- DanglingUnitSIdRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- Date - Class in org.sbml.libsbml
-
Representation of MIRIAM-compliant dates used in
ModelHistory
.
- Date(long, long, long, long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
-
Creates a time and date representation for use in model annotations
and elsewhere.
- Date(long, long, long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
-
Creates a time and date representation for use in model annotations
and elsewhere.
- Date(long, long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
-
Creates a time and date representation for use in model annotations
and elsewhere.
- Date(long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
-
Creates a time and date representation for use in model annotations
and elsewhere.
- Date(long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
-
Creates a time and date representation for use in model annotations
and elsewhere.
- Date(long, long, long, long) - Constructor for class org.sbml.libsbml.Date
-
Creates a time and date representation for use in model annotations
and elsewhere.
- Date(long, long, long) - Constructor for class org.sbml.libsbml.Date
-
Creates a time and date representation for use in model annotations
and elsewhere.
- Date(long, long) - Constructor for class org.sbml.libsbml.Date
-
Creates a time and date representation for use in model annotations
and elsewhere.
- Date(long) - Constructor for class org.sbml.libsbml.Date
-
Creates a time and date representation for use in model annotations
and elsewhere.
- Date() - Constructor for class org.sbml.libsbml.Date
-
Creates a time and date representation for use in model annotations
and elsewhere.
- Date(String) - Constructor for class org.sbml.libsbml.Date
-
Creates a
Date
object from a string expressing a date and time value.
- Date(Date) - Constructor for class org.sbml.libsbml.Date
-
Copy constructor; creates a copy of this
Date
.
- DateList - Class in org.sbml.libsbml
-
- DateList() - Constructor for class org.sbml.libsbml.DateList
-
- deepCopy() - Method in class org.sbml.libsbml.ASTNode
-
Creates a recursive copy of this node and all its children.
- Delay - Class in org.sbml.libsbml
-
Implementation of SBML's Delay construct for Event.
- Delay(long, long) - Constructor for class org.sbml.libsbml.Delay
-
Creates a new
Delay
using the given SBML
level
and
version
values.
- Delay(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Delay
-
- Delay(Delay) - Constructor for class org.sbml.libsbml.Delay
-
Copy constructor; creates a copy of this
Delay
.
- DelayNeedsValuesFromTriggerTime - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DelayUnitsNotTime - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- delete() - Method in class org.sbml.libsbml.AlgebraicRule
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.AssignmentRule
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Association
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ASTNode
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ASTNodeList
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.BoundingBox
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Compartment
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CompartmentGlyph
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CompartmentType
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CompBase
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CompExtension
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CompModelPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CompPkgNamespaces
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CompSBasePlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Constraint
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ConversionOption
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ConversionProperties
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CubicBezier
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Curve
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CVTerm
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CVTermList
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Date
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.DateList
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Delay
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Deletion
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Dimensions
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Event
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.EventAssignment
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FbcExtension
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FbcModelPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FbcPkgNamespaces
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FluxBound
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FluxObjective
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FunctionDefinition
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GeneAssociation
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GeneralGlyph
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GraphicalObject
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.InitialAssignment
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.KineticLaw
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.L3ParserSettings
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Layout
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.LayoutExtension
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.LayoutModelPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.LayoutSpeciesReferencePlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.LineSegment
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOf
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfCompartments
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfConstraints
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfDeletions
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfEventAssignments
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfEvents
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfFluxBounds
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfInitialAssignments
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfLayouts
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfLineSegments
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfLocalParameters
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfObjectives
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfParameters
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfPorts
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfReactions
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfReplacedElements
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfRules
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfSpecies
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfSubmodels
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfUnits
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.LocalParameter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Model
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ModelCreator
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ModelCreatorList
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ModelDefinition
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ModelHistory
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ModifierSpeciesReference
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Objective
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.OFStream
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.OStream
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.OStringStream
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Parameter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Point
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Port
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Priority
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RateRule
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RDFAnnotationParser
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Reaction
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ReactionGlyph
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ReplacedBy
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ReplacedElement
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Replacing
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Rule
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBase
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBaseList
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBasePlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBaseRef
-
Explicitly deletes the underlying native object.
- delete() - Method in exception org.sbml.libsbml.SBMLConstructorException
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLConverter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLConverterRegistry
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLDocument
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLError
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLErrorLog
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLExtensionException
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLExternalValidator
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLFileResolver
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLNamespaces
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLNamespacesList
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLReader
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLResolver
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLResolverRegistry
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLRuleConverter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLUnitsConverter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLUri
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLValidator
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLWriter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBO
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Species
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SpeciesGlyph
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SpeciesReference
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SpeciesType
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.StoichiometryMath
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Submodel
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SyntaxChecker
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.TextGlyph
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Trigger
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Unit
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.UnitDefinition
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.XMLAttributes
-
Explicitly deletes the underlying native object.
- delete() - Method in exception org.sbml.libsbml.XMLConstructorException
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.XMLError
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.XMLErrorLog
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.XMLNamespaces
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.XMLNode
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.XMLToken
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.XMLTriple
-
Explicitly deletes the underlying native object.
- deleteLayoutAnnotation(XMLNode) - Static method in class org.sbml.libsbml.libsbml
-
- deleteLayoutIdAnnotation(XMLNode) - Static method in class org.sbml.libsbml.libsbml
-
- deleteRDFAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
-
Deletes any SBML MIRIAM RDF annotation found in the given
XMLNode
tree and returns
any remaining annotation content.
- deleteRDFCVTermAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
-
Deletes any SBML MIRIAM RDF '
CVTerm
' annotation found in the given
XMLNode
tree and returns
any remaining annotation content.
- deleteRDFHistoryAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
-
Deletes any SBML MIRIAM RDF 'History' annotation found in the given
XMLNode
tree and returns
any remaining annotation content.
- Deletion - Class in org.sbml.libsbml
-
- Deletion(long, long, long) - Constructor for class org.sbml.libsbml.Deletion
-
- Deletion(long, long) - Constructor for class org.sbml.libsbml.Deletion
-
- Deletion(long) - Constructor for class org.sbml.libsbml.Deletion
-
- Deletion() - Constructor for class org.sbml.libsbml.Deletion
-
- Deletion(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.Deletion
-
- Deletion(Deletion) - Constructor for class org.sbml.libsbml.Deletion
-
- depth() - Method in class org.sbml.libsbml.BoundingBox
-
- depth() - Method in class org.sbml.libsbml.Dimensions
-
- Dimensions - Class in org.sbml.libsbml
-
- Dimensions(long, long, long) - Constructor for class org.sbml.libsbml.Dimensions
-
- Dimensions(long, long) - Constructor for class org.sbml.libsbml.Dimensions
-
- Dimensions(long) - Constructor for class org.sbml.libsbml.Dimensions
-
- Dimensions() - Constructor for class org.sbml.libsbml.Dimensions
-
- Dimensions(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.Dimensions
-
- Dimensions(Dimensions) - Constructor for class org.sbml.libsbml.Dimensions
-
- Dimensions(LayoutPkgNamespaces, double, double, double) - Constructor for class org.sbml.libsbml.Dimensions
-
- Dimensions(LayoutPkgNamespaces, double, double) - Constructor for class org.sbml.libsbml.Dimensions
-
- Dimensions(XMLNode, long) - Constructor for class org.sbml.libsbml.Dimensions
-
- Dimensions(XMLNode) - Constructor for class org.sbml.libsbml.Dimensions
-
- disablePackage(String, String) - Method in class org.sbml.libsbml.SBase
-
Disables the given SBML Level 3 package
- disablePackage(String) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Disables the package with the given URI / name.
- disablePackages(SWIGTYPE_p_std__vectorT_std__string_t) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Disables all packages with the given URI / name.
- disableUnusedPackages(SBMLDocument) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Goes through all extensions in the list of plugins of the given document
and disables all plugins that are not being used.
- DisallowedDefinitionURLUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DisallowedMathMLEncodingUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DisallowedMathMLSymbol - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DisallowedMathTypeAttributeUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DisallowedMathTypeAttributeValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DisallowedMathUnitsUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.CompExtension
-
- DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.FbcExtension
-
- DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.LayoutExtension
-
SBMLExtension derived classes must override this method
- DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.CompExtension
-
- DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.FbcExtension
-
- DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.LayoutExtension
-
- DuplicateAnnotationInvalidInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DuplicateAnnotationInvalidInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DuplicateAnnotationInvalidInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DuplicateAnnotationInvalidInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DuplicateAnnotationNamespaces - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DuplicateComponentId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DuplicateLocalParameterId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DuplicateMetaId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DuplicateUnitDefinitionId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- DuplicateXMLAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- GENE_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- GeneAssociation - Class in org.sbml.libsbml
-
- GeneAssociation(long, long, long) - Constructor for class org.sbml.libsbml.GeneAssociation
-
- GeneAssociation(long, long) - Constructor for class org.sbml.libsbml.GeneAssociation
-
- GeneAssociation(long) - Constructor for class org.sbml.libsbml.GeneAssociation
-
- GeneAssociation() - Constructor for class org.sbml.libsbml.GeneAssociation
-
- GeneAssociation(XMLNode, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneAssociation
-
- GeneAssociation(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneAssociation
-
- GeneAssociation(GeneAssociation) - Constructor for class org.sbml.libsbml.GeneAssociation
-
- GeneralGlyph - Class in org.sbml.libsbml
-
- GeneralGlyph(long, long, long) - Constructor for class org.sbml.libsbml.GeneralGlyph
-
- GeneralGlyph(long, long) - Constructor for class org.sbml.libsbml.GeneralGlyph
-
- GeneralGlyph(long) - Constructor for class org.sbml.libsbml.GeneralGlyph
-
- GeneralGlyph() - Constructor for class org.sbml.libsbml.GeneralGlyph
-
- GeneralGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneralGlyph
-
- GeneralGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.GeneralGlyph
-
- GeneralGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.GeneralGlyph
-
- GeneralGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.GeneralGlyph
-
- GeneralGlyph(XMLNode) - Constructor for class org.sbml.libsbml.GeneralGlyph
-
- GeneralGlyph(GeneralGlyph) - Constructor for class org.sbml.libsbml.GeneralGlyph
-
- GeneralWarningNotSpecified - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- get(long) - Method in class org.sbml.libsbml.ASTNodeList
-
- get(long) - Method in class org.sbml.libsbml.CVTermList
-
- get(long) - Method in class org.sbml.libsbml.DateList
-
- get(long) - Method in class org.sbml.libsbml.ListOf
-
Get an item from the list.
- get(long) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfCompartments
-
- get(String) - Method in class org.sbml.libsbml.ListOfCompartments
-
- get(long) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
-
- get(String) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
-
- get(long) - Method in class org.sbml.libsbml.ListOfConstraints
-
- get(long) - Method in class org.sbml.libsbml.ListOfDeletions
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfDeletions
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfEventAssignments
-
- get(String) - Method in class org.sbml.libsbml.ListOfEventAssignments
-
- get(long) - Method in class org.sbml.libsbml.ListOfEvents
-
- get(String) - Method in class org.sbml.libsbml.ListOfEvents
-
- get(long) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfFluxBounds
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfFluxBounds
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
-
- get(String) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
-
- get(long) - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfInitialAssignments
-
- get(String) - Method in class org.sbml.libsbml.ListOfInitialAssignments
-
- get(long) - Method in class org.sbml.libsbml.ListOfLayouts
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfLayouts
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfLineSegments
-
Get an item from the list.
- get(long) - Method in class org.sbml.libsbml.ListOfLocalParameters
-
- get(String) - Method in class org.sbml.libsbml.ListOfLocalParameters
-
Returns the first
LocalParameter
object matching the given identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfObjectives
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfObjectives
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfParameters
-
- get(String) - Method in class org.sbml.libsbml.ListOfParameters
-
Returns the first
Parameter
object matching the given identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfPorts
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfPorts
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfReactions
-
- get(String) - Method in class org.sbml.libsbml.ListOfReactions
-
- get(long) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfReplacedElements
-
Get an item from the list.
- get(long) - Method in class org.sbml.libsbml.ListOfRules
-
- get(String) - Method in class org.sbml.libsbml.ListOfRules
-
- get(long) - Method in class org.sbml.libsbml.ListOfSpecies
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpecies
-
- get(long) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
-
- get(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
-
- get(long) - Method in class org.sbml.libsbml.ListOfSubmodels
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfSubmodels
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
Get an item from the list.
- get(String) - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
Get an item from the list based on its identifier.
- get(long) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
-
- get(String) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
-
- get(long) - Method in class org.sbml.libsbml.ListOfUnits
-
- get(long) - Method in class org.sbml.libsbml.ModelCreatorList
-
- get(long) - Method in class org.sbml.libsbml.SBaseList
-
- get(long) - Method in class org.sbml.libsbml.SBMLNamespacesList
-
- get_ostream() - Method in class org.sbml.libsbml.OStream
-
Returns the stream object.
- getActiveObjective() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getActiveObjective() - Method in class org.sbml.libsbml.ListOfObjectives
-
- getActiveObjectiveId() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getAdditionalGraphicalObject(long) - Method in class org.sbml.libsbml.Layout
-
- getAdditionalGraphicalObject(String) - Method in class org.sbml.libsbml.Layout
-
- getAncestorOfType(int, String) - Method in class org.sbml.libsbml.SBase
-
Returns the first ancestor object that has the given SBML type code.
- getAncestorOfType(int) - Method in class org.sbml.libsbml.SBase
-
Returns the first ancestor object that has the given SBML type code.
- getAnnotation() - Method in class org.sbml.libsbml.SBase
-
Returns the content of the 'annotation' subelement of this object as
a tree of
XMLNode
objects.
- getAnnotationString() - Method in class org.sbml.libsbml.SBase
-
Returns the content of the 'annotation' subelement of this object as a
character string.
- getAreaUnits() - Method in class org.sbml.libsbml.Model
-
Returns the value of the 'areaUnits' attribute of this
Model
.
- getArgument(long) - Method in class org.sbml.libsbml.FunctionDefinition
-
Get the n
th argument to this function.
- getArgument(String) - Method in class org.sbml.libsbml.FunctionDefinition
-
- getArgument(long) - Method in class org.sbml.libsbml.SBMLExternalValidator
-
Returns the argument for the given index.
- getAssociation() - Method in class org.sbml.libsbml.GeneAssociation
-
- getAttributes() - Method in class org.sbml.libsbml.XMLToken
-
Returns the attributes of this element.
- getAttributesLength() - Method in class org.sbml.libsbml.XMLToken
-
Return the number of attributes in the attributes set.
