- DanglingUnitReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DanglingUnitSIdRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- Date - Class in org.sbml.libsbml
-
A MIRIAM-compliant date representation.
- 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
-
Class for managing lists of
Date objects.
- DateList() - Constructor for class org.sbml.libsbml.DateList
-
Explicit constructor for this list.
- deepCopy() - Method in class org.sbml.libsbml.ASTNode
-
Creates a recursive copy of this node and all its children.
- DefaultTerm - Class in org.sbml.libsbml
-
- DefaultTerm(long, long, long) - Constructor for class org.sbml.libsbml.DefaultTerm
-
Creates a new
DefaultTerm with the given level, version, and package version.
- DefaultTerm(long, long) - Constructor for class org.sbml.libsbml.DefaultTerm
-
Creates a new
DefaultTerm with the given level, version, and package version.
- DefaultTerm(long) - Constructor for class org.sbml.libsbml.DefaultTerm
-
Creates a new
DefaultTerm with the given level, version, and package version.
- DefaultTerm() - Constructor for class org.sbml.libsbml.DefaultTerm
-
Creates a new
DefaultTerm with the given level, version, and package version.
- DefaultTerm(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.DefaultTerm
-
- DefaultTerm(DefaultTerm) - Constructor for class org.sbml.libsbml.DefaultTerm
-
- DefaultValues - Class in org.sbml.libsbml
-
render
Encoding of default values.
- DefaultValues(long, long, long) - Constructor for class org.sbml.libsbml.DefaultValues
-
Creates a
DefaultValues object using the given SBML Level, Version and
“render” package version.
- DefaultValues(long, long) - Constructor for class org.sbml.libsbml.DefaultValues
-
Creates a
DefaultValues object using the given SBML Level, Version and
“render” package version.
- DefaultValues(long) - Constructor for class org.sbml.libsbml.DefaultValues
-
Creates a
DefaultValues object using the given SBML Level, Version and
“render” package version.
- DefaultValues() - Constructor for class org.sbml.libsbml.DefaultValues
-
Creates a
DefaultValues object using the given SBML Level, Version and
“render” package version.
- DefaultValues(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.DefaultValues
-
- DefaultValues(DefaultValues) - Constructor for class org.sbml.libsbml.DefaultValues
-
- DefinitionURLRegistry - Class in org.sbml.libsbml
-
Registry of all libSBML SBML DefinitionURLs.
- del(String) - Method in class org.sbml.libsbml.StringSet
-
- Delay - Class in org.sbml.libsbml
-
A delay on the time of execution of an SBML 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
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DelayUnitsNotTime - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- 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.ASTNodeValues_t
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.BindingSiteSpeciesType
-
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.Callback
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.CobraToFbcConverter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ColorDefinition
-
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.CompartmentReference
-
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.CompFlatteningConverter
-
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.DefaultTerm
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.DefaultValues
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.DefinitionURLRegistry
-
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.double_array
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ElementFilter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Ellipse
-
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.FbcAnd
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FbcAssociation
-
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.FbcOr
-
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.FbcReactionPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FbcSBMLDocumentPlugin
-
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.FbcToCobraConverter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FbcV1ToV2Converter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.FbcV2ToV1Converter
-
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.FunctionTerm
-
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.GeneProduct
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GeneProductAssociation
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GeneProductRef
-
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.GlobalRenderInformation
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GlobalStyle
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GradientBase
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GradientStop
-
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.GraphicalPrimitive1D
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Group
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GroupsExtension
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GroupsModelPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.GroupsPkgNamespaces
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Image
-
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.Input
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.int_array
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.IntraSpeciesReaction
-
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.LinearGradient
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.LineEnding
-
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.ListOfColorDefinitions
-
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.ListOfCompartmentReferences
-
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.ListOfCurveElements
-
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.ListOfDrawables
-
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.ListOfFbcAssociations
-
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.ListOfFunctionTerms
-
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.ListOfGeneProducts
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfGlobalStyles
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfGradientDefinitions
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfGradientStops
-
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.ListOfGroups
-
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.ListOfInputs
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfInSpeciesTypeBonds
-
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.ListOfLineEndings
-
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.ListOfLocalRenderInformation
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfLocalStyles
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfMembers
-
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.ListOfMultiSpeciesTypes
-
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.ListOfOutputs
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfOutwardBindingSites
-
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.ListOfPossibleSpeciesFeatureValues
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
-
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.ListOfSpeciesFeatures
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfSpeciesFeatureTypes
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfSpeciesFeatureValues
-
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.ListOfSpeciesTypeComponentIndexes
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentMapInProducts
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.ListOfSpeciesTypeInstances
-
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.ListOfTransitions
-
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.LocalRenderInformation
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.LocalStyle
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Member
-
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.MultiASTPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.MultiExtension
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.MultiListOfReactionsPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.MultiModelPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.MultiPkgNamespaces
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.MultiSBMLDocumentPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.MultiSimpleSpeciesReferencePlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.MultiSpeciesReferencePlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.MultiSpeciesType
-
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.Output
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.OutwardBindingSite
-
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.Polygon
-
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.PossibleSpeciesFeatureValue
-
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.QualExtension
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.QualitativeSpecies
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.QualModelPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.QualPkgNamespaces
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RadialGradient
-
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.Rectangle
-
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.RelAbsVector
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RenderCubicBezier
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RenderCurve
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RenderExtension
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RenderGraphicalObjectPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RenderGroup
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RenderInformationBase
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RenderLayoutPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RenderPkgNamespaces
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.RenderPoint
-
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.SBMLExtension
-
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.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.SBMLIdConverter
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SBMLInferUnitsConverter
-
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.SBMLLevel1Version1Converter
-
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.SBMLLocalParameterConverter
-
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.SBMLReactionConverter
-
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.SpeciesFeature
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SpeciesFeatureValue
-
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.SpeciesTypeComponentIndex
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
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.StringSet
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Style
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
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.Text
-
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.Transformation
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Transformation2D
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.Transition
-
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.XMLInputStream
-
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.XMLOutputStream
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.XMLOwningOutputFileStream
-
Explicitly deletes the underlying native object.
- delete() - Method in class org.sbml.libsbml.XMLOwningOutputStringStream
-
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.
- deleteDisabledPlugins(boolean) - Method in class org.sbml.libsbml.SBase
-
Deletes all information stored in disabled plugins.
- deleteDisabledPlugins() - Method in class org.sbml.libsbml.SBase
-
Deletes all information stored in disabled plugins.
- deleteLayoutAnnotation(XMLNode) - Static method in class org.sbml.libsbml.libsbml
-
Takes an
XMLNode and tries to find the layout annotation node and deletes it if it was found.
- deleteLayoutIdAnnotation(XMLNode) - Static method in class org.sbml.libsbml.libsbml
-
Takes an
XMLNode and tries to find the layoutId annotation node and deletes it if it was found.
- 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.
- deleteResolerRegistryInstance() - Static method in class org.sbml.libsbml.SBMLResolverRegistry
-
deletes the static resolver registry instance
- Deletion - Class in org.sbml.libsbml
-
comp
Deletion of an object from a submodel.
- Deletion(long, long, long) - Constructor for class org.sbml.libsbml.Deletion
-
Creates a new
Deletion with the given level, version, and package version.
- Deletion(long, long) - Constructor for class org.sbml.libsbml.Deletion
-
Creates a new
Deletion with the given level, version, and package version.
- Deletion(long) - Constructor for class org.sbml.libsbml.Deletion
-
Creates a new
Deletion with the given level, version, and package version.
- Deletion() - Constructor for class org.sbml.libsbml.Deletion
-
Creates a new
Deletion with the given level, version, and package version.
- Deletion(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.Deletion
-
- Deletion(Deletion) - Constructor for class org.sbml.libsbml.Deletion
-
Copy constructor.
- depth() - Method in class org.sbml.libsbml.BoundingBox
-
Get the depth of the bounding box.
- depth() - Method in class org.sbml.libsbml.Dimensions
-
Returns the depth.
- determineNumberChildren(String) - Method in class org.sbml.libsbml.XMLInputStream
-
Returns the number of child tokens of the given element in this stream.
- determineNumberChildren() - Method in class org.sbml.libsbml.XMLInputStream
-
Returns the number of child tokens of the given element in this stream.
- determineNumSpecificChildren(String, String) - Method in class org.sbml.libsbml.XMLInputStream
-
Returns the number of child tokens of the specified type within a
given container element.
- Dimensions - Class in org.sbml.libsbml
-
layout
Spatial dimensions of a 2D or 3D shape.
- Dimensions(long, long, long) - Constructor for class org.sbml.libsbml.Dimensions
-
Creates a new
Dimensions object with the given level, version, and package version
and with all sizes set to 0.0.
- Dimensions(long, long) - Constructor for class org.sbml.libsbml.Dimensions
-
Creates a new
Dimensions object with the given level, version, and package version
and with all sizes set to 0.0.
- Dimensions(long) - Constructor for class org.sbml.libsbml.Dimensions
-
Creates a new
Dimensions object with the given level, version, and package version
and with all sizes set to 0.0.
- Dimensions() - Constructor for class org.sbml.libsbml.Dimensions
-
Creates a new
Dimensions object with the given level, version, and package version
and with all sizes set to 0.0.
- Dimensions(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.Dimensions
-
- Dimensions(Dimensions) - Constructor for class org.sbml.libsbml.Dimensions
-
Copy constructor.
- Dimensions(LayoutPkgNamespaces, double, double, double) - Constructor for class org.sbml.libsbml.Dimensions
-
Creates a new
Dimensions object with the given sizes.
- Dimensions(LayoutPkgNamespaces, double, double) - Constructor for class org.sbml.libsbml.Dimensions
-
Creates a new
Dimensions object with the given sizes.
- 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 on this object.
- disablePackage(String) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Disables the package with the given URI or name.
- disableUnusedPackages(SBMLDocument) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Disables unused packages.
- DisallowedDefinitionURLUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DisallowedMathMLEncodingUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DisallowedMathMLSymbol - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DisallowedMathTypeAttributeUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DisallowedMathTypeAttributeValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DisallowedMathUnitsUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- divide(UnitDefinition, UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
-
- double_array - Class in org.sbml.libsbml
-
- double_array(int) - Constructor for class org.sbml.libsbml.double_array
-
- DoubleExponentNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DowncastASTBasePlugin(long, boolean) - Static method in class org.sbml.libsbml.libsbml
-
- DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.GroupsExtension
-
- DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.MultiExtension
-
- DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.RenderExtension
-
- DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.GroupsExtension
-
- DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.MultiExtension
-
- DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.RenderExtension
-
- downIndent() - Method in class org.sbml.libsbml.XMLOutputStream
-
- DuplicateAnnotationInvalidInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DuplicateAnnotationInvalidInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DuplicateAnnotationInvalidInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DuplicateAnnotationInvalidInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DuplicateAnnotationNamespaces - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DuplicateComponentId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DuplicateLocalParameterId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DuplicateMetaId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DuplicateUnitDefinitionId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- DuplicateXMLAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the error and warning codes
returned by the XML layer in libSBML.
- GENE_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible Association types.
- GeneAssociation - Class in org.sbml.libsbml
-
fbc
Annotation helper class for “fbc” Version 1.
- GeneAssociation(long, long, long) - Constructor for class org.sbml.libsbml.GeneAssociation
-
Creates a new
GeneAssociation with the given
level,
version, and
pkgVersion.
- GeneAssociation(long, long) - Constructor for class org.sbml.libsbml.GeneAssociation
-
Creates a new
GeneAssociation with the given
level,
version, and
pkgVersion.
- GeneAssociation(long) - Constructor for class org.sbml.libsbml.GeneAssociation
-
Creates a new
GeneAssociation with the given
level,
version, and
pkgVersion.
- GeneAssociation() - Constructor for class org.sbml.libsbml.GeneAssociation
-
Creates a new
GeneAssociation with the given
level,
version, and
pkgVersion.
- 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
-
Copy constructor.
- GeneProduct - Class in org.sbml.libsbml
-
- GeneProduct(long, long, long) - Constructor for class org.sbml.libsbml.GeneProduct
-
Creates a new
GeneProduct with the given SBML Level, Version, and
“fbc”package version.
- GeneProduct(long, long) - Constructor for class org.sbml.libsbml.GeneProduct
-
Creates a new
GeneProduct with the given SBML Level, Version, and
“fbc”package version.
- GeneProduct(long) - Constructor for class org.sbml.libsbml.GeneProduct
-
Creates a new
GeneProduct with the given SBML Level, Version, and
“fbc”package version.
- GeneProduct() - Constructor for class org.sbml.libsbml.GeneProduct
-
Creates a new
GeneProduct with the given SBML Level, Version, and
“fbc”package version.
- GeneProduct(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneProduct
-
- GeneProduct(GeneProduct) - Constructor for class org.sbml.libsbml.GeneProduct
-
- GeneProductAssociation - Class in org.sbml.libsbml
-
- GeneProductAssociation(long, long, long) - Constructor for class org.sbml.libsbml.GeneProductAssociation
-
- GeneProductAssociation(long, long) - Constructor for class org.sbml.libsbml.GeneProductAssociation
-
- GeneProductAssociation(long) - Constructor for class org.sbml.libsbml.GeneProductAssociation
-
- GeneProductAssociation() - Constructor for class org.sbml.libsbml.GeneProductAssociation
-
- GeneProductAssociation(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneProductAssociation
-
- GeneProductAssociation(GeneProductAssociation) - Constructor for class org.sbml.libsbml.GeneProductAssociation
-
- GeneProductRef - Class in org.sbml.libsbml
-
fbc
Reference to a gene product of a reaction
- GeneProductRef(long, long, long) - Constructor for class org.sbml.libsbml.GeneProductRef
-
Creates a new
GeneProductRef with the given SBML Level, Version, and
“fbc”package version.
- GeneProductRef(long, long) - Constructor for class org.sbml.libsbml.GeneProductRef
-
Creates a new
GeneProductRef with the given SBML Level, Version, and
“fbc”package version.
- GeneProductRef(long) - Constructor for class org.sbml.libsbml.GeneProductRef
-
Creates a new
GeneProductRef with the given SBML Level, Version, and
“fbc”package version.
- GeneProductRef() - Constructor for class org.sbml.libsbml.GeneProductRef
-
Creates a new
GeneProductRef with the given SBML Level, Version, and
“fbc”package version.
- GeneProductRef(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneProductRef
-
- GeneProductRef(GeneProductRef) - Constructor for class org.sbml.libsbml.GeneProductRef
-
- GeneralGlyph - Class in org.sbml.libsbml
-
layout
A glyph for miscellaneous items.
- 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
-
Creates a glyph with the given
LayoutPkgNamespaces, id and set the id of the
associated element to the second argument.
- 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
-
Copy constructor.
- GeneralWarningNotSpecified - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- get(long) - Method in class org.sbml.libsbml.ASTNodeList
-
Returns the nth ASTNode object from this list.
- get(long) - Method in class org.sbml.libsbml.CVTermList
-
Returns the nth CVTerm object from this list.
- get(long) - Method in class org.sbml.libsbml.DateList
-
Returns the nth Date object from this list.
- get(long) - Method in class org.sbml.libsbml.ListOf
-
Get an item from the list.
- get(long) - Method in class org.sbml.libsbml.ListOfColorDefinitions
-
- get(String) - Method in class org.sbml.libsbml.ListOfColorDefinitions
-
- get(long) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
- get(String) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
- get(long) - Method in class org.sbml.libsbml.ListOfCompartmentReferences
-
- get(String) - Method in class org.sbml.libsbml.ListOfCompartmentReferences
-
- 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.ListOfCurveElements
-
- get(String) - Method in class org.sbml.libsbml.ListOfCurveElements
-
- get(long) - Method in class org.sbml.libsbml.ListOfDeletions
-
- get(String) - Method in class org.sbml.libsbml.ListOfDeletions
-
- get(long) - Method in class org.sbml.libsbml.ListOfDrawables
-
- get(String) - Method in class org.sbml.libsbml.ListOfDrawables
-
- 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(String) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
-
- get(long) - Method in class org.sbml.libsbml.ListOfFbcAssociations
-
- get(String) - Method in class org.sbml.libsbml.ListOfFbcAssociations
-
- get(long) - Method in class org.sbml.libsbml.ListOfFluxBounds
-
- get(String) - Method in class org.sbml.libsbml.ListOfFluxBounds
-
- get(long) - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
- get(String) - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
- 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.ListOfFunctionTerms
-
- get(String) - Method in class org.sbml.libsbml.ListOfFunctionTerms
-
- get(long) - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
- get(String) - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
- get(long) - Method in class org.sbml.libsbml.ListOfGeneProducts
-
- get(String) - Method in class org.sbml.libsbml.ListOfGeneProducts
-
- get(long) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- get(String) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- get(long) - Method in class org.sbml.libsbml.ListOfGlobalStyles
-
- get(String) - Method in class org.sbml.libsbml.ListOfGlobalStyles
-
- get(long) - Method in class org.sbml.libsbml.ListOfGradientDefinitions
-
- get(String) - Method in class org.sbml.libsbml.ListOfGradientDefinitions
-
- get(long) - Method in class org.sbml.libsbml.ListOfGradientStops
-
- get(String) - Method in class org.sbml.libsbml.ListOfGradientStops
-
- get(long) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
- get(String) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
- get(long) - Method in class org.sbml.libsbml.ListOfGroups
-
- get(String) - Method in class org.sbml.libsbml.ListOfGroups
-
- 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.ListOfInputs
-
- get(String) - Method in class org.sbml.libsbml.ListOfInputs
-
- get(long) - Method in class org.sbml.libsbml.ListOfInSpeciesTypeBonds
-
- get(String) - Method in class org.sbml.libsbml.ListOfInSpeciesTypeBonds
-
- get(long) - Method in class org.sbml.libsbml.ListOfLayouts
-
- get(String) - Method in class org.sbml.libsbml.ListOfLayouts
-
- get(long) - Method in class org.sbml.libsbml.ListOfLineEndings
-
- get(String) - Method in class org.sbml.libsbml.ListOfLineEndings
-
- get(long) - Method in class org.sbml.libsbml.ListOfLineSegments
-
- 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.ListOfLocalRenderInformation
-
- get(String) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- get(long) - Method in class org.sbml.libsbml.ListOfLocalStyles
-
- get(String) - Method in class org.sbml.libsbml.ListOfLocalStyles
-
- get(long) - Method in class org.sbml.libsbml.ListOfMembers
-
- get(String) - Method in class org.sbml.libsbml.ListOfMembers
-
- get(long) - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
- get(String) - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
- get(long) - Method in class org.sbml.libsbml.ListOfMultiSpeciesTypes
-
- get(String) - Method in class org.sbml.libsbml.ListOfMultiSpeciesTypes
-
- get(long) - Method in class org.sbml.libsbml.ListOfObjectives
-
- get(String) - Method in class org.sbml.libsbml.ListOfObjectives
-
- get(long) - Method in class org.sbml.libsbml.ListOfOutputs
-
- get(String) - Method in class org.sbml.libsbml.ListOfOutputs
-
- get(long) - Method in class org.sbml.libsbml.ListOfOutwardBindingSites
-
- get(String) - Method in class org.sbml.libsbml.ListOfOutwardBindingSites
-
- 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(String) - Method in class org.sbml.libsbml.ListOfPorts
-
- get(long) - Method in class org.sbml.libsbml.ListOfPossibleSpeciesFeatureValues
-
- get(String) - Method in class org.sbml.libsbml.ListOfPossibleSpeciesFeatureValues
-
- get(long) - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
-
- get(String) - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
-
- get(long) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
- get(String) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
- 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(String) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
-
- get(long) - Method in class org.sbml.libsbml.ListOfReplacedElements
-
- 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.ListOfSpeciesFeatures
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
- get(long) - Method in class org.sbml.libsbml.ListOfSpeciesFeatureTypes
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesFeatureTypes
-
- get(long) - Method in class org.sbml.libsbml.ListOfSpeciesFeatureValues
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesFeatureValues
-
- get(long) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
-
- get(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
- 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.ListOfSpeciesTypeComponentIndexes
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentIndexes
-
- get(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentMapInProducts
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentMapInProducts
-
- get(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypeInstances
-
- get(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypeInstances
-
- 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(String) - Method in class org.sbml.libsbml.ListOfSubmodels
-
- get(long) - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
- get(String) - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
- get(long) - Method in class org.sbml.libsbml.ListOfTransitions
-
- get(String) - Method in class org.sbml.libsbml.ListOfTransitions
-
- 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
-
Returns the nth ModelCreator object from this list.
- get(long) - Method in class org.sbml.libsbml.SBaseList
-
Returns the nth SBase object from this list.
- get(long) - Method in class org.sbml.libsbml.SBMLNamespacesList
-
Returns the nth SBMLNamespaces object from this list.
- get(String) - Method in class org.sbml.libsbml.StringSet
-
- get(long) - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- get(String) - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- get_ostream() - Method in class org.sbml.libsbml.OStream
-
Returns the stream object.
- getAbsoluteValue() - Method in class org.sbml.libsbml.RelAbsVector
-
Returns the absolute coordinate value.
- getActiveObjective() - Method in class org.sbml.libsbml.FbcModelPlugin
-
Returns the current active objective.
- getActiveObjective() - Method in class org.sbml.libsbml.ListOfObjectives
-
- getActiveObjectiveId() - Method in class org.sbml.libsbml.FbcModelPlugin
-
Returns the id of the current active objective.
