolstandard.core2.SequenceOntology
A gene that is engineered (SO:0000280).
ENGINEERED_REGION - Static variable in class org.sbolstandard.core2.SequenceOntology
A region that is engineered (SO:0000804).
ENZYMATIC_CATALYST - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed, by lowering the free energy of the transition state (SBO:0000460).
equals(Object) - Method in class org.oboparser.obo.OBOValue
 
equals(Object) - Method in class org.sbolstandard.core2.Annotation
 
equals(Object) - Method in class org.sbolstandard.core2.Collection
 
equals(Object) - Method in class org.sbolstandard.core2.Component
 
equals(Object) - Method in class org.sbolstandard.core2.ComponentDefinition
 
equals(Object) - Method in class org.sbolstandard.core2.ComponentInstance
 
equals(Object) - Method in class org.sbolstandard.core2.Cut
 
equals(Object) - Method in class org.sbolstandard.core2.FunctionalComponent
 
equals(Object) - Method in class org.sbolstandard.core2.GenericLocation
 
equals(Object) - Method in class org.sbolstandard.core2.GenericTopLevel
 
equals(Object) - Method in class org.sbolstandard.core2.Identified
 
equals(Object) - Method in class org.sbolstandard.core2.Interaction
 
equals(Object) - Method in class org.sbolstandard.core2.MapsTo
 
equals(Object) - Method in class org.sbolstandard.core2.Model
 
equals(Object) - Method in class org.sbolstandard.core2.Module
 
equals(Object) - Method in class org.sbolstandard.core2.ModuleDefinition
 
equals(Object) - Method in class org.sbolstandard.core2.Range
 
equals(Object) - Method in class org.sbolstandard.core2.SBOLDocument
 
equals(Object) - Method in class org.sbolstandard.core2.SBOLFactory
 
equals(Object) - Method in class org.sbolstandard.core2.Sequence
 
equals(Object) - Method in class org.sbolstandard.core2.SequenceAnnotation
 
equals(Object) - Method in class org.sbolstandard.core2.SequenceConstraint
 
EQUIVALENCE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Term to signify those material or conceptual entities that are identical in some respect within a frame of reference (SBO:0000392).
ESSENTIAL_ACTIVATOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A substance that is absolutely required for occurrence and stimulation of a reaction (SBO:0000461).

F

FARNESYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Addition of a farnesyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity (SBO:0000222).
FASTAformat - Static variable in class org.sbolstandard.core2.SBOLDocument
Constant representing FASTA file format
FIVE_PRIME_UTR - Static variable in class org.sbolstandard.core2.SequenceOntology
A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein (SO:0000204).
FLUX_BALANCE_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Modelling approach, typically used for metabolic models, where the flow of metabolites (flux) through a network can be calculated (SBO:0000624).
FORMAT - Static variable in class org.sbolstandard.core2.EDAMOntology
A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.
FUNCTIONAL_COMPARTMENT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Logical or physical subset of the event space that contains pools, that is sets of participants considered identical when it comes to the event they are involved into (SBO:0000289).
FunctionalComponent - Class in org.sbolstandard.core2
Represents a FunctionalComponent object in the SBOL data model.

G

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).

H

hasAnnotations() - Method in class org.sbolstandard.core2.Identified
Test if this instance has any annotations.
hashCode() - Method in class org.oboparser.obo.OBOValue
 