- getAttrIndex(String, String) - Method in class org.sbml.libsbml.XMLToken
-
Return the index of an attribute with the given local name and namespace URI.
- getAttrIndex(String) - Method in class org.sbml.libsbml.XMLToken
-
Return the index of an attribute with the given local name and namespace URI.
- getAttrIndex(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
-
Return the index of an attribute with the given
XMLTriple
.
- getAttrName(int) - Method in class org.sbml.libsbml.XMLToken
-
Return the local name of an attribute in the attributes set in this
XMLToken
(by position).
- getAttrPrefix(int) - Method in class org.sbml.libsbml.XMLToken
-
Return the prefix of an attribute in the attribute set in this
XMLToken
(by position).
- getAttrPrefixedName(int) - Method in class org.sbml.libsbml.XMLToken
-
Return the prefixed name of an attribute in the attribute set in this
XMLToken
(by position).
- getAttrURI(int) - Method in class org.sbml.libsbml.XMLToken
-
Return the namespace URI of an attribute in the attribute set in this
XMLToken
(by position).
- getAttrValue(int) - Method in class org.sbml.libsbml.XMLToken
-
Return the value of an attribute in the attribute set in this
XMLToken
(by position).
- getAttrValue(String, String) - Method in class org.sbml.libsbml.XMLToken
-
Return a value of an attribute with the given local name and namespace URI.
- getAttrValue(String) - Method in class org.sbml.libsbml.XMLToken
-
Return a value of an attribute with the given local name and namespace URI.
- getAttrValue(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
-
Return a value of an attribute with the given
XMLTriple
.
- getBasePoint1() - Method in class org.sbml.libsbml.CubicBezier
-
- getBasePoint2() - Method in class org.sbml.libsbml.CubicBezier
-
- getBiologicalQualifierType() - Method in class org.sbml.libsbml.CVTerm
-
Returns the biological qualifier type of this
CVTerm
object.
- getBody() - Method in class org.sbml.libsbml.FunctionDefinition
-
- getBoolValue() - Method in class org.sbml.libsbml.ConversionOption
-
Returns the value of this option as a Boolean.
- getBoolValue(String) - Method in class org.sbml.libsbml.ConversionProperties
-
Returns the value of the given option as a Boolean.
- getBoundaryCondition() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'boundaryCondition' attribute.
- getBoundingBox() - Method in class org.sbml.libsbml.GraphicalObject
-
- getCategory() - Method in class org.sbml.libsbml.XMLError
-
Returns the category of this error.
- getCategoryAsString() - Method in class org.sbml.libsbml.XMLError
-
Returns a string describing the category of this error.
- getCharacter() - Method in class org.sbml.libsbml.ASTNode
-
Get the value of this node as a single character.
- getCharacters() - Method in class org.sbml.libsbml.XMLToken
-
Returns the text of this element.
- getCharge() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
-
- getCharge() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'charge' attribute.
- getChemicalFormula() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
-
- getChild(long) - Method in class org.sbml.libsbml.ASTNode
-
Get a child of this node according to its index number.
- getChild(long) - Method in class org.sbml.libsbml.XMLNode
-
Returns the
n
th child of this
XMLNode
.
- getChild(String) - Method in class org.sbml.libsbml.XMLNode
-
Returns the first child of this
XMLNode
with the corresponding name.
- getClassName() - Method in class org.sbml.libsbml.ASTNode
-
- getCoefficient() - Method in class org.sbml.libsbml.FluxObjective
-
- getColumn() - Method in class org.sbml.libsbml.SBase
-
Returns the column number on which this object first appears in the XML
representation of the SBML document.
- getColumn() - Method in class org.sbml.libsbml.XMLError
-
Returns the column number in the XML input near where the error,
warning or other diagnostic occurred.
- getColumn() - Method in class org.sbml.libsbml.XMLToken
-
Returns the column at which this
XMLToken
occurred in the input
document or data stream.
- getCompartment(long) - Method in class org.sbml.libsbml.Model
-
- getCompartment(String) - Method in class org.sbml.libsbml.Model
-
- getCompartment() - Method in class org.sbml.libsbml.Reaction
-
(SBML Level 3 only) Returns the value of the 'compartment'
attribute on the
Reaction
.
- getCompartment() - Method in class org.sbml.libsbml.Species
-
Get the compartment in which this species is located.
- getCompartmentGlyph(long) - Method in class org.sbml.libsbml.Layout
-
- getCompartmentGlyph(String) - Method in class org.sbml.libsbml.Layout
-
- getCompartmentId() - Method in class org.sbml.libsbml.CompartmentGlyph
-
- getCompartmentType() - Method in class org.sbml.libsbml.Compartment
-
Get the value of the 'compartmentType' attribute of this
Compartment
object.
- getCompartmentType(long) - Method in class org.sbml.libsbml.Model
-
- getCompartmentType(String) - Method in class org.sbml.libsbml.Model
-
- getConstant() - Method in class org.sbml.libsbml.Compartment
-
Get the value of the 'constant' attribute of this
Compartment
.
- getConstant() - Method in class org.sbml.libsbml.Parameter
-
Gets the value of the 'constant' attribute of this
Parameter
instance.
- getConstant() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'constant' attribute.
- getConstant() - Method in class org.sbml.libsbml.SpeciesReference
-
Get the value of the 'constant' attribute.
- getConstraint(long) - Method in class org.sbml.libsbml.Model
-
- getConversionFactor() - Method in class org.sbml.libsbml.Model
-
Returns the value of the 'conversionFactor' attribute of this
Model
.
- getConversionFactor() - Method in class org.sbml.libsbml.ReplacedElement
-
- getConversionFactor() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'conversionFactor' attribute.
- getConverterByIndex(int) - Method in class org.sbml.libsbml.SBMLConverterRegistry
-
Returns the converter with the given index number.
- getConverterFor(ConversionProperties) - Method in class org.sbml.libsbml.SBMLConverterRegistry
-
Returns the converter that best matches the given configuration
properties.
- getCreatedDate() - Method in class org.sbml.libsbml.ModelHistory
-
Returns the 'creation date' portion of this
ModelHistory
object.
- getCreator(long) - Method in class org.sbml.libsbml.ModelHistory
-
- getCurve() - Method in class org.sbml.libsbml.GeneralGlyph
-
- getCurve() - Method in class org.sbml.libsbml.ReactionGlyph
-
- getCurve() - Method in class org.sbml.libsbml.ReferenceGlyph
-
- getCurve() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- getCurveSegment(long) - Method in class org.sbml.libsbml.Curve
-
- getCVTerm(long) - Method in class org.sbml.libsbml.SBase
-
Returns the nth
CVTerm
in the list of CVTerms of this SBML
object.
- getCVTerms() - Method in class org.sbml.libsbml.SBase
-
Returns a list of
CVTerm
objects in the annotations of this SBML
object.
- getDateAsString() - Method in class org.sbml.libsbml.Date
-
Returns the current
Date
value in text-string form.
- getDay() - Method in class org.sbml.libsbml.Date
-
Returns the day from this
Date
.
- getDefaultL3ParserSettings() - Static method in class org.sbml.libsbml.libsbml
-
- getDefaultLevel() - Static method in class org.sbml.libsbml.CompExtension
-
- getDefaultLevel() - Static method in class org.sbml.libsbml.FbcExtension
-
- getDefaultLevel() - Static method in class org.sbml.libsbml.LayoutExtension
-
- getDefaultLevel() - Static method in class org.sbml.libsbml.SBMLDocument
-
- getDefaultPackageVersion() - Static method in class org.sbml.libsbml.CompExtension
-
- getDefaultPackageVersion() - Static method in class org.sbml.libsbml.FbcExtension
-
- getDefaultPackageVersion() - Static method in class org.sbml.libsbml.LayoutExtension
-
- getDefaultProperties() - Method in class org.sbml.libsbml.SBMLConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.SBMLRuleConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.SBMLUnitsConverter
-
Returns the default properties of this converter.
- getDefaultVersion() - Static method in class org.sbml.libsbml.CompExtension
-
- getDefaultVersion() - Static method in class org.sbml.libsbml.FbcExtension
-
- getDefaultVersion() - Static method in class org.sbml.libsbml.LayoutExtension
-
- getDefaultVersion() - Static method in class org.sbml.libsbml.SBMLDocument
-
- getDefinitionURL() - Method in class org.sbml.libsbml.ASTNode
-
Gets the MathML definitionURL
attribute value.
- getDelay() - Method in class org.sbml.libsbml.Event
-
Get the assignment delay portion of this
Event
, if there is one.
- getDeletion() - Method in class org.sbml.libsbml.ReplacedElement
-
- getDeletion(long) - Method in class org.sbml.libsbml.Submodel
-
- getDeletion(String) - Method in class org.sbml.libsbml.Submodel
-
- getDenominator() - Method in class org.sbml.libsbml.ASTNode
-
Get the value of the denominator of this node.
- getDenominator() - Method in class org.sbml.libsbml.SpeciesReference
-
Get the value of the 'denominator' attribute, for the case of a
rational-numbered stoichiometry or a model in SBML Level 1.
- getDepth() - Method in class org.sbml.libsbml.Dimensions
-
- getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Compartment
-
- getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Delay
-
Calculates and returns a
UnitDefinition
that expresses the units
of measurement assumed for the 'math' expression of this
Delay
.
- getDerivedUnitDefinition() - Method in class org.sbml.libsbml.EventAssignment
-
- getDerivedUnitDefinition() - Method in class org.sbml.libsbml.InitialAssignment
-
- getDerivedUnitDefinition() - Method in class org.sbml.libsbml.KineticLaw
-
Calculates and returns a
UnitDefinition
that expresses the units
of measurement assumed for the 'math' expression of this
KineticLaw
.
- getDerivedUnitDefinition() - Method in class org.sbml.libsbml.LocalParameter
-
- getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Parameter
-
- getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Rule
-
Calculates and returns a
UnitDefinition
that expresses the units of
measurement assumed for the 'math' expression of this
Rule
.
- getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Species
-
Constructs and returns a
UnitDefinition
that corresponds to the units
of this
Species
' amount or concentration.
- getDerivedUnitDefinition() - Method in class org.sbml.libsbml.StoichiometryMath
-
- getDescription() - Method in class org.sbml.libsbml.ConversionOption
-
Returns the description string for this option.
- getDescription(String) - Method in class org.sbml.libsbml.ConversionProperties
-
Returns the description string for a given option in this properties
object.
- getDimensions() - Method in class org.sbml.libsbml.BoundingBox
-
- getDimensions() - Method in class org.sbml.libsbml.Layout
-
- getDivider() - Method in class org.sbml.libsbml.CompModelPlugin
-
- getDocument() - Method in class org.sbml.libsbml.SBMLConverter
-
Returns the SBML document that is the subject of the conversions.
- getDocument() - Method in class org.sbml.libsbml.SBMLValidator
-
Returns the current SBML document in use by this validator.
- getDoubleValue() - Method in class org.sbml.libsbml.ConversionOption
-
Returns the value of this option as a double.
- getDoubleValue(String) - Method in class org.sbml.libsbml.ConversionProperties
-
Returns the value of the given option as a double.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.CompModelPlugin
-
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.CompSBasePlugin
-
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.Event
-
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.KineticLaw
-
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.ListOf
-
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.Model
-
Returns the first child element it can find with the given metaid
, or
null if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.Objective
-
Returns the first child element it can find with a specific 'metaid'
attribute value, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.Reaction
-
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.SBase
-
Returns the first child element it can find with a specific 'metaid'
attribute value, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.SBaseRef
-
Returns the first child element it can find with a specific 'metaid'
attribute value, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.SBMLDocument
-
Returns the first child element it can find with the given metaid
, or itself if it has the given metaid
, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.Submodel
-
Returns the first child element it can find with a specific 'metaid'
attribute value, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.UnitDefinition
-
Returns the first child element it can find with the given metaid
, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.CompModelPlugin
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.CompSBasePlugin
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.Event
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.KineticLaw
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.ListOf
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.ListOfEventAssignments
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.ListOfInitialAssignments
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.ListOfLocalParameters
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.ListOfPorts
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.ListOfRules
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.Model
-
Returns the first child element found that has the given id
in the
model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.Objective
-
Returns the first child element found that has the given id
in the
model-wide SId
namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.Reaction
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.SBase
-
Returns the first child element found that has the given id
in the
model-wide SId
namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.SBaseRef
-
Returns the first child element found that has the given id
in the
model-wide SId
namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.SBMLDocument
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.Submodel
-
Returns the first child element found that has the given id
in the
model-wide SId
namespace, or null
if no such object is found.
- getElementBySId(String) - Method in class org.sbml.libsbml.UnitDefinition
-
Returns the first child element found that has the given id
in the model-wide SId namespace, or null
if no such object is found.
- getElementName() - Method in class org.sbml.libsbml.Association
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.BoundingBox
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Compartment
-
Returns the XML element name of this object, which for
Compartment
, is
always
'compartment'.
- getElementName() - Method in class org.sbml.libsbml.CompartmentGlyph
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.CompartmentType
-
Returns the XML element name of this object, which for
CompartmentType
, is always
'compartmentType'.
- getElementName() - Method in class org.sbml.libsbml.Constraint
-
Returns the XML element name of this object, which for
Constraint
, is
always
'constraint'.
- getElementName() - Method in class org.sbml.libsbml.CubicBezier
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Curve
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Delay
-
Returns the XML element name of this object, which for
Delay
, is
always
'delay'.
- getElementName() - Method in class org.sbml.libsbml.Deletion
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Dimensions
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Event
-
Returns the XML element name of this object, which for
Event
, is
always
'event'.
- getElementName() - Method in class org.sbml.libsbml.EventAssignment
-
Returns the XML element name of this object, which for
EventAssignment
, is always
'eventAssignment'.
- getElementName() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.FluxBound
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.FluxObjective
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.FunctionDefinition
-
Returns the XML element name of this object, which for
FunctionDefinition
, is always
'functionDefinition'.
- getElementName() - Method in class org.sbml.libsbml.GeneAssociation
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.GraphicalObject
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.InitialAssignment
-
Returns the XML element name of this object, which for
InitialAssignment
, is always
'initialAssignment'.
- getElementName() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the XML element name of this object, which for
Species
, is
always
'kineticLaw'.
- getElementName() - Method in class org.sbml.libsbml.Layout
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.LineSegment
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOf
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfCompartments
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfConstraints
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfDeletions
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfEventAssignments
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfEvents
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfFluxBounds
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfInitialAssignments
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfLayouts
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfLineSegments
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfLocalParameters
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfObjectives
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfParameters
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfPorts
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfReactions
-
Returns the XML element name of this object
- getElementName() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfReplacedElements
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfRules
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpecies
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSubmodels
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
Returns the XML element name of this object, which for
ListOf
, is
always
'listOf'.