- getAddDefaultUnits() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
-
Returns the flag indicating whether default units should be added when
converting to L3 or not.
- getAdditionalGraphicalObject(long) - Method in class org.sbml.libsbml.Layout
-
Returns the additional graphical object with the given index.
- getAdditionalGraphicalObject(String) - Method in class org.sbml.libsbml.Layout
-
Returns the additional graphical object that has the given id, or null
if no graphical object has the id.
- getAllElementIdList() - Method in class org.sbml.libsbml.Model
-
Returns the internal list of the identifiers of all elements within this
Model object.
- getAllElementMetaIdList() - Method in class org.sbml.libsbml.Model
-
Returns the internal list of the metaids of all elements within this
Model object.
- getAllowedChildrenType() - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- getAllRegisteredPackageNames() - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Returns a list of registered packages.
- getAlpha() - Method in class org.sbml.libsbml.ColorDefinition
-
Returns the alpha color component.
- getAncestorOfType(int, String) - Method in class org.sbml.libsbml.SBase
-
Returns the first ancestor object that has the given SBML type code from the given package.
- getAncestorOfType(int) - Method in class org.sbml.libsbml.SBase
-
Returns the first ancestor object that has the given SBML type code from the given package.
- 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 nth argument to this function.
- getArgument(String) - Method in class org.sbml.libsbml.FunctionDefinition
-
- getAssignmentRule(String) - Method in class org.sbml.libsbml.Model
-
Get a
Rule object based on the variable to which it assigns a value.
- getAssignmentRuleByVariable(String) - Method in class org.sbml.libsbml.Model
-
Get a
Rule object based on the variable to which it assigns a value.
- getAssociatedSpecies() - Method in class org.sbml.libsbml.GeneProduct
-
Returns the value of the 'associatedSpecies' attribute of this
GeneProduct.
- getAssociation(long) - Method in class org.sbml.libsbml.FbcAnd
-
- getAssociation(String) - Method in class org.sbml.libsbml.FbcAnd
-
- getAssociation(long) - Method in class org.sbml.libsbml.FbcOr
-
- getAssociation(String) - Method in class org.sbml.libsbml.FbcOr
-
- getAssociation() - Method in class org.sbml.libsbml.GeneAssociation
-
- getAssociation() - Method in class org.sbml.libsbml.GeneProductAssociation
-
- getASTPlugin(SBMLNamespaces) - Method in class org.sbml.libsbml.ASTNode
-
- getASTPlugin(int) - Method in class org.sbml.libsbml.ASTNode
-
- getASTPlugin(String, boolean, boolean) - Method in class org.sbml.libsbml.ASTNode
-
- getASTPlugin(String, boolean) - Method in class org.sbml.libsbml.ASTNode
-
- getASTPlugin(String) - Method in class org.sbml.libsbml.ASTNode
-
- getASTPlugin(long) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
- getASTPlugins() - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
- getAttributes() - Method in class org.sbml.libsbml.XMLToken
-
Returns the attributes of the XML element represented by this token.
- getAttributesLength() - Method in class org.sbml.libsbml.XMLToken
-
Returns the number of attributes on this
XMLToken object.
- getAttrIndex(String, String) - Method in class org.sbml.libsbml.XMLToken
-
Returns the index of the attribute with the given name and namespace
URI.
- getAttrIndex(String) - Method in class org.sbml.libsbml.XMLToken
-
Returns the index of the attribute with the given name and namespace
URI.
- getAttrIndex(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
-
Returns the index of the attribute defined by the given
XMLTriple
object.
- getAttrName(int) - Method in class org.sbml.libsbml.XMLToken
-
Returns the name of the nth attribute in this token's list of
attributes.
- getAttrPrefix(int) - Method in class org.sbml.libsbml.XMLToken
-
Returns the prefix of the nth attribute in this token's list of
attributes.
- getAttrPrefixedName(int) - Method in class org.sbml.libsbml.XMLToken
-
Returns the prefixed name of the nth attribute in this token's
list of attributes.
- getAttrURI(int) - Method in class org.sbml.libsbml.XMLToken
-
Returns the XML namespace URI of the nth attribute in this
token's list of attributes.
- getAttrValue(int) - Method in class org.sbml.libsbml.XMLToken
-
Returns the value of the nth attribute in this token's list of
attributes.
- getAttrValue(String, String) - Method in class org.sbml.libsbml.XMLToken
-
Returns the value of the attribute with a given name and XML namespace URI.
- getAttrValue(String) - Method in class org.sbml.libsbml.XMLToken
-
Returns the value of the attribute with a given name and XML namespace URI.
- getAttrValue(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
-
Returns the value of the attribute specified by a given
XMLTriple object.
- getBackgroundColor() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'backgroundColor' attribute of this
DefaultValues object.
- getBackgroundColor() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getBasePoint1() - Method in class org.sbml.libsbml.CubicBezier
-
Returns the first base point of the curve (the one closer to the
starting point).
- getBasePoint1_x() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- getBasePoint1_y() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- getBasePoint1_z() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- getBasePoint2() - Method in class org.sbml.libsbml.CubicBezier
-
Returns the second base point of the curve (the one closer to the end
point).
- getBasePoint2_x() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- getBasePoint2_y() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- getBasePoint2_z() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- getBindingSite1() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- getBindingSite2() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- getBindingStatus() - Method in class org.sbml.libsbml.OutwardBindingSite
-
- getBiologicalQualifierType() - Method in class org.sbml.libsbml.CVTerm
-
Returns the biological qualifier type of this
CVTerm object.
- getBlue() - Method in class org.sbml.libsbml.ColorDefinition
-
Returns the blue color component.
- 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
-
- getBoundingBox() - Method in class org.sbml.libsbml.LineEnding
-
Returns the value of the 'boundingBox' element of this
LineEnding.
- getBoundingBoxExplicitlySet() - Method in class org.sbml.libsbml.GraphicalObject
-
- getByIdRef(String) - Method in class org.sbml.libsbml.ListOfMembers
-
- getBySpecies(String) - Method in class org.sbml.libsbml.ListOfInputs
-
Get a
Input from the
ListOfInputs
based on the qualitativeSpecies to which it refers.
- getBySpecies(String) - Method in class org.sbml.libsbml.ListOfOutputs
-
- 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.
- getCenterX() - Method in class org.sbml.libsbml.RadialGradient
-
Returns the x coordinate for the start point as a reference.
- getCenterY() - Method in class org.sbml.libsbml.RadialGradient
-
Returns the y coordinate for the start point as a reference.
- getCenterZ() - Method in class org.sbml.libsbml.RadialGradient
-
Returns the z coordinate for the start point as a reference.
- getCharacter() - Method in class org.sbml.libsbml.ASTNode
-
Gets the value of this node as a single character.
- getCharacters() - Method in class org.sbml.libsbml.XMLToken
-
Returns the character text of token.
- 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
-
Gets a child of this node according to its index number.
- getChild(long) - Method in class org.sbml.libsbml.XMLNode
-
Returns the
nth 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
-
Returns the value of the 'coefficient' attribute of this
FluxObjective.
- getColorDefinition(long) - Method in class org.sbml.libsbml.RenderInformationBase
-
- getColorDefinition(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- getColumn() - Method in class org.sbml.libsbml.SBase
-
Returns the column number where 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 number at which this token occurs in the input.
- getComparisonCaseSensitivity() - Method in class org.sbml.libsbml.L3ParserSettings
-
Returns true if the parser is configured to match built-in symbols
in a case-insensitive way.
- getCompartment() - Method in class org.sbml.libsbml.CompartmentReference
-
- 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.MultiSpeciesType
-
- getCompartment() - Method in class org.sbml.libsbml.QualitativeSpecies
-
- 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
-
Returns the compartment glyph with the given index.
- getCompartmentGlyph(String) - Method in class org.sbml.libsbml.Layout
-
Returns the compartment glyph that has the given id, or null if no
compartment glyph has the id.
- getCompartmentId() - Method in class org.sbml.libsbml.CompartmentGlyph
-
Returns the id of the associated compartment.
- getCompartmentReference(long) - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
- getCompartmentReference(String) - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
- getCompartmentReference() - Method in class org.sbml.libsbml.MultiSimpleSpeciesReferencePlugin
-
- getCompartmentReference() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- 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
-
- getCompartmentType() - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
Returns the value of the 'compartmentType' attribute of this compartment.
- getComponent() - Method in class org.sbml.libsbml.OutwardBindingSite
-
- getComponent() - Method in class org.sbml.libsbml.SpeciesFeature
-
Returns the value of the 'component' attribute of this
SpeciesFeature.
- getComponent() - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- getComponent() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- getConstant() - Method in class org.sbml.libsbml.Compartment
-
Get the value of the 'constant' attribute of this
Compartment object.
- 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.QualitativeSpecies
-
- 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
-
Returns the value of the 'conversionFactor' attribute of this
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.
- getCoordinate() - Method in class org.sbml.libsbml.RelAbsVector
-
Returns the coordinate value.
- getCoreDefinitionsAdded() - Static method in class org.sbml.libsbml.DefinitionURLRegistry
-
- 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
-
- getCsymbolURL() - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- getCurve() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the curve object for the reaction glyph
- getCurve() - Method in class org.sbml.libsbml.ReactionGlyph
-
Returns the curve object for the reaction glyph
- getCurve() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Returns the curve object for the reference glyph
- getCurve() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Returns the curve object for the species reference glyph
- getCurveElement(long) - Method in class org.sbml.libsbml.RenderCurve
-
Returns a pointer to the curve segment with the given index or null if
the id is invalid.
- getCurveExplicitlySet() - Method in class org.sbml.libsbml.GeneralGlyph
-
- getCurveExplicitlySet() - Method in class org.sbml.libsbml.ReactionGlyph
-
- getCurveExplicitlySet() - Method in class org.sbml.libsbml.ReferenceGlyph
-
- getCurveExplicitlySet() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- getCurveSegment(long) - Method in class org.sbml.libsbml.Curve
-
Returns a pointer to the curve segment with the given index.
- 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.
- getCX() - Method in class org.sbml.libsbml.Ellipse
-
Returns the x coordinate for the center point as a reference.
- getCx() - Method in class org.sbml.libsbml.RadialGradient
-
- getCY() - Method in class org.sbml.libsbml.Ellipse
-
Returns the y coordinate for the center point as a reference.
- getCy() - Method in class org.sbml.libsbml.RadialGradient
-
- getCZ() - Method in class org.sbml.libsbml.Ellipse
-
Returns the z coordinate for the center point as a reference.
- getCz() - Method in class org.sbml.libsbml.RadialGradient
-
- getDashByIndex(long) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
Returns the dash at the given index of the 'stroke-dasharray' attribute.
- 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.
- getDefault_z() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'default_z' attribute of this
DefaultValues object.
- getDefaultL3ParserSettings() - Static method in class org.sbml.libsbml.libsbml
-
Returns a copy of the default Level 3 ('L3') formula parser settings.
- getDefaultLevel() - Static method in class org.sbml.libsbml.CompExtension
-
Returns the default SBML Level used by this libSBML package extension.
- getDefaultLevel() - Static method in class org.sbml.libsbml.FbcExtension
-
Returns the default SBML Level used by this libSBML package extension.
- getDefaultLevel() - Static method in class org.sbml.libsbml.GroupsExtension
-
Returns the default SBML Level implemented by this libSBML extension.
- getDefaultLevel() - Static method in class org.sbml.libsbml.LayoutExtension
-
Returns the default SBML Level used by this libSBML package extension.
- getDefaultLevel() - Static method in class org.sbml.libsbml.MultiExtension
-
Returns the default SBML Level used by this libSBML package extension.
- getDefaultLevel() - Static method in class org.sbml.libsbml.QualExtension
-
Returns the default SBML Level used by this libSBML package extension.
- getDefaultLevel() - Static method in class org.sbml.libsbml.RenderExtension
-
Returns the default SBML Level this extension.
- getDefaultLevel() - Static method in class org.sbml.libsbml.SBMLDocument
-
- getDefaultPackageVersion() - Static method in class org.sbml.libsbml.CompExtension
-
Returns the default version of the SBML Level 3 package implemented
by this libSBML extension.
- getDefaultPackageVersion() - Static method in class org.sbml.libsbml.FbcExtension
-
Returns the default version of the SBML Level 3 package implemented
by this libSBML extension.
- getDefaultPackageVersion() - Static method in class org.sbml.libsbml.GroupsExtension
-
Returns the default version of the SBML Level 3 package implemented
by this libSBML extension.
- getDefaultPackageVersion() - Static method in class org.sbml.libsbml.LayoutExtension
-
Returns the default version of the SBML Level 3 package implemented
by this libSBML extension.
- getDefaultPackageVersion() - Static method in class org.sbml.libsbml.MultiExtension
-
Returns the default version of the SBML Level 3 package implemented
by this libSBML extension.
- getDefaultPackageVersion() - Static method in class org.sbml.libsbml.QualExtension
-
Returns the default version of the SBML Level 3 package implemented
by this libSBML extension.
- getDefaultPackageVersion() - Static method in class org.sbml.libsbml.RenderExtension
-
Returns the default SBML version this extension.
- getDefaultProperties() - Method in class org.sbml.libsbml.CobraToFbcConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.CompFlatteningConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.FbcToCobraConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.FbcV1ToV2Converter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.FbcV2ToV1Converter
-
Returns the default properties of this converter.
- 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.SBMLIdConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.SBMLInferUnitsConverter
-
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.SBMLLevel1Version1Converter
-
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.SBMLLocalParameterConverter
-
Returns the default properties of this converter.
- getDefaultProperties() - Method in class org.sbml.libsbml.SBMLReactionConverter
-
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.
- getDefaultTerm() - Method in class org.sbml.libsbml.ListOfFunctionTerms
-
- getDefaultTerm() - Method in class org.sbml.libsbml.Transition
-
- getDefaultValues() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- getDefaultValues() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- getDefaultVersion() - Static method in class org.sbml.libsbml.CompExtension
-
Returns the default SBML Version used by this libSBML package extension.
- getDefaultVersion() - Static method in class org.sbml.libsbml.FbcExtension
-
Returns the default SBML Version used by this libSBML package extension.
- getDefaultVersion() - Static method in class org.sbml.libsbml.GroupsExtension
-
Returns the default SBML Version implemented by this libSBML extension.
- getDefaultVersion() - Static method in class org.sbml.libsbml.LayoutExtension
-
Returns the default SBML Version used by this libSBML package extension.
- getDefaultVersion() - Static method in class org.sbml.libsbml.MultiExtension
-
Returns the default SBML Version used by this libSBML package extension.
- getDefaultVersion() - Static method in class org.sbml.libsbml.QualExtension
-
Returns the default SBML Version used by this libSBML package extension.
- getDefaultVersion() - Static method in class org.sbml.libsbml.RenderExtension
-
Returns the default SBML Version this extension.
- getDefaultVersion() - Static method in class org.sbml.libsbml.SBMLDocument
-
- getDefinitionURL() - Method in class org.sbml.libsbml.ASTNode
-
Gets the MathML 'definitionURL' attribute value.
- getDefinitionUrlByIndex(int) - Static method in class org.sbml.libsbml.DefinitionURLRegistry
-
- getDefinitionURLString() - Method in class org.sbml.libsbml.ASTNode
-
Returns the MathML definitionURL attribute value as a string.
- 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
-
Returns the deletion with the given index.
- getDeletion(String) - Method in class org.sbml.libsbml.Submodel
-
Returns the deletion with the given id.
- getDenominator() - Method in class org.sbml.libsbml.ASTNode
-
Gets 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
-
Returns the depth.
- 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.
- getDExplicitlySet() - Method in class org.sbml.libsbml.Dimensions
-
Checks whether the depth has been explicitly set.
- getDimensions() - Method in class org.sbml.libsbml.BoundingBox
-
- getDimensions() - Method in class org.sbml.libsbml.Layout
-
Returns the dimensions of the layout.
- getDimensionsExplicitlySet() - Method in class org.sbml.libsbml.BoundingBox
-
Return
true or
false based on whether
Dimensions have been set.
- getDimensionsExplicitlySet() - Method in class org.sbml.libsbml.Layout
-
Predicate returning true if the dimensions has been set
- getDisabledPlugin(long) - Method in class org.sbml.libsbml.SBase
-
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3
package extension.
- getDivider() - Method in class org.sbml.libsbml.CompModelPlugin
-
Get the string used as the divider between names when renaming and
flattening models.
- 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.
- getElement(long) - Method in class org.sbml.libsbml.Polygon
-
- getElement(long) - Method in class org.sbml.libsbml.RenderCurve
-
- getElement(long) - Method in class org.sbml.libsbml.RenderGroup
-
- getElement(String) - Method in class org.sbml.libsbml.RenderGroup
-
Returns pointer to the element with the given id.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.CompModelPlugin
-
Returns the first child element it can find with the given meta
identifier, or itself if it has 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
itself if it has 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
itself if it has 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.GlobalRenderInformation
-
Returns the first child element that has the given metaid, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.GradientBase
-
Returns the first child element that has the given metaid, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.Group
-
Returns the first child element that has the given metaid, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.GroupsModelPlugin
-
Returns the first child element that has 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.LineEnding
-
Returns the first child element that has 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 found with the given meta-identifier.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
Returns the first child element that has the given metaid, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
Returns the first child element that has the given metaid, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.LocalRenderInformation
-
Returns the first child element that has 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.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.Polygon
-
Returns the first child element that has the given metaid, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.QualModelPlugin
-
Returns the first child element that has the given metaid, 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.RenderCurve
-
Returns the first child element that has the given metaid, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.RenderGroup
-
Returns the first child element that has the given metaid, or null
if no such object is found.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
Returns the first child element that has 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
-
Return the first child object found with a given meta identifier.
- getElementByMetaId(String) - Method in class org.sbml.libsbml.SBaseRef
-
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.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.Style
-
Returns the first child element that 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 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.Transition
-
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.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.GlobalRenderInformation
-
Returns the first child element 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.GradientBase
-
Returns the first child element 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.Group
-
Returns the first child element 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.GroupsModelPlugin
-
Returns the first child element 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.LineEnding
-
Returns the first child element 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 identifier.
- 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.ListOfGlobalRenderInformation
-
Returns the first child element 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.ListOfLocalRenderInformation
-
Returns the first child element 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.LocalRenderInformation
-
Returns the first child element 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.
- getElementBySId(String) - Method in class org.sbml.libsbml.Polygon
-
Returns the first child element 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.QualModelPlugin
-
Returns the first child element 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.RenderCurve
-
Returns the first child element 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.RenderGroup
-
Returns the first child element 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.RenderInformationBase
-
Returns the first child element 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
-
Return the first child object found with a given identifier.
- 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.Style
-
Returns the first child element 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.Transition
-
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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.BindingSiteSpeciesType
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.BoundingBox
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ColorDefinition
-
- getElementName() - Method in class org.sbml.libsbml.Compartment
-
Returns the XML element name of this object
- getElementName() - Method in class org.sbml.libsbml.CompartmentGlyph
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.CompartmentReference
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.CompartmentType
-
Returns the XML element name of this object
- 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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.Curve
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.DefaultTerm
-
Returns the XML name of this object.
- getElementName() - Method in class org.sbml.libsbml.DefaultValues
-
- 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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.Dimensions
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.Ellipse
-
Returns the XML element name of this
Ellipse 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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.FbcAnd
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.FbcAssociation
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.FbcOr
-
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.FunctionTerm
-
Returns the XML name of this object.
- getElementName() - Method in class org.sbml.libsbml.GeneAssociation
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.GeneProduct
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.GeneProductAssociation
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.GeneProductRef
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- getElementName() - Method in class org.sbml.libsbml.GlobalStyle
-
Returns the XML element name of this
GlobalStyle object.
- getElementName() - Method in class org.sbml.libsbml.GradientBase
-
- getElementName() - Method in class org.sbml.libsbml.GradientStop
-
- getElementName() - Method in class org.sbml.libsbml.GraphicalObject
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- getElementName() - Method in class org.sbml.libsbml.Group
-
Returns the XML element name of this
Group object.
- getElementName() - Method in class org.sbml.libsbml.Image
-
Returns the XML element name of this
Image 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.Input
-
Returns the XML name of this object.
- getElementName() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.IntraSpeciesReaction
-
Returns the XML element name of this object.
- 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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.LinearGradient
-
- getElementName() - Method in class org.sbml.libsbml.LineEnding
-
Returns the XML element name of this
LineEnding object.
- getElementName() - Method in class org.sbml.libsbml.LineSegment
-
Returns the XML element name of
this SBML 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.ListOfColorDefinitions
-
- getElementName() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfCompartmentReferences
-
- 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.ListOfCurveElements
-
- getElementName() - Method in class org.sbml.libsbml.ListOfDeletions
-
Returns the XML element name of this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfDrawables
-
- 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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfFbcAssociations
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfFluxBounds
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfFunctionTerms
-
Returns the XML name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfGeneProducts
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- getElementName() - Method in class org.sbml.libsbml.ListOfGlobalStyles
-
- getElementName() - Method in class org.sbml.libsbml.ListOfGradientDefinitions
-
- getElementName() - Method in class org.sbml.libsbml.ListOfGradientStops
-
- getElementName() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfGroups
-
- getElementName() - Method in class org.sbml.libsbml.ListOfInitialAssignments
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfInputs
-
Returns the XML name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfInSpeciesTypeBonds
-
- getElementName() - Method in class org.sbml.libsbml.ListOfLayouts
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfLineEndings
-
- getElementName() - Method in class org.sbml.libsbml.ListOfLineSegments
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfLocalParameters
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- getElementName() - Method in class org.sbml.libsbml.ListOfLocalStyles
-
- getElementName() - Method in class org.sbml.libsbml.ListOfMembers
-
- getElementName() - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfMultiSpeciesTypes
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfObjectives
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfOutputs
-
Returns the XML name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfOutwardBindingSites
-
- 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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfPossibleSpeciesFeatureValues
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
-
Returns the XML name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
Returns the XML element name of
this SBML object.