hashCode() - Method in class org.sbolstandard.core2.Annotation
 
hashCode() - Method in class org.sbolstandard.core2.Collection
 
hashCode() - Method in class org.sbolstandard.core2.Component
 
hashCode() - Method in class org.sbolstandard.core2.ComponentDefinition
 
hashCode() - Method in class org.sbolstandard.core2.ComponentInstance
 
hashCode() - Method in class org.sbolstandard.core2.Cut
 
hashCode() - Method in class org.sbolstandard.core2.FunctionalComponent
 
hashCode() - Method in class org.sbolstandard.core2.GenericLocation
 
hashCode() - Method in class org.sbolstandard.core2.GenericTopLevel
 
hashCode() - Method in class org.sbolstandard.core2.Identified
 
hashCode() - Method in class org.sbolstandard.core2.Interaction
 
hashCode() - Method in class org.sbolstandard.core2.MapsTo
 
hashCode() - Method in class org.sbolstandard.core2.Model
 
hashCode() - Method in class org.sbolstandard.core2.Module
 
hashCode() - Method in class org.sbolstandard.core2.ModuleDefinition
 
hashCode() - Method in class org.sbolstandard.core2.Range
 
hashCode() - Method in class org.sbolstandard.core2.SBOLDocument
 
hashCode() - Method in class org.sbolstandard.core2.SBOLFactory
 
hashCode() - Method in class org.sbolstandard.core2.Sequence
 
hashCode() - Method in class org.sbolstandard.core2.SequenceAnnotation
 
hashCode() - Method in class org.sbolstandard.core2.SequenceConstraint
 
hasValue(String) - Method in class org.oboparser.obo.OBOStanza
 
HYDROLYSIS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Decomposition of a compound by reaction with water, where the hydroxyl and H groups are incorporated into different products (SBO:0000376).
HYDROXYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Addition of an hydroxyl group (-OH) to a chemical entity (SBO:0000233).

I

Identified - Class in org.sbolstandard.core2
Represents an Identified object in the SBOL data model.
IdentifiedMetadata - Class in org.synbiohub.frontend
The metadata common to all SBOL data objects
IdentifiedMetadata() - Constructor for class org.synbiohub.frontend.IdentifiedMetadata
 
INHIBITED - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Conceptual or material entity that is the object of an inhibition process, and is acted upon by an inhibitor (SBO:0000642).
INHIBITION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Negative modulation of the execution of a process (SBO:0000169).
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 (SBO:0000020).
INSULATOR - Static variable in class org.sbolstandard.core2.SequenceOntology
A transcriptional cis regulatory region that, when located between a CM and a gene's promoter, prevents the CRM from modulating that genes expression (SO:0000627)
Interaction - Class in org.sbolstandard.core2
Represents an Interaction object in the SOBL data model.
INTERACTOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Entity participating in a physical or functional interaction (SBO:0000336).
intersectionOf() - Method in class org.oboparser.obo.OBOTerm
 
IONISATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Ionization is the physical process of converting an atom or molecule into an ion by changing the difference between the number of protons and electrons (SBO:0000209).
isa() - Method in class org.oboparser.obo.OBOTerm
 
isBooleanValue() - Method in class org.sbolstandard.core2.Annotation
Checks if the annotation has a boolean value property.
isComplete() - Method in class org.sbolstandard.core2.SBOLDocument
Returns the value of the complete flag for this SBOL document.
isComplete() - Static method in class org.sbolstandard.core2.SBOLFactory
Returns the value of the complete flag in the factory's internal SBOL document.
isCompliant() - Method in class org.sbolstandard.core2.SBOLDocument
Returns the value of the compliant flag in this SBOL document.
isCompliant() - Static method in class org.sbolstandard.core2.SBOLFactory
Returns the value of the compliant flag in the factory's internal SBOL document.
isCompliant() - Static method in class org.sbolstandard.core2.SBOLReader
Check if document is to be read as being compliant.
isCreateDefaults() - Method in class org.sbolstandard.core2.SBOLDocument
Returns the value of the createDefaults flag in this SBOL document.
isCreateDefaults() - Static method in class org.sbolstandard.core2.SBOLFactory
Returns the value of the createDefaults flag in the factory's internal SBOL document.
isDescendantOf(OBOStanza, OBOStanza) - Method in class org.oboparser.obo.OBOOntology
 
isDescendantOf(String, String) - Method in class org.sbolstandard.core2.EDAMOntology
Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
isDescendantOf(URI, URI) - Method in class org.sbolstandard.core2.EDAMOntology
Returns true if the stanza with childURI is a descendant of the stanza with parentURI.
isDescendantOf(String, String) - Method in class org.sbolstandard.core2.SequenceOntology
Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
isDescendantOf(URI, URI) - Method in class org.sbolstandard.core2.SequenceOntology
Returns true if the stanza with childURI is a descendant of the stanza with parentURI.
isDescendantOf(URI, URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
Returns true if the stanza with childURI is a descendant of the stanza with parentURI.
isDescendantOf(String, String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
isDoubleValue() - Method in class org.sbolstandard.core2.Annotation
Checks if the annotation has a double value property.
isDropObjectsWithDuplicateURIs() - Static method in class org.sbolstandard.core2.SBOLReader
Check if objects with duplicate URIs should be dropped.
isIntegerValue() - Method in class org.sbolstandard.core2.Annotation
Checks if the annotation has an integer value property.
isKeepGoing() - Static method in class org.sbolstandard.core2.SBOLReader
Checks if reading should continue after encountering an SBOL validation exception.
isKeepGoing() - Static method in class org.sbolstandard.core2.SBOLWriter
Returns the value of the keepGoing flag.
isNestedAnnotations() - Method in class org.sbolstandard.core2.Annotation
Checks if the annotation has a nested value property.
isObsolete() - Method in class org.oboparser.obo.OBOTerm
 
ISOMERISATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A reaction in which the principal reactant and principal product are isomers of each other (SBO:0000377).
isSetComponent() - Method in class org.sbolstandard.core2.SequenceAnnotation
Test if the reference component is set.
isSetDescription() - Method in class org.sbolstandard.core2.Identified
Test if the description property is set.
isSetDisplayId() - Method in class org.sbolstandard.core2.Identified
Test if the display ID is set.
isSetName() - Method in class org.sbolstandard.core2.Identified
Test if the name property is set.
isSetOrientation() - Method in class org.sbolstandard.core2.Location
Checks if the orientation property is set.
isSetPersistentIdentity() - Method in class org.sbolstandard.core2.Identified
Test if the persistent identity URI is set.
isSetRoleIntegration() - Method in class org.sbolstandard.core2.Component
Test if the roleIntegration property is set.
isSetVersion() - Method in class org.sbolstandard.core2.Identified
Test if the version is set.
isSetWasDerivedFrom() - Method in class org.sbolstandard.core2.Identified
Deprecated.
isStringValue() - Method in class org.sbolstandard.core2.Annotation
Checks if the annotation has a string value property.
isTypesInURIs() - Method in class org.sbolstandard.core2.SBOLDocument
Returns the value of the typesInURI flag in this SBOL document.
isTypesInURIs() - Static method in class org.sbolstandard.core2.SBOLFactory
Returns the value of the typesInURI flag in the factory's internal SBOL document.
isURIValue() - Method in class org.sbolstandard.core2.Annotation
Checks if the annotation is a URI value property.
IUPAC_DNA - Static variable in class org.sbolstandard.core2.Sequence
Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (IUPAC_DNA).
IUPAC_PROTEIN - Static variable in class org.sbolstandard.core2.Sequence
Nomenclature and Symbolism for Amino Acids and Peptides (IUPAC_PROTEIN).
IUPAC_RNA - Static variable in class org.sbolstandard.core2.Sequence
Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (IUPAC_RNA).

J

JSON - Static variable in class org.sbolstandard.core2.SBOLDocument
Constant representing JSON file format

K

keepGoing - Static variable in class org.sbolstandard.core2.SBOLReader
A true value of the keepGoing flag tells the SBOL reader to continue reading an SBOL input file, after it encounters an SBOL validation exception; a false value forces the reader to stop reading after it encounters an SBOL validation exception.
keepGoing - Static variable in class org.sbolstandard.core2.SBOLWriter
A true value of the keepGoing flag tells the SBOL writer to continue writing an output file, after it encounters an SBOL conversion exception; a false value forces the writer to stop writing after it encounters an SBOL conversion exception.
keys() - Method in class org.oboparser.obo.OBOStanza
 

L

LINEAR - Static variable in class org.sbolstandard.core2.SequenceOntology
A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.
Location - Class in org.sbolstandard.core2
Represents a Location object in the SOBL data model.
LOGICAL_COMBINATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Combining the influence of several entities or events in a unique influence (SBO:0000237).
LOGICAL_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Modelling approach, pioneered by Rene Thomas and Stuart Kaufman, where the evolution of a system is described by the transitions between discrete activity states of "genes" that control each other (SBO:0000234).
LOGICAL_RELATIONSHIP - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Relationship between entities (material or conceptual) and logical operators, or between logical operators themselves (SBO:0000398).
login(String, String) - Method in class org.synbiohub.frontend.SynBioHubFrontend
Login to the SynBioHub.
logout() - Method in class org.synbiohub.frontend.SynBioHubFrontend
Sets the user to null to indicate that no user is logged in.