- getElementName() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfUnits
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.LocalParameter
-
Returns the XML element name of this object, which for
LocalParameter
,
is always
'localParameter'.
- getElementName() - Method in class org.sbml.libsbml.Model
-
Returns the XML element name of this object, which for
Model
, is
always
'model'.
- getElementName() - Method in class org.sbml.libsbml.ModelDefinition
-
Returns the XML element name of this object, which for
Model
, is
always
'model'.
- getElementName() - Method in class org.sbml.libsbml.ModifierSpeciesReference
-
Returns the XML element name of this object, which for
Species
, is
always
'modifierSpeciesReference'.
- getElementName() - Method in class org.sbml.libsbml.Objective
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Parameter
-
Returns the XML element name of this object, which for
Parameter
, is
always
'parameter'.
- getElementName() - Method in class org.sbml.libsbml.Point
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Port
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Priority
-
Returns the XML element name of this object, which for
Priority
, is
always
'priority'.
- getElementName() - Method in class org.sbml.libsbml.Reaction
-
Returns the XML element name of this object, which for
Reaction
, is
always
'reaction'.
- getElementName() - Method in class org.sbml.libsbml.ReactionGlyph
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ReplacedBy
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ReplacedElement
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Rule
-
Returns the XML element name of this object
- getElementName() - Method in class org.sbml.libsbml.SBase
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.SBaseRef
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.SBMLDocument
-
Returns the XML element name of this object, which for
SBMLDocument
,
is always
'sbml'.
- getElementName() - Method in class org.sbml.libsbml.Species
-
Returns the XML element name of this object, which for
Species
, is
always
'species'.
- getElementName() - Method in class org.sbml.libsbml.SpeciesGlyph
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.SpeciesReference
-
Returns the XML element name of this object, which for
SpeciesReference
, is always
'speciesReference'.
- getElementName() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.SpeciesType
-
Returns the XML element name of this object, which for
SpeciesType
, is always
'compartmentType'.
- getElementName() - Method in class org.sbml.libsbml.StoichiometryMath
-
Returns the XML element name of this object, which for
StoichiometryMath
, is
always
'stoichiometryMath'.
- getElementName() - Method in class org.sbml.libsbml.Submodel
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.TextGlyph
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Trigger
-
Returns the XML element name of this object, which for
Trigger
, is
always
'trigger'.
- getElementName() - Method in class org.sbml.libsbml.Unit
-
Returns the XML element name of this object, which for
Unit
, is
always
'unit'.
- getElementName() - Method in class org.sbml.libsbml.UnitDefinition
-
Returns the XML element name of this object, which for
UnitDefinition
,
is always
'unitDefinition'.
- getElementNamespace() - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the XML namespace (URI) of the package extension
of this plugin object.
- getEmail() - Method in class org.sbml.libsbml.ModelCreator
-
- getEnd() - Method in class org.sbml.libsbml.LineSegment
-
- getError(long) - Method in class org.sbml.libsbml.SBMLDocument
-
Returns the nth error or warning encountered during parsing,
consistency checking, or attempted translation of this model.
- getError(long) - Method in class org.sbml.libsbml.SBMLErrorLog
-
Returns the
nth
SBMLError
object in this log.
- getError(long) - Method in class org.sbml.libsbml.XMLErrorLog
-
Returns the
nth
XMLError
object in this log.
- getErrorId() - Method in class org.sbml.libsbml.XMLError
-
Returns the identifier of this error.
- getErrorIdOffset() - Method in class org.sbml.libsbml.XMLError
-
Returns a copy of the message string associated with the given
predefined
XMLError
code.
- getErrorLog() - Method in class org.sbml.libsbml.SBMLDocument
-
Returns the list of errors or warnings logged during parsing,
consistency checking, or attempted translation of this model.
- getErrorLog() - Method in class org.sbml.libsbml.SBMLValidator
-
Returns the list of errors or warnings logged during parsing,
consistency checking, or attempted translation of this model.
- getEvent(long) - Method in class org.sbml.libsbml.Model
-
- getEvent(String) - Method in class org.sbml.libsbml.Model
-
Get an
Event
object based on its identifier.
- getEventAssignment(long) - Method in class org.sbml.libsbml.Event
-
- getEventAssignment(String) - Method in class org.sbml.libsbml.Event
-
Return the event assignment indicated by the given variable
.
- getExponent() - Method in class org.sbml.libsbml.ASTNode
-
Get the exponent value of this
ASTNode
.
- getExponent() - Method in class org.sbml.libsbml.Unit
-
Returns the value of the 'exponent' attribute of this unit.
- getExponentAsDouble() - Method in class org.sbml.libsbml.Unit
-
Returns the value of the 'exponent' attribute of this unit.
- getExtension(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Returns an SBMLExtension
object with the given package URI or package name (string).
- getExtentConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
- getExtentUnits() - Method in class org.sbml.libsbml.Model
-
Returns the value of the 'extentUnits' attribute of this
Model
.
- getExternalModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- getExternalModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- getFailure(long) - Method in class org.sbml.libsbml.SBMLValidator
-
Returns the failure object at index n in this validator's list of
failures logged during the last run.
- getFamilyName() - Method in class org.sbml.libsbml.ModelCreator
-
Returns the 'family name' stored in this
ModelCreator
object.
- getFast() - Method in class org.sbml.libsbml.Reaction
-
Returns the value of the 'fast' attribute of this
Reaction
.
- getFloatValue() - Method in class org.sbml.libsbml.ConversionOption
-
Returns the value of this option as a float.
- getFloatValue(String) - Method in class org.sbml.libsbml.ConversionProperties
-
Returns the value of the given option as a float.
- getFluxBound(long) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getFluxBound(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getFluxBoundOperation() - Method in class org.sbml.libsbml.FluxBound
-
- getFluxBoundsForReaction(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getFluxObjective(long) - Method in class org.sbml.libsbml.Objective
-
- getFluxObjective(String) - Method in class org.sbml.libsbml.Objective
-
- getFormula() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the mathematical formula for this
KineticLaw
object and return
it as as a text string.
- getFormula() - Method in class org.sbml.libsbml.Rule
-
Returns the mathematical expression of this
Rule
in text-string form.
- getFunctionDefinition(long) - Method in class org.sbml.libsbml.Model
-
Get the nth FunctionDefinitions object in this
Model
.
- getFunctionDefinition(String) - Method in class org.sbml.libsbml.Model
-
- getGeneAssociation(long) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getGeneAssociation(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getGeneralGlyph(long) - Method in class org.sbml.libsbml.Layout
-
- getGeneralGlyph(String) - Method in class org.sbml.libsbml.Layout
-
- getGivenName() - Method in class org.sbml.libsbml.ModelCreator
-
Returns the 'given name' stored in this
ModelCreator
object.
- getGlyphId() - Method in class org.sbml.libsbml.ReferenceGlyph
-
- getGraphicalObjectId() - Method in class org.sbml.libsbml.TextGlyph
-
- getHasOnlySubstanceUnits() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'hasOnlySubstanceUnits' attribute.
- getHeight() - Method in class org.sbml.libsbml.Dimensions
-
- getHost() - Method in class org.sbml.libsbml.SBMLUri
-
- getHour() - Method in class org.sbml.libsbml.Date
-
Returns the hour from this
Date
.
- getHoursOffset() - Method in class org.sbml.libsbml.Date
-
Returns the hours of the time zone offset from this
Date
.
- getId() - Method in class org.sbml.libsbml.ASTNode
-
- getId() - Method in class org.sbml.libsbml.Compartment
-
Returns the value of the 'id' attribute of this
Compartment
object.
- getId() - Method in class org.sbml.libsbml.CompartmentType
-
- getId() - Method in class org.sbml.libsbml.Event
-
Returns the value of the 'id' attribute of this
Event
.
- getId() - Method in class org.sbml.libsbml.FunctionDefinition
-
- getId() - Method in class org.sbml.libsbml.InitialAssignment
-
Predicate returning
true
if
all the required elements for this
InitialAssignment
object
have been set.
- getId() - Method in class org.sbml.libsbml.Model
-
Returns the value of the 'id' attribute of this
Model
.
- getId() - Method in class org.sbml.libsbml.Parameter
-
Returns the value of the 'id' attribute of this
Parameter
.
- getId() - Method in class org.sbml.libsbml.Reaction
-
Returns the value of the 'id' attribute of this
Reaction
.
- getId() - Method in class org.sbml.libsbml.Rule
-
Renames all the UnitSIdRef attributes on this element
- getId() - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
- getId() - Method in class org.sbml.libsbml.Species
-
Returns the value of the 'id' attribute of this
Species
object.
- getId() - Method in class org.sbml.libsbml.SpeciesType
-
Returns the value of the 'id' attribute of this
SpeciesType
.
- getId() - Method in class org.sbml.libsbml.UnitDefinition
-
- getIdRef() - Method in class org.sbml.libsbml.SBaseRef
-
- getIndex(String) - Method in class org.sbml.libsbml.XMLAttributes
-
Return the index of an attribute with the given name.
- getIndex(String, String) - Method in class org.sbml.libsbml.XMLAttributes
-
Return the index of an attribute with the given local name and namespace URI.
- getIndex(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
-
Return the index of an attribute with the given
XMLTriple
.
- getIndex(String) - Method in class org.sbml.libsbml.XMLNamespaces
-
Look up the index of an XML namespace declaration by URI.
- getIndex(String) - Method in class org.sbml.libsbml.XMLNode
-
Return the index of the first child of this
XMLNode
with the given name.
- getIndexByPrefix(String) - Method in class org.sbml.libsbml.XMLNamespaces
-
Look up the index of an XML namespace declaration by prefix.
- getIndexForReferenceGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
-
- getIndexForSpeciesReferenceGlyph(String) - Method in class org.sbml.libsbml.ReactionGlyph
-
- getIndexForSubGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
-
- getInitialAmount() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'initialAmount' attribute.
- getInitialAssignment(long) - Method in class org.sbml.libsbml.Model
-
- getInitialAssignment(String) - Method in class org.sbml.libsbml.Model
-
- getInitialConcentration() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'initialConcentration' attribute.
- getInitialValue() - Method in class org.sbml.libsbml.Trigger
-
(SBML Level 3 only) Get the value of the 'initialValue' attribute
of this
Trigger
.
- getInstance() - Static method in class org.sbml.libsbml.SBMLConverterRegistry
-
Returns the singleton instance for the converter registry.
- getInstance() - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
-
- getInstance() - Static method in class org.sbml.libsbml.SBMLResolverRegistry
-
- getInstantiation() - Method in class org.sbml.libsbml.Submodel
-
- getInteger() - Method in class org.sbml.libsbml.ASTNode
-
Get the value of this node as an integer.
- getIntValue() - Method in class org.sbml.libsbml.ConversionOption
-
Returns the value of this option as an integer.
- getIntValue(String) - Method in class org.sbml.libsbml.ConversionProperties
-
Returns the value of the given option as an integer.
- getIsSetListOfFluxObjectives() - Method in class org.sbml.libsbml.Objective
-
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOf
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartments
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Compartment
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
CompartmentType
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfConstraints
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Constraint
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfDeletions
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfEventAssignments
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
EventAssignment
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfEvents
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Event
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFluxBounds
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
FunctionDefinition
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfInitialAssignments
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
InitialAssignment
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLayouts
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLineSegments
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLocalParameters
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
LocalParameter
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfObjectives
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfParameters
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Parameter
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfPorts
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReactions
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Reaction
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReplacedElements
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfRules
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Rule
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpecies
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Species
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
SpeciesReference
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
SpeciesType
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSubmodels
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
Get the type code of the objects contained in this
ListOf
.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
UnitDefinition
objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfUnits
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Unit
objects, if the list is non-empty).
- getKey() - Method in class org.sbml.libsbml.ConversionOption
-
Returns the key for this option.
- getKind() - Method in class org.sbml.libsbml.Unit
-
Returns the 'kind' of
Unit
this is.
- getKineticLaw() - Method in class org.sbml.libsbml.Reaction
-
- getL1TypeCode() - Method in class org.sbml.libsbml.Rule
-
Returns the SBML Level 1 type code for this
Rule
object.
- getLastParseL3Error() - Static method in class org.sbml.libsbml.libsbml
-
Returns the last error reported by the parser.
- getLayout(long) - Method in class org.sbml.libsbml.LayoutModelPlugin
-
- getLayout(String) - Method in class org.sbml.libsbml.LayoutModelPlugin
-
- getLeftChild() - Method in class org.sbml.libsbml.ASTNode
-
Get the left child of this node.
- getLength() - Method in class org.sbml.libsbml.XMLAttributes
-
Return the number of attributes in the set.
- getLength() - Method in class org.sbml.libsbml.XMLNamespaces
-
Returns the total number of URI-and-prefix pairs stored in this
particular
XMLNamespaces
instance.
- getLengthUnits() - Method in class org.sbml.libsbml.Model
-
Returns the value of the 'lengthUnits' attribute of this
Model
.
- getLevel() - Method in class org.sbml.libsbml.SBase
-
Returns the SBML Level of the
SBMLDocument
object containing this
object.
- getLevel() - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the SBML level of the package extension of
this plugin object.
- getLevel() - Method in class org.sbml.libsbml.SBMLNamespaces
-
- getLibSBMLDottedVersion() - Static method in class org.sbml.libsbml.libsbml
-
Returns the version number of this copy of libSBML as a string.
- getLibSBMLVersion() - Static method in class org.sbml.libsbml.libsbml
-
Returns the version number of this copy of libSBML as an integer.
- getLibSBMLVersionString() - Static method in class org.sbml.libsbml.libsbml
-
Returns the version number of this copy of libSBML as a string without
periods.
- getLine() - Method in class org.sbml.libsbml.SBase
-
Returns the line number on which this object first appears in the XML
representation of the SBML document.
- getLine() - Method in class org.sbml.libsbml.XMLError
-
Returns the line number in the XML input near where the error, warning
or other diagnostic occurred.
- getLine() - Method in class org.sbml.libsbml.XMLToken
-
Returns the line at which this
XMLToken
occurred in the input document
or data stream.
- getListCreators() - Method in class org.sbml.libsbml.ModelHistory
-
- getListModifiedDates() - Method in class org.sbml.libsbml.ModelHistory
-
Returns the list of 'modified date' values (as
Date
objects) stored in
this
ModelHistory
object.