- 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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfReplacedElements
-
Returns the XML element name of
this SBML object.
- 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.ListOfSpeciesFeatures
-
Returns the XML element name of this object, which for
ListOfSpeciesFeatures, is
always
'listOfSpeciesFeatures'.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesFeatureTypes
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesFeatureValues
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentIndexes
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentMapInProducts
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesTypeInstances
-
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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ListOfTransitions
-
Returns the XML name of this object.
- 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.LocalRenderInformation
-
- getElementName() - Method in class org.sbml.libsbml.LocalStyle
-
Returns the XML element name of this
LocalStyle object.
- getElementName() - Method in class org.sbml.libsbml.Member
-
Returns the XML element name of this
Member object.
- 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.
- 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.MultiSpeciesType
-
Returns the XML element name of this object, which for
MultiSpeciesType, is
always
'multiSpeciesType'.
- getElementName() - Method in class org.sbml.libsbml.Objective
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Output
-
Returns the XML name of this object.
- getElementName() - Method in class org.sbml.libsbml.OutwardBindingSite
-
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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.Polygon
-
Returns the XML element name of this
Polygon object.
- getElementName() - Method in class org.sbml.libsbml.Port
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
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.QualitativeSpecies
-
Returns the XML name of this object.
- getElementName() - Method in class org.sbml.libsbml.RadialGradient
-
- 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 SBML object.
- getElementName() - Method in class org.sbml.libsbml.Rectangle
-
Returns the XML element name of this
Rectangle object.
- getElementName() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- getElementName() - Method in class org.sbml.libsbml.RenderCurve
-
Returns the XML element name of this
RenderCurve object.
- getElementName() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the XML element name of this
RenderGroup object.
- getElementName() - Method in class org.sbml.libsbml.RenderPoint
-
Returns the XML element name of this
RenderPoint object.
- getElementName() - Method in class org.sbml.libsbml.ReplacedBy
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.ReplacedElement
-
Returns the XML element name of
this SBML 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 SBML 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.SpeciesFeature
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.SpeciesFeatureValue
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.SpeciesGlyph
-
Returns the XML element name of
this SBML 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 SBML 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.SpeciesTypeComponentIndex
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
Returns the XML element name of this object.
- 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.Style
-
Returns the XML element name of this
Style object.
- getElementName() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.libsbml.Submodel
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.Text
-
Returns the XML element name of this
Text object.
- getElementName() - Method in class org.sbml.libsbml.TextGlyph
-
Returns the XML element name of
this SBML object.
- getElementName() - Method in class org.sbml.libsbml.Transformation
-
- getElementName() - Method in class org.sbml.libsbml.Transformation2D
-
- getElementName() - Method in class org.sbml.libsbml.Transition
-
Returns the XML 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 namespace URI of the package to which this plugin object
belongs.
- getEmail() - Method in class org.sbml.libsbml.ModelCreator
-
- getEnableRotationalMapping() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'enableRotationalMapping' attribute of this
DefaultValues object.
- getEnableRotationalMapping() - Method in class org.sbml.libsbml.LineEnding
-
Returns the value of the 'enableRotationalMapping' attribute of this
LineEnding.
- getEncoding() - Method in class org.sbml.libsbml.XMLInputStream
-
Returns the encoding of the XML stream.
- getEnd() - Method in class org.sbml.libsbml.LineSegment
-
Returns the end point of the line.
- getEndHead() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'endHead' attribute of this
DefaultValues
object.
- getEndHead() - Method in class org.sbml.libsbml.RenderCurve
-
Returns the value of the 'endHead' attribute of this
RenderCurve.
- getEndHead() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'endHead' attribute of this
RenderGroup.
- 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 libSBML's internal numerical offset for the error code
associated with this error.
- 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.
- getErrorLog() - Method in class org.sbml.libsbml.XMLInputStream
-
- getErrorWithSeverity(long, long) - Method in class org.sbml.libsbml.SBMLDocument
-
Returns the nth error or warning with the given severity
encountered during parsing, consistency checking, or attempted
translation of this model.
- getErrorWithSeverity(long, long) - Method in class org.sbml.libsbml.SBMLErrorLog
-
Returns the
nth
SBMLError object with given severity in this log.
- 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
-
Gets 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.
- getExtentConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
Returns the value of the 'extentConversionFactor' attribute of this
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
-
Returns the model definition object based on its identifier.
- 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.
- getFill() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'fill' attribute of this
DefaultValues object.
- getFill() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- getFillColor() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- getFillRule() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'fill-rule' attribute of this
DefaultValues object.
- getFillRule() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- getFillRuleAsString() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'fill-rule' attribute of this
DefaultValues object.
- getFillRuleAsString() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- 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
-
Returns the
FluxBound object that belongs to the given index.
- getFluxBound(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
Returns the
FluxBound object based on its identifier.
- getFluxBoundOperation() - Method in class org.sbml.libsbml.FluxBound
-
Returns the value of the 'operation' attribute of this
FluxBound object.
- 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
-
- getFocalPointX() - Method in class org.sbml.libsbml.RadialGradient
-
Returns the x coordinate for the start point as a reference.
- getFocalPointY() - Method in class org.sbml.libsbml.RadialGradient
-
Returns the y coordinate for the start point as a reference.
- getFocalPointZ() - Method in class org.sbml.libsbml.RadialGradient
-
Returns the z coordinate for the start point as a reference.
- getFontFamily() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'font-family' attribute of this
DefaultValues object.
- getFontFamily() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'font-family' attribute of this
RenderGroup.
- getFontFamily() - Method in class org.sbml.libsbml.Text
-
Returns the value of the 'font-family' attribute of this
Text.
- getFontSize() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'font-size' attribute of this
DefaultValues object.
- getFontSize() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'font-size' element of this
RenderGroup.
- getFontSize() - Method in class org.sbml.libsbml.Text
-
Returns the font size as a reference.
- getFontStyle() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'font-style' attribute of this
DefaultValues
object.
- getFontStyle() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'font-style' attribute of this
RenderGroup.
- getFontStyle() - Method in class org.sbml.libsbml.Text
-
Returns the value of the 'font-style' attribute of this
Text.
- getFontStyleAsString() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'font-style' attribute of this
DefaultValues
object.
- getFontStyleAsString() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'font-style' attribute of this
RenderGroup.
- getFontStyleAsString() - Method in class org.sbml.libsbml.Text
-
Returns the value of the 'font-style' attribute of this
Text.
- getFontWeight() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'font-weight' attribute of this
DefaultValues object.
- getFontWeight() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'font-weight' attribute of this
RenderGroup.
- getFontWeight() - Method in class org.sbml.libsbml.Text
-
Returns the value of the 'font-weight' attribute of this
Text.
- getFontWeightAsString() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'font-weight' attribute of this
DefaultValues object.
- getFontWeightAsString() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'font-weight' attribute of this
RenderGroup.
- getFontWeightAsString() - Method in class org.sbml.libsbml.Text
-
Returns the value of the 'font-weight' attribute of this
Text.
- 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
-
- getFunctionTerm(long) - Method in class org.sbml.libsbml.Transition
-
- getFunctionTerm(String) - Method in class org.sbml.libsbml.Transition
-
- getFx() - Method in class org.sbml.libsbml.RadialGradient
-
- getFy() - Method in class org.sbml.libsbml.RadialGradient
-
- getFz() - Method in class org.sbml.libsbml.RadialGradient
-
- getGeneAssociation(long) - Method in class org.sbml.libsbml.FbcModelPlugin
-
Returns the
GeneAssociation annotation object that belongs to the given index.
- getGeneAssociation(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getGeneProduct(long) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getGeneProduct(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getGeneProduct() - Method in class org.sbml.libsbml.GeneProductRef
-
Returns the value of the 'geneProduct' attribute of this
GeneProductRef.
- getGeneProductAssociation() - Method in class org.sbml.libsbml.FbcReactionPlugin
-
- getGeneProductByLabel(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getGeneralGlyph(long) - Method in class org.sbml.libsbml.Layout
-
Returns the general glyph with the given index.
- getGeneralGlyph(String) - Method in class org.sbml.libsbml.Layout
-
Returns the general glyph that has the given id, or null
if no graphical object has the id.
- getGivenName() - Method in class org.sbml.libsbml.ModelCreator
-
Returns the 'given name' stored in this
ModelCreator object.
- getGlobalStyle(long) - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- getGlobalStyle(String) - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- getGlyphId() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Returns the id of the associated glyph.
- getGradientDefinition(long) - Method in class org.sbml.libsbml.RenderInformationBase
-
- getGradientDefinition(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- getGradientStop(long) - Method in class org.sbml.libsbml.GradientBase
-
- getGradientStop(String) - Method in class org.sbml.libsbml.GradientBase
-
- getGraphicalObjectId() - Method in class org.sbml.libsbml.TextGlyph
-
Returns the id of the associated graphical object.
- getGreen() - Method in class org.sbml.libsbml.ColorDefinition
-
Returns the green color component.
- getGroup(long) - Method in class org.sbml.libsbml.GroupsModelPlugin
-
- getGroup(String) - Method in class org.sbml.libsbml.GroupsModelPlugin
-
- getGroup() - Method in class org.sbml.libsbml.LineEnding
-
Returns the value of the 'group' element of this
LineEnding.
- getGroup() - Method in class org.sbml.libsbml.Style
-
Returns the value of the 'group' element of this
Style.
- getHasOnlySubstanceUnits() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'hasOnlySubstanceUnits' attribute.
- getHeight() - Method in class org.sbml.libsbml.Dimensions
-
Returns the height.
- getHeight() - Method in class org.sbml.libsbml.Image
-
Returns a reference to the height of the image.
- getHeight() - Method in class org.sbml.libsbml.Rectangle
-
Returns the height of the rectangle
- getHost() - Method in class org.sbml.libsbml.SBMLUri
-
Returns the host portion of the stored URI.
- 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.
- getHref() - Method in class org.sbml.libsbml.Image
-
Returns the value of the 'href' attribute of this
Image.
- getId() - Method in class org.sbml.libsbml.ASTNode
-
- getId() - Method in class org.sbml.libsbml.BoundingBox
-
Returns the value of the 'id' attribute of this
BoundingBox.
- getId() - Method in class org.sbml.libsbml.ColorDefinition
-
- getId() - Method in class org.sbml.libsbml.Compartment
-
Returns the value of the 'id' attribute of this
Compartment.
- getId() - Method in class org.sbml.libsbml.CompartmentReference
-
- getId() - Method in class org.sbml.libsbml.CompartmentType
-
- getId() - Method in class org.sbml.libsbml.Deletion
-
Returns the value of the 'id' attribute of this
Deletion.
- getId() - Method in class org.sbml.libsbml.Dimensions
-
Returns the value of the 'id' attribute of this
Dimensions.
- 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.EventAssignment
-
Returns the value of the 'variable' attribute of this
EventAssignment (NOT the 'id').
- getId() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- getId() - Method in class org.sbml.libsbml.FluxBound
-
Returns the value of the 'id' attribute of this
FluxBound.
- getId() - Method in class org.sbml.libsbml.FluxObjective
-
- getId() - Method in class org.sbml.libsbml.FunctionDefinition
-
- getId() - Method in class org.sbml.libsbml.GeneAssociation
-
- getId() - Method in class org.sbml.libsbml.GeneProduct
-
Returns the value of the 'id' attribute of this
GeneProduct.
- getId() - Method in class org.sbml.libsbml.GeneProductAssociation
-
- getId() - Method in class org.sbml.libsbml.GeneProductRef
-
- getId() - Method in class org.sbml.libsbml.GradientBase
-
Returns the value of the 'id' attribute of this
GradientBase.
- getId() - Method in class org.sbml.libsbml.GraphicalObject
-
- getId() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- getId() - Method in class org.sbml.libsbml.Group
-
Returns the value of the 'id' attribute of this
Group.
- getId() - Method in class org.sbml.libsbml.Image
-
Returns the value of the 'id' attribute of this
Image.
- getId() - Method in class org.sbml.libsbml.InitialAssignment
-
Returns the value of the 'symbol' attribute of this
InitialAssignment (NOT the 'id').
- getId() - Method in class org.sbml.libsbml.Input
-
Returns the value of the 'id' attribute of this
Input.
- getId() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- getId() - Method in class org.sbml.libsbml.Layout
-
Returns the value of the 'id' attribute of this
Layout.
- getId() - Method in class org.sbml.libsbml.LineEnding
-
Returns the value of the 'id' attribute of this
LineEnding.
- getId() - Method in class org.sbml.libsbml.ListOfMembers
-
- getId() - Method in class org.sbml.libsbml.Member
-
Returns the value of the 'id' attribute of this
Member.
- 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.MultiSpeciesType
-
- getId() - Method in class org.sbml.libsbml.Objective
-
Returns the value of the 'id' attribute of this
Objective.
- getId() - Method in class org.sbml.libsbml.Output
-
Returns the value of the 'id' attribute of this
Output.
- getId() - Method in class org.sbml.libsbml.OutwardBindingSite
-
- 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.Point
-
Returns the value of the 'id' attribute of this
Point.
- getId() - Method in class org.sbml.libsbml.Port
-
Returns the value of the 'id' attribute of this
Port.
- getId() - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
- getId() - Method in class org.sbml.libsbml.QualitativeSpecies
-
- 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.RenderInformationBase
-
- getId() - Method in class org.sbml.libsbml.Rule
-
Returns the value of the 'variable' attribute of this
Rule (NOT the 'id').
- getId() - Method in class org.sbml.libsbml.SBase
-
Returns the value of the 'id' attribute of this SBML object, if it has one,
or the 'variable' attribute of a
Rule, or the 'symbol' attribute of
an
InitialAssignment.
- 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.
- getId() - Method in class org.sbml.libsbml.SpeciesFeature
-
- getId() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- 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.SpeciesTypeComponentIndex
-
- getId() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- getId() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- getId() - Method in class org.sbml.libsbml.Style
-
Returns the value of the 'id' attribute of this
Style.
- getId() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- getId() - Method in class org.sbml.libsbml.Submodel
-
Returns the value of the 'id' attribute of this
Submodel.
- getId() - Method in class org.sbml.libsbml.Transition
-
Returns the value of the 'id' attribute of this
Transition.
- getId() - Method in class org.sbml.libsbml.UnitDefinition
-
- getIdAttribute() - Method in class org.sbml.libsbml.SBase
-
Returns the value of the 'id' attribute of this SBML object.
- getIdentifyingParent() - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- getIdentityMatrix() - Static method in class org.sbml.libsbml.Transformation
-
Returns a 3D identity matrix.
- getIdentityMatrix2D() - Static method in class org.sbml.libsbml.Transformation2D
-
Returns a 2D identity matrix.
- getIdList() - Method in class org.sbml.libsbml.LocalStyle
-
Returns the value of the 'idList' attribute of this
LocalStyle.
- getIdRef() - Method in class org.sbml.libsbml.Member
-
Returns the value of the 'idRef' attribute of this
Member.
- getIdRef() - Method in class org.sbml.libsbml.SBaseRef
-
Returns the value of the 'idRef' attribute of this
SBaseRef.
- getImageReference() - Method in class org.sbml.libsbml.Image
-
Returns the image reference URL string.
- getIndex(String) - Method in class org.sbml.libsbml.XMLAttributes
-
Returns the index of an attribute having a given name.
- getIndex(String, String) - Method in class org.sbml.libsbml.XMLAttributes
-
Returns the index of the attribute having a given name and XML namespace
URI.
- getIndex(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
-
Returns the index of the attribute defined by the given
XMLTriple object.
- 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
-
Returns the index of the reference glyph with the given id.
- getIndexForSpeciesReferenceGlyph(String) - Method in class org.sbml.libsbml.ReactionGlyph
-
Returns the index of the species reference glyph with the given id.
- getIndexForSubGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the index of the subglyph with the given id.
- 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
-
- getInitialAssignmentBySymbol(String) - Method in class org.sbml.libsbml.Model
-
- getInitialConcentration() - Method in class org.sbml.libsbml.Species
-
Get the value of the 'initialConcentration' attribute.
- getInitialLevel() - Method in class org.sbml.libsbml.QualitativeSpecies
-
- getInitialValue() - Method in class org.sbml.libsbml.Trigger
-
(SBML Level 3 only) Get the value of the 'initialValue' attribute
of this
Trigger.
- getInput(long) - Method in class org.sbml.libsbml.Transition
-
- getInput(String) - Method in class org.sbml.libsbml.Transition
-
- getInputBySpecies(String) - Method in class org.sbml.libsbml.Transition
-
- getInSpeciesTypeBond(long) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getInSpeciesTypeBond(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getInstance() - Static method in class org.sbml.libsbml.DefinitionURLRegistry
-
Returns the singleton instance for the DefinitionURL registry.
- 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
-
Returns a singleton instance of the registry.
- getInstance() - Static method in class org.sbml.libsbml.SBMLResolverRegistry
-
Returns the singleton instance for the resolver registry.
- getInstantiation() - Method in class org.sbml.libsbml.Submodel
-
Get the instantiated
Model this
Submodel contains rules to create.
- getInteger() - Method in class org.sbml.libsbml.ASTNode
-
Gets 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.
- getIsEnabledRotationalMapping() - Method in class org.sbml.libsbml.LineEnding
-
Returns whether rotational mapping is enabled or not.
- getIsFunction() - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- getIsType() - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
Returns the value of the 'isType' attribute.
- getitem(int) - Method in class org.sbml.libsbml.double_array
-
- getitem(int) - Method in class org.sbml.libsbml.int_array
-
- 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.ListOfColorDefinitions
-
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentReferences
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object
- 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.ListOfCurveElements
-
Returns the libSBML type code for the SBML objects contained in this
ListOfCurveElements object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfDeletions
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Deletion objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfDrawables
-
Returns the libSBML type code for the SBML objects contained in this
ListOfDrawables object.
- 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
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Model objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFbcAssociations
-
Returns the libSBML type code for the objects contained in this
ListOf.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFluxBounds
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
Returns the libSBML type code for 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.ListOfFunctionTerms
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGeneProducts
-
Returns the libSBML type code for the objects contained in this
ListOf.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGlobalStyles
-
Returns the libSBML type code for the SBML objects contained in this
ListOfGlobalStyles object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGradientDefinitions
-
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGradientStops
-
Returns the libSBML type code for the SBML objects contained in this
ListOfGradientStops object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGroups
-
Returns the libSBML type code for the SBML objects contained in this
ListOfGroups object.
- 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.ListOfInputs
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfInSpeciesTypeBonds
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLayouts
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLineEndings
-
Returns the libSBML type code for the SBML objects contained in this
ListOfLineEndings object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLineSegments
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- 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.ListOfLocalRenderInformation
-
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLocalStyles
-
Returns the libSBML type code for the SBML objects contained in this
ListOfLocalStyles object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfMembers
-
Returns the libSBML type code for the SBML objects contained in this
ListOfMembers object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
ModelDefinition objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfMultiSpeciesTypes
-
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.ListOfObjectives
-
Returns the libSBML type code for the objects contained in this
ListOf.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfOutputs
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfOutwardBindingSites
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object
- 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
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Port objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfPossibleSpeciesFeatureValues
-
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.ListOfQualitativeSpecies
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- 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
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReplacedElements
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e., ReplacedElements objects, if the list is non-empty).
- 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.ListOfSpeciesFeatures
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesFeatureTypes
-
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.ListOfSpeciesFeatureValues
-
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.ListOfSpeciesGlyphs
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- 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.ListOfSpeciesTypeComponentIndexes
-
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.ListOfSpeciesTypeComponentMapInProducts
-
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.ListOfSpeciesTypeInstances
-
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.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
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Submodel objects, if the list is non-empty).
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- getItemTypeCode() - Method in class org.sbml.libsbml.ListOfTransitions
-
Returns the libSBML type code for the SBML objects
contained in this
ListOf object.
- 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).
- getItemTypeCode() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
Returns the libSBML type code for the objects contained in this
ListOf
(i.e.,
Compartment 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.Group
-
Returns the value of the 'kind' attribute of this
Group.
- getKind() - Method in class org.sbml.libsbml.Unit
-
Returns the 'kind' of
Unit this is.
- getKindAsString() - Method in class org.sbml.libsbml.Group
-
Returns the value of the 'kind' attribute of this
Group.
- 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.
- getLabel() - Method in class org.sbml.libsbml.GeneProduct
-
Returns the value of the 'label' attribute of this
GeneProduct.
- getLastParseL3Error() - Static method in class org.sbml.libsbml.libsbml
-
Returns the last error reported by the 'L3' mathematical formula parser.
- getLayout(long) - Method in class org.sbml.libsbml.LayoutModelPlugin
-
Returns the layout object that belongs to the given index.
- getLayout(String) - Method in class org.sbml.libsbml.LayoutModelPlugin
-
Returns the layout object with the given sid attribute.
