- 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
-
- 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).
- Activity - Class in org.sbolstandard.core2
-
Represents a Activity object in the SBOL data model.
- ACTIVITY - Static variable in class org.sbolstandard.core2.TopLevel
-
The abbreviation for the Activity type in URI
- ActivityRoleType - Enum in org.sbolstandard.core2
-
Represents the roles used in Associations and Usages in Activities for Design-Build-Test-Learn workflow.
- addAttachment(Attachment) - Method in class org.sbolstandard.core2.TopLevel
-
Adds the URI of the given Attachment instance to this top level's
set of attachment URIs.
- addAttachment(String, String) - Method in class org.sbolstandard.core2.TopLevel
-
Constructs a compliant attachment URI with the given display ID and version, and then adds this URI
to this top level's set of attachment URIs.
- addAttachment(String) - Method in class org.sbolstandard.core2.TopLevel
-
Constructs a compliant sequence URI using the given attachment display ID, and then adds this URI to
this top level's set of attachment URIs.
- addCriteria(SearchCriteria) - Method in class org.synbiohub.frontend.SearchQuery
-
Add a search criterion
- addCut(String, int) - Method in class org.sbolstandard.core2.Component
-
Creates a cut with the given arguments and then adds it to this component's
list of locations.
- addCut(String, int, OrientationType) - Method in class org.sbolstandard.core2.Component
-
Creates a cut with the given arguments and then adds it to this component's
list of locations.
- 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.
- addExperimentalData(URI) - Method in class org.sbolstandard.core2.Experiment
-
Adds the given experimentalData URI to this Experiment's
set of reference experimentalData URIs.
- addGenericLocation(String) - Method in class org.sbolstandard.core2.Component
-
Creates a generic location with the given arguments and then adds it to this component's
list of locations.
- addGenericLocation(String, OrientationType) - Method in class org.sbolstandard.core2.Component
-
Creates a generic location with the given arguments and then adds it to this component'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.
- addGenericSourceLocation(String) - Method in class org.sbolstandard.core2.Component
-
Creates a generic location with the given arguments and then adds it to this components's
list of source locations.
- addGenericSourceLocation(String, OrientationType) - Method in class org.sbolstandard.core2.Component
-
Creates a generic location with the given arguments and then adds it to this component's
list of source 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.
- addRange(String, int, int) - Method in class org.sbolstandard.core2.Component
-
Creates a range with the given arguments and then adds it to this component's
list of locations.
- addRange(String, int, int, OrientationType) - Method in class org.sbolstandard.core2.Component
-
Creates a range with the given arguments and then adds it to this component's
list of locations.
- 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.Association
-
Adds the given role URI to this association's set of role URIs.
- addRole(ActivityRoleType) - Method in class org.sbolstandard.core2.Association
-
Adds the given role to this association's set of roles.
- 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.
- addRole(URI) - Method in class org.sbolstandard.core2.Usage
-
Adds the given role URI to this usage's set of role URIs.
- addRole(ActivityRoleType) - Method in class org.sbolstandard.core2.Usage
-
Adds the given role to this usage'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.
- addSourceCut(String, int) - Method in class org.sbolstandard.core2.Component
-
Creates a cut with the given arguments and then adds it to this component's
list of source locations.
- addSourceCut(String, int, OrientationType) - Method in class org.sbolstandard.core2.Component
-
Creates a cut with the given arguments and then adds it to this component's
list of source locations.
- addSourceRange(String, int, int) - Method in class org.sbolstandard.core2.Component
-
Creates a range with the given arguments and then adds it to this component's
list of source locations.
- addSourceRange(String, int, int, OrientationType) - Method in class org.sbolstandard.core2.Component
-
Creates a range with the given arguments and then adds it to this component's
list of source locations.
- addToCollection(URI, boolean, SBOLDocument) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Add SBOL document to an existing private collection on SynBioHub
- addToCollection(URI, boolean, String) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Add file to an existing private collection on SynBioHub
- addToCollection(URI, boolean, File) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Add file to an existing private collection on SynBioHub
- addToCollection(URI, boolean, InputStream) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Add file to an existing private collection on SynBioHub
- addType(URI) - Method in class org.sbolstandard.core2.Activity
-
Adds the given type URI to this activity's set of type 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.
- addType(URI) - Method in class org.sbolstandard.core2.Measure
-
Adds the given type URI to this measure's set of type URIs.
- addVariant(URI) - Method in class org.sbolstandard.core2.VariableComponent
-
Adds the given variant URI to the list of variant URIs.
- addVariant(String, String, String) - Method in class org.sbolstandard.core2.VariableComponent
-
Adds the given variant to the list of variants.
- addVariantCollection(URI) - Method in class org.sbolstandard.core2.VariableComponent
-
Adds the given variant collection URI to the list of variant collection URIs.
- addVariantCollection(String, String, String) - Method in class org.sbolstandard.core2.VariableComponent
-
Adds the given variant collection to the list of variant collections.
- addVariantDerivation(URI) - Method in class org.sbolstandard.core2.VariableComponent
-
Adds the given variant derivation URI to the list of variant derivations URIs.
- addVariantDerivation(String, String, String) - Method in class org.sbolstandard.core2.VariableComponent
-
Adds the given variant derivation to the list of variant derivations.
- addWasDerivedFrom(URI) - Method in class org.sbolstandard.core2.Identified
-
Adds the given wasDerivedFrom URI to the set of wasDerivedFrom URIs.
- addWasGeneratedBy(URI) - Method in class org.sbolstandard.core2.Identified
-
Adds the given wasGeneratedBy URI to the set of wasGeneratedBy URIs.
- addWasInformedBy(Activity) - Method in class org.sbolstandard.core2.Activity
-
Adds the URI of the given Activity instance to this Activity's
set of wasInformdBy URIs.
- addWasInformedBy(URI) - Method in class org.sbolstandard.core2.Activity
-
Adds the given activity URI to this Activity's set of wasInformedBy URIs.
- addWasInformedBy(String, String) - Method in class org.sbolstandard.core2.Activity
-
Constructs a compliant activity URI with the given display ID and version, and then adds this URI
to this activity's set of wasInformedBy URIs.
- addWasInformedBy(String) - Method in class org.sbolstandard.core2.Activity
-
Constructs a compliant activity URI using the given activity display ID, and then adds this URI to
this activity's set of wasInformedBy URIs.
- Agent - Class in org.sbolstandard.core2
-
Represents an Agent object in the SBOL data model.
- AGENT - Static variable in class org.sbolstandard.core2.TopLevel
-
The abbreviation for the Agent type in URI
- 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 - Static variable in class org.sbolstandard.core2.TopLevel
-
The abbreviation for the Annotation type in URI
- Association - Class in org.sbolstandard.core2
-
Represents an Association object in the SBOL data model.
- attachFile(URI, String) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Attach a file to an object in SynBioHub.
- attachFile(URI, File) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Attach a file to an object in SynBioHub.
- attachFile(URI, InputStream) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Attach a file to an object in SynBioHub.
- attachFile(URI, InputStream, String) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Attach a file to an object in SynBioHub.
- Attachment - Class in org.sbolstandard.core2
-
Represents a Attachment object in the SBOL data model.
- ATTACHMENT - Static variable in class org.sbolstandard.core2.TopLevel
-
The abbreviation for the Attachment type in URI