- 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
.
- 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.
- setAdministratorEmail(String) - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- setAgent(URI) - Method in class org.sbolstandard.core2.Association
-
- setAnnotations(List<Annotation>) - Method in class org.sbolstandard.core2.Annotation
-
Sets the list of Annotations of the nested value property.
- setApproved(String) - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- setAt(int) - Method in class org.sbolstandard.core2.Cut
-
Sets the at property of this Cut instance to the given one.
- setAttachments(Set<URI>) - Method in class org.sbolstandard.core2.TopLevel
-
Clears the existing set of attachments first, and then adds the given set of
the attachments to this top level.
- setBooleanValue(boolean) - Method in class org.sbolstandard.core2.Annotation
-
Sets the boolean representation of the value property.
- setBuilt(URI) - Method in class org.sbolstandard.core2.Implementation
-
Sets the URI of the built property to the given one.
- setBuilt(TopLevel) - Method in class org.sbolstandard.core2.Implementation
-
Sets the the built property to the given one.
- setCombinatorialDerivation(CombinatorialDerivation) - Method in class org.sbolstandard.core2.VariableComponent
-
Sets the parent combinatorial derivation to the given one.
- setComplete(boolean) - Method in class org.sbolstandard.core2.SBOLDocument
-
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.
- 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.
- 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
-
- setDescription(String) - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- setDirection(DirectionType) - Method in class org.sbolstandard.core2.FunctionalComponent
-
Sets the direction property of this functional component to the given one.
- setDisplayId(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the SBOL default displayId for this reader.
- 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.
- setEndedAtTime(DateTime) - Method in class org.sbolstandard.core2.Activity
-
- setEntity(URI) - Method in class org.sbolstandard.core2.Usage
-
- setExperimentalData(Set<URI>) - Method in class org.sbolstandard.core2.Experiment
-
Clears the existing set of experimentalData of this Experiment instance first, then adds the given
set of the experimentalData references to it.
- setFormat(URI) - Method in class org.sbolstandard.core2.Attachment
-
Sets the URI of this attachment's format property
- setFramework(URI) - Method in class org.sbolstandard.core2.Model
-
Sets the framework property to the given one.
- setHash(String) - Method in class org.sbolstandard.core2.Attachment
-
sets this attachment's hash property
- setId(String) - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- setInstanceUrl(String) - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- 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
-
- setName(String) - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- 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.
- setNumericalValue(Double) - Method in class org.sbolstandard.core2.Measure
-
- 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
- setOperator(OperatorType) - Method in class org.sbolstandard.core2.VariableComponent
-
Sets the operator property to the given one.
- 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.
- setPlan(URI) - Method in class org.sbolstandard.core2.Association
-
- 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.Association
-
Clears the existing set of roles first, and then adds the given
set of the roles to this association.
- 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.
- setRoles(Set<URI>) - Method in class org.sbolstandard.core2.Usage
-
Clears the existing set of roles first, and then adds the given
set of the roles to this usage.
- setSequence(URI) - Method in class org.sbolstandard.core2.Location
-
Sets the sequence property 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.
- setSize(long) - Method in class org.sbolstandard.core2.Attachment
-
Sets the value of this attachment's size property
- setSource(URI) - Method in class org.sbolstandard.core2.Attachment
-
Sets the source property to the given one.
- 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.
- setStartedAtTime(DateTime) - Method in class org.sbolstandard.core2.Activity
-
- setStrategy(StrategyType) - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Sets the strategy property to the given one.
- 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
.
- setTemplate(URI) - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Sets the template property to the given one.
- setType(String) - Method in class org.synbiohub.frontend.IdentifiedMetadata
-
Set the type
- setTypes(Set<URI>) - Method in class org.sbolstandard.core2.Activity
-
Clears the existing set of types first, then adds the given
set of the types to this activity.
- 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.
- setTypes(Set<URI>) - Method in class org.sbolstandard.core2.Measure
-
Clears the existing set of types first, and then adds the given
set of the types to this measure.
- 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.
- setUnit(URI) - Method in class org.sbolstandard.core2.Measure
-
- setUpdateWorking(String) - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- 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.
- setUriPrefix(String) - Method in class org.synbiohub.frontend.WebOfRegistriesData
-
- 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
- setVariable(URI) - Method in class org.sbolstandard.core2.VariableComponent
-
Sets the variable property to the given one.
- setVariableComponents(Set<VariableComponent>) - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Clears the existing set of variable components first, and then adds the given
set of the variable components to this combinatorial derivation.
- setVariantCollections(Set<URI>) - Method in class org.sbolstandard.core2.VariableComponent
-
Clears the existing set of variant collections first, and then adds the given
set of the variant collections to this variable component.
- setVariantDerivations(Set<URI>) - Method in class org.sbolstandard.core2.VariableComponent
-
Clears the existing set of variant derivations first, and then adds the given
set of the variant derivations to this variable component.
- setVariants(Set<URI>) - Method in class org.sbolstandard.core2.VariableComponent
-
Clears the existing set of variants first, and then adds the given
set of the variants to this variable component.
- setVersion(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Sets the SBOL default 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.
- setWasGeneratedBys(Set<URI>) - Method in class org.sbolstandard.core2.Identified
-
Clears the existing set of wasGeneratedBys first, and then adds the given
set of the wasGeneratedBys.
- setWasInformedBys(Set<URI>) - Method in class org.sbolstandard.core2.Activity
-
- 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
-
- 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).
- SNAPGENE - Static variable in class org.sbolstandard.core2.SBOLDocument
-
Constant representing SnapGene file format
- SnapGene - Class in org.sbolstandard.core2
-
Provides a Java API to a SnapGene Server instance.
- SnapGene() - Constructor for class org.sbolstandard.core2.SnapGene
-
- sparqlQuery(String) - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Perform a SPARQL query
- 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.
- StrategyType - Enum in org.sbolstandard.core2
-
- 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.
- SynBioHubFrontend(String, int) - Constructor for class org.synbiohub.frontend.SynBioHubFrontend
-
Creates an instance of the SynBioHub API.
- SynBioHubFrontend(String, String, int) - 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).
- SYSTEMS_DESCRIPTION_PARAMETER - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
A value, numerical or symbolic, that defines certain characteristics of systems
or system functions, or is necessary in their derivation.
- SystemsBiologyOntology - Class in org.sbolstandard.core2
-
- 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.