- Identified - Class in org.sbolstandard.core2
-
Represents an Identified object in the SBOL data model.
- IdentifiedMetadata - Class in org.synbiohub.frontend
-
The metadata common to all SBOL data objects
- IdentifiedMetadata() - Constructor for class org.synbiohub.frontend.IdentifiedMetadata
-
- IdentifiedVisitor - Class in org.sbolstandard.core2
-
A visitor for every identified object in an SBOLDocument
- IdentifiedVisitor() - Constructor for class org.sbolstandard.core2.IdentifiedVisitor
-
- Implementation - Class in org.sbolstandard.core2
-
Represents an Implementation object in the SBOL data model.
- IMPLEMENTATION - Static variable in class org.sbolstandard.core2.TopLevel
-
The abbreviation for the Implementation type in URI
- INHIBITED - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Conceptual or material entity that is the object of an inhibition process, and is
acted upon by an inhibitor (
SBO:0000642).
- INHIBITION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Negative modulation of the execution of a process
(
SBO:0000169).
- INHIBITOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Substance that decreases the probability of a chemical reaction without itself being
consumed or transformed by the reaction
(
SBO:0000020).
- INSULATOR - Static variable in class org.sbolstandard.core2.SequenceOntology
-
A transcriptional cis regulatory region that, when located between a CM and a gene's promoter, prevents the CRM
from modulating that genes expression (
SO:0000627)
- Interaction - Class in org.sbolstandard.core2
-
Represents an Interaction object in the SOBL data model.
- INTERACTOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Entity participating in a physical or functional interaction
(
SBO:0000336).
- IONISATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Ionization is the physical process of converting an atom or molecule into an ion by
changing the difference between the number of protons and electrons
(
SBO:0000209).
- isBooleanValue() - Method in class org.sbolstandard.core2.Annotation
-
Checks if the annotation has a boolean value property.
- isComplete() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the value of the complete flag for this SBOL document.
- isCompliant() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the value of the compliant flag in this SBOL document.
- isCompliant() - Static method in class org.sbolstandard.core2.SBOLReader
-
Check if document is to be read as being compliant.
- isCreateDefaults() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the value of the createDefaults flag in this SBOL document.
- isDescendantOf(String, String) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
- isDescendantOf(URI, URI) - Method in class org.sbolstandard.core2.EDAMOntology
-
Returns true if the stanza with childURI is a descendant of the stanza with parentURI.
- isDescendantOf(String, String) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
- isDescendantOf(URI, URI) - Method in class org.sbolstandard.core2.SequenceOntology
-
Returns true if the stanza with childURI is a descendant of the stanza with parentURI.
- isDescendantOf(URI, URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns true if the stanza with childURI is a descendant of the stanza with parentURI.
- isDescendantOf(String, String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
- isDoubleValue() - Method in class org.sbolstandard.core2.Annotation
-
Checks if the annotation has a double value property.
- isDropObjectsWithDuplicateURIs() - Static method in class org.sbolstandard.core2.SBOLReader
-
Check if objects with duplicate URIs should be dropped.
- isFastaFile(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Check if a file begins with ">" or ";" indicating that it is Fasta file
- isFastaString(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Check if a string begins with ">" or ";" indicating that it is Fasta file string
- isGenBankFile(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Check if a file begins with LOCUS indicating that it is GenBank file
- isGenBankString(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Check if a string begins with LOCUS indicating that it is GenBank file string
- isIntegerValue() - Method in class org.sbolstandard.core2.Annotation
-
Checks if the annotation has an integer value property.
- isKeepGoing() - Static method in class org.sbolstandard.core2.SBOLReader
-
Checks if reading should continue after encountering an SBOL validation exception.
- isKeepGoing() - Static method in class org.sbolstandard.core2.SBOLWriter
-
Returns the value of the keepGoing flag.
- isNestedAnnotations() - Method in class org.sbolstandard.core2.Annotation
-
Checks if the annotation has a nested value property.
- ISOMERISATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
A reaction in which the principal reactant and principal product are isomers of each other
(
SBO:0000377).
- isSetBuilt() - Method in class org.sbolstandard.core2.Implementation
-
Checks if the built property is set.
- isSetComponent() - Method in class org.sbolstandard.core2.SequenceAnnotation
-
Test if the reference component is set.
- isSetDescription() - Method in class org.sbolstandard.core2.Identified
-
Test if the description property is set.
- isSetDisplayId() - Method in class org.sbolstandard.core2.Identified
-
Test if the display ID is set.
- isSetEndedAtTime() - Method in class org.sbolstandard.core2.Activity
-
Test if the endedAtTime is set.
- isSetFormat() - Method in class org.sbolstandard.core2.Attachment
-
Checks if the format property is set.
- isSetHash() - Method in class org.sbolstandard.core2.Attachment
-
Checks if the hash property is set.
- isSetName() - Method in class org.sbolstandard.core2.Identified
-
Test if the name property is set.
- isSetOrientation() - Method in class org.sbolstandard.core2.Location
-
Checks if the orientation property is set.
- isSetPersistentIdentity() - Method in class org.sbolstandard.core2.Identified
-
Test if the persistent identity URI is set.
- isSetPlan() - Method in class org.sbolstandard.core2.Association
-
Test if the plan is set.
- isSetRoleIntegration() - Method in class org.sbolstandard.core2.Component
-
Test if the roleIntegration property is set.
- isSetSequence() - Method in class org.sbolstandard.core2.Location
-
Checks if the sequence property is set.
- isSetSize() - Method in class org.sbolstandard.core2.Attachment
-
Checks if the size property is set.
- isSetStartedAtTime() - Method in class org.sbolstandard.core2.Activity
-
Test if the startedAtTime is set.
- isSetStrategy() - Method in class org.sbolstandard.core2.CombinatorialDerivation
-
Checks if the strategy property is set.
- isSetUsername() - Method in class org.synbiohub.frontend.SynBioHubFrontend
-
Returns if a user is logged in
- isSetVersion() - Method in class org.sbolstandard.core2.Identified
-
Test if the version is set.
- isSetWasDerivedFrom() - Method in class org.sbolstandard.core2.Identified
-
Deprecated.
- isSnapGeneFile(String) - Static method in class org.sbolstandard.core2.SBOLReader
-
Check if a file begins with the byte sequence indicating it is a SnapGene file
- isStringValue() - Method in class org.sbolstandard.core2.Annotation
-
Checks if the annotation has a string value property.
- isTypesInURIs() - Method in class org.sbolstandard.core2.SBOLDocument
-
Returns the value of the typesInURI flag in this SBOL document.
- isURIValue() - Method in class org.sbolstandard.core2.Annotation
-
Checks if the annotation is a URI value property.
- IUPAC_DNA - Static variable in class org.sbolstandard.core2.Sequence
-
Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences
(
IUPAC_DNA).
- IUPAC_PROTEIN - Static variable in class org.sbolstandard.core2.Sequence
-
Nomenclature and Symbolism for Amino Acids and Peptides
(
IUPAC_PROTEIN).
- IUPAC_RNA - Static variable in class org.sbolstandard.core2.Sequence
-
Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences
(
IUPAC_RNA).