- getLeftChild() - Method in class org.sbml.libsbml.ASTNode
-
Gets the left child of this node.
- getLength() - Method in class org.sbml.libsbml.XMLAttributes
-
Returns the number of attributes in this list of attributes.
- 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(String) - Method in class org.sbml.libsbml.CompExtension
-
Returns the SBML Level for the given URI of this package.
- getLevel(String) - Method in class org.sbml.libsbml.FbcExtension
-
Returns the SBML Level for the given URI of this package.
- getLevel(String) - Method in class org.sbml.libsbml.GroupsExtension
-
Returns the SBML Level for the given URI of this package.
- getLevel(String) - Method in class org.sbml.libsbml.LayoutExtension
-
Returns the SBML Level for the given URI of this package.
- getLevel(String) - Method in class org.sbml.libsbml.MultiExtension
-
Returns the SBML Level for the given URI of this package.
- getLevel(String) - Method in class org.sbml.libsbml.QualExtension
-
Returns the SBML Level for the given URI of this package.
- getLevel(String) - Method in class org.sbml.libsbml.RenderExtension
-
Returns the SBML level with the given URI of this package.
- 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(String) - Method in class org.sbml.libsbml.SBMLExtension
-
Returns the SBML Level associated with the given XML namespace URI.
- getLevel() - Method in class org.sbml.libsbml.SBMLNamespaces
-
- getLibraryName() - Static method in class org.sbml.libsbml.XMLOutputStream
-
- getLibraryVersion() - Static method in class org.sbml.libsbml.XMLOutputStream
-
- getLibSBMLDependencyVersionOf(String) - Static method in class org.sbml.libsbml.libsbml
-
Returns the version string for the dependency library used.
- 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 where 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 number at which this token occurs in the input.
- getLinearGradient_x1() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'linearGradient_x1' attribute of this
DefaultValues object.
- getLinearGradient_x2() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'linearGradient_x2' attribute of this
DefaultValues object.
- getLinearGradient_y1() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'linearGradient_y1' attribute of this
DefaultValues object.
- getLinearGradient_y2() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'linearGradient_y2' attribute of this
DefaultValues object.
- getLinearGradient_z1() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'linearGradient_z1' attribute of this
DefaultValues object.
- getLinearGradient_z2() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'linearGradient_z2' attribute of this
DefaultValues object.
- getLineEnding(long) - Method in class org.sbml.libsbml.RenderInformationBase
-
- getLineEnding(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- 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.
- getListNestedCVTerms() - Method in class org.sbml.libsbml.CVTerm
-
Returns a list of
CVTerm objects contained within this
CVTerm
object.
- getListOfAdditionalGraphicalObjects() - Method in class org.sbml.libsbml.Layout
-
Returns the
ListOf object that holds all additional graphical objects.
- getListOfAllElements(ElementFilter) - Method in class org.sbml.libsbml.SBase
-
Returns an
SBaseList of all child
SBase objects,
including those nested to an arbitrary depth.
- getListOfAllElements() - Method in class org.sbml.libsbml.SBase
-
Returns an
SBaseList of all child
SBase objects,
including those nested to an arbitrary depth.
- getListOfAllElements(ElementFilter) - Method in class org.sbml.libsbml.SBasePlugin
-
Returns an
SBaseList of all child
SBase objects,
including those nested to an arbitrary depth.
- getListOfAllElements() - Method in class org.sbml.libsbml.SBasePlugin
-
Returns an
SBaseList of all child
SBase objects,
including those nested to an arbitrary depth.
- getListOfAllElementsFromPlugins(ElementFilter) - Method in class org.sbml.libsbml.SBase
-
Returns an
SBaseList of all child
SBase objects
contained in SBML package plugins.
- getListOfAllElementsFromPlugins() - Method in class org.sbml.libsbml.SBase
-
Returns an
SBaseList of all child
SBase objects
contained in SBML package plugins.
- getListOfAllInstantiatedElements() - Method in class org.sbml.libsbml.Submodel
-
- getListOfAssociations() - Method in class org.sbml.libsbml.FbcAnd
-
- getListOfAssociations() - Method in class org.sbml.libsbml.FbcOr
-
- getListOfColorDefinitions() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getListOfCompartmentGlyphs() - Method in class org.sbml.libsbml.Layout
-
Returns the
ListOf object that holds all compartment glyphs.
- getListOfCompartmentReferences() - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
- 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
-
Returns a refernce to the
ListOf object That holds all the curve
segments.
- getListOfDeletions() - Method in class org.sbml.libsbml.Submodel
-
Returns the
ListOf object that holds all deletions.
- getListOfElements() - Method in class org.sbml.libsbml.Polygon
-
- getListOfElements() - Method in class org.sbml.libsbml.RenderCurve
-
- getListOfElements() - Method in class org.sbml.libsbml.RenderGroup
-
- 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
-
- getListOfFunctionTerms() - Method in class org.sbml.libsbml.Transition
-
- getListOfGeneAssociations() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getListOfGeneProducts() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getListOfGlobalRenderInformation() - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
-
Returns a pointer to the list object that contains local render information.
- getListOfGlobalStyles() - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- getListOfGradientDefinitions() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getListOfGradientStops() - Method in class org.sbml.libsbml.GradientBase
-
- getListOfGroups() - Method in class org.sbml.libsbml.GroupsModelPlugin
-
- getListOfInitialAssignments() - Method in class org.sbml.libsbml.Model
-
- getListOfInputs() - Method in class org.sbml.libsbml.Transition
-
- getListOfInSpeciesTypeBonds() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getListOfLayouts() - Method in class org.sbml.libsbml.LayoutModelPlugin
-
- getListOfLineEndings() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getListOfLocalParameters() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the list of local parameters in this
KineticLaw object.
- getListOfLocalRenderInformation() - Method in class org.sbml.libsbml.RenderLayoutPlugin
-
Returns a pointer to the list object that contains local render information.
- getListOfLocalStyles() - Method in class org.sbml.libsbml.LocalRenderInformation
-
- getListOfMembers() - Method in class org.sbml.libsbml.Group
-
- 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.
- getListOfMultiSpeciesTypes() - Method in class org.sbml.libsbml.MultiModelPlugin
-
- getListOfNodes() - Method in class org.sbml.libsbml.ASTNode
-
- getListOfObjectives() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getListOfOutputs() - Method in class org.sbml.libsbml.Transition
-
- getListOfOutwardBindingSites() - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getListOfParameters() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the list of parameters in this
KineticLaw object.
- getListOfParameters() - Method in class org.sbml.libsbml.Model
-
- getListOfPorts() - Method in class org.sbml.libsbml.CompModelPlugin
-
- getListOfPossibleSpeciesFeatureValues() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- getListOfProducts() - Method in class org.sbml.libsbml.Reaction
-
Returns the list of products in this
Reaction object.
- getListOfQualitativeSpecies() - Method in class org.sbml.libsbml.QualModelPlugin
-
- 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
-
Returns the
ListOf object that holds all reaction glyphs.
- getListOfReactions() - Method in class org.sbml.libsbml.Model
-
- getListOfReferenceGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the
ListOf object that hold the reference glyphs.
- getListOfReplacedElements() - Method in class org.sbml.libsbml.CompSBasePlugin
-
Returns the
ListOf object that holds all replacedElements.
- getListOfRules() - Method in class org.sbml.libsbml.Model
-
- getListOfSpecies() - Method in class org.sbml.libsbml.Model
-
- getListOfSpeciesFeatures() - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getListOfSpeciesFeatureTypes() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getListOfSpeciesFeatureValues() - Method in class org.sbml.libsbml.SpeciesFeature
-
- getListOfSpeciesGlyphs() - Method in class org.sbml.libsbml.Layout
-
Returns the
ListOf object that holds all species glyphs.
- getListOfSpeciesReferenceGlyphs() - Method in class org.sbml.libsbml.ReactionGlyph
-
Returns the
ListOf object that hold the species reference glyphs.
- getListOfSpeciesTypeComponentIndexes() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getListOfSpeciesTypeComponentMapInProducts() - Method in class org.sbml.libsbml.MultiSpeciesReferencePlugin
-
- getListOfSpeciesTypeInstances() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getListOfSpeciesTypes() - Method in class org.sbml.libsbml.Model
-
- getListOfStyles() - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- getListOfStyles() - Method in class org.sbml.libsbml.LocalRenderInformation
-
- getListOfSubGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the
ListOf object that hold the sub glyphs.
- getListOfSubmodels() - Method in class org.sbml.libsbml.CompModelPlugin
-
- getListOfTextGlyphs() - Method in class org.sbml.libsbml.Layout
-
Returns the
ListOf object that holds all text glyphs.
- getListOfTransitions() - Method in class org.sbml.libsbml.QualModelPlugin
-
- 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.
- getLocalStyle(long) - Method in class org.sbml.libsbml.LocalRenderInformation
-
- getLocalStyle(String) - Method in class org.sbml.libsbml.LocalRenderInformation
-
Returns a pointer to the style with the given id.
- getLocationURI() - Method in class org.sbml.libsbml.SBMLDocument
-
- getLowerFluxBound() - Method in class org.sbml.libsbml.FbcReactionPlugin
-
- getMajorVersion() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- getMajorVersion() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- getMantissa() - Method in class org.sbml.libsbml.ASTNode
-
Gets 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.FunctionTerm
-
- 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.
- getMatrix() - Method in class org.sbml.libsbml.Transformation
-
Returns the value of the 'transform' attribute of this
Transformation.
- getMatrix2D() - Method in class org.sbml.libsbml.Transformation2D
-
Returns the 2D matrix which is an array of double values of length 6.
- getMaxLevel() - Method in class org.sbml.libsbml.QualitativeSpecies
-
- getMd5() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- getMember(long) - Method in class org.sbml.libsbml.Group
-
- getMember(String) - Method in class org.sbml.libsbml.Group
-
- getMemberByIdRef(String) - Method in class org.sbml.libsbml.Group
-
Get a
Member from the
Group based on the element to which it refers.
- 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 SBML object.
- getMetaIdRef() - Method in class org.sbml.libsbml.GraphicalObject
-
- getMetaIdRef() - Method in class org.sbml.libsbml.Member
-
Returns the value of the 'metaIdRef' attribute of this
Member.
- getMetaIdRef() - Method in class org.sbml.libsbml.SBaseRef
-
Returns the value of the 'metaIdRef' attribute of this
SBaseRef.
- getMinorVersion() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- getMinorVersion() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- 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
-
Searches the model namespace of the document and returns the
Model,
ModelDefinition, or ExternalModelDefintion object with the given
identifier.
- getModel() - Method in class org.sbml.libsbml.L3ParserSettings
-
- getModel() - Method in class org.sbml.libsbml.SBase
-
Returns the
Model object for the SBML Document 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
-
Returns the model definition object based on its identifier.
- 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
-
Returns the value of the 'modelRef' attribute of this
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
-
- getModifierSpeciesReference(String) - Method in class org.sbml.libsbml.Model
-
- 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.
- getMultiSpeciesType(long) - Method in class org.sbml.libsbml.MultiModelPlugin
-
- getMultiSpeciesType(String) - Method in class org.sbml.libsbml.MultiModelPlugin
-
- getName() - Method in class org.sbml.libsbml.ASTNode
-
Gets the value of this node as a string.
- getName() - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- getName() - Method in class org.sbml.libsbml.ColorDefinition
-
- 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.CompartmentReference
-
- getName() - Method in class org.sbml.libsbml.CompartmentType
-
- getName() - Method in class org.sbml.libsbml.CompExtension
-
Returns the name of this package as a short-form label
("comp").
- getName() - Method in class org.sbml.libsbml.Deletion
-
Returns the value of the 'name' attribute of this
Deletion object.
- 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.ExternalModelDefinition
-
- getName() - Method in class org.sbml.libsbml.FbcExtension
-
Returns the name of this SBML Level 3 package ('fbc').
- getName() - Method in class org.sbml.libsbml.FluxBound
-
Returns the value of the 'name' attribute of this
FluxBound object.
- getName() - Method in class org.sbml.libsbml.FluxObjective
-
Returns the value of the 'name' attribute of this
FluxObjective object.
- getName() - Method in class org.sbml.libsbml.FunctionDefinition
-
- getName() - Method in class org.sbml.libsbml.GeneProduct
-
Returns the value of the 'name' attribute of this
GeneProduct object.
- getName() - Method in class org.sbml.libsbml.GeneProductAssociation
-
- getName() - Method in class org.sbml.libsbml.GeneProductRef
-
Returns the value of the 'name' attribute of this
GeneProductRef object.
- getName() - Method in class org.sbml.libsbml.GradientBase
-
Returns the value of the 'name' attribute of this
GradientBase.
- getName() - Method in class org.sbml.libsbml.Group
-
Returns the value of the 'name' attribute of this
Group.
- getName() - Method in class org.sbml.libsbml.GroupsExtension
-
Returns the name of this SBML Level 3 package ('groups').
- getName() - Method in class org.sbml.libsbml.Input
-
Returns the value of the 'name' attribute of this
Input object.
- getName() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- getName() - Method in class org.sbml.libsbml.Layout
-
Returns the value of the 'name' attribute of this
Layout object.
- getName() - Method in class org.sbml.libsbml.LayoutExtension
-
Returns the name of this package ('layout')
- getName() - Method in class org.sbml.libsbml.ListOfMembers
-
- getName() - Method in class org.sbml.libsbml.Member
-
Returns the value of the 'name' attribute of this
Member.
- getName() - Method in class org.sbml.libsbml.Model
-
Returns the value of the 'name' attribute of this
Model object.
- getName() - Method in class org.sbml.libsbml.ModelCreator
-
Returns the 'fn' stored in this
ModelCreator object when using vCard4.
- getName() - Method in class org.sbml.libsbml.MultiExtension
-
Returns the name of this package ('multi')
- getName() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getName() - Method in class org.sbml.libsbml.Objective
-
Returns the value of the 'name' attribute of this
Objective object.
- getName() - Method in class org.sbml.libsbml.Output
-
Returns the value of the 'name' attribute of this
Output object.
- getName() - Method in class org.sbml.libsbml.OutwardBindingSite
-
- getName() - Method in class org.sbml.libsbml.Parameter
-
Returns the value of the 'name' attribute of this
Parameter object.
- getName() - Method in class org.sbml.libsbml.Port
-
Returns the value of the 'name' attribute of this
Port object.
- getName() - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
- getName() - Method in class org.sbml.libsbml.QualExtension
-
Returns the name of this package ('qual')
- getName() - Method in class org.sbml.libsbml.QualitativeSpecies
-
- getName() - Method in class org.sbml.libsbml.Reaction
-
Returns the value of the 'name' attribute of this
Reaction object.
- getName() - Method in class org.sbml.libsbml.RenderExtension
-
Returns the name of this package ('render')
- getName() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getName() - Method in class org.sbml.libsbml.SBase
-
Returns the value of the 'name' attribute of this SBML object.
- getName() - Method in class org.sbml.libsbml.SBMLConverter
-
Returns the name of this converter.
- getName() - Method in class org.sbml.libsbml.SBMLExtension
-
Returns the nickname of this package.
- 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.SpeciesFeature
-
- getName() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- getName() - Method in class org.sbml.libsbml.SpeciesType
-
Returns the value of the 'name' attribute of this
SpeciesType object.
- getName() - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- getName() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- getName() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- getName() - Method in class org.sbml.libsbml.Style
-
Returns the value of the 'name' attribute of this
Style.
- getName() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- getName() - Method in class org.sbml.libsbml.Submodel
-
Returns the value of the 'name' attribute of this
Submodel object.
- getName() - Method in class org.sbml.libsbml.Transformation
-
- getName() - Method in class org.sbml.libsbml.Transition
- getName() - Method in class org.sbml.libsbml.UnitDefinition
-
Returns the value of the 'name' attribute of this
UnitDefinition object.
- getName(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Returns the name of the nth attribute in this list of
attributes.
- getName() - Method in class org.sbml.libsbml.XMLToken
-
Returns the (unqualified) name of token.
- getName() - Method in class org.sbml.libsbml.XMLTriple
-
Returns the
name portion of this
XMLTriple object.
- getNamespaceIndex(String) - Method in class org.sbml.libsbml.XMLToken
-
Returns the index of an XML namespace declaration based on its URI.
- getNamespaceIndexByPrefix(String) - Method in class org.sbml.libsbml.XMLToken
-
Returns the index of an XML namespace declaration based on its prefix.
- getNamespacePrefix(int) - Method in class org.sbml.libsbml.XMLToken
-
Returns the prefix of the nth XML namespace declaration.
- getNamespacePrefix(String) - Method in class org.sbml.libsbml.XMLToken
-
Returns the prefix associated with a given XML namespace URI on this
token.
- getNamespaces() - Method in class org.sbml.libsbml.SBase
-
Returns a list of the XML Namespaces declared on the SBML document
owning this object.
- 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 namespaces declared for this token.
- getNamespacesLength() - Method in class org.sbml.libsbml.XMLToken
-
Returns the number of XML namespaces declared on this token.
- getNamespaceURI(int) - Method in class org.sbml.libsbml.XMLToken
-
Returns the URI of the nth XML namespace declared on this token.
- getNamespaceURI(String) - Method in class org.sbml.libsbml.XMLToken
-
Returns the URI of an XML namespace with a given prefix.
- getNamespaceURI() - Method in class org.sbml.libsbml.XMLToken
-
Returns the URI of an XML namespace with a given prefix.
- getNestedCVTerm(long) - Method in class org.sbml.libsbml.CVTerm
-
Returns the nth
CVTerm in the list of CVTerms of this
CVTerm
object.
- 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
-
Returns the number of additional graphical objects for the layout.
- getNumAllowedChildren() - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- getNumArguments() - Method in class org.sbml.libsbml.FunctionDefinition
-
- getNumAssociations() - Method in class org.sbml.libsbml.Association
-
Returns the number of child Associations of this
Association object.
- getNumAssociations() - Method in class org.sbml.libsbml.FbcAnd
-
- getNumAssociations() - Method in class org.sbml.libsbml.FbcOr
-
- getNumASTPlugins() - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
- getNumAttributes() - Method in class org.sbml.libsbml.XMLAttributes
-
Returns the number of attributes in this list of attributes.
- getNumChildren() - Method in class org.sbml.libsbml.ASTNode
-
Gets the number of children that this node has.
- getNumChildren() - Method in class org.sbml.libsbml.XMLNode
-
Returns the number of children for this
XMLNode.
- getNumColorDefinitions() - Method in class org.sbml.libsbml.ListOfColorDefinitions
-
- getNumColorDefinitions() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getNumCompartmentGlyphs() - Method in class org.sbml.libsbml.Layout
-
Returns the number of compartment glyphs for the layout.
- getNumCompartmentReferences() - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
- 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
-
Returns the number of curve segments.
- getNumCVTerms() - Method in class org.sbml.libsbml.SBase
-
Returns the number of
CVTerm objects in the annotations of this SBML
object.
- getNumDashes() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
Returns the number of defined dashes in the 'stroke-dasharray' attribute.
- getNumDefinitionURLs() - Static method in class org.sbml.libsbml.DefinitionURLRegistry
-
Returns the number of DefinitionURLs known by the registry.
- getNumDeletions() - Method in class org.sbml.libsbml.Submodel
-
Returns the number of deletions for this
Submodel.
- getNumDisabledPlugins() - Method in class org.sbml.libsbml.SBase
-
Returns the number of disabled plug-in objects (extension interfaces)
for SBML Level 3 package extensions known.
- getNumElements() - Method in class org.sbml.libsbml.Polygon
-
- getNumElements() - Method in class org.sbml.libsbml.RenderCurve
-
- getNumElements() - Method in class org.sbml.libsbml.RenderGroup
-
- getNumerator() - Method in class org.sbml.libsbml.ASTNode
-
Gets the value of the numerator of this node.
- getNumericValue() - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
- 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 extensions that have a 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.
- getNumFbcAssociations() - Method in class org.sbml.libsbml.ListOfFbcAssociations
-
- getNumFluxBounds() - Method in class org.sbml.libsbml.FbcModelPlugin
-
Returns the number of
FluxBound object in this plugin object.
- getNumFluxObjectives() - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
- getNumFluxObjectives() - Method in class org.sbml.libsbml.Objective
-
- getNumFunctionDefinitions() - Method in class org.sbml.libsbml.Model
-
- getNumFunctionTerms() - Method in class org.sbml.libsbml.Transition
-
- getNumGeneAssociations() - Method in class org.sbml.libsbml.FbcModelPlugin
-
Returns the number of
GeneAssociation annotation object in this plugin object.
- getNumGeneProducts() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getNumGeneProducts() - Method in class org.sbml.libsbml.ListOfGeneProducts
-
- getNumGeneralGlyphs() - Method in class org.sbml.libsbml.Layout
-
Returns the number of general glyphs for the layout.
- getNumGlobalRenderInformation() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- getNumGlobalRenderInformationObjects() - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
-
Returns the number of local render information objects.
- getNumGlobalStyles() - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- getNumGlobalStyles() - Method in class org.sbml.libsbml.ListOfGlobalStyles
-
- getNumGradientBases() - Method in class org.sbml.libsbml.ListOfGradientDefinitions
-
- getNumGradientDefinitions() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getNumGradientStops() - Method in class org.sbml.libsbml.GradientBase
-
- getNumGradientStops() - Method in class org.sbml.libsbml.ListOfGradientStops
-
- getNumGroups() - Method in class org.sbml.libsbml.GroupsModelPlugin
-
- getNumGroups() - Method in class org.sbml.libsbml.ListOfGroups
-
- getNumIds() - Method in class org.sbml.libsbml.LocalStyle
-
Returns the number of ids in the id set.