M

main(String[]) - Static method in class org.oboparser.obo.OBOParser
 
main(String[]) - Static method in class org.oboparser.obo.OBOValue
 
main(String[]) - Static method in class org.sbolstandard.core2.SBOLValidate
Command line method for reading an input file and producing an output file.
MapsTo - Class in org.sbolstandard.core2
Represents a MapsTo object in the SBOL data model.
METHYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Addition of a methyl group (-CH3) to a chemical entity (SBO:0000214).
Model - Class in org.sbolstandard.core2
Represents a Model object in the SBOL data model.
MODEL - Static variable in class org.sbolstandard.core2.TopLevel
The abbreviation for the Model type in URI
MODELING_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Set of assumptions that underlay a mathematical description (SBO:0000004).
MODIFIED - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Conceptual or material entity that is the object of a modification process, and is acted upon by a modifier (SBO:0000644).
MODIFIER - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Substance that changes the velocity of a process without itself being consumed or transformed by the reaction (SBO:0000019).
MODIFIER_OF_UNKNOWN_ACTIVITY - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A modifier whose activity is not known or has not been specified (SBO:0000596).
Module - Class in org.sbolstandard.core2
Represents a Module object in the SBOL data model.
MODULE_DEFINITION - Static variable in class org.sbolstandard.core2.TopLevel
The abbreviation for the ModuleDefinition type in URI
ModuleDefinition - Class in org.sbolstandard.core2
Represents a ModuleDefinition object in the SBOL data model.
MOLECULAR_INTERACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Relationship between molecular entities, based on contacts, direct or indirect (SBO:0000344).
MOLECULAR_OR_GENETIC_INTERACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Mutual or reciprocal action or influence between molecular entities (SBO:0000342).
MRNA - Static variable in class org.sbolstandard.core2.SequenceOntology
Messenger RNA is the intermediate molecule between DNA and protein.
MYRISTOYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Addition of a myristoyl (CH3-[CH2]12-CO-) to a chemical entity (SBO:0000219).

N

NAMESPACE - Static variable in class org.sbolstandard.core2.EDAMOntology
Namespace of the EDAM Ontology (http://identifiers.org/edam/).
NAMESPACE - Static variable in class org.sbolstandard.core2.SequenceOntology
Namespace of the Sequence Ontology (http://identifiers.org/so/).
NAMESPACE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Namespace of the Systems Biology Ontology (http://identifiers.org/biomodels.sbo/).
NECESSARY_STIMULATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Control that is necessary to the execution of a process (SBO:0000171).
NEUTRAL_PARTICIPANT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A participant whose presence does not alter the velocity of a process or event (SBO:0000594).
NON_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, and without sterically hindering the interaction between reactants (SBO:0000207).
NON_COVALENT_BINDING - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Interaction between several biochemical entities that results in the formation of a non-covalent complex (SBO:0000177).
NON_ESSENTIAL_ACTIVATOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
An activator which is not necessary for an enzymatic reaction, but whose presence will further increase enzymatic activity (SBO:0000462).
NON_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:0000293).
NON_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:0000295).
NOT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
The preceding event or participating entity cannot participate to the control (SBO:0000238).

O

OBOException - Exception in org.oboparser.obo
 
OBOException(String) - Constructor for exception org.oboparser.obo.OBOException
 
OBOException(Throwable) - Constructor for exception org.oboparser.obo.OBOException
 
OBOException(String, Throwable) - Constructor for exception org.oboparser.obo.OBOException
 
OBOIndividual - Class in org.oboparser.obo
 
OBOIndividual() - Constructor for class org.oboparser.obo.OBOIndividual
 
OBOOntology - Class in org.oboparser.obo
 
OBOOntology() - Constructor for class org.oboparser.obo.OBOOntology
 
OBOParser - Class in org.oboparser.obo
 
OBOParser() - Constructor for class org.oboparser.obo.OBOParser
 
OBOProperties - Class in org.oboparser.obo
 
OBOProperties() - Constructor for class org.oboparser.obo.OBOProperties
 
OBOStanza - Class in org.oboparser.obo
 
OBOStanza(String) - Constructor for class org.oboparser.obo.OBOStanza
 
OBOTerm - Class in org.oboparser.obo
OBOTerm represent an OBO stanza that begins with the "[Term]" string.
OBOTerm() - Constructor for class org.oboparser.obo.OBOTerm
 
OBOTypedef - Class in org.oboparser.obo
 
OBOTypedef() - Constructor for class org.oboparser.obo.OBOTypedef
 
OBOValue - Class in org.oboparser.obo
 
OBOValue(String) - Constructor for class org.oboparser.obo.OBOValue
 
OBOValue(String, String, String...) - Constructor for class org.oboparser.obo.OBOValue
 