- getListOfAdditionalGraphicalObjects() - Method in class org.sbml.libsbml.Layout
-
- getListOfAllElements() - Method in class org.sbml.libsbml.SBase
-
- getListOfAllElements() - Method in class org.sbml.libsbml.SBasePlugin
-
- getListOfAllElementsFromPlugins() - Method in class org.sbml.libsbml.SBase
-
- getListOfAllInstantiatedElements() - Method in class org.sbml.libsbml.Submodel
-
- getListOfCompartmentGlyphs() - Method in class org.sbml.libsbml.Layout
-
- getListOfCompartments() - Method in class org.sbml.libsbml.Model
-
- getListOfCompartmentTypes() - Method in class org.sbml.libsbml.Model
-
- getListOfConstraints() - Method in class org.sbml.libsbml.Model
-
- getListOfCurveSegments() - Method in class org.sbml.libsbml.Curve
-
- getListOfDeletions() - Method in class org.sbml.libsbml.Submodel
-
- getListOfEventAssignments() - Method in class org.sbml.libsbml.Event
-
Returns the list of event assignments for this
Event
.
- getListOfEvents() - Method in class org.sbml.libsbml.Model
-
- getListOfExternalModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- getListOfFluxBounds() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getListOfFluxObjectives() - Method in class org.sbml.libsbml.Objective
-
- getListOfFunctionDefinitions() - Method in class org.sbml.libsbml.Model
-
- getListOfGeneAssociations() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getListOfInitialAssignments() - Method in class org.sbml.libsbml.Model
-
- getListOfLayouts() - Method in class org.sbml.libsbml.LayoutModelPlugin
-
- getListOfLocalParameters() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the list of local parameters in this
KineticLaw
object.
- getListOfModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- getListOfModifiers() - Method in class org.sbml.libsbml.Reaction
-
Returns the list of modifiers in this
Reaction
object.
- getListOfNodes() - Method in class org.sbml.libsbml.ASTNode
-
- getListOfObjectives() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getListOfParameters() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the list of local parameters in this
KineticLaw
object.
- getListOfParameters() - Method in class org.sbml.libsbml.Model
-
- getListOfPorts() - Method in class org.sbml.libsbml.CompModelPlugin
-
- getListOfProducts() - Method in class org.sbml.libsbml.Reaction
-
Returns the list of products in this
Reaction
object.
- getListOfReactants() - Method in class org.sbml.libsbml.Reaction
-
Returns the list of reactants in this
Reaction
object.
- getListOfReactionGlyphs() - Method in class org.sbml.libsbml.Layout
-
- getListOfReactions() - Method in class org.sbml.libsbml.Model
-
- getListOfReferenceGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
-
- getListOfReplacedElements() - Method in class org.sbml.libsbml.CompSBasePlugin
-
- getListOfRules() - Method in class org.sbml.libsbml.Model
-
- getListOfSpecies() - Method in class org.sbml.libsbml.Model
-
- getListOfSpeciesGlyphs() - Method in class org.sbml.libsbml.Layout
-
- getListOfSpeciesReferenceGlyphs() - Method in class org.sbml.libsbml.ReactionGlyph
-
- getListOfSpeciesTypes() - Method in class org.sbml.libsbml.Model
-
- getListOfSubGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
-
- getListOfSubmodels() - Method in class org.sbml.libsbml.CompModelPlugin
-
- getListOfTextGlyphs() - Method in class org.sbml.libsbml.Layout
-
- getListOfUnitDefinitions() - Method in class org.sbml.libsbml.Model
-
- getListOfUnits() - Method in class org.sbml.libsbml.UnitDefinition
-
- getLocalParameter(long) - Method in class org.sbml.libsbml.KineticLaw
-
- getLocalParameter(String) - Method in class org.sbml.libsbml.KineticLaw
-
Returns a local parameter based on its identifier.
- getLocationURI() - Method in class org.sbml.libsbml.SBMLDocument
-
- getMantissa() - Method in class org.sbml.libsbml.ASTNode
-
Get the mantissa value of this node.
- getMath() - Method in class org.sbml.libsbml.Constraint
-
Get the mathematical expression of this
Constraint
- getMath() - Method in class org.sbml.libsbml.Delay
-
Get the mathematical formula for the delay and return it
as an AST.
- getMath() - Method in class org.sbml.libsbml.EventAssignment
-
Get the mathematical expression in this
EventAssignment
's 'math'
subelement.
- getMath() - Method in class org.sbml.libsbml.FunctionDefinition
-
- getMath() - Method in class org.sbml.libsbml.InitialAssignment
-
- getMath() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the mathematical formula for this
KineticLaw
object and return
it as as an AST.
- getMath() - Method in class org.sbml.libsbml.Priority
-
Get the mathematical formula for the priority and return it
as an AST.
- getMath() - Method in class org.sbml.libsbml.Rule
-
Get the mathematical formula of this
Rule
as an
ASTNode
tree.
- getMath() - Method in class org.sbml.libsbml.StoichiometryMath
-
Retrieves the mathematical formula within this
StoichiometryMath
and
return it as an AST.
- getMath() - Method in class org.sbml.libsbml.Trigger
-
Get the mathematical formula for the trigger and return it
as an AST.
- getMd5() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- getMessage() - Method in class org.sbml.libsbml.Constraint
-
Get the message, if any, associated with this
Constraint
- getMessage() - Method in class org.sbml.libsbml.XMLError
-
Returns the message text of this error.
- getMessageString() - Method in class org.sbml.libsbml.Constraint
-
Get the message string, if any, associated with this
Constraint
- getMetaId() - Method in class org.sbml.libsbml.SBase
-
Returns the value of the 'metaid' attribute of this object.
- getMetaIdRef() - Method in class org.sbml.libsbml.GraphicalObject
-
- getMetaIdRef() - Method in class org.sbml.libsbml.SBaseRef
-
- getMinute() - Method in class org.sbml.libsbml.Date
-
Returns the minute from this
Date
.
- getMinutesOffset() - Method in class org.sbml.libsbml.Date
-
Returns the minutes of the time zone offset from this
Date
.
- getModel(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- getModel() - Method in class org.sbml.libsbml.L3ParserSettings
-
- getModel() - Method in class org.sbml.libsbml.SBase
-
Returns the
Model
object in which the current object is located.
- getModel() - Method in class org.sbml.libsbml.SBMLDocument
-
- getModel() - Method in class org.sbml.libsbml.SBMLValidator
-
- getModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- getModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- getModelHistory() - Method in class org.sbml.libsbml.SBase
-
Returns the
ModelHistory
object, if any, attached to this object.
- getModelQualifierType() - Method in class org.sbml.libsbml.CVTerm
-
Returns the model qualifier type of this
CVTerm
object.
- getModelRef() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- getModelRef() - Method in class org.sbml.libsbml.Submodel
-
- getModifiedDate() - Method in class org.sbml.libsbml.ModelHistory
-
Returns the 'modified date' portion of this
ModelHistory
object.
- getModifiedDate(long) - Method in class org.sbml.libsbml.ModelHistory
-
Get the nth
Date
object in the list of 'modified date' values stored
in this
ModelHistory
object.
- getModifier(long) - Method in class org.sbml.libsbml.Reaction
-
- getModifier(String) - Method in class org.sbml.libsbml.Reaction
-
- getMonth() - Method in class org.sbml.libsbml.Date
-
Returns the month from this
Date
.
- getMultiplier() - Method in class org.sbml.libsbml.Unit
-
Returns the value of the 'multiplier' attribute of this
Unit
.
- getName() - Method in class org.sbml.libsbml.ASTNode
-
Get the value of this node as a string.
- getName() - Method in class org.sbml.libsbml.Compartment
-
Returns the value of the 'name' attribute of this
Compartment
object.
- getName() - Method in class org.sbml.libsbml.CompartmentType
-
- getName() - Method in class org.sbml.libsbml.Event
-
Returns the value of the 'name' attribute of this
Event
.
- getName() - Method in class org.sbml.libsbml.FunctionDefinition
-
- getName() - Method in class org.sbml.libsbml.Model
-
Returns the value of the 'name' attribute of this
Model
.
- getName() - Method in class org.sbml.libsbml.Parameter
-
Returns the value of the 'name' attribute of this
Parameter
.
- getName() - Method in class org.sbml.libsbml.Reaction
-
Returns the value of the 'name' attribute of this
Reaction
.
- getName() - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
- getName() - Method in class org.sbml.libsbml.Species
-
Returns the value of the 'name' attribute of this
Species
object.
- getName() - Method in class org.sbml.libsbml.SpeciesType
-
Returns the value of the 'name' attribute of this
SpeciesType
.
- getName() - Method in class org.sbml.libsbml.UnitDefinition
-
- getName(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Return the local name of an attribute in this
XMLAttributes
set (by position).
- getName() - Method in class org.sbml.libsbml.XMLToken
-
Returns the (unqualified) name of this XML element.
- getName() - Method in class org.sbml.libsbml.XMLTriple
-
- getNamespaceIndex(String) - Method in class org.sbml.libsbml.XMLToken
-
Look up the index of an XML namespace declaration by URI.
- getNamespaceIndexByPrefix(String) - Method in class org.sbml.libsbml.XMLToken
-
Look up the index of an XML namespace declaration by prefix.
- getNamespacePrefix(int) - Method in class org.sbml.libsbml.XMLToken
-
Look up the prefix of an XML namespace declaration by position.
- getNamespacePrefix(String) - Method in class org.sbml.libsbml.XMLToken
-
Look up the prefix of an XML namespace declaration by its URI.
- getNamespaces() - Method in class org.sbml.libsbml.SBase
-
Returns a list of the XML Namespaces declared on this SBML document.
- getNamespaces() - Method in class org.sbml.libsbml.SBMLDocument
-
Returns a list of XML Namespaces associated with the XML content
of this SBML document.
- getNamespaces() - Method in class org.sbml.libsbml.SBMLNamespaces
-
- getNamespaces() - Method in class org.sbml.libsbml.XMLToken
-
Returns the XML namespace declarations for this XML element.
- getNamespacesLength() - Method in class org.sbml.libsbml.XMLToken
-
- getNamespaceURI(int) - Method in class org.sbml.libsbml.XMLToken
-
Look up the URI of an XML namespace declaration by its position.
- getNamespaceURI(String) - Method in class org.sbml.libsbml.XMLToken
-
Look up the URI of an XML namespace declaration by its prefix.
- getNamespaceURI() - Method in class org.sbml.libsbml.XMLToken
-
Look up the URI of an XML namespace declaration by its prefix.
- getNotes() - Method in class org.sbml.libsbml.SBase
-
Returns the content of the 'notes' subelement of this object as
a tree of
XMLNode
objects.
- getNotesString() - Method in class org.sbml.libsbml.SBase
-
Returns the content of the 'notes' subelement of this object as a
string.
- getNumAdditionalGraphicalObjects() - Method in class org.sbml.libsbml.Layout
-
- getNumArguments() - Method in class org.sbml.libsbml.FunctionDefinition
-
- getNumArguments() - Method in class org.sbml.libsbml.SBMLExternalValidator
-
- getNumAssociations() - Method in class org.sbml.libsbml.Association
-
- getNumAttributes() - Method in class org.sbml.libsbml.XMLAttributes
-
Return the number of attributes in the set.
- getNumChildren() - Method in class org.sbml.libsbml.ASTNode
-
Get the number of children that this node has.
- getNumChildren() - Method in class org.sbml.libsbml.XMLNode
-
Returns the number of children for this
XMLNode
.
- getNumCompartmentGlyphs() - Method in class org.sbml.libsbml.Layout
-
- getNumCompartments() - Method in class org.sbml.libsbml.Model
-
- getNumCompartmentTypes() - Method in class org.sbml.libsbml.Model
-
- getNumConstraints() - Method in class org.sbml.libsbml.Model
-
- getNumConverters() - Method in class org.sbml.libsbml.SBMLConverterRegistry
-
Returns the number of converters known by the registry.
- getNumCreators() - Method in class org.sbml.libsbml.ModelHistory
-
- getNumCurveSegments() - Method in class org.sbml.libsbml.Curve
-
- getNumCVTerms() - Method in class org.sbml.libsbml.SBase
-
Returns the number of
CVTerm
objects in the annotations of this SBML
object.
- getNumDeletions() - Method in class org.sbml.libsbml.Submodel
-
- getNumerator() - Method in class org.sbml.libsbml.ASTNode
-
Get the value of the numerator of this node.
- getNumErrors() - Method in class org.sbml.libsbml.SBMLDocument
-
Returns the number of errors or warnings encountered during parsing,
consistency checking, or attempted translation of this model.
- getNumErrors(long) - Method in class org.sbml.libsbml.SBMLDocument
-
Returns the number of errors or warnings encountered with the given
severity during parsing,
consistency checking, or attempted translation of this model.
- getNumErrors() - Method in class org.sbml.libsbml.XMLErrorLog
-
Returns the number of errors that have been logged.
- getNumEventAssignments() - Method in class org.sbml.libsbml.Event
-
- getNumEvents() - Method in class org.sbml.libsbml.Model
-
- getNumExtension(SBaseExtensionPoint) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Returns the number of SBMLExtension
with the given extension point.
- getNumExternalModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- getNumFailsWithSeverity(long) - Method in class org.sbml.libsbml.SBMLErrorLog
-
Returns the number of errors that have been logged with the given
severity code.
- getNumFailures() - Method in class org.sbml.libsbml.SBMLValidator
-
Returns the number of failures encountered in the last validation run.
- getNumFluxBounds() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getNumFluxObjectives() - Method in class org.sbml.libsbml.Objective
-
- getNumFunctionDefinitions() - Method in class org.sbml.libsbml.Model
-
- getNumGeneAssociations() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getNumGeneralGlyphs() - Method in class org.sbml.libsbml.Layout
-
- getNumInitialAssignments() - Method in class org.sbml.libsbml.Model
-
- getNumLayouts() - Method in class org.sbml.libsbml.LayoutModelPlugin
-
- getNumLocalParameters() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the number of local parameters in this
KineticLaw
instance.
- getNumModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- getNumModifiedDates() - Method in class org.sbml.libsbml.ModelHistory
-
Get the number of
Date
objects in this
ModelHistory
object's list of
'modified dates'.
- getNumModifiers() - Method in class org.sbml.libsbml.Reaction
-
Returns the number of modifier species in this
Reaction
.
- getNumNamespaces() - Method in class org.sbml.libsbml.XMLNamespaces
-
Returns the total number of URI-and-prefix pairs stored in this
particular
XMLNamespaces
instance.