- getNumInitialAssignments() - Method in class org.sbml.libsbml.Model
-
- getNumInputs() - Method in class org.sbml.libsbml.Transition
-
- getNumInSpeciesTypeBonds() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getNumLayouts() - Method in class org.sbml.libsbml.LayoutModelPlugin
-
Returns the number of layout objects.
- getNumLineEndings() - Method in class org.sbml.libsbml.ListOfLineEndings
-
- getNumLineEndings() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getNumLocalParameters() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the number of local parameters in this
KineticLaw instance.
- getNumLocalRenderInformation() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- getNumLocalRenderInformationObjects() - Method in class org.sbml.libsbml.RenderLayoutPlugin
-
Returns the number of local render information objects.
- getNumLocalStyles() - Method in class org.sbml.libsbml.ListOfLocalStyles
-
- getNumLocalStyles() - Method in class org.sbml.libsbml.LocalRenderInformation
-
- getNumMembers() - Method in class org.sbml.libsbml.Group
-
- getNumMembers() - Method in class org.sbml.libsbml.ListOfMembers
-
- 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.
- getNumMultiSpeciesTypes() - Method in class org.sbml.libsbml.MultiModelPlugin
-
- getNumNamespaces() - Method in class org.sbml.libsbml.XMLNamespaces
-
Returns the total number of URI-and-prefix pairs stored in this
particular
XMLNamespaces instance.
- getNumNestedCVTerms() - Method in class org.sbml.libsbml.CVTerm
-
Returns the number of
CVTerm objects nested within this
CVTerm
object.
- getNumObjectives() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getNumObjectives() - Method in class org.sbml.libsbml.ListOfObjectives
-
- getNumOfSBasePlugins() - Method in class org.sbml.libsbml.SBMLExtension
-
Returns the number of SBasePluginCreatorBase objects stored in this
object.
- getNumOfSupportedPackageURI() - Method in class org.sbml.libsbml.SBMLExtension
-
Returns the number of supported package namespace URIs.
- getNumOptions() - Method in class org.sbml.libsbml.ConversionProperties
-
Returns the number of options in this Conversion Properties object
- getNumOutputs() - Method in class org.sbml.libsbml.Transition
-
- getNumOutwardBindingSites() - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getNumParameters() - Method in class org.sbml.libsbml.KineticLaw
-
Returns the number of 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
-
- getNumPossibleSpeciesFeatureValues() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- getNumProducts() - Method in class org.sbml.libsbml.Reaction
-
Returns the number of product species in this
Reaction.
- getNumQualitativeSpecies() - Method in class org.sbml.libsbml.QualModelPlugin
-
- 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
-
Returns the number of reaction glyphs for the layout.
- getNumReactions() - Method in class org.sbml.libsbml.Model
-
- getNumReferenceGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the number of reference glyph objects.
- getNumReferents() - Method in class org.sbml.libsbml.ReplacedElement
-
- getNumReferents() - Method in class org.sbml.libsbml.SBaseRef
-
Returns how many elements are being referred to by this
SBaseRef.
- getNumRegisteredPackages() - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Returns the number of registered packages.
- getNumRenderPoints() - Method in class org.sbml.libsbml.ListOfCurveElements
-
- getNumReplacedElements() - Method in class org.sbml.libsbml.CompSBasePlugin
-
- getNumResolvers() - Method in class org.sbml.libsbml.SBMLResolverRegistry
-
Returns the number of resolvers known by the registry.
- getNumResources() - Method in class org.sbml.libsbml.CVTerm
-
Returns the number of resources for this
CVTerm object.
- getNumRoles() - Method in class org.sbml.libsbml.Style
-
Returns the number of ids in the role list.
- 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
-
Gets the number of semantic annotation elements inside this node.
- getNumSpecies() - Method in class org.sbml.libsbml.Model
-
- getNumSpeciesFeatures() - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
- getNumSpeciesFeatures() - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getNumSpeciesFeatures() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- getNumSpeciesFeatureTypes() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getNumSpeciesFeatureValues() - Method in class org.sbml.libsbml.SpeciesFeature
-
- getNumSpeciesGlyphs() - Method in class org.sbml.libsbml.Layout
-
Returns the number of species glyphs for the layout.
- getNumSpeciesReferenceGlyphs() - Method in class org.sbml.libsbml.ReactionGlyph
-
Returns the number of species reference glyph objects.
- getNumSpeciesTypeComponentIndexes() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getNumSpeciesTypeComponentMapInProducts() - Method in class org.sbml.libsbml.MultiSpeciesReferencePlugin
-
- getNumSpeciesTypeInstances() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- 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.
- getNumStyles() - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- getNumStyles() - Method in class org.sbml.libsbml.LocalRenderInformation
-
- getNumSubGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the number of subglyph objects.
- getNumSubListOfSpeciesFeatures() - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
- getNumSubListOfSpeciesFeatures() - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getNumSubmodels() - Method in class org.sbml.libsbml.CompModelPlugin
-
- getNumTextGlyphs() - Method in class org.sbml.libsbml.Layout
-
Returns the number of text glyphs for the layout.
- getNumTransformation2Ds() - Method in class org.sbml.libsbml.ListOfDrawables
-
- getNumTransitions() - Method in class org.sbml.libsbml.QualModelPlugin
-
Returns the number of
Transition object in this plugin object.
- getNumTypes() - Method in class org.sbml.libsbml.Style
-
Returns the number of types in the type list.
- 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
-
Returns the enumeration value of the 'type' attribute of this
Objective.
- getObjectRole() - Method in class org.sbml.libsbml.RenderGraphicalObjectPlugin
-
Returns the object role string for the object.
- getOccur() - Method in class org.sbml.libsbml.SpeciesFeature
-
- getOccur() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- getOffset() - Method in class org.sbml.libsbml.GradientStop
-
Returns the value of the 'offset' element of this
GradientStop.
- 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
-
Returns the value of the 'operation' attribute of this
FluxBound object.
- getOperatorName() - Method in class org.sbml.libsbml.ASTNode
-
Gets the value of this operator node as a string.
- getOption(String) - Method in class org.sbml.libsbml.ConversionProperties
-
- getOption(int) - Method in class org.sbml.libsbml.ConversionProperties
-
- getOrder() - Method in class org.sbml.libsbml.CompartmentGlyph
-
Returns the compartment order.
- 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
-
Returns the id of the origin of text.
- getOutput(long) - Method in class org.sbml.libsbml.Transition
-
- getOutput(String) - Method in class org.sbml.libsbml.Transition
-
- getOutputBySpecies(String) - Method in class org.sbml.libsbml.Transition
-
- getOutputLevel() - Method in class org.sbml.libsbml.Output
-
Returns the value of the 'outputLevel' attribute of this
Output.
- getOutside() - Method in class org.sbml.libsbml.Compartment
-
Get the identifier, if any, of the
Compartment object that is designated
as being outside of
this one.
- getOutwardBindingSite(long) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getOutwardBindingSite(String) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getPackage() - Method in class org.sbml.libsbml.XMLError
-
Returns the SBML Level 3 package extension (if any) that logged
this error.
- getPackageCoreVersion() - Method in class org.sbml.libsbml.SBase
-
Returns the SBML Core Version within the SBML Level of the actual object.
- getPackageName() - Method in class org.sbml.libsbml.CompBase
-
Returns the package name of this plugin object.
- getPackageName() - Static method in class org.sbml.libsbml.CompExtension
-
Returns the nickname of the SBML Level 3 package implemented by
this libSBML extension.
- getPackageName() - Method in class org.sbml.libsbml.CompPkgNamespaces
-
Returns the short-form name or label for the package.
- getPackageName() - Static method in class org.sbml.libsbml.FbcExtension
-
Returns the nickname of the SBML Level 3 package implemented by
this libSBML extension.
- getPackageName() - Method in class org.sbml.libsbml.FbcPkgNamespaces
-
Returns the short-form name or label for the package.
- getPackageName() - Static method in class org.sbml.libsbml.GroupsExtension
-
Returns the nickname of the SBML Level 3 package implemented by this
libSBML extension.
- getPackageName() - Method in class org.sbml.libsbml.GroupsPkgNamespaces
-
Returns the short-form name or label for the package.
- getPackageName() - Static method in class org.sbml.libsbml.LayoutExtension
-
Returns the nickname of the SBML Level 3 package implemented by
this libSBML extension.
- getPackageName() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
-
Returns the short-form name or label for the package.
- getPackageName() - Static method in class org.sbml.libsbml.MultiExtension
-
Returns the nickname of the SBML Level 3 package implemented by
this libSBML extension.
- getPackageName() - Method in class org.sbml.libsbml.MultiPkgNamespaces
-
Returns the short-form name or label for the package.
- getPackageName() - Static method in class org.sbml.libsbml.QualExtension
-
Returns the nickname of the SBML Level 3 package implemented by
this libSBML extension.
- getPackageName() - Method in class org.sbml.libsbml.QualPkgNamespaces
-
Returns the short-form name or label for the package.
- getPackageName() - Static method in class org.sbml.libsbml.RenderExtension
-
Returns the package name of this extension.
- getPackageName() - Method in class org.sbml.libsbml.RenderPkgNamespaces
-
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 short-form name of the package to which this plugin
object belongs.
- 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.
- getPackageToStrip() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
-
- getPackageURI() - Method in class org.sbml.libsbml.CompBase
-
Returns the XML namespace (URI) of the package extension
of this object.
- getPackageVersion() - Method in class org.sbml.libsbml.CompBase
-
Returns the package version of the package extension of
this plugin object.
- getPackageVersion(String) - Method in class org.sbml.libsbml.CompExtension
-
Returns the SBML Level 3 package version for the given URI of this
package.
- getPackageVersion() - Method in class org.sbml.libsbml.CompPkgNamespaces
-
Returns the package's version number.
- getPackageVersion(String) - Method in class org.sbml.libsbml.FbcExtension
-
Returns the SBML Level 3 package version for the given URI of this
package.
- getPackageVersion() - Method in class org.sbml.libsbml.FbcPkgNamespaces
-
Returns the package's version number.
- getPackageVersion(String) - Method in class org.sbml.libsbml.GroupsExtension
-
Returns the SBML Level 3 package version for the given URI of this
package.
- getPackageVersion() - Method in class org.sbml.libsbml.GroupsPkgNamespaces
-
Returns the package's version number.
- getPackageVersion(String) - Method in class org.sbml.libsbml.LayoutExtension
-
Returns the SBML Level 3 package version for the given URI of this
package.
- getPackageVersion() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
-
Returns the package's version number.
- getPackageVersion(String) - Method in class org.sbml.libsbml.MultiExtension
-
Returns the SBML Level 3 package version for the given URI of this
package.
- getPackageVersion() - Method in class org.sbml.libsbml.MultiPkgNamespaces
-
Returns the package's version number.
- getPackageVersion(String) - Method in class org.sbml.libsbml.QualExtension
-
Returns the SBML Level 3 package version for the given URI of this
package.
- getPackageVersion() - Method in class org.sbml.libsbml.QualPkgNamespaces
-
Returns the package's version number.
- getPackageVersion(String) - Method in class org.sbml.libsbml.RenderExtension
-
Returns the package version with the given URI of this package.
- getPackageVersion() - Method in class org.sbml.libsbml.RenderPkgNamespaces
-
- 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.
- getPackageVersion(String) - Method in class org.sbml.libsbml.SBMLExtension
-
Returns the package version associated with the given XML namespace URI.
- getParameter(long) - Method in class org.sbml.libsbml.KineticLaw
-
- getParameter(String) - Method in class org.sbml.libsbml.KineticLaw
-
Returns a 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
-
Returns the
Model object to which the referenced child object belongs.
- 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 object to which this plugin object is connected.
- getParseAvogadroCsymbol() - Method in class org.sbml.libsbml.L3ParserSettings
-
Indicates the current behavior set for handling avogadro for SBML
Level 3.
- getParseCollapseMinus() - Method in class org.sbml.libsbml.L3ParserSettings
-
Indicates the current behavior set for handling multiple unary minuses
in formulas.
- getParseL3v2Functions() - Method in class org.sbml.libsbml.L3ParserSettings
-
Indicates the current behavior set for handling whether to
parse the functions added in L3v2 as that MathML or not.
- getParseLog() - Method in class org.sbml.libsbml.L3ParserSettings
-
Indicates the current behavior set for handling the function log with
one argument.
- getParseModuloL3v2() - Method in class org.sbml.libsbml.L3ParserSettings
-
Indicates the current behavior set for handling the '%' sumbol in
mathematical formulas.
- getParsePackageMath(int) - Method in class org.sbml.libsbml.L3ParserSettings
-
Indicates the current behavior set for handling whether to
parse the functions added in the given package as that MathML or not.
- getParseUnits() - Method in class org.sbml.libsbml.L3ParserSettings
-
Indicates the current behavior set for handling units in text-string
mathematical formulas.
- getPath() - Method in class org.sbml.libsbml.SBMLUri
-
Returns the path and filename portion of the stored URI.
- getPersistent() - Method in class org.sbml.libsbml.Trigger
-
(SBML Level 3 only) Get the value of the 'persistent' attribute
of this
Trigger.
- getPkgRequired(String) - Method in class org.sbml.libsbml.SBMLDocument
-
- 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
-
Returns the port with the given index.
- getPort(String) - Method in class org.sbml.libsbml.CompModelPlugin
-
Returns the port with the given identifier.
- getPortRef() - Method in class org.sbml.libsbml.SBaseRef
-
Returns the value of the 'portRef' attribute of this
SBaseRef.
- getPosition() - Method in class org.sbml.libsbml.BoundingBox
-
- getPositionExplicitlySet() - Method in class org.sbml.libsbml.BoundingBox
-
Return true or false based on whether Position has been set.
- getPossibleSpeciesFeatureValue(long) - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- getPossibleSpeciesFeatureValue(String) - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- getPrecedence() - Method in class org.sbml.libsbml.ASTNode
-
Gets the precedence of this node in the infix math syntax of SBML
Level 1.
- getPrefix() - Method in class org.sbml.libsbml.SBase
-
Returns the XML namespace prefix of this element.
- getPrefix() - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the XML namespace prefix of the package to which this plugin
object belongs.
- getPrefix(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Returns the namespace prefix of the nth attribute in this
attribute set.
- 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 XML namespace prefix of token.
- getPrefix() - Method in class org.sbml.libsbml.XMLTriple
-
Returns the
prefix portion of this
XMLTriple object.
- getPrefixedName(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Returns the prefix name of the nth attribute in this attribute
set.
- 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
-
- getProductComponent() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- getProgramName() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getProgramVersion() - Method in class org.sbml.libsbml.RenderInformationBase
-
- 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.
- getQualitativeSpecies() - Method in class org.sbml.libsbml.Input
-
Returns the value of the 'qualitativeSpecies' attribute of this
Input.
- getQualitativeSpecies() - Method in class org.sbml.libsbml.Output
-
Returns the value of the 'qualitativeSpecies' attribute of this
Output.
- getQualitativeSpecies(long) - Method in class org.sbml.libsbml.QualModelPlugin
-
- getQualitativeSpecies(String) - Method in class org.sbml.libsbml.QualModelPlugin
-
Returns the qualitativeSpecies object based on its identifier.
- getQuery() - Method in class org.sbml.libsbml.SBMLUri
-
Returns the query portion of the stored URI.
- getR() - Method in class org.sbml.libsbml.RadialGradient
-
- getRadialGradient_cx() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'radialGradient_cx' attribute of this
DefaultValues object.
- getRadialGradient_cy() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'radialGradient_cy' attribute of this
DefaultValues object.
- getRadialGradient_cz() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'radialGradient_cz' attribute of this
DefaultValues object.
- getRadialGradient_fx() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'radialGradient_fx' attribute of this
DefaultValues object.
- getRadialGradient_fy() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'radialGradient_fy' attribute of this
DefaultValues object.
- getRadialGradient_fz() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'radialGradient_fz' attribute of this
DefaultValues object.
- getRadialGradient_r() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'radialGradient_r' attribute of this
DefaultValues object.
- getRadius() - Method in class org.sbml.libsbml.RadialGradient
-
Returns the radius as a reference.
- getRadiusX() - Method in class org.sbml.libsbml.Rectangle
-
Returns the corner radius along the x axis
- getRadiusY() - Method in class org.sbml.libsbml.Rectangle
-
Returns the corner radius along the y axis
- getRateRule(String) - Method in class org.sbml.libsbml.Model
-
Get a
Rule object based on the variable to which it assigns a value.
- getRateRuleByVariable(String) - Method in class org.sbml.libsbml.Model
-
Get a
Rule object based on the variable to which it assigns a value.
- getRatio() - Method in class org.sbml.libsbml.Ellipse
-
Returns the value of the 'ratio' attribute of this
Ellipse.
- getRatio() - Method in class org.sbml.libsbml.Rectangle
-
Returns the value of the 'ratio' attribute of this
Rectangle.
- getReactant(long) - Method in class org.sbml.libsbml.Reaction
-
- getReactant(String) - Method in class org.sbml.libsbml.Reaction
-
- getReactant() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- getReactantComponent() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- getReaction() - Method in class org.sbml.libsbml.FluxBound
-
Returns the value of the 'reaction' attribute of this
FluxBound object.
- getReaction() - Method in class org.sbml.libsbml.FluxObjective
-
Returns the value of the 'reaction' attribute of this
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
-
Returns the reaction glyph with the given index.
- getReactionGlyph(String) - Method in class org.sbml.libsbml.Layout
-
Returns the reaction glyph that has the given id, or null if no
reaction glyph has the id.
- getReactionId() - Method in class org.sbml.libsbml.ReactionGlyph
-
Returns the id of the associated reaction.
- getReal() - Method in class org.sbml.libsbml.ASTNode
-
Gets the real-numbered value of this node.
- getRed() - Method in class org.sbml.libsbml.ColorDefinition
-
Returns the red color component.
- getReference() - Method in class org.sbml.libsbml.Association
-
Returns the string of the 'reference' attribute of this
Association object.
- getReferencedElement() - Method in class org.sbml.libsbml.SBaseRef
-
Returns the object pointed to by this element.
- getReferencedElementFrom(Model) - Method in class org.sbml.libsbml.ReplacedElement
-
- getReferencedElementFrom(Model) - Method in class org.sbml.libsbml.SBaseRef
-
Examines the referenced
Model for the referenced object, and returns it, if found.
- getReferencedModel() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- getReferenceGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the reference glyph with the given index.
- getReferenceId() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the id of the associated element.
- getReferenceId() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Returns the id of the associated sbml reference.
- getReferenceRenderInformation() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getReferenceRenderInformationId() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getRegisteredPackageName(long) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Returns the nth registered package.
- getRelation() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- getRelativeValue() - Method in class org.sbml.libsbml.RelAbsVector
-
Returns the relative coordinate value.
- getRenderInformation(long) - Method in class org.sbml.libsbml.RenderLayoutPlugin
-
Returns a pointer to the local render information object with the given
index.
- getRenderInformation(String) - Method in class org.sbml.libsbml.RenderLayoutPlugin
-
Returns a pointer to the local render information object with the given
id.
- getRenderInformation(long) - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
-
Returns a pointer to the local render information object with the given
index.
- getRenderInformation(String) - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
-
Returns a pointer to the local render information object with the given
id.
- getReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
-
- getReplacedElement(long) - Method in class org.sbml.libsbml.CompSBasePlugin
-
- getRepresentationType() - Method in class org.sbml.libsbml.MultiASTPlugin
-
Returns the value of the 'representationType' attribute of this
MultiASTPlugin.
- getRequired() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
-
Returns the value of the 'required' attribute.
- getResolverByIndex(int) - Method in class org.sbml.libsbml.SBMLResolverRegistry
-
Returns the resolver with the given index number.
- 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.
- getResultLevel() - Method in class org.sbml.libsbml.DefaultTerm
-
Returns the value of the 'resultLevel' attribute of this
DefaultTerm.
- getResultLevel() - Method in class org.sbml.libsbml.FunctionTerm
-
Returns the value of the 'resultLevel' attribute of this
FunctionTerm.
- 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
-
Gets the right child of this node.
- getRole() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Returns a string representation of the role.
- getRole() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Returns the role.
- getRoleList() - Method in class org.sbml.libsbml.Style
-
Returns the value of the 'roleList' attribute of this
Style.
- getRoleString() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Returns a string representation of the role.
- 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.
- getRuleByVariable(String) - Method in class org.sbml.libsbml.Model
-
Get a
Rule object based on the variable to which it assigns a value.
- getRX() - Method in class org.sbml.libsbml.Ellipse
-
Returns the radius along the x axis as a reference.
- getRX() - Method in class org.sbml.libsbml.Rectangle
-
Returns the value of the 'rX' element of this
Rectangle.
- getRY() - Method in class org.sbml.libsbml.Ellipse
-
Returns the radius along the y axis as a reference.
- getRY() - Method in class org.sbml.libsbml.Rectangle
-
Returns the value of the 'rY' element of this
Rectangle.
- getSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
-
Get the child sBaseRef of this 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
-
Returns the
SBMLDocument object containing this object instance.
- getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.CompExtension
-
- getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.FbcExtension
-
- getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.GroupsExtension
-
- getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.LayoutExtension
-
- getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.MultiExtension
-
- getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.QualExtension
-
- getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.RenderExtension
-
- getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.SBMLExtension
-
Returns a specialized
SBMLNamespaces object corresponding to a given
namespace URI.
- getSBMLNamespaces() - Method in class org.sbml.libsbml.XMLInputStream
-
- getSBMLNamespaces() - Method in class org.sbml.libsbml.XMLOutputStream
-
- 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 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
-
Returns the scheme of the stored URI.
- getSecond() - Method in class org.sbml.libsbml.Date
-
Returns the seconds from this
Date.
- getSemanticsAnnotation(long) - Method in class org.sbml.libsbml.ASTNode
-
Gets 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.
- getSeverityOverride() - Method in class org.sbml.libsbml.XMLErrorLog
-
Returns the current override.
- getShortMessage() - Method in class org.sbml.libsbml.XMLError
-
Returns a brief message for this error.
- getSign() - Method in class org.sbml.libsbml.Input
-
Returns the value of the 'sign' attribute of this
Input.
- 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
-
Returns the number of items in this list.
- getSize() - Method in class org.sbml.libsbml.Compartment
-
- getSize() - Method in class org.sbml.libsbml.CVTermList
-
Returns the number of items in this list.
- getSize() - Method in class org.sbml.libsbml.DateList
-
Returns the number of items in this list.
- getSize() - Method in class org.sbml.libsbml.ModelCreatorList
-
Returns the number of items in this list.
- getSize() - Method in class org.sbml.libsbml.SBaseList
-
Returns the number of items in this list.
- getSize() - Method in class org.sbml.libsbml.SBMLNamespacesList
-
Returns the number of items in this list.
- 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.
- getSpeciesFeature(long) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getSpeciesFeature(String) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getSpeciesFeatureType(long) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getSpeciesFeatureType(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getSpeciesFeatureType() - Method in class org.sbml.libsbml.SpeciesFeature
-
Returns the value of the 'speciesFeatureType' attribute of this
SpeciesFeature.
- getSpeciesFeatureValue(long) - Method in class org.sbml.libsbml.SpeciesFeature
-
- getSpeciesFeatureValue(String) - Method in class org.sbml.libsbml.SpeciesFeature
-
- getSpeciesGlyph(long) - Method in class org.sbml.libsbml.Layout
-
Returns the species glyph with the given index.
- getSpeciesGlyph(String) - Method in class org.sbml.libsbml.Layout
-
Returns the species glyph that has the given id, or null if no species
glyph has the id.
- getSpeciesGlyphId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- getSpeciesId() - Method in class org.sbml.libsbml.SpeciesGlyph
-
Returns the id of the associated species object.
- getSpeciesReference(String) - Method in class org.sbml.libsbml.Model
-
- getSpeciesReference() - Method in class org.sbml.libsbml.MultiASTPlugin
-
Returns the value of the 'speciesReference' attribute of this
MultiASTPlugin.
- getSpeciesReferenceGlyph(long) - Method in class org.sbml.libsbml.ReactionGlyph
-
Returns the species reference glyph with the given index.
- getSpeciesReferenceId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Returns the id of the associated species reference.
- 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.MultiSpeciesPlugin
-
Returns the value of the 'speciesType' attribute of this 'multi'
Species.
- getSpeciesType() - Method in class org.sbml.libsbml.Species
-
Get the type of this
Species object object.
- getSpeciesType() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- getSpeciesTypeComponentIndex(long) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getSpeciesTypeComponentIndex(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getSpeciesTypeComponentMapInProduct(long) - Method in class org.sbml.libsbml.MultiSpeciesReferencePlugin
-
- getSpeciesTypeComponentMapInProduct(String) - Method in class org.sbml.libsbml.MultiSpeciesReferencePlugin
-
- getSpeciesTypeInstance(long) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getSpeciesTypeInstance(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- getSpreadMethod() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'spreadMethod' attribute of this
DefaultValues
object.
- getSpreadMethod() - Method in class org.sbml.libsbml.GradientBase
-
Returns the value of the 'spreadMethod' attribute of this
GradientBase.
- getSpreadMethodAsString() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'spreadMethod' attribute of this
DefaultValues
object.
- getSpreadMethodAsString() - Method in class org.sbml.libsbml.GradientBase
-
Returns the value of the 'spreadMethod' attribute of this
GradientBase.
- getSpreadMethodString() - Method in class org.sbml.libsbml.GradientBase
-
Returns the value of the 'spreadMethod' attribute of this
GradientBase.
- 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
-
Returns the start point of the line.
- getStartHead() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'startHead' attribute of this
DefaultValues
object.
- getStartHead() - Method in class org.sbml.libsbml.RenderCurve
-
Returns the value of the 'startHead' attribute of this
RenderCurve.
- getStartHead() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'startHead' attribute of this
RenderGroup.
- 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.
- getStopColor() - Method in class org.sbml.libsbml.GradientStop
-
Returns the value of the 'stop-color' attribute of this
GradientStop.
- getStrict() - Method in class org.sbml.libsbml.FbcModelPlugin
-
- getStrict() - Method in class org.sbml.libsbml.FbcV1ToV2Converter
-
- getStringFromTypeCode(int) - Method in class org.sbml.libsbml.CompExtension
-
Takes a type code of the “comp” package and returns a string
describing the code.
- getStringFromTypeCode(int) - Method in class org.sbml.libsbml.FbcExtension
-
Takes a type code of the “fbc” package and returns a string
describing the code.
- getStringFromTypeCode(int) - Method in class org.sbml.libsbml.GroupsExtension
-
Takes a type code of the “groups” package and returns a string
describing the code.
- getStringFromTypeCode(int) - Method in class org.sbml.libsbml.LayoutExtension
-
Takes a type code of the “layout” package and returns a string
describing the code.
- getStringFromTypeCode(int) - Method in class org.sbml.libsbml.MultiExtension
-
Takes a type code of the 'multi' package and returns a string
describing the code.
- getStringFromTypeCode(int) - Method in class org.sbml.libsbml.QualExtension
-
Takes a type code of the “qual” package and returns a string
describing the code.
- getStringFromTypeCode(int) - Method in class org.sbml.libsbml.RenderExtension
-
This method takes a type code of groups package and returns a string representing
the code.
- getStringFromTypeCode(int) - Method in class org.sbml.libsbml.SBMLExtension
-
Returns a string representation of a type code.
- getStroke() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'stroke' attribute of this
DefaultValues object.
- getStroke() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- getStrokeDashArray() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- getStrokeWidth() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'stroke-width' attribute of this
DefaultValues object.
- getStrokeWidth() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- getStyle() - Method in class org.sbml.libsbml.ASTNode
-
- getStyle(long) - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- getStyle(String) - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- getStyle(long) - Method in class org.sbml.libsbml.LocalRenderInformation
-
- getStyle(String) - Method in class org.sbml.libsbml.LocalRenderInformation
-
Returns a pointer to the style with the given id.
- getSubGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the sub glyph with the given index.
- getSubListOfSpeciesFeatures(long) - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
- getSubListOfSpeciesFeatures(String) - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
- getSubListOfSpeciesFeatures(long) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getSubListOfSpeciesFeatures(String) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- getSubmodel(long) - Method in class org.sbml.libsbml.CompModelPlugin
-
Returns the submodel with the given index.
- getSubmodel(String) - Method in class org.sbml.libsbml.CompModelPlugin
-
Returns the submodel with the given identifier.
- getSubmodelRef() - Method in class org.sbml.libsbml.Replacing
-
Returns the value of the 'submodelRef' attribute of this
SBaseRef.
- getSubstanceConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
Returns an empty string, since 'substanceConversionFactor' is not a part of the comp spec.
- 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
-
Returns a list of all supported
SBMLNamespaces in this version of
libsbml.
- getSupportedPackageURI(long) - Method in class org.sbml.libsbml.SBMLExtension
-
Returns the nth XML namespace URI.
- 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.Text
-
Returns the text for the
Text object.
- getText() - Method in class org.sbml.libsbml.TextGlyph
-
Returns the text to be displayed by the text glyph.
- getTextAnchor() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'text-anchor' attribute of this
DefaultValues
object.
- getTextAnchor() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'text-anchor' attribute of this
RenderGroup.
- getTextAnchor() - Method in class org.sbml.libsbml.Text
-
Returns the value of the 'text-anchor' attribute of this
Text.
- getTextAnchorAsString() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'text-anchor' attribute of this
DefaultValues
object.
- getTextAnchorAsString() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'text-anchor' attribute of this
RenderGroup.
- getTextAnchorAsString() - Method in class org.sbml.libsbml.Text
-
Returns the value of the 'text-anchor' attribute of this
Text.
- getTextGlyph(long) - Method in class org.sbml.libsbml.Layout
-
Returns the text glyph with the given index.
- getTextGlyph(String) - Method in class org.sbml.libsbml.Layout
-
Returns the text glyph that has the given id, or null if no text glyph
has the id.
- getThresholdLevel() - Method in class org.sbml.libsbml.Input
-
Returns the value of the 'thresholdLevel' attribute of this
Input.
- getTimeConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
Returns the value of the 'timeConversionFactor' attribute of this
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.
- getTransform(SWIGTYPE_p_double) - Method in class org.sbml.libsbml.Transformation
-
Returns the value of the 'transform' attribute of this
Transformation.
- getTransformer() - Method in class org.sbml.libsbml.CompModelPlugin
-
- getTransition(long) - Method in class org.sbml.libsbml.QualModelPlugin
-
Returns the
Transition object that belongs to the given index.
- getTransition(String) - Method in class org.sbml.libsbml.QualModelPlugin
-
Returns the qualitativeSpecies object based on its identifier.
- getTransitionEffect() - Method in class org.sbml.libsbml.Input
-
Returns the value of the 'transitionEffect' attribute of this
Input.
- getTransitionEffect() - Method in class org.sbml.libsbml.Output
-
Returns the value of the 'transitionEffect' attribute of this
Output.
- getTrigger() - Method in class org.sbml.libsbml.Event
-
Get the event trigger portion of this
Event.
- getType() - Method in class org.sbml.libsbml.Association
-
Returns the string of the 'type' attribute of this
Association object.
- getType() - Method in class org.sbml.libsbml.ASTNode
-
- getType() - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- 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(String) - Static method in class org.sbml.libsbml.DefinitionURLRegistry
-
- getType() - Method in class org.sbml.libsbml.Objective
-
Returns the string of the 'type' attribute of this
Objective.
- getType() - Method in class org.sbml.libsbml.Rule
-
Returns a code representing the type of rule this is.
- getTypeCode() - Method in class org.sbml.libsbml.Association
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.BindingSiteSpeciesType
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.BoundingBox
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.ColorDefinition
-
- 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 of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.CompartmentReference
-
Returns the libSBML type code for this SBML 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 of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Curve
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.DefaultTerm
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.DefaultValues
-
- 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 of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Dimensions
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Ellipse
-
Returns the libSBML type code for this
Ellipse 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 of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.FbcAnd
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.FbcAssociation
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.FbcOr
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.FluxBound
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.FluxObjective
-
Returns the libSBML type code for this SBML 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.FunctionTerm
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.GeneAssociation
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.GeneProduct
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.GeneProductAssociation
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.GeneProductRef
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- getTypeCode() - Method in class org.sbml.libsbml.GlobalStyle
-
Returns the libSBML type code for this
GlobalStyle object.
- getTypeCode() - Method in class org.sbml.libsbml.GradientBase
-
- getTypeCode() - Method in class org.sbml.libsbml.GradientStop
-
- getTypeCode() - Method in class org.sbml.libsbml.GraphicalObject
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- getTypeCode() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- getTypeCode() - Method in class org.sbml.libsbml.Group
-
Returns the libSBML type code for this
Group object.
- getTypeCode() - Method in class org.sbml.libsbml.Image
-
Returns the libSBML type code for this
Image 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.Input
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.IntraSpeciesReaction
-
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 of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.LinearGradient
-
- getTypeCode() - Method in class org.sbml.libsbml.LineEnding
-
Returns the libSBML type code for this
LineEnding object.
- getTypeCode() - Method in class org.sbml.libsbml.LineSegment
-
Returns the libSBML type code of this object instance.
- 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.ListOfColorDefinitions
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentReferences
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfCurveElements
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfDrawables
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfFbcAssociations
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfGeneProducts
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfGlobalStyles
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfGradientDefinitions
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfGradientStops
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfGroups
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfInSpeciesTypeBonds
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfLineEndings
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfLocalStyles
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfMembers
-
- getTypeCode() - Method in class org.sbml.libsbml.ListOfMultiSpeciesTypes
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfObjectives
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfOutwardBindingSites
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfPossibleSpeciesFeatureValues
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesFeatureTypes
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesFeatureValues
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentIndexes
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentMapInProducts
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesTypeInstances
-
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.LocalRenderInformation
-
- getTypeCode() - Method in class org.sbml.libsbml.LocalStyle
-
Returns the libSBML type code for this
LocalStyle object.
- getTypeCode() - Method in class org.sbml.libsbml.Member
-
Returns the libSBML type code for this
Member 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 of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.ModifierSpeciesReference
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.MultiSpeciesType
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.Objective
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.Output
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.OutwardBindingSite
-
Returns the libSBML type code for this SBML 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 of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Polygon
-
Returns the libSBML type code for this
Polygon object.
- getTypeCode() - Method in class org.sbml.libsbml.Port
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
Returns the libSBML type code for this SBML 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.QualitativeSpecies
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.RadialGradient
-
- 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 of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Rectangle
-
Returns the libSBML type code for this
Rectangle object.
- getTypeCode() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- getTypeCode() - Method in class org.sbml.libsbml.RenderCurve
-
Returns the libSBML type code for this
RenderCurve object.
- getTypeCode() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the libSBML type code for this
RenderGroup object.
- getTypeCode() - Method in class org.sbml.libsbml.RenderInformationBase
-
- getTypeCode() - Method in class org.sbml.libsbml.RenderPoint
-
Returns the libSBML type code for this
RenderPoint object.
- getTypeCode() - Method in class org.sbml.libsbml.ReplacedBy
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.ReplacedElement
-
Returns the libSBML type code of this object instance.
- 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 of this object instance.
- 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.SpeciesFeature
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesFeatureValue
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesGlyph
-
Returns the libSBML type code of this object instance.
- 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 of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesType
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
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.Style
-
Returns the libSBML type code for this
Style object.
- getTypeCode() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
Returns the libSBML type code for this SBML object.
- getTypeCode() - Method in class org.sbml.libsbml.Submodel
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Text
-
Returns the libSBML type code for this
Text object.
- getTypeCode() - Method in class org.sbml.libsbml.TextGlyph
-
Returns the libSBML type code of this object instance.
- getTypeCode() - Method in class org.sbml.libsbml.Transformation
-
- getTypeCode() - Method in class org.sbml.libsbml.Transformation2D
-
- getTypeCode() - Method in class org.sbml.libsbml.Transition
-
Returns the libSBML type code of this object instance.
- 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.
- getTypeList() - Method in class org.sbml.libsbml.Style
-
Returns the type list.
- 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
-
Returns the value of the 'unitRef' attribute of this
SBaseRef.
- getUnits() - Method in class org.sbml.libsbml.ASTNode
-
- getUnits() - Method in class org.sbml.libsbml.Compartment
-
- 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.
- getUpperFluxBound() - Method in class org.sbml.libsbml.FbcReactionPlugin
-
- getURI(long, long, long) - Method in class org.sbml.libsbml.CompExtension
-
Returns a string representing the SBML XML namespace of this SBML
Level 3 package.
- getURI() - Method in class org.sbml.libsbml.CompPkgNamespaces
-
Returns a string representing the package's XML namespace.
- getURI(long, long, long) - Method in class org.sbml.libsbml.FbcExtension
-
Returns a string representing the SBML XML namespace of this
SBML Level 3 package.
- getURI() - Method in class org.sbml.libsbml.FbcPkgNamespaces
-
Returns a string representing the package's XML namespace.
- getURI(long, long, long) - Method in class org.sbml.libsbml.GroupsExtension
-
Returns a string representing the SBML XML namespace of this SBML
Level 3 package.
- getURI() - Method in class org.sbml.libsbml.GroupsPkgNamespaces
-
Returns a string representing the package's XML namespace.
- getURI(long, long, long) - Method in class org.sbml.libsbml.LayoutExtension
-
Returns a string representing the SBML XML namespace of this SBML
Level 3 package.
- getURI() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
-
Returns a string representing the package's XML namespace.
- getURI(long, long, long) - Method in class org.sbml.libsbml.MultiExtension
-
Returns a string representing the SBML XML namespace of this SBML
Level 3 package.
- getURI() - Method in class org.sbml.libsbml.MultiPkgNamespaces
-
Returns a string representing the package's XML namespace.
- getURI(long, long, long) - Method in class org.sbml.libsbml.QualExtension
-
Returns a string representing the SBML XML namespace of this SBML
Level 3 package.
- getURI() - Method in class org.sbml.libsbml.QualPkgNamespaces
-
Returns a string representing the package's XML namespace.
- getURI(long, long, long) - Method in class org.sbml.libsbml.RenderExtension
-
Returns the URI (namespace) of the package corresponding to the combination of
the given sbml level, sbml version, and package version.
- getURI() - Method in class org.sbml.libsbml.RenderPkgNamespaces
-
Returns a string representing the SBML XML namespace of this
object.
- getURI() - Method in class org.sbml.libsbml.SBase
-
Gets the namespace URI to which this element belongs to.
- getURI() - Method in class org.sbml.libsbml.SBasePlugin
-
Returns the XML namespace URI for the package to which this object belongs.
- getURI(long, long, long) - Method in class org.sbml.libsbml.SBMLExtension
-
Returns the XML namespace URI for a given Level and Version.
- 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
-
Returns the full stored URI, after replacing backslashes with slashes.
- getURI(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Returns the XML namespace URI of the nth attribute in this
attribute set.
- 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 XML namespace URI of token.
- getURI() - Method in class org.sbml.libsbml.XMLTriple
-
Returns the
URI portion of this
XMLTriple object.
- 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.ASTNode
-
Returns the numerical value of this
ASTNode.
- getValue() - Method in class org.sbml.libsbml.ColorDefinition
-
- 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
-
Returns the value of the 'value' attribute of this
FluxBound object.
- getValue() - Method in class org.sbml.libsbml.Parameter
-
- getValue() - Method in class org.sbml.libsbml.SpeciesFeatureValue
-
- getValue(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Returns the value of the nth attribute in this list of attributes.
- getValue(String) - Method in class org.sbml.libsbml.XMLAttributes
-
Returns a named attribute's value.
- getValue(String, String) - Method in class org.sbml.libsbml.XMLAttributes
-
Returns a named attribute's value.
- getValue(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
-
Return the value of an attribute described by a given
XMLTriple object.
- 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(String) - Method in class org.sbml.libsbml.CompExtension
-
Returns the Version within the SBML Level for the given URI of this
package.
- getVersion(String) - Method in class org.sbml.libsbml.FbcExtension
-
Returns the Version within the SBML Level for the given URI of this
package.
- getVersion(String) - Method in class org.sbml.libsbml.GroupsExtension
-
Returns the Version within the SBML Level for the given URI of this
package.
- getVersion(String) - Method in class org.sbml.libsbml.LayoutExtension
-
Returns the Version within the SBML Level for the given URI of this
package.
- getVersion(String) - Method in class org.sbml.libsbml.MultiExtension
-
Returns the Version within the SBML Level for the given URI of this
package.
- getVersion(String) - Method in class org.sbml.libsbml.QualExtension
-
Returns the Version within the SBML Level for the given URI of this
package.
- getVersion(String) - Method in class org.sbml.libsbml.RenderExtension
-
Returns the SBML version with the given URI of this package.
- 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 Version within the SBML Level of the package extension of
this plugin object.
- getVersion(String) - Method in class org.sbml.libsbml.SBMLExtension
-
Returns the SBML Version associated with the given XML namespace URI.
- getVersion() - Method in class org.sbml.libsbml.SBMLNamespaces
-
- getVersion() - Method in class org.sbml.libsbml.XMLInputStream
-
Returns the version of the XML stream.
- getVersionString() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
Returns the version as a string.
- getVersionString() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
Returns the version as a string.
- 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.
- getVTextAnchor() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'vtext-anchor' attribute of this
DefaultValues
object.
- getVTextAnchor() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'vtext-anchor' attribute of this
RenderGroup.
- getVTextAnchor() - Method in class org.sbml.libsbml.Text
-
Returns the value of the 'vtext-anchor' attribute of this
Text.
- getVTextAnchorAsString() - Method in class org.sbml.libsbml.DefaultValues
-
Returns the value of the 'vtext-anchor' attribute of this
DefaultValues
object.
- getVTextAnchorAsString() - Method in class org.sbml.libsbml.RenderGroup
-
Returns the value of the 'vtext-anchor' attribute of this
RenderGroup.
- getVTextAnchorAsString() - Method in class org.sbml.libsbml.Text
-
Returns the value of the 'vtext-anchor' attribute of this
Text.
- getWidth() - Method in class org.sbml.libsbml.Dimensions
-
Returns the width.
- getWidth() - Method in class org.sbml.libsbml.Image
-
Returns a reference to the width of the image.
