- 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.
- getActivities() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of activities owned by this SBOL document.
- getActivity(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the activity matching the given display ID and version from this SBOL
document's list of activities.
- getActivity(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the activity matching the given display identity URI from this SBOL
document's list of activities.
- getAdministratorEmail() - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- getAgent() - Method in class org.sbolstandard.core2.Association
-
Returns the agent referenced by this association.
- getAgent(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the agent matching the given display ID and version from this SBOL
document's list of agents.
- getAgent(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the agent matching the given display identity URI from this SBOL
document's list of agents.
- getAgentIdentity() - Method in class org.sbolstandard.core2.Association
-
Returns the agent identity referenced by this association.
- getAgents() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of agents owned by this SBOL document.
- getAgentURI() - Method in class org.sbolstandard.core2.Association
-
Returns the reference agent URI.
- 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.
- getApproved() - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- getAssociation(String) - Method in class org.sbolstandard.core2.Activity
-
Returns the association matching the given association's display ID.
- getAssociation(URI) - Method in class org.sbolstandard.core2.Activity
-
Returns the instance matching the given association's identity URI.
- getAssociations() - Method in class org.sbolstandard.core2.Activity
-
Returns the set of associations owned by this activity.
- getAt() - Method in class org.sbolstandard.core2.Cut
-
Returns the at property of this Cut instance.
- getAttachment(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the attachment matching the given display ID and version from this SBOL
document's list of attachments.
- getAttachment(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the attachment matching the given identity URI from this SBOL document's
list of attachments.
- getAttachment(URI, String) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Retrieve an attachment from a SynBioHub instance using its URI,
and save to the path provided.
- getAttachment(URI, OutputStream) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Retrieve an attachment from a SynBioHub instance using its URI,
and save into the provided output stream.
- getAttachments() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of attachments owned by this SBOL document.
- getAttachments() - Method in class org.sbolstandard.core2.TopLevel
-
Returns the set of attachments referenced by this top level.
- getAttachmentURIs() - Method in class org.sbolstandard.core2.TopLevel
-
Returns the set of attachment URIs referenced by this top level.
- 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.
- getBuilt() - Method in class org.sbolstandard.core2.Implementation
-
Returns the component definition or module definition referenced by the built field.
- getBuiltURI() - Method in class org.sbolstandard.core2.Implementation
-
Returns the URI of the component definition or module definition built
- 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.
- 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.
- getCollections() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of Collection instances owned by this SBOL document.
- getCombinatorialDerivation(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the combinatorial derivation matching the given display ID and
version from this SBOL document's list of combinatorial derivations.
- getCombinatorialDerivation(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the combinatorial derivation matching the given identity URI from
this SBOL document's list of combinatorial derivations.
- getCombinatorialDerivations() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of combinatorial derivations owned by this SBOL document.
- 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() - 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.
- getComponentIdentity() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns the component identity this sequence annotation refers to.
- 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.
- 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.
- getDefinitionIdentity() - Method in class org.sbolstandard.core2.ComponentInstance
-
Returns the component definition identity referenced by this component or functional component.
- getDefinitionIdentity() - Method in class org.sbolstandard.core2.Module
-
Returns the module definition identity 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(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
-
- getDescription() - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- 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() - Static method in class org.sbolstandard.core2.SBOLReader
-
Get the SBOL default displayId for this reader.
- getDisplayId() - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
- 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.
- getEndedAtTime() - Method in class org.sbolstandard.core2.Activity
-
- getEntity() - Method in class org.sbolstandard.core2.Usage
-
Returns the entity referenced by this usage.
- getEntityIdentity() - Method in class org.sbolstandard.core2.Usage
-
Returns the entity identity referenced by this usage.
- getEntityURI() - Method in class org.sbolstandard.core2.Usage
-
Returns the reference entity URI.
- 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.
- getExperiment(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the experiment matching the given display ID and version from this
SBOL document's list of experiments.