OCCURRING_ENTITY_REPRESENTATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Representation of an entity that manifests, unfolds or develops through time, such as a discrete event, or a mutual or reciprocal action or influence that happens between participating physical entities, and/or other occurring entities (SBO:0000231).
OMITTED_PROCESS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
One or more processes that are not represented in certain representations or interpretations of a model (SBO:0000397).
OPERATOR - Static variable in class org.sbolstandard.core2.SequenceOntology
A regulatory element of an operon to which activators or repressors bind, thereby effecting translation of genes in that operon (SO:0000057).
OR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Any of the preceding events or participating entities are necessary to perform the control (SBO:0000174).
org.oboparser.obo - package org.oboparser.obo
 
org.sbolstandard.core2 - package org.sbolstandard.core2
 
org.synbiohub.frontend - package org.synbiohub.frontend
 
OrientationType - Enum in org.sbolstandard.core2
Represents the orientation type for extended classes of the Location class.
ORIGIN_OF_REPLICATION - Static variable in class org.sbolstandard.core2.SequenceOntology
The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies (SO:0000296).
OXIDATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Chemical process during which a molecular entity loses electrons (SBO:0000201).

P

PALMITOYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Addition of a palmitoyl group (CH3-[CH2]14-CO-) to a chemical entity (SBO:0000218).
parse(Reader) - Method in class org.oboparser.obo.OBOParser
 
parse(BufferedReader) - Method in class org.oboparser.obo.OBOParser
 
parse(File) - Method in class org.oboparser.obo.OBOParser
 
PARTICIPANT_ROLE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
The function of a physical or conceptual entity, that is its role, in the execution of an event or process (SBO:0000003).
Participation - Class in org.sbolstandard.core2
Represents a Participation object in the SBOL data model.
PETRI_NET_TRANSITION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A process that can modify the state of petri net 'places' (SBO:0000591).
PHENOTYPE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A biochemical network can generate phenotypes or affects biological processes (SBO:0000358).
PHOSPHORYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Addition of a phosphate group (-H2PO4) to a chemical entity (SBO:0000216).
POSITIONAL_RELATIONSHIP - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
The connectedness between entities as related by their position (SBO:0000413).
POTENTIATOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Substance that increases the probability of a chemical reaction without itself being consumed or transformed by the reaction (SBO:0000021).
PRENYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Addition of a prenyl group (generic sense) to a chemical entity (SBO:0000221).
PRIMER_BINDING_SITE - Static variable in class org.sbolstandard.core2.SequenceOntology
Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription (SO:0005850)
print(PrintWriter) - Method in class org.oboparser.obo.OBOOntology
 
print(PrintWriter) - Method in class org.oboparser.obo.OBOStanza
 
PROCESS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A sequential series of actions, motions, or occurrences, such as chemical reactions, that affect one or more entities in a phenomenologically characteristic manner (SBO:0000375).
PRODUCT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Substance that is produced in a reaction (SBO:0000011).
PRODUCTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Generation of a material or conceptual entity (SBO:0000393).
PROMOTER - Static variable in class org.sbolstandard.core2.SequenceOntology
A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery (SO:0000167).
PROMOTER - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A region of DNA to which various transcription factors and RNA polymerase must bind in order to initiate transcription for a gene (SBO:0000598).
PROTEIN - Static variable in class org.sbolstandard.core2.ComponentDefinition
A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain (Protein).
PROTEIN_COMPLEX_FORMATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
The process by which two or more proteins interact non-covalently to form a protein complex (SBO:0000526).
PROTONATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Addition of a proton (H+) to a chemical entity (SBO:0000212).

R

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.

S

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
A small bioactive molecule (SmallMolecule).
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
This class provides methods for accessing Systems Biology Ontology (SBO) terms and querying about their relationships.
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.