- getNumObjectives() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getNumParameters() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the number of local parameters in this
KineticLaw
instance.
- getNumParameters() - Method in class org.sbml.libsbml.Model
-
- getNumPlugins() - Method in class org.sbml.libsbml.SBase
-
Returns the number of plug-in objects (extenstion interfaces) for SBML
Level 3 package extensions known.
- getNumPorts() - Method in class org.sbml.libsbml.CompModelPlugin
-
- getNumProducts() - Method in class org.sbml.libsbml.Reaction
-
Returns the number of product species in this
Reaction
.
- getNumReactants() - Method in class org.sbml.libsbml.Reaction
-
Returns the number of reactant species in this
Reaction
.
- getNumReactionGlyphs() - Method in class org.sbml.libsbml.Layout
-
- getNumReactions() - Method in class org.sbml.libsbml.Model
-
- getNumReferenceGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
-
- getNumReferents() - Method in class org.sbml.libsbml.ReplacedElement
-
- getNumReferents() - Method in class org.sbml.libsbml.SBaseRef
-
- getNumRegisteredPackages() - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Returns the number of registered packages.
- getNumReplacedElements() - Method in class org.sbml.libsbml.CompSBasePlugin
-
- getNumResolvers() - Method in class org.sbml.libsbml.SBMLResolverRegistry
-
- getNumResources() - Method in class org.sbml.libsbml.CVTerm
-
Returns the number of resources for this
CVTerm
object.
- getNumRules() - Method in class org.sbml.libsbml.Model
-
Get the number of
Rule
objects in this
Model
.
- getNumSemanticsAnnotations() - Method in class org.sbml.libsbml.ASTNode
-
Get the number of semantic annotation elements inside this node.
- getNumSpecies() - Method in class org.sbml.libsbml.Model
-
Get the number of Specie objects in this
Model
.
- getNumSpeciesGlyphs() - Method in class org.sbml.libsbml.Layout
-
- getNumSpeciesReferenceGlyphs() - Method in class org.sbml.libsbml.ReactionGlyph
-
- getNumSpeciesTypes() - Method in class org.sbml.libsbml.Model
-
- getNumSpeciesWithBoundaryCondition() - Method in class org.sbml.libsbml.Model
-
Get the number of
Species
in this
Model
having their
'boundaryCondition' attribute value set to
true.
- getNumSubGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
-
- getNumSubmodels() - Method in class org.sbml.libsbml.CompModelPlugin
-
- getNumTextGlyphs() - Method in class org.sbml.libsbml.Layout
-
- getNumUnitDefinitions() - Method in class org.sbml.libsbml.Model
-
- getNumUnits() - Method in class org.sbml.libsbml.UnitDefinition
-
- getObjective(long) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getObjective(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getObjectiveType() - Method in class org.sbml.libsbml.Objective
-
- getOffset() - Method in class org.sbml.libsbml.Unit
-
Returns the value of the 'offset' attribute of this
Unit
.
- getOperation() - Method in class org.sbml.libsbml.FluxBound
-
- getOperatorName() - Method in class org.sbml.libsbml.ASTNode
-
Get the value of this operator node as a string.
- getOption(String) - Method in class org.sbml.libsbml.ConversionProperties
-
- getOrganisation() - Method in class org.sbml.libsbml.ModelCreator
-
(Alternate spelling) Returns the 'organization' stored in this
ModelCreator
object.
- getOrganization() - Method in class org.sbml.libsbml.ModelCreator
-
Returns the 'organization' stored in this
ModelCreator
object.
- getOriginOfTextId() - Method in class org.sbml.libsbml.TextGlyph
-
- getOutputFileName() - Method in class org.sbml.libsbml.SBMLExternalValidator
-
- getOutside() - Method in class org.sbml.libsbml.Compartment
-
Get the identifier, if any, of the compartment that is designated
as being outside of this one.
- getPackage() - Method in class org.sbml.libsbml.XMLError
-
Returns a copy of the message string associated with the given
predefined
XMLError
code.
- getPackageName() - Method in class org.sbml.libsbml.CompBase
-
Returns the name of the SBML Level 3 package in which this
element is defined.
- getPackageName() - Static method in class org.sbml.libsbml.CompExtension
-
- getPackageName() - Method in class org.sbml.libsbml.CompPkgNamespaces
-
Returns the name of the main package for this namespace.
- getPackageName() - Static method in class org.sbml.libsbml.FbcExtension
-
- getPackageName() - Method in class org.sbml.libsbml.FbcPkgNamespaces
-
Returns the name of the main package for this namespace.
- getPackageName() - Static method in class org.sbml.libsbml.LayoutExtension
-
- getPackageName() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
-
Returns the name of the main package for this namespace.
- getPackageName() - Method in class org.sbml.libsbml.SBase
-
Returns the name of the SBML Level 3 package in which this
element is defined.
- getPackageName() - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the package name of this plugin object.
- getPackageName() - Method in class org.sbml.libsbml.SBMLNamespaces
-
Returns the name of the main package for this namespace.
- getPackageRequired(String) - Method in class org.sbml.libsbml.SBMLDocument
-
Returns the required
attribute of the given package
extension.
- getPackageURI() - Method in class org.sbml.libsbml.CompBase
-
- getPackageVersion() - Method in class org.sbml.libsbml.CompBase
-
Returns the Version of the SBML Level 3 package to which this
element belongs to.
- getPackageVersion() - Method in class org.sbml.libsbml.CompPkgNamespaces
-
- getPackageVersion() - Method in class org.sbml.libsbml.FbcPkgNamespaces
-
- getPackageVersion() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
-
- getPackageVersion() - Method in class org.sbml.libsbml.SBase
-
Returns the Version of the SBML Level 3 package to which this
element belongs to.
- getPackageVersion() - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the package version of the package extension of
this plugin object.
- getParameter(long) - Method in class org.sbml.libsbml.KineticLaw
-
- getParameter(String) - Method in class org.sbml.libsbml.KineticLaw
-
Returns a local parameter based on its identifier.
- getParameter(long) - Method in class org.sbml.libsbml.Model
-
- getParameter(String) - Method in class org.sbml.libsbml.Model
-
Get a
Parameter
object based on its identifier.
- getParentModel(SBase) - Static method in class org.sbml.libsbml.CompBase
-
- getParentSBMLObject() - Method in class org.sbml.libsbml.ASTNode
-
Returns the parent SBML object.
- getParentSBMLObject() - Method in class org.sbml.libsbml.SBase
-
Returns the parent SBML object containing this object.
- getParentSBMLObject() - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the parent
SBase
object to which this plugin
object connected.
- getParseAvogadroCsymbol() - Method in class org.sbml.libsbml.L3ParserSettings
-
Returns true
if the current settings are oriented towards handling
avogadro
for SBML Level 3.
- getParseCollapseMinus() - Method in class org.sbml.libsbml.L3ParserSettings
-
Returns a flag indicating the current behavior set for handling
multiple unary minuses in formulas.
- getParseLog() - Method in class org.sbml.libsbml.L3ParserSettings
-
Returns the current setting indicating what to do with formulas
containing the function log
with one argument.
- getParseUnits() - Method in class org.sbml.libsbml.L3ParserSettings
-
Returns if
the current settings allow units in text-string
mathematical formulas.
- getPath() - Method in class org.sbml.libsbml.SBMLUri
-
- getPersistent() - Method in class org.sbml.libsbml.Trigger
-
(SBML Level 3 only) Get the value of the 'persistent' attribute
of this
Trigger
.
- getPlugin(String) - Method in class org.sbml.libsbml.SBase
-
Returns a plug-in object (extension interface) for an SBML Level 3
package extension with the given package name or URI.
- getPlugin(long) - Method in class org.sbml.libsbml.SBase
-
Returns the nth plug-in object (extension interface) for an SBML Level 3
package extension.
- getPort(long) - Method in class org.sbml.libsbml.CompModelPlugin
-
- getPort(String) - Method in class org.sbml.libsbml.CompModelPlugin
-
- getPortRef() - Method in class org.sbml.libsbml.SBaseRef
-
- getPosition() - Method in class org.sbml.libsbml.BoundingBox
-
- getPrecedence() - Method in class org.sbml.libsbml.ASTNode
-
Get the precedence of this node in the infix math syntax of SBML
Level 1.
- getPrefix() - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the prefix of the package extension of this plugin object.
- getPrefix(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Return the prefix of an attribute in this
XMLAttributes
set (by position).
- getPrefix(int) - Method in class org.sbml.libsbml.XMLNamespaces
-
Look up the prefix of an XML namespace declaration by its position.
- getPrefix(String) - Method in class org.sbml.libsbml.XMLNamespaces
-
Look up the prefix of an XML namespace declaration by its URI.
- getPrefix() - Method in class org.sbml.libsbml.XMLToken
-
Returns the namespace prefix of this XML element.
- getPrefix() - Method in class org.sbml.libsbml.XMLTriple
-
Returns the
prefix portion of this
XMLTriple
.
- getPrefixedName(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Return the prefixed name of an attribute in this
XMLAttributes
set (by position).
- getPrefixedName() - Method in class org.sbml.libsbml.XMLTriple
-
Returns the prefixed name from this
XMLTriple
.
- getPriority() - Method in class org.sbml.libsbml.Event
-
(SBML Level 3 only) Get the event priority portion of this
Event
.
- getProduct(long) - Method in class org.sbml.libsbml.Reaction
-
- getProduct(String) - Method in class org.sbml.libsbml.Reaction
-
- getProgram() - Method in class org.sbml.libsbml.SBMLExternalValidator
-
- getProperties() - Method in class org.sbml.libsbml.SBMLConverter
-
Returns the current properties in effect for this converter.
- getQualifierType() - Method in class org.sbml.libsbml.CVTerm
-
Returns the qualifier type of this
CVTerm
object.
- getQuery() - Method in class org.sbml.libsbml.SBMLUri
-
- getReactant(long) - Method in class org.sbml.libsbml.Reaction
-
- getReactant(String) - Method in class org.sbml.libsbml.Reaction
-
- getReaction() - Method in class org.sbml.libsbml.FluxBound
-
- getReaction() - Method in class org.sbml.libsbml.FluxObjective
-
- getReaction() - Method in class org.sbml.libsbml.GeneAssociation
-
- getReaction(long) - Method in class org.sbml.libsbml.Model
-
- getReaction(String) - Method in class org.sbml.libsbml.Model
-
Get a
Reaction
object based on its identifier.
- getReactionGlyph(long) - Method in class org.sbml.libsbml.Layout
-
- getReactionGlyph(String) - Method in class org.sbml.libsbml.Layout
-
- getReactionId() - Method in class org.sbml.libsbml.ReactionGlyph
-
- getReal() - Method in class org.sbml.libsbml.ASTNode
-
Get the real-numbered value of this node.
- getReference() - Method in class org.sbml.libsbml.Association
-
- getReferencedElement() - Method in class org.sbml.libsbml.SBaseRef
-
- getReferencedElementFrom(Model) - Method in class org.sbml.libsbml.ReplacedElement
-
- getReferencedElementFrom(Model) - Method in class org.sbml.libsbml.SBaseRef
-
- getReferencedModel() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- getReferenceGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
-
- getReferenceId() - Method in class org.sbml.libsbml.GeneralGlyph
-
- getReferenceId() - Method in class org.sbml.libsbml.ReferenceGlyph
-
- getRegisteredPackageName(long) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Returns the registered package name at the given index
- getReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
-
- getReplacedElement(long) - Method in class org.sbml.libsbml.CompSBasePlugin
-
- getRequired() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
-
Returns the bool value of 'required' attribute of corresponding
package in
SBMLDocument
element.
- getResolverByIndex(int) - Method in class org.sbml.libsbml.SBMLResolverRegistry
-
- getResourceBiologicalQualifier(String) - Method in class org.sbml.libsbml.SBase
-
Returns the MIRIAM biological qualifier associated with the
given resource.
- getResourceModelQualifier(String) - Method in class org.sbml.libsbml.SBase
-
Returns the MIRIAM model qualifier associated with the
given resource.
- getResources() - Method in class org.sbml.libsbml.CVTerm
-
Returns the resource references for this
CVTerm
object.
- getResourceURI(long) - Method in class org.sbml.libsbml.CVTerm
-
Returns the value of the
nth resource for this
CVTerm
object.
- getReversible() - Method in class org.sbml.libsbml.Reaction
-
Returns the value of the 'reversible' attribute on the
Reaction
as a
boolean value.
- getRightChild() - Method in class org.sbml.libsbml.ASTNode
-
Get the right child of this node.
- getRole() - Method in class org.sbml.libsbml.ReferenceGlyph
-
- getRole() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- getRoleString() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- getRule(long) - Method in class org.sbml.libsbml.Model
-
- getRule(String) - Method in class org.sbml.libsbml.Model
-
Get a
Rule
object based on the variable to which it assigns a value.
- getSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
-
- getSBMLDocument() - Method in class org.sbml.libsbml.SBase
-
Returns the
SBMLDocument
object containing
this object instance.
- getSBMLDocument() - Method in class org.sbml.libsbml.SBasePlugin
-
- getSBMLErrMsg() - Method in exception org.sbml.libsbml.SBMLConstructorException
-
Returns the message associated with this SBML exception.
- getSBMLFileName() - Method in class org.sbml.libsbml.SBMLExternalValidator
-
- getSBMLNamespaceURI(long, long) - Static method in class org.sbml.libsbml.SBMLNamespaces
-
Returns a string representing the SBML XML namespace for the
given level
and version
of SBML.
- getSBOTerm() - Method in class org.sbml.libsbml.SBase
-
Returns the integer portion of the value of the 'sboTerm' attribute of
this object.
- getSBOTermAsURL() - Method in class org.sbml.libsbml.SBase
-
Returns the identifiers.org URL representation of the 'sboTerm' attribute of
this object.
- getSBOTermID() - Method in class org.sbml.libsbml.SBase
-
Returns the string representation of the 'sboTerm' attribute of
this object.
- getScale() - Method in class org.sbml.libsbml.Unit
-
Returns the value of the 'scale' attribute of this unit.
- getScheme() - Method in class org.sbml.libsbml.SBMLUri
-
- getSecond() - Method in class org.sbml.libsbml.Date
-
Returns the seconds from this
Date
.
- getSemanticsAnnotation(long) - Method in class org.sbml.libsbml.ASTNode
-
Get the nth semantic annotation of this node.
- getSeverity() - Method in class org.sbml.libsbml.XMLError
-
Returns the severity of this error.
- getSeverityAsString() - Method in class org.sbml.libsbml.XMLError
-
Returns a string describing the severity level of this error.