- getExperiment(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the experiment matching the given identity URI from this SBOL
document's list of experiments.
- getExperimentalData() - Method in class org.sbolstandard.core2.Experiment
-
Returns the set of objects referenced by this Experiment's experimentalData.
- getExperimentalData(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the experimentalData matching the given display ID and version from this
SBOL document's list of experimentalData.
- getExperimentalData(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the experimentalData matching the given identity URI from this SBOL
document's list of experimentalDatas.
- getExperimentalData() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of ExperimentalData instances owned by this SBOL document.
- getExperimentalDataIdentities() - Method in class org.sbolstandard.core2.Experiment
-
Returns the set of experimentalData identities referenced by this Experiment instance.
- getExperimentalDataURIs() - Method in class org.sbolstandard.core2.Experiment
-
Returns the set of experimentalData URIs referenced by this Experiment instance.
- getExperiments() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of Experiment instances owned by this SBOL document.
- getFormat() - Method in class org.sbolstandard.core2.Attachment
-
Returns this attachment's format property
- 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.
- getGenericTopLevels() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of generic top-levels owned by this SBOL document.
- getHash() - Method in class org.sbolstandard.core2.Attachment
-
Returns this attachment's hash property
- 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.
- getId() - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- getIdentity() - Method in class org.sbolstandard.core2.Identified
-
Returns the identity URI of this instance.
- getImplementation(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the implementation matching the given display ID and
version from this SBOL document's list of implementations.
- getImplementation(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the implementation matching the given identity URI from
this SBOL document's list of implementations.
- getImplementations() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of implementations owned by this SBOL document.
- getImpliedNucleicAcidSequence() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Return the elements of a nucleic acid sequence implied by the hierarchically included components.
- getInstanceUrl() - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- 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.
- getLocalIdentity() - Method in class org.sbolstandard.core2.MapsTo
-
Returns this mapsTo's local component instance identity.
- 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.Component
-
Returns the location owned by this component
that matches the given display ID.
- getLocation(URI) - Method in class org.sbolstandard.core2.Component
-
Returns the location owned by this component
that matches the given identity 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.Component
-
Returns the set of locations referenced by this component.
- 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 referenceURI
- 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
- getMeasure(String) - Method in class org.sbolstandard.core2.Measured
-
Returns the measure matching the given display ID from
this measured object's list of measures.
- getMeasure(URI) - Method in class org.sbolstandard.core2.Measured
-
Returns the measure matching the given measure URI from this
measured object's list of measures.
- getMeasures() - Method in class org.sbolstandard.core2.Measured
-
Returns the set of measures owned by this
measured object.
- getMemberIdentities() - Method in class org.sbolstandard.core2.Collection
-
Returns the set of member identities referenced by this Collection instance.
- getMembers() - Method in class org.sbolstandard.core2.Collection
-
Returns the set of objects 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.
- getModelIdentities() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the set of models identities referenced by this module definition.
- 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.
- getModelURIs() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the set of model URIs referenced by this module definition.
- 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.
- getModuleDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of module definitions owned by this SBOLDocument object.
- getModules() - Method in class org.sbolstandard.core2.ModuleDefinition
-
Returns the set of modules owned by this module definition.
- 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
-
- getName() - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- 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.
- getNamespaces() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the list of namespaces owned by this 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.
- getNumericalValue() - Method in class org.sbolstandard.core2.Measure
-
Returns the numerical value.
- 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.
- getObjectIdentity() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the object component identity this sequence constraint refers to.
- 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
- getOperator() - Method in class org.sbolstandard.core2.VariableComponent
-
Returns the operator of the given variable component.
- 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.
- getParticipantIdentity() - Method in class org.sbolstandard.core2.Participation
-
Returns the functional component identity this participation refers to.
- 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.
- getPlan() - Method in class org.sbolstandard.core2.Association
-
Returns the plan referenced by this association.