T

tag() - Method in class org.oboparser.obo.OBOTerm
 
TEMPLATE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
An entity that acts as the starting material for genetic production (SBO:0000645).
TERMINATOR - Static variable in class org.sbolstandard.core2.SequenceOntology
The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription (SO:0000141).
toFullString() - Method in class org.oboparser.obo.OBOValue
 
TopLevel - Class in org.sbolstandard.core2
Represents a TopLevel object in the SBOL data model.
TOPOLOGY_ATTRIBUTE - Static variable in class org.sbolstandard.core2.SequenceOntology
Attributes added to describe the different kinds of replicon.
toString() - Method in class org.oboparser.obo.OBOStanza
 
toString() - Method in class org.oboparser.obo.OBOTerm
 
toString() - Method in class org.oboparser.obo.OBOValue
 
toString() - Method in enum org.sbolstandard.core2.AccessType
 
toString() - Method in class org.sbolstandard.core2.Annotation
 
toString() - Method in class org.sbolstandard.core2.Collection
 
toString() - Method in class org.sbolstandard.core2.Component
 
toString() - Method in class org.sbolstandard.core2.ComponentDefinition
 
toString() - Method in class org.sbolstandard.core2.ComponentInstance
 
toString() - Method in class org.sbolstandard.core2.Cut
 
toString() - Method in enum org.sbolstandard.core2.DirectionType
 
toString() - Method in class org.sbolstandard.core2.FunctionalComponent
 
toString() - Method in class org.sbolstandard.core2.GenericLocation
 
toString() - Method in class org.sbolstandard.core2.GenericTopLevel
 
toString() - Method in class org.sbolstandard.core2.Identified
 
toString() - Method in class org.sbolstandard.core2.Interaction
 
toString() - Method in class org.sbolstandard.core2.Location
 
toString() - Method in class org.sbolstandard.core2.MapsTo
 
toString() - Method in class org.sbolstandard.core2.Model
 
toString() - Method in class org.sbolstandard.core2.Module
 
toString() - Method in class org.sbolstandard.core2.ModuleDefinition
 
toString() - Method in enum org.sbolstandard.core2.OrientationType
 
toString() - Method in class org.sbolstandard.core2.Participation
 
toString() - Method in class org.sbolstandard.core2.Range
 
toString() - Method in enum org.sbolstandard.core2.RefinementType
 
toString() - Method in enum org.sbolstandard.core2.RestrictionType
 
toString() - Method in enum org.sbolstandard.core2.RoleIntegrationType
 
toString() - Method in class org.sbolstandard.core2.SBOLDocument
 
toString() - Method in class org.sbolstandard.core2.SBOLFactory
 
toString() - Method in class org.sbolstandard.core2.Sequence
 
toString() - Method in class org.sbolstandard.core2.SequenceAnnotation
 
toString() - Method in class org.sbolstandard.core2.SequenceConstraint
 
toString() - Method in class org.synbiohub.frontend.IdentifiedMetadata
 
TRANS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Positional relationship between entities on different sides, or strands (SBO:0000415).
TRANSAMINATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
The transfer of an amino group between two molecules (SBO:0000403).
TRANSCELLULAR_MEMBRANE_EFFLUX_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A transport reaction which results in the removal of the transported entity from the cell (SBO:0000588).
TRANSCELLULAR_MEMBRANE_INFLUX_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
A transport reaction which results in the entry of the transported entity, into the cell (SBO:0000587).
TRANSCRIPTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Process through which a DNA sequence is copied to produce a complementary RNA (SBO:0000183).
TRANSFER_OF_A_CHEMICAL_GROUP - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Covalent reaction that results in the transfer of a chemical group from one molecule to another (SBO:0000402).
TRANSLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Process in which a polypeptide chain is produced from a messenger RNA (SBO:0000184).
TRANSPORT_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Movement of a physical entity without modification of the structure of the entity (SBO:0000185).
TURTLE - Static variable in class org.sbolstandard.core2.SBOLDocument
Constant representing TURTLE file format

U

UBIQUITINATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Covalent linkage to the protein ubiquitin (SBO:0000224).
UNCERTAIN_PROCESS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
An equivocal or conjectural process, whose existence is assumed but not proven (SBO:0000396).
unsetComponent() - Method in class org.sbolstandard.core2.SequenceAnnotation
Sets the reference component to null.
unsetDescription() - Method in class org.sbolstandard.core2.Identified
Sets the description property to null.
unsetName() - Method in class org.sbolstandard.core2.Identified
Sets the name of this instance to null.
unsetOrientation() - Method in class org.sbolstandard.core2.Location
Sets the orientation property of this location to null.
unsetRoleIntegration() - Method in class org.sbolstandard.core2.Component
Sets the roleIntegration property of this object to null.
unsetURIPrefix() - Static method in class org.sbolstandard.core2.SBOLReader
Sets the URI prefix for this reader to null.
unsetWasDerivedFrom() - Method in class org.sbolstandard.core2.Identified
Deprecated.