- getShortMessage() - Method in class org.sbml.libsbml.XMLError
-
Returns a brief message for this error.
- getSignOffset() - Method in class org.sbml.libsbml.Date
-
Returns the sign of the time zone offset from this
Date
.
- getSize() - Method in class org.sbml.libsbml.ASTNodeList
-
- getSize() - Method in class org.sbml.libsbml.Compartment
-
- getSize() - Method in class org.sbml.libsbml.CVTermList
-
- getSize() - Method in class org.sbml.libsbml.DateList
-
- getSize() - Method in class org.sbml.libsbml.ModelCreatorList
-
- getSize() - Method in class org.sbml.libsbml.SBaseList
-
- getSize() - Method in class org.sbml.libsbml.SBMLNamespacesList
-
- getSource() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- getSpatialDimensions() - Method in class org.sbml.libsbml.Compartment
-
Get the number of spatial dimensions of this
Compartment
object.
- getSpatialDimensionsAsDouble() - Method in class org.sbml.libsbml.Compartment
-
Get the number of spatial dimensions of this
Compartment
object
as a double.
- getSpatialSizeUnits() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'spatialSizeUnits' attribute.
- getSpecies(long) - Method in class org.sbml.libsbml.Model
-
- getSpecies(String) - Method in class org.sbml.libsbml.Model
-
Get a
Species
object based on its identifier.
- getSpecies() - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
Get the value of the 'species' attribute.
- getSpeciesGlyph(long) - Method in class org.sbml.libsbml.Layout
-
- getSpeciesGlyph(String) - Method in class org.sbml.libsbml.Layout
-
- getSpeciesGlyphId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- getSpeciesId() - Method in class org.sbml.libsbml.SpeciesGlyph
-
- getSpeciesReference(String) - Method in class org.sbml.libsbml.Model
-
- getSpeciesReferenceGlyph(long) - Method in class org.sbml.libsbml.ReactionGlyph
-
- getSpeciesReferenceId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- getSpeciesType(long) - Method in class org.sbml.libsbml.Model
-
- getSpeciesType(String) - Method in class org.sbml.libsbml.Model
-
- getSpeciesType() - Method in class org.sbml.libsbml.Species
-
Get the type of this
Species
object object.
- getStandardMessage(int) - Static method in class org.sbml.libsbml.XMLError
-
Returns a copy of the message string associated with the given
predefined
XMLError
code.
- getStart() - Method in class org.sbml.libsbml.LineSegment
-
- getStoichiometry() - Method in class org.sbml.libsbml.SpeciesReference
-
Get the value of the 'stoichiometry' attribute.
- getStoichiometryMath() - Method in class org.sbml.libsbml.SpeciesReference
-
Get the content of the 'stoichiometryMath' subelement as an
ASTNode
tree.
- getStyle() - Method in class org.sbml.libsbml.ASTNode
-
- getSubGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
-
- getSubmodel(long) - Method in class org.sbml.libsbml.CompModelPlugin
-
- getSubmodel(String) - Method in class org.sbml.libsbml.CompModelPlugin
-
- getSubmodelRef() - Method in class org.sbml.libsbml.Replacing
-
- getSubstanceConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
- getSubstanceUnits() - Method in class org.sbml.libsbml.KineticLaw
-
(SBML Level 2 Version 1 only) Returns the value of the
'substanceUnits' attribute of this
KineticLaw
object.
- getSubstanceUnits() - Method in class org.sbml.libsbml.Model
-
Returns the value of the 'substanceUnits' attribute of this
Model
.
- getSubstanceUnits() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'substanceUnits' attribute.
- getSupportedNamespaces() - Static method in class org.sbml.libsbml.SBMLNamespaces
-
- getSymbol() - Method in class org.sbml.libsbml.InitialAssignment
-
- getTargetLevel() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
-
Returns the target SBML Level for the conversion.
- getTargetNamespaces() - Method in class org.sbml.libsbml.ConversionProperties
-
Returns the current target SBML namespace.
- getTargetNamespaces() - Method in class org.sbml.libsbml.SBMLConverter
-
Returns the target SBML namespaces of the currently set properties.
- getTargetVersion() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
-
Returns the target SBML Version for the conversion.
- getText() - Method in class org.sbml.libsbml.TextGlyph
-
- getTextGlyph(long) - Method in class org.sbml.libsbml.Layout
-
- getTextGlyph(String) - Method in class org.sbml.libsbml.Layout
-
- getTimeConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
- getTimeUnits() - Method in class org.sbml.libsbml.Event
-
Get the value of the 'timeUnits' attribute of this
Event
, if it has one.
- getTimeUnits() - Method in class org.sbml.libsbml.KineticLaw
-
(SBML Level 2 Version 1 only) Returns the value of the
'timeUnits' attribute of this
KineticLaw
object.
- getTimeUnits() - Method in class org.sbml.libsbml.Model
-
Returns the value of the 'timeUnits' attribute of this
Model
.
- getTrigger() - Method in class org.sbml.libsbml.Event
-
Get the event trigger portion of this
Event
.
- getType() - Method in class org.sbml.libsbml.Association
-
- getType() - Method in class org.sbml.libsbml.ASTNode
-
- getType() - Method in class org.sbml.libsbml.ConversionOption
-
Returns the type of this option
- getType(String) - Method in class org.sbml.libsbml.ConversionProperties
-
Returns the type of a given option in this properties object.
- getType() - Method in class org.sbml.libsbml.Objective
-
- getType() - Method in class org.sbml.libsbml.Rule
-
Get the type of rule this is.
- getTypeCode() - Method in class org.sbml.libsbml.Association
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.BoundingBox
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.Compartment
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.CompartmentGlyph
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.CompartmentType
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.Constraint
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.CubicBezier
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.Curve
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.Delay
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Deletion
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.Dimensions
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.Event
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.EventAssignment
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.FluxBound
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.FluxObjective
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.FunctionDefinition
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.GeneAssociation
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.GraphicalObject
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.InitialAssignment
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.Layout
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.LineSegment
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOf
-
Returns the libSBML type code for this object, namely,
SBML_LIST_OF.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfCompartments
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfConstraints
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfEventAssignments
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfEvents
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfInitialAssignments
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfLocalParameters
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfParameters
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfReactions
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfRules
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfSpecies
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfUnits
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.LocalParameter
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.Model
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ModelDefinition
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ModifierSpeciesReference
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.Objective
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.Parameter
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.Point
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.Port
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.Priority
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Reaction
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ReactionGlyph
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.ReplacedBy
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.ReplacedElement
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.Rule
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.SBase
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.SBaseRef
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.SBMLDocument
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.Species
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesGlyph
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesReference
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesType
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.StoichiometryMath
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Submodel
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.TextGlyph
-
Returns the libSBML type code for this object.
- getTypeCode() - Method in class org.sbml.libsbml.Trigger
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Unit
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.UnitDefinition
-
Returns the libSBML type code for this object instance.
- getUnit(long) - Method in class org.sbml.libsbml.UnitDefinition
-
- getUnitDefinition(long) - Method in class org.sbml.libsbml.Model
-
- getUnitDefinition(String) - Method in class org.sbml.libsbml.Model
-
- getUnitRef() - Method in class org.sbml.libsbml.SBaseRef
-
- getUnits() - Method in class org.sbml.libsbml.ASTNode
-
- getUnits() - Method in class org.sbml.libsbml.Compartment
-
Get the units of this compartment's size.
- getUnits() - Method in class org.sbml.libsbml.Parameter
-
- getUnits() - Method in class org.sbml.libsbml.Rule
-
Returns the units for the
mathematical formula of this
Rule
.
- getUnits() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'units' attribute.
- getURI() - Method in class org.sbml.libsbml.CompPkgNamespaces
-
Returns a string representing the SBML XML namespace of this
object.
- getURI() - Method in class org.sbml.libsbml.FbcPkgNamespaces
-
Returns a string representing the SBML XML namespace of this
object.
- getURI() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
-
Returns a string representing the SBML XML namespace of this
object.
- getURI() - Method in class org.sbml.libsbml.SBasePlugin
-
Gets the URI to which this element belongs to.
- getURI() - Method in class org.sbml.libsbml.SBMLNamespaces
-
Returns a string representing the SBML XML namespace of this
object.
- getUri() - Method in class org.sbml.libsbml.SBMLUri
-
- getURI(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Return the namespace URI of an attribute in this
XMLAttributes
set (by position).
- getURI(int) - Method in class org.sbml.libsbml.XMLNamespaces
-
Look up the URI of an XML namespace declaration by its position.
- getURI(String) - Method in class org.sbml.libsbml.XMLNamespaces
-
Look up the URI of an XML namespace declaration by its prefix.
- getURI() - Method in class org.sbml.libsbml.XMLNamespaces
-
Look up the URI of an XML namespace declaration by its prefix.
- getURI() - Method in class org.sbml.libsbml.XMLToken
-
Returns the namespace URI of this XML element.
- getURI() - Method in class org.sbml.libsbml.XMLTriple
-
- getUseValuesFromTriggerTime() - Method in class org.sbml.libsbml.Event
-
Get the value of the 'useValuesFromTriggerTime' attribute of this
Event
.
- getValidityFlag() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
-
Returns the flag indicating whether the conversion has been set to 'strict'.
- getValue() - Method in class org.sbml.libsbml.ConversionOption
-
Returns the value of this option.
- getValue(String) - Method in class org.sbml.libsbml.ConversionProperties
-
Returns the value of the given option as a string.
- getValue() - Method in class org.sbml.libsbml.FluxBound
-
- getValue() - Method in class org.sbml.libsbml.Parameter
-
- getValue(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Return the value of an attribute in this
XMLAttributes
set (by position).
- getValue(String) - Method in class org.sbml.libsbml.XMLAttributes
-
Return an attribute's value by name.
- getValue(String, String) - Method in class org.sbml.libsbml.XMLAttributes
-
Return a value of an attribute with the given local name and namespace URI.
- getValue(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
-
Return a value of an attribute with the given
XMLTriple
.
- getVariable() - Method in class org.sbml.libsbml.EventAssignment
-
- getVariable() - Method in class org.sbml.libsbml.Rule
-
Get the value of the 'variable' attribute of this
Rule
object.
- getVersion() - Method in class org.sbml.libsbml.SBase
-
Returns the Version within the SBML Level of the
SBMLDocument
object
containing this object.
- getVersion() - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the SBML version of the package extension of
this plugin object.
- getVersion() - Method in class org.sbml.libsbml.SBMLNamespaces
-
- getVolume() - Method in class org.sbml.libsbml.Compartment
-
- getVolumeUnits() - Method in class org.sbml.libsbml.Model
-
Returns the value of the 'volumeUnits' attribute of this
Model
.
- getWidth() - Method in class org.sbml.libsbml.Dimensions
-
- getXmlnsL2() - Static method in class org.sbml.libsbml.LayoutExtension
-
- getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.CompExtension
-
- getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.FbcExtension
-
- getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.LayoutExtension
-
- getXmlnsXSI() - Static method in class org.sbml.libsbml.LayoutExtension
-
- getXOffset() - Method in class org.sbml.libsbml.Point
-
- getYear() - Method in class org.sbml.libsbml.Date
-
Returns the year from this
Date
.
- getYOffset() - Method in class org.sbml.libsbml.Point
-
- getZOffset() - Method in class org.sbml.libsbml.Point
-
- GlobalUnitsNotDeclared - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- GraphicalObject - Class in org.sbml.libsbml
-
- GraphicalObject(long, long, long) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(long, long) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(long) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject() - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(LayoutPkgNamespaces, String, double, double, double, double) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(LayoutPkgNamespaces, String, double, double, double, double, double, double) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(LayoutPkgNamespaces, String, Point, Dimensions) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(LayoutPkgNamespaces, String, BoundingBox) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(XMLNode, long) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(XMLNode) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- GraphicalObject(GraphicalObject) - Constructor for class org.sbml.libsbml.GraphicalObject
-
- IdCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- IdCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- IdNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InconsistentArgUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InconsistentArgUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InconsistentExponUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InconsistentKineticLawUnitsL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InconsistentPowerUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- IncorrectCompartmentSpatialDimensions - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- IncorrectOrderInConstraint - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- IncorrectOrderInEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- IncorrectOrderInKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- IncorrectOrderInModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- IncorrectOrderInReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- init() - Static method in class org.sbml.libsbml.CompExtension
-
- init() - Static method in class org.sbml.libsbml.FbcExtension
-
- init() - Static method in class org.sbml.libsbml.LayoutExtension
-
- init() - Static method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
-
- init() - Static method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
-
- init() - Static method in class org.sbml.libsbml.SBMLLevelVersionConverter
-
- init() - Static method in class org.sbml.libsbml.SBMLRuleConverter
-
- init() - Static method in class org.sbml.libsbml.SBMLStripPackageConverter
-
- init() - Static method in class org.sbml.libsbml.SBMLUnitsConverter
-
- InitAssignCompartmenMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InitAssignmentAndRuleForSameId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InitAssignParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InitAssignSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InitAssignStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- initDefaults() - Method in class org.sbml.libsbml.BoundingBox
-
- initDefaults() - Method in class org.sbml.libsbml.Compartment
-
Initializes the fields of this
Compartment
object to 'typical' default
values.
- initDefaults() - Method in class org.sbml.libsbml.CompartmentGlyph
-
- initDefaults() - Method in class org.sbml.libsbml.CubicBezier
-
- initDefaults() - Method in class org.sbml.libsbml.Curve
-
- initDefaults() - Method in class org.sbml.libsbml.Dimensions
-
- initDefaults() - Method in class org.sbml.libsbml.GeneralGlyph
-
- initDefaults() - Method in class org.sbml.libsbml.GraphicalObject
-
- initDefaults() - Method in class org.sbml.libsbml.Layout
-
- initDefaults() - Method in class org.sbml.libsbml.LineSegment
-
- initDefaults() - Method in class org.sbml.libsbml.Parameter
-
Initializes the fields of this
Parameter
object to 'typical' defaults
values.
- initDefaults() - Method in class org.sbml.libsbml.Point
-
- initDefaults() - Method in class org.sbml.libsbml.Reaction
-
Initializes the fields of this
Reaction
object to 'typical' default
values.
- initDefaults() - Method in class org.sbml.libsbml.ReactionGlyph
-
- initDefaults() - Method in class org.sbml.libsbml.ReferenceGlyph
-
- initDefaults() - Method in class org.sbml.libsbml.Species
-
Initializes the fields of this
Species
object to 'typical' defaults
values.