- getPlan(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the plan matching the given display ID and version from this SBOL
document's list of plans.
- getPlan(URI) - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the plan matching the given display identity URI from this SBOL
document's list of plans.
- getPlanIdentity() - Method in class org.sbolstandard.core2.Association
-
Returns the plan identity referenced by this association.
- getPlans() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of plans owned by this SBOL document.
- getPlanURI() - Method in class org.sbolstandard.core2.Association
-
Returns the reference plan URI.
- getPreciseLocations() - Method in class org.sbolstandard.core2.Component
-
Returns the set of Range/Cut locations referenced by this component.
- getPreciseLocations() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Returns the set of Range/Cut locations referenced by this sequence annotation.
- getPreciseSourceLocations() - Method in class org.sbolstandard.core2.Component
-
Returns the set of Range/Cut sourceLocations referenced by this component.
- getQName() - Method in class org.sbolstandard.core2.Annotation
-
Returns the QName of this Annotation instance.
- 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.
- getRegistries() - Static method in class org.synbiohub.frontend.SynBioHubFrontend
-
Fetch data about all registries in the web of registries.
- getRegistries(String) - Static method in class org.synbiohub.frontend.SynBioHubFrontend
-
Fetch data about all registries in the web of registries.
- 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.
- getRemoteIdentity() - Method in class org.sbolstandard.core2.MapsTo
-
Returns this mapsTo's remote component instance identity.
- 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.Association
-
Returns the set of role URIs owned by this association.
- 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.
- getRoles() - Method in class org.sbolstandard.core2.Usage
-
Returns the set of role URIs owned by this usage.
- 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.
- 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.
- getSBOL(URI, boolean) - 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() - Method in class org.sbolstandard.core2.Location
-
Returns the sequence referenced by this location.
- 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.
- 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.
- getSequenceIdentities() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the set of sequences identities referenced by this component definition.
- getSequenceIdentity() - Method in class org.sbolstandard.core2.Location
-
Returns the sequence identity referenced by this location.
- 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.
- getSequenceURI() - Method in class org.sbolstandard.core2.Location
-
Returns the sequence URI referenced by this location.
- getSequenceURIs() - Method in class org.sbolstandard.core2.ComponentDefinition
-
Returns the set of sequence URIs referenced by this component definition.
- getSize() - Method in class org.sbolstandard.core2.Attachment
-
Returns this attachment's size property
- 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.Component
-
Returns a sorted list of locations owned by this component.
- 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.
- getSortedSourceLocations() - Method in class org.sbolstandard.core2.Component
-
Returns a sorted list of sourceLocations owned by this component.
- getSource() - Method in class org.sbolstandard.core2.Attachment
-
Returns this attachment's source property
- getSource() - Method in class org.sbolstandard.core2.Model
-
Returns the this model's source property.
- getSourceLocation(String) - Method in class org.sbolstandard.core2.Component
-
Returns a source location owned by this component
that matches the given display ID.
- getSourceLocation(URI) - Method in class org.sbolstandard.core2.Component
-
Returns a sourceLocation owned by this component
that matches the given identity URI.
- getSourceLocations() - Method in class org.sbolstandard.core2.Component
-
Returns the set of sourceLocations referenced by this component.
- getStart() - Method in class org.sbolstandard.core2.Range
-
Returns the start position of this range.
- getStartedAtTime() - Method in class org.sbolstandard.core2.Activity
-
- getStrategy() - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Returns the strategy property.
- 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.
- getSubjectIdentity() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the subject component identity this sequence constraint refers to.
- getSubjectURI() - Method in class org.sbolstandard.core2.SequenceConstraint
-
Returns the subject component's identity URI that this sequence constraint refers to.
- getTemplate() - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Returns the component definition referenced by this combinatorial derivation.
- getTemplateIdentity() - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Returns the component definition identity referenced by this combinatorial
derivation.
- getTemplateURI() - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Returns the reference component definition URI.
- 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.
