| Class | Description |
|---|---|
| Activity |
Represents a Activity object in the SBOL data model.
|
| Agent |
Represents an Agent object in the SBOL data model.
|
| Annotation |
Represents an Annotation object in the cSBOL data model.
|
| Association |
Represents an Association object in the SBOL data model.
|
| Attachment |
Represents a Attachment object in the SBOL data model.
|
| Collection |
Represents an Collection object in the SBOL data model.
|
| CombinatorialDerivation |
Represents a CombinatorialDerivation object in the SBOL data model.
|
| Component |
Represents a Component object in the SBOL data model.
|
| ComponentDefinition |
Represents a ComponentDefinition object in the SBOL data model.
|
| ComponentInstance |
Represents a ComponentInstance object in the SBOL data model.
|
| Cut |
Represents the Cut extension of the SBOL Location class.
|
| EDAMOntology |
This class provides methods for accessing EMBRACE Data and Methods (EDAM) terms
and querying about their relationships.
|
| Experiment |
Represents an Collection object in the SBOL data model.
|
| ExperimentalData |
Represents an Collection object in the SBOL data model.
|
| FunctionalComponent |
Represents a FunctionalComponent object in the SBOL data model.
|
| GenericLocation |
Represents a GenericLocation extension object of the SBOL Location class.
|
| GenericTopLevel |
Represents a GenericTopLevel object in the SBOL data model.
|
| Identified |
Represents an Identified object in the SBOL data model.
|
| IdentifiedVisitor |
A visitor for every identified object in an SBOLDocument
|
| Implementation |
Represents an Implementation object in the SBOL data model.
|
| Interaction |
Represents an Interaction object in the SOBL data model.
|
| Location |
Represents a Location object in the SOBL data model.
|
| MapsTo |
Represents a MapsTo object in the SBOL data model.
|
| Measure |
Represents an Measure object in the SBOL data model.
|
| Measured |
Represents a Measured object in the SBOL data model.
|
| Model |
Represents a Model object in the SBOL data model.
|
| Module |
Represents a Module object in the SBOL data model.
|
| ModuleDefinition |
Represents a ModuleDefinition object in the SBOL data model.
|
| Participation |
Represents a Participation object in the SBOL data model.
|
| Plan |
Represents an Plan object in the SBOL data model.
|
| Range |
Represents a Range extension object of the SBOL Location class.
|
| SBOLDocument |
Represents the SBOL document where all top-level instances can be created and
manipulated.
|
| SBOLReader |
Provides methods to read input SBOL files.
|
| SBOLValidate |
Provides functionality for validating SBOL data models.
|
| SBOLWriter |
Provides methods to output SBOL files in XML/RDF format.
|
| Sequence |
Represents a Sequence object in the SBOL data model.
|
| SequenceAnnotation |
Represents a SequenceAnnotation object in the SBOL data model.
|
| SequenceConstraint |
Represents a SequenceConstraint object in the SBOL data model.
|
| SequenceOntology |
This class provides methods for accessing Sequence Ontology (SO) terms
and querying about their relationships.
|
| SnapGene |
Provides a Java API to a SnapGene Server instance.
|
| SystemsBiologyOntology |
This class provides methods for accessing Systems Biology Ontology (SBO) terms
and querying about their relationships.
|
| TopLevel |
Represents a TopLevel object in the SBOL data model.
|
| Usage |
Represents an Usage object in the SBOL data model.
|
| VariableComponent |
Represents a VariableComponent in the SBOL data model
|
| Enum | Description |
|---|---|
| AccessType |
Represents all access types for a
ComponentInstance object. |
| ActivityRoleType |
Represents the roles used in Associations and Usages in Activities for Design-Build-Test-Learn workflow.
|
| DirectionType |
Represents all direction types for a
FunctionalComponent object. |
| OperatorType |
Represents all operator types for a
VariableComponent object. |
| OrientationType |
Represents the orientation type for extended classes of the Location class.
|
| RefinementType |
Represents the refinement relationship between a MapsTo instance's local and remote components.
|
| RestrictionType |
Represents the relationship between a sequence constraint's subject and object components.
|
| RoleIntegrationType |
Represents the role integration relationship between roles specified in related objects.
|
| StrategyType |
Represents all strategy types for a
CombinatorialDerivation object. |
| Exception | Description |
|---|---|
| SBOLConversionException |
Signals that an exception related to conversion between SBOL and other file formats has occurred.
|
| SBOLValidationException |
Signals that an SBOL validation rule violation has occurred.
|