- initDefaults() - Method in class org.sbml.libsbml.SpeciesGlyph
-
- initDefaults() - Method in class org.sbml.libsbml.SpeciesReference
-
Initializes the fields of this
SpeciesReference
object to 'typical'
default values.
- initDefaults() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- initDefaults() - Method in class org.sbml.libsbml.TextGlyph
-
- initDefaults() - Method in class org.sbml.libsbml.Unit
-
Initializes the fields of this
Unit
object to 'typical' default
values.
- InitialAssignment - Class in org.sbml.libsbml
-
Implementation of SBML's InitialAssignment construct.
- InitialAssignment(long, long) - Constructor for class org.sbml.libsbml.InitialAssignment
-
- InitialAssignment(SBMLNamespaces) - Constructor for class org.sbml.libsbml.InitialAssignment
-
- InitialAssignment(InitialAssignment) - Constructor for class org.sbml.libsbml.InitialAssignment
-
- InitialAssignNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InitialValueFalseEventNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InitialValueNotBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- insert(int, SBase) - Method in class org.sbml.libsbml.ListOf
-
Inserts the item at the given position of this
ListOf
- insertAndOwn(int, SBase) - Method in class org.sbml.libsbml.ListOf
-
Inserts the item at the given position of this
ListOf
- insertChild(long, ASTNode) - Method in class org.sbml.libsbml.ASTNode
-
Insert the given
ASTNode
at point n in the list of children
of this
ASTNode
.
- insertChild(long, XMLNode) - Method in class org.sbml.libsbml.XMLNode
-
Inserts a copy of the given node as the
n
th child of this
XMLNode
.
- instantiate() - Method in class org.sbml.libsbml.Submodel
-
- IntegerSpatialDimensions - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InternalXMLParserError - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- intToString(int) - Static method in class org.sbml.libsbml.SBO
-
Returns the integer as a correctly formatted SBO identifier string.
- Invalid1DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- Invalid2DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- Invalid3DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidAfterXMLContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidApplyCiInLambda - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidAreaRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidAssignRuleVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidCharInXML - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidCiInLambda - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidCompartmentSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidCompartmentTypeRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidCompartmentTypeSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidConstraintContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidConstraintSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidDelaySBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidEventAssignmentSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidEventAssignmentVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidEventSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidFunctionDefReturnType - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidFunctionDefSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidInitAssignSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidInitAssignSymbol - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidKineticLawSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidL1CompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidLengthRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidMathElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidMetaidSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidModelSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidModifiersList - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidNamespaceOnSBML - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidNameSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidNoArgsPassedToFunctionDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidNotesContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidParameterSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidParameterUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidRateRuleVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidReactantsProductsList - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidReactionSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidRuleOrdering - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidRuleSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidSBMLLevelVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidSBOTermSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidSpeciesCompartmentRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidSpeciesReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidSpeciesReferenceSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidSpeciesSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidSpeciesSusbstanceUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidSpeciesTypeRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidSpeciesTypeSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidSubstanceRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidTargetLevelVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidTimeRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidTriggerSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidUnitDefId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidUnitIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidUnitKind - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidUnitsValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidVolumeRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- InvalidXMLConstruct - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- is_open() - Method in class org.sbml.libsbml.OFStream
-
Returns true
if this stream object is currently
associated with a file.
- isAlgebraic() - Method in class org.sbml.libsbml.Rule
-
- isAmpere() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
ampere.
- isAssignment() - Method in class org.sbml.libsbml.Rule
-
- isAttributesEmpty() - Method in class org.sbml.libsbml.XMLToken
-
Predicate returning
true
or
false
depending on whether
the attribute set in this
XMLToken
set is empty.
- isAvogadro() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node is the special
symbol avogadro.
The predicate returns false
(zero) otherwise.
- isAvogadro() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
avogadro.
- isBecquerel() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
becquerel
- isBoolean() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node has a boolean type
(a logical operator, a relational operator, or the constants true
or false
).
- isBuiltIn(String, long) - Static method in class org.sbml.libsbml.Unit
-
Predicate to test whether a given string is the name of a
predefined SBML unit.
- isCandela() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
candela
- isCelsius() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
Celsius
- isCompartmentVolume() - Method in class org.sbml.libsbml.Rule
-
Predicate returning
true
if this
Rule
is an CompartmentVolumeRule
or equivalent.
- isConservationLaw(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isConstant() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node represents a MathML
constant (e.g., true
, Pi
).
- isContinuousFramework(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isCoulomb() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
coulomb
- isDimensionless() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
dimensionless.
- isDiscreteFramework(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isElement() - Method in class org.sbml.libsbml.XMLToken
-
Predicate returning
true
or
false
depending on whether
this
XMLToken
is an XML element.
- isEmpty() - Method in class org.sbml.libsbml.XMLAttributes
-
Predicate returning
true
or
false
depending on whether
this
XMLAttributes
set is empty.
- isEmpty() - Method in class org.sbml.libsbml.XMLNamespaces
-
Predicate returning
true
or
false
depending on whether this
XMLNamespaces
list is empty.
- isEmpty() - Method in class org.sbml.libsbml.XMLTriple
-
Predicate returning
true
or
false
depending on whether
this
XMLTriple
is empty.
- isEnabled(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Checks if the extension with the given URI is enabled (true) or
disabled (false)
- isEnabledDefaultNS(String) - Method in class org.sbml.libsbml.SBMLDocument
-
Returns true
if a default namespace is added to each top-level
element defined in the given package extension, otherwise returns
false.
- isEnd() - Method in class org.sbml.libsbml.XMLToken
-
Predicate returning
true
or
false
depending on whether
this
XMLToken
is an XML end element.
- isEndFor(XMLToken) - Method in class org.sbml.libsbml.XMLToken
-
Predicate returning
true
or
false
depending on whether
this
XMLToken
is an XML end element for the given start element.
- isEntity(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isEOF() - Method in class org.sbml.libsbml.XMLToken
-
Predicate returning
true
or
false
depending on whether
this
XMLToken
is an end of file marker.
- isError() - Method in class org.sbml.libsbml.XMLError
-
Predicate returning true
or false
depending on whether this
error is a significant error.
- isEvent(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isFarad() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
farad
- isFatal() - Method in class org.sbml.libsbml.XMLError
-
Predicate returning true
or false
depending on whether this
error is a fatal run-time error.
- isFunction() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node represents a
MathML function (e.g., abs()
), or an SBML Level 1
function, or a user-defined function.
- isFunctionalCompartment(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isFunctionalEntity(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isGram() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
gram
- isGray() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
gray
- isHenry() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
henry
- isHertz() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
hertz
- isIgnoredPackage(String) - Method in class org.sbml.libsbml.SBMLDocument
-
Returns true
if the given package extension is one of an ignored
packages, otherwise returns false.
- isInfinity() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node represents
the special IEEE 754 value infinity, false
(zero) otherwise.
- isInfo() - Method in class org.sbml.libsbml.XMLError
-
Predicate returning true
or false
depending on whether this
error object is for information purposes only.
- isInteger() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node contains an
integer value, false
(zero) otherwise.
- isInteraction(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isInternal() - Method in class org.sbml.libsbml.XMLError
-
Predicate returning true
or false
depending on whether this
error resulted from an internal program error.
- isItem() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
item
- isJoule() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
joule
- isKatal() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
katal
- isKelvin() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
kelvin
- isKilogram() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
kilogram
- isKineticConstant(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isLambda() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node is a MathML
<lambda>
, false
(zero) otherwise.
- isLitre() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
litre
- isLog10() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node represents a
log10
function, false
(zero) otherwise.
- isLogical() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node is a MathML
logical operator (i.e., and
, or
, not
, xor
).
- isLogicalFramework(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isLumen() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
lumen
- isLux() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
lux
- isMaterialEntity(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isMathematicalExpression(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isMetadataRepresentation(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isMetre() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
metre
- isModellingFramework(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isModifier(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isModifier() - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
- isMole() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
mole
- isName() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node is a user-defined
variable name in SBML L1, L2 (MathML), or the special symbols delay
or time.
The predicate returns false
(zero) otherwise.
- isNamespacesEmpty() - Method in class org.sbml.libsbml.XMLToken
-
- isNaN() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node represents the
special IEEE 754 value 'not a number' (NaN), false
(zero)
otherwise.
- isNegInfinity() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node represents the
special IEEE 754 value 'negative infinity', false
(zero) otherwise.
- isNewton() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
newton
- isNumber() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node contains a number,
false
(zero) otherwise.
- isObselete(long) - Static method in class org.sbml.libsbml.SBO
-
Predicate for checking whether the given term is obsolete.
- isOccurringEntityRepresentation(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isOhm() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
ohm
- isOperator() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node is a mathematical
operator, meaning, +
, -
, *
,
/
or ^
(power).
- isPackageEnabled(String) - Method in class org.sbml.libsbml.SBase
-
Predicate returning true
if the given SBML Level 3 package is
enabled with this object.
- isPackageEnabled(String) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
-
- isPackageURIEnabled(String) - Method in class org.sbml.libsbml.SBase
-
Predicate returning true
if an SBML Level 3 package with the
given URI is enabled with this object.
- isParameter() - Method in class org.sbml.libsbml.Rule
-
Predicate returning
true
if this
Rule
is an ParameterRule or
equivalent.
- isParticipant(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isParticipantRole(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isPascal() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
pascal
- isPhysicalEntityRepresentation(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isPhysicalParticipant(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isPiecewise() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node is the MathML
<piecewise>
construct, false
(zero) otherwise.
- isPopulatedListFormulaUnitsData() - Method in class org.sbml.libsbml.Model
-
Predicate returning true
if
the list of FormulaUnitsData is populated.
- isProduct(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isQuantitativeParameter(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isRadian() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
radian
- isRate() - Method in class org.sbml.libsbml.Rule
-
Predicate returning
true
if this
Rule
is a
RateRule
(SBML Levels 2–3) or has a 'type' attribute
value of
'rate'
(SBML Level 1).
- isRateLaw(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isRational() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node represents a rational
number, false
(zero) otherwise.
- isReactant(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isReal() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node can represent a
real number, false
(zero) otherwise.
- isRegistered(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Checks if the extension with the given URI is registered (true)
or not (false)
- isRelational() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node is a MathML
relational operator, meaning ==
, >=
,
>
, <
, and !=
.
- isSBMLNamespace(String) - Static method in class org.sbml.libsbml.SBMLNamespaces
-
Predicate returning true
if the given
URL is one of SBML XML namespaces.
- isScalar() - Method in class org.sbml.libsbml.Rule
-
Predicate returning
true
if this
Rule
is an
AssignmentRule
(SBML Levels 2–3) or has a 'type'
attribute value of
'scalar'
(SBML Level 1).
- isSecond() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
second
- isSetActiveObjective() - Method in class org.sbml.libsbml.ListOfObjectives
-
- isSetAnnotation() - Method in class org.sbml.libsbml.SBase
-
Predicate returning true
if this
object's 'annotation' subelement exists and has content.
- isSetAreaUnits() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true
if this
Model
's 'areaUnits' attribute is set.
- isSetAssociation() - Method in class org.sbml.libsbml.GeneAssociation
-
- isSetBody() - Method in class org.sbml.libsbml.FunctionDefinition
-
- isSetBoundaryCondition() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'boundaryCondition' attribute is set.
- isSetCharge() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
-
- isSetCharge() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'charge' attribute is set.
- isSetChemicalFormula() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
-
- isSetClass() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node has the mathml attribute
class
.
- isSetCoefficient() - Method in class org.sbml.libsbml.FluxObjective
-
- isSetCompartment() - Method in class org.sbml.libsbml.Reaction
-
Predicate returning
true
if this
Reaction
's 'compartment' attribute is set.
- isSetCompartment() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'compartment' attribute is set.
- isSetCompartmentId() - Method in class org.sbml.libsbml.CompartmentGlyph
-
- isSetCompartmentType() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true
if this
Compartment
's 'compartmentType' attribute is set.
- isSetConstant() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true
if this
Compartment
's 'constant' attribute is set.
- isSetConstant() - Method in class org.sbml.libsbml.Parameter
-
Predicate returning
true
if the
'constant' attribute of this
Parameter
is set.
- isSetConstant() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'constant' attribute is set.
- isSetConstant() - Method in class org.sbml.libsbml.SpeciesReference
-
- isSetConversionFactor() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true
if this
Model
's 'conversionFactor' attribute is set.
- isSetConversionFactor() - Method in class org.sbml.libsbml.ReplacedElement
-
- isSetConversionFactor() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'conversionFactor' attribute is set.
- isSetCreatedDate() - Method in class org.sbml.libsbml.ModelHistory
-
Predicate returning
true
or
false
depending on whether this
ModelHistory
's 'creation date' is set.
- isSetCurve() - Method in class org.sbml.libsbml.GeneralGlyph
-
- isSetCurve() - Method in class org.sbml.libsbml.ReactionGlyph
-
- isSetCurve() - Method in class org.sbml.libsbml.ReferenceGlyph
-
- isSetCurve() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- isSetDelay() - Method in class org.sbml.libsbml.Event
-
Predicate for testing whether the delay for this
Event
is set.
- isSetDeletion() - Method in class org.sbml.libsbml.ReplacedElement
-
- isSetEmail() - Method in class org.sbml.libsbml.ModelCreator
-
Predicate returning
true
or
false
depending on whether this
ModelCreator
's 'email' part is set.
- isSetExponent() - Method in class org.sbml.libsbml.Unit
-
Predicate to test whether the 'exponent' attribute of this
Unit
is set.
- isSetExtentConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
- isSetExtentUnits() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true
if this
Model
's 'extentUnits' attribute is set.
- isSetFamilyName() - Method in class org.sbml.libsbml.ModelCreator
-
Predicate returning
true
or
false
depending on whether this
ModelCreator
's 'family name' part is set.
- isSetFast() - Method in class org.sbml.libsbml.Reaction
-
Predicate returning
true
if the value of
the 'fast' attribute on this
Reaction
.
- isSetFormula() - Method in class org.sbml.libsbml.KineticLaw
-
Predicate returning
true
if this
KineticLaw
's 'formula' attribute is set.
- isSetFormula() - Method in class org.sbml.libsbml.Rule
-
Predicate returning
true
if this
Rule
's mathematical expression is set.
- isSetGivenName() - Method in class org.sbml.libsbml.ModelCreator
-
Predicate returning
true
or
false
depending on whether this
ModelCreator
's 'given name' part is set.
- isSetGlyphId() - Method in class org.sbml.libsbml.ReferenceGlyph
-
- isSetGraphicalObjectId() - Method in class org.sbml.libsbml.TextGlyph
-
- isSetHasOnlySubstanceUnits() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'hasOnlySubstanceUnits' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node has the mathml attribute
id
.