- getTopLevels() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the set of all top-levels owned by this SBOL document.
- getType() - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
Return the type
- getTypes() - Method in class org.sbolstandard.core2.Activity
-
Returns the set of type URIs owned by this activity.
- 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.
- getTypes() - Method in class org.sbolstandard.core2.Measure
-
Returns the set of type URIs owned by this measure.
- getUnit() - Method in class org.sbolstandard.core2.Measure
-
Returns the unit referenced by this measure.
- getUnitIdentity() - Method in class org.sbolstandard.core2.Measure
-
Returns the unit identity referenced by this measure.
- getUnitURI() - Method in class org.sbolstandard.core2.Measure
-
Returns the unit URI.
- getUpdateWorking() - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- 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.
- getURIPrefix() - Static method in class org.sbolstandard.core2.SBOLReader
-
Returns the specified authority prefix.
- getUriPrefix() - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- getURIValue() - Method in class org.sbolstandard.core2.Annotation
-
Returns a URI representation of the value property.
- getUsage(String) - Method in class org.sbolstandard.core2.Activity
-
Returns the usage matching the given usage's display ID.
- getUsage(URI) - Method in class org.sbolstandard.core2.Activity
-
Returns the instance matching the given usage's identity URI.
- getUsages() - Method in class org.sbolstandard.core2.Activity
-
Returns the set of usages owned by this activity.
- getUsername() - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Returns the username of the logged in user
- getValue() - Method in class org.synbiohub.frontend.SearchCriteria
-
Return the search value
- getVariable() - Method in class org.sbolstandard.core2.VariableComponent
-
Returns the instance matching the given variable component's variable.
- getVariableComponent(URI) - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Returns the instance matching the given variable component's identity URI.
- getVariableComponent(String) - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Returns the variable component matching the given variable component's
display ID.
- getVariableComponents() - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Returns the set of variable components owned by this combinatorial
derivation.
- getVariableURI() - Method in class org.sbolstandard.core2.VariableComponent
-
Returns the URI of the instance matching the given variable component's variable.
- getVariantCollections() - Method in class org.sbolstandard.core2.VariableComponent
-
Returns a set of collections belonging to the variable component.
- getVariantCollectionURIs() - Method in class org.sbolstandard.core2.VariableComponent
-
Returns a set of collection URIs belonging to the variable component.
- getVariantDerivations() - Method in class org.sbolstandard.core2.VariableComponent
-
Returns a set of combinatorial derivations belonging to the variable component.
- getVariantDerivationURIs() - Method in class org.sbolstandard.core2.VariableComponent
-
Returns a set of combinatorial derivation URIs belonging to the variable component.
- getVariants() - Method in class org.sbolstandard.core2.VariableComponent
-
Returns a set of component definitions belonging to the variable component.
- getVariantURIs() - Method in class org.sbolstandard.core2.VariableComponent
-
Returns a set of component definition URIs belonging to the variable component.
- getVersion() - Method in class org.sbolstandard.core2.Identified
-
Returns this instance's version.
- getVersion() - Static method in class org.sbolstandard.core2.SBOLReader
-
Get the SBOL default version for this reader.
- 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.
- getWasGeneratedBys() - Method in class org.sbolstandard.core2.Identified
-
Returns the set of wasGeneratedBy URIs.
- getWasInformedByIdentities() - Method in class org.sbolstandard.core2.Activity
-
Returns the set of wasInformedBys identities referenced by this activity.
- getWasInformedBys() - Method in class org.sbolstandard.core2.Activity
-
Returns the set of wasInformedBys referenced by this activity.
- getWasInformedByURIs() - Method in class org.sbolstandard.core2.Activity
-
Returns the set of wasInformedBy URIs referenced by this activity.
- GLYCOSYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Addition of a saccharide group to a chemical entity
(
SBO:0000217).
- GROWTH_RATE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
A measure of the rate of growth of an organism, usually in culture.