- getWidth() - Method in class org.sbml.libsbml.Rectangle
-
Returns the with of the rectangle
- getWriteComment() - Static method in class org.sbml.libsbml.XMLOutputStream
-
- getWriteTimestamp() - Static method in class org.sbml.libsbml.XMLOutputStream
-
- getX() - Method in class org.sbml.libsbml.Image
-
Returns a reference to the x coordinate of the image position.
- getX() - Method in class org.sbml.libsbml.Rectangle
-
Returns the x coordinate of the rectangle's position
- getX() - Method in class org.sbml.libsbml.RenderPoint
-
Returns the value of the 'x' element of this
RenderPoint.
- getX() - Method in class org.sbml.libsbml.Text
-
Returns the x position offset as a reference.
- getX1() - Method in class org.sbml.libsbml.LinearGradient
-
- getX2() - Method in class org.sbml.libsbml.LinearGradient
-
- getXmlnsL2() - Static method in class org.sbml.libsbml.LayoutExtension
-
Returns the XML namespace URI of the SBML Level 2 version
of the package implemented by this libSBML Extension.
- getXmlnsL2() - Static method in class org.sbml.libsbml.RenderExtension
-
Returns URI of L2 version of supported versions of this package.
- getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.CompExtension
-
Returns the XML namespace URI of the SBML Level 3 package
implemented by this libSBML extension.
- getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.FbcExtension
-
Returns the XML namespace URI of the SBML Level 3 package
implemented by this libSBML extension.
- getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.GroupsExtension
-
Returns the XML namespace URI of the SBML Level 3 package implemented
by this libSBML extension.
- getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.LayoutExtension
-
Returns the XML namespace URI of the SBML Level 3 package
implemented by this libSBML extension.
- getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.MultiExtension
-
Returns the XML namespace URI of the SBML Level 3 package
implemented by this libSBML extension.
- getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.QualExtension
-
Returns the XML namespace URI of the SBML Level 3 package
implemented by this libSBML extension.
- getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.RenderExtension
-
Returns URI of supported versions of this package.
- getXmlnsL3V1V2() - Static method in class org.sbml.libsbml.FbcExtension
-
Returns the XML namespace URI of the SBML Level 3 package
implemented by this libSBML extension.
- getXmlnsXSI() - Static method in class org.sbml.libsbml.LayoutExtension
-
Returns the XML namespace URI of any additional XML namespaces needed
or used by this SBML Level 3 package.
- getXOffset() - Method in class org.sbml.libsbml.Point
-
Returns the x offset.
- getXPoint1() - Method in class org.sbml.libsbml.LinearGradient
-
Returns the x coordinate for the start point as a reference.
- getXPoint2() - Method in class org.sbml.libsbml.LinearGradient
-
Returns the x coordinate for the end point as a reference.
- getY() - Method in class org.sbml.libsbml.Image
-
Returns a reference to the y coordinate of the image position.
- getY() - Method in class org.sbml.libsbml.Rectangle
-
Returns the y coordinate of the rectangle's position
- getY() - Method in class org.sbml.libsbml.RenderPoint
-
Returns the value of the 'y' element of this
RenderPoint.
- getY() - Method in class org.sbml.libsbml.Text
-
Returns the y position offset as a reference.
- getY1() - Method in class org.sbml.libsbml.LinearGradient
-
- getY2() - Method in class org.sbml.libsbml.LinearGradient
-
- getYear() - Method in class org.sbml.libsbml.Date
-
Returns the year from this
Date.
- getYOffset() - Method in class org.sbml.libsbml.Point
-
Returns the y offset.
- getYPoint1() - Method in class org.sbml.libsbml.LinearGradient
-
Returns the y coordinate for the start point as a reference.
- getYPoint2() - Method in class org.sbml.libsbml.LinearGradient
-
Returns the y coordinate for the end point as a reference.
- getZ() - Method in class org.sbml.libsbml.Image
-
Returns a reference to the z coordinate of the image position.
- getZ() - Method in class org.sbml.libsbml.Rectangle
-
Returns the z coordinate of the rectangle's position
- getZ() - Method in class org.sbml.libsbml.RenderPoint
-
Returns the value of the 'z' element of this
RenderPoint.
- getZ() - Method in class org.sbml.libsbml.Text
-
Returns the z position offset as a reference.
- getZ1() - Method in class org.sbml.libsbml.LinearGradient
-
- getZ2() - Method in class org.sbml.libsbml.LinearGradient
-
- getZOffset() - Method in class org.sbml.libsbml.Point
-
Returns the z offset.
- getZOffsetExplicitlySet() - Method in class org.sbml.libsbml.Point
-
- getZPoint1() - Method in class org.sbml.libsbml.LinearGradient
-
Returns the z coordinate for the start point as a reference.
- getZPoint2() - Method in class org.sbml.libsbml.LinearGradient
-
Returns the z coordinate for the end point as a reference.
- GlobalRenderInformation - Class in org.sbml.libsbml
-
- GlobalRenderInformation(long, long, long) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
-
- GlobalRenderInformation(long, long) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
-
- GlobalRenderInformation(long) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
-
- GlobalRenderInformation() - Constructor for class org.sbml.libsbml.GlobalRenderInformation
-
- GlobalRenderInformation(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
-
- GlobalRenderInformation(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
-
- GlobalRenderInformation(GlobalRenderInformation) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
-
- GlobalStyle - Class in org.sbml.libsbml
-
render
A style that can be associated with a layout.
- GlobalStyle(long, long, long) - Constructor for class org.sbml.libsbml.GlobalStyle
-
Creates a new
GlobalStyle using the given SBML Level, Version and
“render” package version.
- GlobalStyle(long, long) - Constructor for class org.sbml.libsbml.GlobalStyle
-
Creates a new
GlobalStyle using the given SBML Level, Version and
“render” package version.
- GlobalStyle(long) - Constructor for class org.sbml.libsbml.GlobalStyle
-
Creates a new
GlobalStyle using the given SBML Level, Version and
“render” package version.
- GlobalStyle() - Constructor for class org.sbml.libsbml.GlobalStyle
-
Creates a new
GlobalStyle using the given SBML Level, Version and
“render” package version.
- GlobalStyle(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.GlobalStyle
-
- GlobalStyle(XMLNode, long) - Constructor for class org.sbml.libsbml.GlobalStyle
-
- GlobalStyle(XMLNode) - Constructor for class org.sbml.libsbml.GlobalStyle
-
- GlobalStyle(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.GlobalStyle
-
Constructor which creates a
GlobalStyle with the given
id
and all lists empty.
- GlobalStyle(GlobalStyle) - Constructor for class org.sbml.libsbml.GlobalStyle
-
- GlobalUnitsNotDeclared - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- GRADIENT_SPREAD_METHOD_INVALID - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- GRADIENT_SPREADMETHOD_PAD - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- GRADIENT_SPREADMETHOD_REFLECT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- GRADIENT_SPREADMETHOD_REPEAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- GradientBase - Class in org.sbml.libsbml
-
render
Abstract base class for linear and radial gradients.
- GradientStop - Class in org.sbml.libsbml
-
render
A color at a certain location in a color gradient.
- GradientStop(long, long, long) - Constructor for class org.sbml.libsbml.GradientStop
-
Creates a new
GradientStop using the given SBML Level, Version and
“render” package version.
- GradientStop(long, long) - Constructor for class org.sbml.libsbml.GradientStop
-
Creates a new
GradientStop using the given SBML Level, Version and
“render” package version.
- GradientStop(long) - Constructor for class org.sbml.libsbml.GradientStop
-
Creates a new
GradientStop using the given SBML Level, Version and
“render” package version.
- GradientStop() - Constructor for class org.sbml.libsbml.GradientStop
-
Creates a new
GradientStop using the given SBML Level, Version and
“render” package version.
- GradientStop(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.GradientStop
-
- GradientStop(XMLNode, long) - Constructor for class org.sbml.libsbml.GradientStop
-
- GradientStop(XMLNode) - Constructor for class org.sbml.libsbml.GradientStop
-
- GradientStop(GradientStop) - Constructor for class org.sbml.libsbml.GradientStop
-
- GraphicalObject - Class in org.sbml.libsbml
-
layout
Base class of objects that store layouts.
- 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
-
Creates a new
GraphicalObject with the given
id and 2D coordinates for
the bounding box.
- GraphicalObject(LayoutPkgNamespaces, String, double, double, double, double, double, double) - Constructor for class org.sbml.libsbml.GraphicalObject
-
Creates a new
GraphicalObject with the given
id and 3D coordinates for
the bounding box.
- GraphicalObject(LayoutPkgNamespaces, String, Point, Dimensions) - Constructor for class org.sbml.libsbml.GraphicalObject
-
Creates a new
GraphicalObject with the given
id and 3D coordinates for
the bounding box.
- GraphicalObject(LayoutPkgNamespaces, String, BoundingBox) - Constructor for class org.sbml.libsbml.GraphicalObject
-
Creates a new
GraphicalObject with the given
id and 3D coordinates for
the bounding box.
- 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
-
Copy constructor.
- GraphicalPrimitive1D - Class in org.sbml.libsbml
-
render
Base class for graphical primitives implementing 1D attributes.
- GraphicalPrimitive2D - Class in org.sbml.libsbml
-
render
Base class for graphical primitives implementing 2D attributes.
- Group - Class in org.sbml.libsbml
-
groups
Representation of a group of SBML components.
- Group(long, long, long) - Constructor for class org.sbml.libsbml.Group
-
Creates a new
Group using the given SBML Level, Version and
“groups” package version.
- Group(long, long) - Constructor for class org.sbml.libsbml.Group
-
Creates a new
Group using the given SBML Level, Version and
“groups” package version.
- Group(long) - Constructor for class org.sbml.libsbml.Group
-
Creates a new
Group using the given SBML Level, Version and
“groups” package version.
- Group() - Constructor for class org.sbml.libsbml.Group
-
Creates a new
Group using the given SBML Level, Version and
“groups” package version.
- Group(GroupsPkgNamespaces) - Constructor for class org.sbml.libsbml.Group
-
- Group(Group) - Constructor for class org.sbml.libsbml.Group
-
Copy constructor for
Group.
- GROUP_KIND_CLASSIFICATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups One of the
possible Group kinds.
- GROUP_KIND_COLLECTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups One of the
possible Group kinds.
- GROUP_KIND_PARTONOMY - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups One of the
possible Group kinds.
- GROUP_KIND_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups One of the
possible Group kinds.
- GroupKind_fromString(String) - Static method in class org.sbml.libsbml.libsbml
-
Returns the enumeration value corresponding to the given string or
GROUP_KIND_UNKNOWN if there is no such match.
- GroupKind_isValid(int) - Static method in class org.sbml.libsbml.libsbml
-
Predicate returning 1 (true) or 0 (false) depending on whether the
given enumeration value is valid.
- GroupKind_isValidString(String) - Static method in class org.sbml.libsbml.libsbml
-
Predicate returning 1 (true) or 0 (false) depending on whether the
given string is a valid enumeration value.
- GroupKind_toString(int) - Static method in class org.sbml.libsbml.libsbml
-
Returns the string version of the provided enumeration value.
- GroupsAttributeRequiredMissing - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsAttributeRequiredMustBeBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsAttributeRequiredMustHaveValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsDuplicateComponentId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsElementNotInNs - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsExtension - Class in org.sbml.libsbml
-
groups
Base extension class for the package.
- GroupsExtension() - Constructor for class org.sbml.libsbml.GroupsExtension
-
- GroupsExtension(GroupsExtension) - Constructor for class org.sbml.libsbml.GroupsExtension
-
- GroupsGroupAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsGroupAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsGroupAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsGroupAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsGroupEmptyLOElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsGroupKindMustBeGroupKindEnum - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsGroupLOMembersAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsGroupLOMembersAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsGroupLOMembersAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsGroupNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsIdSyntaxRule - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsLOMembersConsistentReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsLOMembersNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsMemberAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsMemberAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsMemberAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsMemberIdRefMustBeSBase - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsMemberIdRefMustBeSId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsMemberMetaIdRefMustBeID - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsMemberMetaIdRefMustBeSBase - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsMemberNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsModelAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsModelEmptyLOElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsModelLOGroupsAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsModelLOGroupsAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsModelPlugin - Class in org.sbml.libsbml
-
- GroupsModelPlugin(String, String, GroupsPkgNamespaces) - Constructor for class org.sbml.libsbml.GroupsModelPlugin
-
- GroupsModelPlugin(GroupsModelPlugin) - Constructor for class org.sbml.libsbml.GroupsModelPlugin
-
- GroupsNotCircularReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsNSUndeclared - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- GroupsPkgNamespaces - Class in org.sbml.libsbml
-
groups
Class to store SBML Level, Version, and XML namespace for the
SBML Level 3 Groups (“groups”) package.
- GroupsPkgNamespaces() - Constructor for class org.sbml.libsbml.GroupsPkgNamespaces
-
- GroupsUnknown - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups A value in the
enumeration of all the error and warning codes generated by the
libSBML “groups” extension for objects of class
SBMLError.
- IdNameSBaseInL3V2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- IdNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- Image - Class in org.sbml.libsbml
-
render
Representation of images.
- Image(long, long, long) - Constructor for class org.sbml.libsbml.Image
-
Creates a new
Image using the given SBML Level, Version and
“render” package version.
- Image(long, long) - Constructor for class org.sbml.libsbml.Image
-
Creates a new
Image using the given SBML Level, Version and
“render” package version.
- Image(long) - Constructor for class org.sbml.libsbml.Image
-
Creates a new
Image using the given SBML Level, Version and
“render” package version.
- Image() - Constructor for class org.sbml.libsbml.Image
-
Creates a new
Image using the given SBML Level, Version and
“render” package version.
- Image(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.Image
-
- Image(XMLNode, long) - Constructor for class org.sbml.libsbml.Image
-
- Image(XMLNode) - Constructor for class org.sbml.libsbml.Image
-
- Image(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.Image
-
Instantiates an
Image object with the given
id.
- Image(Image) - Constructor for class org.sbml.libsbml.Image
-
Copy constructor for
Image.
- InconsistentArgUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InconsistentArgUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InconsistentExponUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InconsistentKineticLawUnitsL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InconsistentPowerUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- IncorrectCompartmentSpatialDimensions - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- IncorrectOrderInConstraint - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- IncorrectOrderInEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- IncorrectOrderInKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- IncorrectOrderInModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- IncorrectOrderInReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- INFIX_SYNTAX_CURLY_BRACES - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- INFIX_SYNTAX_CURLY_BRACES_SEMICOLON - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- INFIX_SYNTAX_NAMED_SQUARE_BRACKETS - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
- INHERIT - Static variable in class org.sbml.libsbml.GraphicalPrimitive2D
-
- InitAssignCompartmenMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InitAssignmentAndRuleForSameId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InitAssignmentCannotRef0DComp - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InitAssignParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InitAssignSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InitAssignStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- initDefaults() - Method in class org.sbml.libsbml.BoundingBox
-
Does nothing since there are no defaults for a
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
-
Does nothing since no defaults are defined for
Curve.
- initDefaults() - Method in class org.sbml.libsbml.Dimensions
-
Sets the depth to 0.0.
- initDefaults() - Method in class org.sbml.libsbml.Event
-
Initializes the fields of this
Event object to 'typical' default
values.
- initDefaults() - Method in class org.sbml.libsbml.GeneralGlyph
-
- initDefaults() - Method in class org.sbml.libsbml.GraphicalObject
-
Does nothing.
- initDefaults() - Method in class org.sbml.libsbml.Layout
-
Does nothing since no defaults are defined for
Layout.
- initDefaults() - Method in class org.sbml.libsbml.LineSegment
-
Does nothing since no defaults are defined for
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
-
Sets the Z offset to 0.0.
- 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.RenderPoint
-
Sets the Z offset to 0.0.
- 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
-
An SBML initial assignment, evaluated once only.
- 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
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InitialValueFalseEventNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InitialValueNotBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- Input - Class in org.sbml.libsbml
-
- Input(long, long, long) - Constructor for class org.sbml.libsbml.Input
-
Creates a new
Input with the given level, version, and package version.
- Input(long, long) - Constructor for class org.sbml.libsbml.Input
-
Creates a new
Input with the given level, version, and package version.
- Input(long) - Constructor for class org.sbml.libsbml.Input
-
Creates a new
Input with the given level, version, and package version.
- Input() - Constructor for class org.sbml.libsbml.Input
-
Creates a new
Input with the given level, version, and package version.
- Input(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.Input
-
- Input(Input) - Constructor for class org.sbml.libsbml.Input
-
Copy constructor for
Input.
- INPUT_SIGN_DUAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible Input "sign" attribute values.
- INPUT_SIGN_NEGATIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible Input "sign" attribute values.
- INPUT_SIGN_POSITIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible Input "sign" attribute values.
- INPUT_SIGN_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible Input "sign" attribute values.
- INPUT_SIGN_VALUE_NOTSET - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible Input "sign" attribute values.
- INPUT_TRANSITION_EFFECT_CONSUMPTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible Input transition effects.
- INPUT_TRANSITION_EFFECT_NONE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible Input transition effects.
- INPUT_TRANSITION_EFFECT_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible Input transition effects.
- insert(int, SBase) - Method in class org.sbml.libsbml.ListOf
-
Inserts an item at a given position in this
ListOf's list of items.
- insert(String) - Method in class org.sbml.libsbml.StringSet
-
- insertAndOwn(int, SBase) - Method in class org.sbml.libsbml.ListOf
-
Inserts an item at a given position in this
ListOf's list of items.
- insertChild(long, ASTNode) - Method in class org.sbml.libsbml.ASTNode
-
Inserts 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
nth child of this
XMLNode.
- insertDash(long, long) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
Inserts the given integer value for the dash length at the
given position.
- InSpeciesTypeBond - Class in org.sbml.libsbml
-
- InSpeciesTypeBond(long, long, long) - Constructor for class org.sbml.libsbml.InSpeciesTypeBond
-
- InSpeciesTypeBond(long, long) - Constructor for class org.sbml.libsbml.InSpeciesTypeBond
-
- InSpeciesTypeBond(long) - Constructor for class org.sbml.libsbml.InSpeciesTypeBond
-
- InSpeciesTypeBond() - Constructor for class org.sbml.libsbml.InSpeciesTypeBond
-
- InSpeciesTypeBond(MultiPkgNamespaces) - Constructor for class org.sbml.libsbml.InSpeciesTypeBond
-
- InSpeciesTypeBond(InSpeciesTypeBond) - Constructor for class org.sbml.libsbml.InSpeciesTypeBond
-
- instantiate() - Method in class org.sbml.libsbml.Submodel
-
Find and create a local copy of the
Model object referenced by this
Submodel.
- int_array - Class in org.sbml.libsbml
-
- int_array(int) - Constructor for class org.sbml.libsbml.int_array
-
- IntegerSpatialDimensions - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InternalXMLParserError - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the error and warning codes
returned by the XML layer in libSBML.
- IntraSpeciesReaction - Class in org.sbml.libsbml
-
multi
A subclass of
Reaction for changes of an internal species bond.
- IntraSpeciesReaction(long, long, long) - Constructor for class org.sbml.libsbml.IntraSpeciesReaction
-
- IntraSpeciesReaction(long, long) - Constructor for class org.sbml.libsbml.IntraSpeciesReaction
-
- IntraSpeciesReaction(long) - Constructor for class org.sbml.libsbml.IntraSpeciesReaction
-
- IntraSpeciesReaction() - Constructor for class org.sbml.libsbml.IntraSpeciesReaction
-
- IntraSpeciesReaction(MultiPkgNamespaces) - Constructor for class org.sbml.libsbml.IntraSpeciesReaction
-
- IntraSpeciesReaction(IntraSpeciesReaction) - Constructor for class org.sbml.libsbml.IntraSpeciesReaction
-
- intToString(int) - Static method in class org.sbml.libsbml.SBO
-
Returns the integer as a correctly formatted SBO identifier string.
- INVALID - Static variable in class org.sbml.libsbml.GradientBase
-
- INVALID - Static variable in class org.sbml.libsbml.GraphicalPrimitive2D
-
- Invalid1DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- Invalid2DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- Invalid3DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidAfterXMLContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the error and warning codes
returned by the XML layer in libSBML.
- InvalidApplyCiInLambda - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidAreaRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidAssignRuleVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidCharInXML - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the error and warning codes
returned by the XML layer in libSBML.
- InvalidCiInLambda - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidCompartmentSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidCompartmentTypeRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidCompartmentTypeSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidConstraintContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidConstraintSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidDelaySBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidEventAssignmentSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidEventAssignmentVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidEventSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidFunctionDefReturnType - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidFunctionDefSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidInitAssignSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidInitAssignSymbol - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidKineticLawSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidL1CompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidLengthRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidLocalParameterSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidMathElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidMathMLAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidMetaidSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidModelSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidModifiersList - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidNamespaceOnSBML - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidNameSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidNoArgsPassedToFunctionDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidNotesContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidPackageLevelVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidParameterSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidParameterUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidRateRuleVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidReactantsProductsList - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidReactionSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidRuleOrdering - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidRuleSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSBMLElementSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSBMLLevelVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSBOTermSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSpeciesCompartmentRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSpeciesReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSpeciesReferenceSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSpeciesSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSpeciesSusbstanceUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSpeciesTypeRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSpeciesTypeSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidSubstanceRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidTargetLevelVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidTimeRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidTriggerSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidUnitDefId - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidUnitIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidUnitKind - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidUnitsValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidVolumeRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- InvalidXMLConstruct - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the error and warning codes
returned by the XML layer in libSBML.