V

validate(String, String, boolean, boolean, boolean, boolean, String, boolean, String, String, String, String, boolean, boolean, boolean, String, boolean, boolean) - Static method in class org.sbolstandard.core2.SBOLValidate
The validate function will: - perform validation on the given input SBOL file - perform comparison between 2 SBOL files - perform interconversion between SBOL1 and SBOL2 - convert from SBOL to GenBank - convert from SBOL to FASTA
validateSBOL(SBOLDocument, boolean, boolean, boolean) - Static method in class org.sbolstandard.core2.SBOLValidate
Validates the given SBOL document.
valueOf(String) - Static method in enum org.sbolstandard.core2.AccessType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbolstandard.core2.DirectionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbolstandard.core2.OrientationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbolstandard.core2.RefinementType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbolstandard.core2.RestrictionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbolstandard.core2.RoleIntegrationType
Returns the enum constant of this type with the specified name.
values(String) - Method in class org.oboparser.obo.OBOStanza
 
values() - Static method in enum org.sbolstandard.core2.AccessType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbolstandard.core2.DirectionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbolstandard.core2.OrientationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbolstandard.core2.RefinementType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbolstandard.core2.RestrictionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbolstandard.core2.RoleIntegrationType
Returns an array containing the constants of this enum type, in the order they are declared.

W

write(String) - Method in class org.sbolstandard.core2.SBOLDocument
Outputs this SBOL document's data from the RDF/XML serialization to a new file with the given file name.
write(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
Outputs this SBOL document's data from serialization in the given serialization format to a new file with the given file name.
write(File) - Method in class org.sbolstandard.core2.SBOLDocument
Outputs this SBOL document's data from the RDF/XML serialization to the given file.
write(File, String) - Method in class org.sbolstandard.core2.SBOLDocument
Outputs this SBOL document's data from the serialization in the given serialization format to the given file.
write(OutputStream) - Method in class org.sbolstandard.core2.SBOLDocument
Outputs this SBOL document's data from the RDF/XML serialization to the given output stream.
write(OutputStream, String) - Method in class org.sbolstandard.core2.SBOLDocument
Outputs this SBOL document's data from the serialization in the given serialization format to the given output stream.
write(String) - Static method in class org.sbolstandard.core2.SBOLFactory
Outputs the factory's internal SBOL document's data from the RDF/XML serialization to a new file with the given file name.
write(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
Outputs the factory's internal SBOL document's data from serialization in the given serialization format to a new file with the given file name.
write(File) - Static method in class org.sbolstandard.core2.SBOLFactory
Outputs the factory's internal SBOL document's data from the RDF/XML serialization to the given file.
write(File, String) - Static method in class org.sbolstandard.core2.SBOLFactory
Outputs the factory's internal SBOL document's data from the serialization in the given serialization format to the given file.
write(OutputStream) - Static method in class org.sbolstandard.core2.SBOLFactory
Outputs the factory's internal SBOL document's data from the RDF/XML serialization to the given output stream.
write(OutputStream, String) - Static method in class org.sbolstandard.core2.SBOLFactory
Outputs the factory's internal SBOL document's data from the serialization in the given serialization format to the given output stream.
write(SBOLDocument, File) - Static method in class org.sbolstandard.core2.SBOLWriter
Outputs the given SBOL document's data from the RDF/XML serialization to the given file.
write(SBOLDocument, File, String) - Static method in class org.sbolstandard.core2.SBOLWriter
Outputs this SBOL document's data from the serialization in the given serialization format to the given file.
write(SBOLDocument, OutputStream) - Static method in class org.sbolstandard.core2.SBOLWriter
Outputs this SBOL document's data from the RDF/XML serialization to the given output stream.
write(SBOLDocument, String) - Static method in class org.sbolstandard.core2.SBOLWriter
Outputs this SBOL document's data from the RDF/XML serialization to a new file with the given file name.
write(SBOLDocument, String, String) - Static method in class org.sbolstandard.core2.SBOLWriter
Outputs this SBOL document's data from serialization in the given serialization format to a new file with the given file name.
write(SBOLDocument, OutputStream, String) - Static method in class org.sbolstandard.core2.SBOLWriter
Serializes a given SBOLDocument and outputs the data from the serialization to the given output stream in the specified fileType format.

X

XOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
Only one of the preceding events or participating entities can perform the control at one time (SBO:0000175).
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