- isSetId() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true
if this
Compartment
's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.CompartmentType
-
- isSetId() - Method in class org.sbml.libsbml.Event
-
Predicate returning
true
if this
Event
's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.FunctionDefinition
-
- isSetId() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true
if this
Model
's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.Parameter
-
Predicate returning
true
if this
Parameter
's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.Reaction
-
Predicate returning
true
if this
Reaction
's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
- isSetId() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.SpeciesType
-
Predicate returning
true
if this
SpeciesType
's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.UnitDefinition
-
Predicate returning
true
if this
UnitDefinition
's 'id' attribute is set.
- isSetIdRef() - Method in class org.sbml.libsbml.SBaseRef
-
- isSetInitialAmount() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'initialAmount' attribute is set.
- isSetInitialConcentration() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'initialConcentration' attribute is set.
- isSetInitialValue() - Method in class org.sbml.libsbml.Trigger
-
(SBML Level 3 only) Predicate to test whether the 'initialValue'
attribute for this trigger is set.
- isSetKind() - Method in class org.sbml.libsbml.Unit
-
Predicate to test whether the 'kind' attribute of this
Unit
is set.
- isSetKineticLaw() - Method in class org.sbml.libsbml.Reaction
-
Predicate returning
true
if this
Reaction
contains a kinetic law object.
- isSetLengthUnits() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true
if this
Model
's 'lengthUnits' attribute is set.
- isSetMath() - Method in class org.sbml.libsbml.Constraint
-
Predicate returning
true
if a
mathematical formula is defined for this
Constraint
.
- isSetMath() - Method in class org.sbml.libsbml.Delay
-
Predicate to test whether the formula for this delay is set.
- isSetMath() - Method in class org.sbml.libsbml.EventAssignment
-
Predicate for testing whether the 'math' subelement of this
EventAssignment
is set.
- isSetMath() - Method in class org.sbml.libsbml.FunctionDefinition
-
- isSetMath() - Method in class org.sbml.libsbml.InitialAssignment
-
Predicate returning
true
if this
InitialAssignment
's 'math' subelement contains a value.
- isSetMath() - Method in class org.sbml.libsbml.KineticLaw
-
Predicate returning true
if this
Kinetic's 'math' subelement is set.
- isSetMath() - Method in class org.sbml.libsbml.Priority
-
Predicate to test whether the formula for this delay is set.
- isSetMath() - Method in class org.sbml.libsbml.Rule
-
Predicate returning
true
if this
Rule
's mathematical expression is set.
- isSetMath() - Method in class org.sbml.libsbml.StoichiometryMath
-
- isSetMath() - Method in class org.sbml.libsbml.Trigger
-
Predicate to test whether the math for this trigger is set.
- isSetMd5() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- isSetMessage() - Method in class org.sbml.libsbml.Constraint
-
Predicate returning
true
if a
message is defined for this
Constraint
.
- isSetMetaId() - Method in class org.sbml.libsbml.SBase
-
Predicate returning true
if this object's 'metaid' attribute is set.
- isSetMetaIdRef() - Method in class org.sbml.libsbml.GraphicalObject
-
- isSetMetaIdRef() - Method in class org.sbml.libsbml.SBaseRef
-
- isSetModelHistory() - Method in class org.sbml.libsbml.SBase
-
Predicate returning
true
if this
object has a
ModelHistory
object attached to it.
- isSetModelRef() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- isSetModelRef() - Method in class org.sbml.libsbml.Submodel
-
- isSetModifiedDate() - Method in class org.sbml.libsbml.ModelHistory
-
Predicate returning
true
or
false
depending on whether this
ModelHistory
's 'modified date' is set.
- isSetMultiplier() - Method in class org.sbml.libsbml.Unit
-
Predicate to test whether the 'multiplier' attribute of this
Unit
is set.
- isSetName() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true
if this
Compartment
's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.CompartmentType
-
Predicate returning
true
if this
CompartmentType
's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.Event
-
Predicate returning
true
if this
Event
's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.FunctionDefinition
-
- isSetName() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true
if this
Model
's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.Parameter
-
Predicate returning
true
if this
Parameter
's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.Reaction
-
Predicate returning
true
if this
Reaction
's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
- isSetName() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.SpeciesType
-
Predicate returning
true
if this
SpeciesType
's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.UnitDefinition
-
Predicate returning
true
if this
UnitDefinition
's 'name' attribute is set.
- isSetNotes() - Method in class org.sbml.libsbml.SBase
-
Predicate returning true
if this
object's 'notes' subelement exists and has content.
- isSetOperation() - Method in class org.sbml.libsbml.FluxBound
-
- isSetOrganisation() - Method in class org.sbml.libsbml.ModelCreator
-
(Alternate spelling) Predicate returning
true
or
false
depending
on whether this
ModelCreator
's 'organization' part is set.
- isSetOrganization() - Method in class org.sbml.libsbml.ModelCreator
-
Predicate returning
true
or
false
depending on whether this
ModelCreator
's 'organization' part is set.
- isSetOriginOfTextId() - Method in class org.sbml.libsbml.TextGlyph
-
- isSetOutside() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true
if this
Compartment
's 'outside' attribute is set.
- isSetPackageRequired(String) - Method in class org.sbml.libsbml.SBMLDocument
-
Returns true
if the required attribute of the given package extension
is defined, otherwise returns false.
- isSetPersistent() - Method in class org.sbml.libsbml.Trigger
-
(SBML Level 3 only) Predicate to test whether the 'persistent'
attribute for this trigger is set.
- isSetPortRef() - Method in class org.sbml.libsbml.SBaseRef
-
- isSetPriority() - Method in class org.sbml.libsbml.Event
-
(SBML Level 3 only) Predicate for testing whether the priority
for this
Event
is set.
- isSetReaction() - Method in class org.sbml.libsbml.FluxBound
-
- isSetReaction() - Method in class org.sbml.libsbml.FluxObjective
-
- isSetReaction() - Method in class org.sbml.libsbml.GeneAssociation
-
- isSetReactionId() - Method in class org.sbml.libsbml.ReactionGlyph
-
- isSetReference() - Method in class org.sbml.libsbml.Association
-
- isSetReferenceId() - Method in class org.sbml.libsbml.GeneralGlyph
-
- isSetReferenceId() - Method in class org.sbml.libsbml.ReferenceGlyph
-
- isSetReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
-
- isSetRequired() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
-
Predicate returning
true
or
false
depending on whether this
SBMLDocumentPlugin
's 'required' attribute has been set.
- isSetReversible() - Method in class org.sbml.libsbml.Reaction
-
Predicate returning
true
if this
Reaction
's 'reversible' attribute is set.
- isSetRole() - Method in class org.sbml.libsbml.ReferenceGlyph
-
- isSetRole() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- isSetSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
-
- isSetSBOTerm() - Method in class org.sbml.libsbml.SBase
-
Predicate returning true
if this
object's 'sboTerm' attribute is set.
- isSetScale() - Method in class org.sbml.libsbml.Unit
-
Predicate to test whether the 'scale' attribute of this
Unit
is set.
- isSetSize() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true
if this
Compartment
's 'size' attribute is set.
- isSetSource() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- isSetSpatialDimensions() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true
if this
Compartment
's 'spatialDimensions' attribute is set.
- isSetSpatialSizeUnits() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'spatialSizeUnits' attribute is set.
- isSetSpecies() - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
- isSetSpeciesGlyphId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- isSetSpeciesId() - Method in class org.sbml.libsbml.SpeciesGlyph
-
- isSetSpeciesReferenceId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- isSetSpeciesType() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's
'speciesType' attribute is set.
- isSetStoichiometry() - Method in class org.sbml.libsbml.SpeciesReference
-
Predicate returning
true
if this
SpeciesReference
's 'stoichiometry' attribute is set.
- isSetStoichiometryMath() - Method in class org.sbml.libsbml.SpeciesReference
-
Predicate returning
true
if this
SpeciesReference
's 'stoichiometryMath' subelement is set
- isSetStyle() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node has the mathml attribute
style
.
- isSetSubmodelRef() - Method in class org.sbml.libsbml.Replacing
-
- isSetSubstanceConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
- isSetSubstanceUnits() - Method in class org.sbml.libsbml.KineticLaw
-
(SBML Level 2 Version 1 only) Predicate returning
true
if
this
SpeciesReference
's 'substanceUnits' attribute is set.
- isSetSubstanceUnits() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true
if this
Model
's 'substanceUnits' attribute is set.
- isSetSubstanceUnits() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if this
Species
object's 'substanceUnits' attribute is set.
- isSetSymbol() - Method in class org.sbml.libsbml.InitialAssignment
-
- isSetText() - Method in class org.sbml.libsbml.TextGlyph
-
- isSetTimeConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
- isSetTimeUnits() - Method in class org.sbml.libsbml.Event
-
Predicate for testing whether the 'timeUnits' attribute of this
Event
is set.
- isSetTimeUnits() - Method in class org.sbml.libsbml.KineticLaw
-
(SBML Level 2 Version 1 only) Predicate returning
true
if
this
SpeciesReference
's 'timeUnits' attribute is set.
- isSetTimeUnits() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true
if this
Model
's 'timeUnits' attribute is set.
- isSetTrigger() - Method in class org.sbml.libsbml.Event
-
Predicate for testing whether the trigger for this
Event
is set.
- isSetType() - Method in class org.sbml.libsbml.Association
-
- isSetType() - Method in class org.sbml.libsbml.Objective
-
- isSetUnitRef() - Method in class org.sbml.libsbml.SBaseRef
-
- isSetUnits() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node has the attribute
sbml:units
.
- isSetUnits() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true
if this
Compartment
's 'units' attribute is set.
- isSetUnits() - Method in class org.sbml.libsbml.Parameter
-
Predicate returning
true
if the
'units' attribute of this
Parameter
is set.
- isSetUnits() - Method in class org.sbml.libsbml.Rule
-
Predicate returning
true
if this
Rule
's 'units' attribute is set.
- isSetUnits() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true
if
this
Species
object's 'units' attribute is set.
- isSetUseValuesFromTriggerTime() - Method in class org.sbml.libsbml.Event
-
Predicate for testing whether the 'useValuesFromTriggerTime' attribute of this
Event
is set.
- isSetValue() - Method in class org.sbml.libsbml.FluxBound
-
- isSetValue() - Method in class org.sbml.libsbml.Parameter
-
Predicate returning
true
if the
'value' attribute of this
Parameter
is set.
- isSetVariable() - Method in class org.sbml.libsbml.EventAssignment
-
Predicate for testing whether the attribute 'variable' of this
EventAssignment
is set.
- isSetVariable() - Method in class org.sbml.libsbml.Rule
-
Predicate returning
true
if this
Rule
's 'variable' attribute is set.
- isSetVolume() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true
if this
Compartment
's
'volume' attribute is set.
- isSetVolumeUnits() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true
if this
Model
's 'volumeUnits' attribute is set.
- isSiemens() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
siemens
- isSievert() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
sievert
- isSpeciesConcentration() - Method in class org.sbml.libsbml.Rule
-
Predicate returning
true
if this
Rule
is a
SpeciesConcentrationRule or equivalent.
- isSqrt() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node represents a
square root function, false
(zero) otherwise.
- isStart() - Method in class org.sbml.libsbml.XMLToken
-
Predicate returning
true
or
false
depending on whether
this
XMLToken
is an XML start element.
- isSteadyStateExpression(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isSteradian() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
steradian
- isSystem() - Method in class org.sbml.libsbml.XMLError
-
Predicate returning true
or false
depending on whether this
error was generated by the operating system.
- isSystemsDescriptionParameter(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true
if the given term identifier comes from the stated branch of SBO.
- isTesla() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
tesla
- isText() - Method in class org.sbml.libsbml.XMLToken
-
Predicate returning
true
or
false
depending on whether
this
XMLToken
is an XML text element.
- isUMinus() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node is a unary minus
operator, false
(zero) otherwise.
- isUnitKind(String, long, long) - Static method in class org.sbml.libsbml.Unit
-
Predicate to test whether a given string is the name of a valid
base unit in SBML (such as 'gram'
or 'mole'
).
- isUnknown() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node has an unknown type.
- isUPlus() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning true
(non-zero) if this node is a unary plus
operator, false
(zero) otherwise.
- isValid() - Method in class org.sbml.libsbml.XMLError
-
Predicate returning true
or false
depending on whether this
error resulted from a problem or whether it was logged as an unknown
error.
- isValidCombination() - Method in class org.sbml.libsbml.SBMLNamespaces
-
Predicate returning true
if the given
set of namespaces represent a valid set
- isValidSBMLSId(String) - Static method in class org.sbml.libsbml.SyntaxChecker
-
Returns true true
or false
depending on whether the argument
string conforms to the syntax of SBML identifiers.
- isValidUnitSId(String) - Static method in class org.sbml.libsbml.SyntaxChecker
-
Returns true
or false
depending on whether the argument string
conforms to the syntax of SBML unit identifiers.
- isValidXMLID(String) - Static method in class org.sbml.libsbml.SyntaxChecker
-
Returns true
or false
depending on whether the argument string
conforms to the XML data type ID
.
- isVariantOfArea() - Method in class org.sbml.libsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier 'area'.
- isVariantOfDimensionless() - Method in class org.sbml.libsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a
variant of the unit 'dimensionless'.
- isVariantOfLength() - Method in class org.sbml.libsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier 'length'.
- isVariantOfMass() - Method in class org.sbml.libsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier 'mass'.
- isVariantOfSubstance() - Method in class org.sbml.libsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier 'substance'.
- isVariantOfSubstancePerTime() - Method in class org.sbml.libsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a
variant of the predefined unit 'substance'
divided by the predefined
unit 'time'.
- isVariantOfTime() - Method in class org.sbml.libsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier 'time'.
- isVariantOfVolume() - Method in class org.sbml.libsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a
variant of the predefined unit identifier 'volume'.
- isVolt() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
volt
- isWarning() - Method in class org.sbml.libsbml.XMLError
-
Predicate returning true
or false
depending on whether
this error object is a warning.
- isWatt() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
watt
- isWeber() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit
is of the kind
weber
- isWellFormedASTNode() - Method in class org.sbml.libsbml.ASTNode
-
Predicate returning
true
or
false
depending on whether this
ASTNode
is well-formed.
- isXML() - Method in class org.sbml.libsbml.XMLError
-
Predicate returning true
or false
depending on whether this
error resulted from a problem in the XML input (e.g., an XML syntax
error).