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.
|