- 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
-
Returns true if this token has no attributes.
- isAvogadro() - Method in class org.sbml.libsbml.ASTNode
-
Returns 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
-
Returns 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 built-in SBML
unit, depending on the SBML level, since new predefined units were added
between level 2 versions 1 and 2, and then all predefined units were removed
again in SBML Level 3.
- 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
- isCiNumber() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node represents a MathML
ci element representing a value not a function (e.g., true, Pi).
- 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
-
Returns true (non-zero) if this node represents a MathML
constant (e.g., true, Pi).
- isConstantNumber() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node represents a MathML
constant with numeric value(e.g., 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
- isCSymbolFunction() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node represents a MathML
csymbol representing a function.
- isDimensionless() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit is of the kind
dimensionless.
- isDisabledIgnoredPackage(String) - Method in class org.sbml.libsbml.SBMLDocument
-
Returns true if the given package extension is one of an ignored
packages that has been disabled, otherwise returns false.
- 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
-
Returns true if this token represents an XML element.
- isEllipse() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- isEllipse() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- isEllipse() - Method in class org.sbml.libsbml.Transformation
-
- isEllipse() - Method in class org.sbml.libsbml.Transformation2D
-
- isEmpty() - Method in class org.sbml.libsbml.XMLAttributes
-
Returns true if this list of attributes 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
-
Returns
true if this
XMLTriple object is empty.
- isEnabled() - Method in class org.sbml.libsbml.SBMLExtension
-
Returns true if this package is enabled.
- isEnabled(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Returns true if the given extension is enabled.
- 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
-
Returns true if this token represents an XML end element.
- isEndFor(XMLToken) - Method in class org.sbml.libsbml.XMLToken
-
Returns true if this token represents an XML end element for a
particular 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.XMLInputStream
-
Returns true if end of file (stream) has been reached.
- isEOF() - Method in class org.sbml.libsbml.XMLToken
-
Returns true if this token 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.
- isError() - Method in class org.sbml.libsbml.XMLInputStream
-
Returns true if a fatal error occurred while reading from this
stream.
- 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.
- isFbcAnd() - Method in class org.sbml.libsbml.Association
-
- isFbcAnd() - Method in class org.sbml.libsbml.FbcAssociation
-
- isFbcOr() - Method in class org.sbml.libsbml.Association
-
- isFbcOr() - Method in class org.sbml.libsbml.FbcAssociation
-
- isFunction() - Method in class org.sbml.libsbml.ASTNode
-
Returns 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.
- isGeneProductRef() - Method in class org.sbml.libsbml.Association
-
- isGeneProductRef() - Method in class org.sbml.libsbml.FbcAssociation
-
- isGlobalRenderInformation() - Method in class org.sbml.libsbml.RenderInformationBase
-
- isGlobalStyle() - Method in class org.sbml.libsbml.Style
-
- isGood() - Method in class org.sbml.libsbml.XMLInputStream
-
Returns true if the stream is in a good state.
- 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.
- isIgnoredPkg(String) - Method in class org.sbml.libsbml.SBMLDocument
-
- isImage() - Method in class org.sbml.libsbml.Transformation
-
- isImage() - Method in class org.sbml.libsbml.Transformation2D
-
- isInfinity() - Method in class org.sbml.libsbml.ASTNode
-
Returns 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.
- isInIdList(String) - Method in class org.sbml.libsbml.LocalStyle
-
Checks whether a given id is in the id list.
- isInRoleList(String) - Method in class org.sbml.libsbml.Style
-
Checks whether a given role is in the role list.
- isInteger() - Method in class org.sbml.libsbml.ASTNode
-
Returns 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.
- isInTypeList(String) - Method in class org.sbml.libsbml.Style
-
Checks whether a given type string is in the type list.
- isInUse(SBMLDocument) - Method in class org.sbml.libsbml.LayoutExtension
-
Determines whether this extension is being used by the given
SBMLDocument
- isInUse(SBMLDocument) - Method in class org.sbml.libsbml.RenderExtension
-
Determines whether this extension is being used by the given
SBMLDocument
- isInUse(SBMLDocument) - Method in class org.sbml.libsbml.SBMLExtension
-
Indicates whether this extension is being used by the given
SBMLDocument.
- 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
-
Returns true (non-zero) if this node is a MathML
<lambda>, false (zero) otherwise.
- isLibSBMLCompiledWith(String) - Static method in class org.sbml.libsbml.libsbml
-
Returns an indication whether libSBML has been compiled with
against a specific library.
- isLinearGradient() - Method in class org.sbml.libsbml.GradientBase
-
- isLineEnding() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- isLineEnding() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- isLineEnding() - Method in class org.sbml.libsbml.Transformation
-
- isLineEnding() - Method in class org.sbml.libsbml.Transformation2D
-
- isLitre() - Method in class org.sbml.libsbml.Unit
-
Predicate for testing whether this
Unit is of the kind
litre
- isLocalRenderInformation() - Method in class org.sbml.libsbml.RenderInformationBase
-
- isLocalStyle() - Method in class org.sbml.libsbml.Style
-
- isLog10() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node represents a
log10 function, false (zero) otherwise.
- isLogical() - Method in class org.sbml.libsbml.ASTNode
-
Returns 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
-
Returns true (non-zero) if this node is a user-defined
variable name in SBML L1, L2 (MathML), or the special symbols time
or avogadro. The predicate returns false (zero) otherwise.
- isNamespacesEmpty() - Method in class org.sbml.libsbml.XMLToken
-
Returns true if there are no namespaces declared on this token.
- isNaN() - Method in class org.sbml.libsbml.ASTNode
-
Returns 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
-
Returns 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
-
Returns 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
-
Returns 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
-
Returns true if the named package is enabled.
- 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
-
Returns true (non-zero) if this node is the MathML
<piecewise> construct, false (zero) otherwise.
- isPkgEnabled(String) - Method in class org.sbml.libsbml.SBase
-
- isPkgURIEnabled(String) - Method in class org.sbml.libsbml.SBase
-
- isPolygon() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- isPolygon() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- isPolygon() - Method in class org.sbml.libsbml.Transformation
-
- isPolygon() - Method in class org.sbml.libsbml.Transformation2D
-
- isPopulatedAllElementIdList() - Method in class org.sbml.libsbml.Model
-
Predicate returning true if libSBML has a list of the ids of all
components of this model.
- isPopulatedAllElementMetaIdList() - Method in class org.sbml.libsbml.Model
-
Predicate returning true if libSBML has a list of the metaids of all
components of this model.
- isPopulatedListFormulaUnitsData() - Method in class org.sbml.libsbml.Model
-
Predicate returning true if libSBML has derived units for the
components of this model.
- 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.
- isQuantitativeSystemsDescriptionParameter(long) - Static method in class org.sbml.libsbml.SBO
-
Returns true if the given term identifier comes from the stated branch of SBO.
- isRadialGradient() - Method in class org.sbml.libsbml.GradientBase
-
- 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
-
Returns 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
-
Returns true (non-zero) if this node can represent a
real number, false (zero) otherwise.
- isRectangle() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- isRectangle() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- isRectangle() - Method in class org.sbml.libsbml.Transformation
-
- isRectangle() - Method in class org.sbml.libsbml.Transformation2D
-
- isRegistered(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Returns true if a package extension is registered for the
corresponding package URI.
- isRelational() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node is a MathML
relational operator, meaning ==, >=,
>, <, and !=.
- isRenderCubicBezier() - Method in class org.sbml.libsbml.RenderPoint
-
- isRenderCurve() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- isRenderCurve() - Method in class org.sbml.libsbml.Transformation
-
- isRenderCurve() - Method in class org.sbml.libsbml.Transformation2D
-
- isRenderGroup() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- isRenderGroup() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- isRenderGroup() - Method in class org.sbml.libsbml.Transformation
-
- isRenderGroup() - Method in class org.sbml.libsbml.Transformation2D
-
- isRenderPoint() - Method in class org.sbml.libsbml.RenderPoint
-
- 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
- isSetAbsoluteValue() - Method in class org.sbml.libsbml.RelAbsVector
-
Predicate returning
true if this
RelAbsVector's 'abs' attribute is set.
- isSetActiveObjective() - Method in class org.sbml.libsbml.ListOfObjectives
-
Predicate returning true if this ListOfObjective's 'activeObjective'
attribute is set.
- 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.
- isSetAssociatedSpecies() - Method in class org.sbml.libsbml.GeneProduct
-
Predicate returning
true if this
GeneProduct's 'associatedSpecies'
attribute is set.
- isSetAssociation() - Method in class org.sbml.libsbml.GeneAssociation
-
Predicate returning
true if this
GeneAssociation's 'association'
element is set.
- isSetAssociation() - Method in class org.sbml.libsbml.GeneProductAssociation
-
- isSetBackgroundColor() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'backgroundColor' attribute is set.
- isSetBackgroundColor() - Method in class org.sbml.libsbml.RenderInformationBase
-
- isSetBasePoint1_x() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- isSetBasePoint1_y() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- isSetBasePoint1_z() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- isSetBasePoint2_x() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- isSetBasePoint2_y() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- isSetBasePoint2_z() - Method in class org.sbml.libsbml.RenderCubicBezier
-
- isSetBindingSite1() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- isSetBindingSite2() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- isSetBindingStatus() - Method in class org.sbml.libsbml.OutwardBindingSite
-
- 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.
- isSetBoundingBox() - Method in class org.sbml.libsbml.LineEnding
-
Predicate returning
true if this
LineEnding's 'boundingBox' element is
set.
- isSetCharge() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
-
Predicate returning
true or
false depending on whether this
FbcSpeciesPlugin's 'charge' attribute has been set.
- 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
-
Predicate returning
true or
false depending on whether this
FbcSpeciesPlugin's 'chemicalFormula' attribute has been set.
- isSetClass() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node has a value for the MathML
attribute 'class'.
- isSetCoefficient() - Method in class org.sbml.libsbml.FluxObjective
-
Predicate returning
true if this
FluxObjective's 'coefficient'
attribute is set.
- isSetCompartment() - Method in class org.sbml.libsbml.CompartmentReference
-
- isSetCompartment() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- isSetCompartment() - Method in class org.sbml.libsbml.QualitativeSpecies
-
Predicate returning
true or
false depending on whether this
QualitativeSpecies's 'compartment' attribute has been set.
- 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
-
Returns true if the id of the associated compartment is not the empty
string.
- isSetCompartmentReference() - Method in class org.sbml.libsbml.MultiSimpleSpeciesReferencePlugin
-
- isSetCompartmentReference() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- isSetCompartmentType() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true if this
Compartment object's
'compartmentType' attribute is set.
- isSetCompartmentType() - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
Returns true if this compartment's 'compartmentType' attribute has
been set.
- isSetComponent() - Method in class org.sbml.libsbml.OutwardBindingSite
-
- isSetComponent() - Method in class org.sbml.libsbml.SpeciesFeature
-
Returns
true if this
SpeciesFeature's 'component' attribute has been
set.
- isSetComponent() - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- isSetComponent() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- isSetConstant() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true if this
Compartment object'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.QualitativeSpecies
-
Predicate returning
true or
false depending on whether this
QualitativeSpecies's 'constant' attribute has been 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
-
Predicate returning
true or
false depending on whether this
ReplacedElement's 'conversionFactor' attribute has been set.
- isSetConversionFactor() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true if this
Species object's 'conversionFactor' attribute is set.
- isSetCoordinate() - Method in class org.sbml.libsbml.RelAbsVector
-
Predicate returning
true if this
RelAbsVector's coordinate 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
-
Returns true if the curve consists of one or more segments.
- isSetCurve() - Method in class org.sbml.libsbml.ReactionGlyph
-
Returns true if the curve consists of one or more segments.
- isSetCurve() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Returns true if the curve consists of one or more segments.
- isSetCurve() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Returns true if the curve consists of one or more segments.
- isSetCX() - Method in class org.sbml.libsbml.Ellipse
-
Predicate returning
true if this
Ellipse's 'cx' element is set.
- isSetCx() - Method in class org.sbml.libsbml.RadialGradient
-
Predicate returning
true if this
RadialGradient's 'cx' element is set.
- isSetCY() - Method in class org.sbml.libsbml.Ellipse
-
Predicate returning
true if this
Ellipse's 'cy' element is set.
- isSetCy() - Method in class org.sbml.libsbml.RadialGradient
-
Predicate returning
true if this
RadialGradient's 'cy' element is set.
- isSetCZ() - Method in class org.sbml.libsbml.Ellipse
-
Predicate returning
true if this
Ellipse's 'cz' element is set.
- isSetCz() - Method in class org.sbml.libsbml.RadialGradient
-
Predicate returning
true if this
RadialGradient's 'cz' element is set.
- isSetDashArray() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
Returns true if the dash array has been set or false otherwise.
- isSetDefault_z() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'default_z'
attribute is set.
- isSetDefaultTerm() - Method in class org.sbml.libsbml.ListOfFunctionTerms
-
- isSetDefaultTerm() - Method in class org.sbml.libsbml.Transition
-
Predicate returning
true if the defaultTerm
for this
Transition object has been set.
- isSetDefaultValues() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- isSetDefaultValues() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- 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
-
Predicate returning
true or
false depending on whether this
SBaseRef's 'deletion' attribute has been set.
- isSetEmail() - Method in class org.sbml.libsbml.ModelCreator
-
Predicate returning
true or
false depending on whether this
ModelCreator's 'email' part is set.
- isSetEnableRotationalMapping() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'enableRotationalMapping' attribute is set.
- isSetEnableRotationalMapping() - Method in class org.sbml.libsbml.LineEnding
-
Predicate returning
true if this
LineEnding's 'enableRotationalMapping'
attribute is set.
- isSetEndHead() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'endHead'
attribute is set.
- isSetEndHead() - Method in class org.sbml.libsbml.RenderCurve
-
Predicate returning
true if this
RenderCurve's 'endHead' attribute is
set.
- isSetEndHead() - Method in class org.sbml.libsbml.RenderGroup
-
Predicate returning
true if this
RenderGroup's 'endHead' attribute 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
-
Predicate returning
true or
false depending on whether this
Submodel's 'extentConversionFactor' attribute has been set.
- 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 is set.
- isSetFill() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'fill'
attribute is set.
- isSetFill() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- isSetFillColor() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
Returns true if the fill attribute is set or false otherwise.
- isSetFillRule() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'fill-rule'
attribute is set.
- isSetFillRule() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- isSetFontFamily() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'font-family'
attribute is set.
- isSetFontFamily() - Method in class org.sbml.libsbml.RenderGroup
-
Predicate returning
true if this
RenderGroup's 'font-family' attribute
is set.
- isSetFontFamily() - Method in class org.sbml.libsbml.Text
-
Predicate returning
true if this
Text's 'font-family' attribute is set.
- isSetFontSize() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'font-size'
attribute is set.
- isSetFontSize() - Method in class org.sbml.libsbml.RenderGroup
-
Predicate returning
true if this
RenderGroup's 'font-size' element is
set.
- isSetFontSize() - Method in class org.sbml.libsbml.Text
-
Predicate returning
true if this
Text's 'font-size' element is set.
- isSetFontStyle() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'font-style'
attribute is set.
- isSetFontStyle() - Method in class org.sbml.libsbml.RenderGroup
-
Predicate returning
true if this
RenderGroup's 'font-style' attribute
is set.
- isSetFontStyle() - Method in class org.sbml.libsbml.Text
-
Predicate returning
true if this
Text's 'font-style' attribute is set.
- isSetFontWeight() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'font-weight'
attribute is set.
- isSetFontWeight() - Method in class org.sbml.libsbml.RenderGroup
-
Predicate returning
true if this
RenderGroup's 'font-weight' attribute
is set.
- isSetFontWeight() - Method in class org.sbml.libsbml.Text
-
Predicate returning
true if this
Text's 'font-weight' attribute is set.
- 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.
- isSetFx() - Method in class org.sbml.libsbml.RadialGradient
-
Predicate returning
true if this
RadialGradient's 'fx' element is set.
- isSetFy() - Method in class org.sbml.libsbml.RadialGradient
-
Predicate returning
true if this
RadialGradient's 'fy' element is set.
- isSetFz() - Method in class org.sbml.libsbml.RadialGradient
-
Predicate returning
true if this
RadialGradient's 'fz' element is set.
- isSetGeneProduct() - Method in class org.sbml.libsbml.GeneProductRef
-
Predicate returning
true if this
GeneProductRef's 'geneProduct'
attribute is set.
- isSetGeneProductAssociation() - Method in class org.sbml.libsbml.FbcReactionPlugin
-
Predicate returning
true if this
FbcReactionPlugin's
'GeneProductAssociation' element has been 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
-
Returns true if the id of the associated glyph is not the
empty string.
- isSetGraphicalObjectId() - Method in class org.sbml.libsbml.TextGlyph
-
Returns true if the id of the associated graphical object is not the
empty string.
- isSetGroup() - Method in class org.sbml.libsbml.LineEnding
-
Predicate returning
true if this
LineEnding's 'group' element is set.
- isSetGroup() - Method in class org.sbml.libsbml.Style
-
Predicate returning
true if this
Style's 'group' element is set.
- isSetHasOnlySubstanceUnits() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true if this
Species object's 'hasOnlySubstanceUnits' attribute is set.
- isSetHeight() - Method in class org.sbml.libsbml.Image
-
Predicate returning
true if this
Image's 'height' element is set.
- isSetHeight() - Method in class org.sbml.libsbml.Rectangle
-
Predicate returning
true if this
Rectangle's 'height' attribute is set.
- isSetHref() - Method in class org.sbml.libsbml.Image
-
Predicate returning
true if this
Image's 'href' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node has a value for the MathML
attribute 'id'.
- isSetId() - Method in class org.sbml.libsbml.BoundingBox
-
Predicate returning
true or
false depending on whether this
BoundingBox's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.ColorDefinition
-
- isSetId() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true if this
Compartment object's 'id' attribute
is set.
- isSetId() - Method in class org.sbml.libsbml.CompartmentReference
-
- isSetId() - Method in class org.sbml.libsbml.CompartmentType
-
Predicate returning
true if this
CompartmentType object's 'id'
attribute is set.
- isSetId() - Method in class org.sbml.libsbml.Deletion
-
Predicate returning true or false depending on whether this
object's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.Dimensions
-
Predicate returning
true or
false depending on whether this
Dimensions's 'id' attribute has been set.
- 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.ExternalModelDefinition
-
Predicate returning true or false depending on whether this
object's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.FluxBound
-
Predicate returning
true if this
FluxBound's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.FluxObjective
-
Predicate returning
true if this
FluxObjective's 'id' attribute is
set.
- isSetId() - Method in class org.sbml.libsbml.FunctionDefinition
-
- isSetId() - Method in class org.sbml.libsbml.GeneAssociation
-
- isSetId() - Method in class org.sbml.libsbml.GeneProduct
-
Predicate returning
true if this
GeneProduct's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.GeneProductAssociation
-
- isSetId() - Method in class org.sbml.libsbml.GeneProductRef
-
Predicate returning
true if this
GeneProductRef's 'id' attribute is
set.
- isSetId() - Method in class org.sbml.libsbml.GradientBase
-
Predicate returning
true if this
GradientBase's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.GraphicalObject
-
Predicate returning
true or
false depending on whether this
GraphicalObject's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- isSetId() - Method in class org.sbml.libsbml.Group
-
Predicate returning
true if this
Group's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.Image
-
Predicate returning
true if this
Image's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.Input
-
Predicate returning
true or
false depending on whether this
Input's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- isSetId() - Method in class org.sbml.libsbml.Layout
-
Predicate returning
true or
false depending on whether this
Layout's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.LineEnding
-
Predicate returning
true if this
LineEnding's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.ListOfMembers
-
Predicate returning
true if this
ListOfMembers's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.Member
-
Predicate returning
true if this
Member's 'id' attribute is set.
- 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.MultiSpeciesType
-
- isSetId() - Method in class org.sbml.libsbml.Objective
-
Predicate returning
true if this
Objective's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.Output
-
Predicate returning
true or
false depending on whether this
Output's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.OutwardBindingSite
-
- 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.Point
-
Predicate returning
true or
false depending on whether this
Point's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.Port
-
Predicate returning
true or
false depending on whether this
Port's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
- isSetId() - Method in class org.sbml.libsbml.QualitativeSpecies
-
Predicate returning
true or
false depending on whether this
QualitativeSpecies's 'id' attribute has been 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.RenderInformationBase
-
- isSetId() - Method in class org.sbml.libsbml.SBase
-
Predicate returning true if a call to getId() returns a
non-empty string.
- 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.SpeciesFeature
-
- isSetId() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- 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.SpeciesTypeComponentIndex
-
- isSetId() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- isSetId() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- isSetId() - Method in class org.sbml.libsbml.Style
-
Predicate returning
true if this
Style's 'id' attribute is set.
- isSetId() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- isSetId() - Method in class org.sbml.libsbml.Submodel
-
Predicate returning
true or
false depending on whether this
Submodel's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.Transition
-
Predicate returning
true or
false depending on whether this
Transition's 'id' attribute has been set.
- isSetId() - Method in class org.sbml.libsbml.UnitDefinition
-
Predicate returning
true if this
UnitDefinition's 'id' attribute is set.
- isSetIdAttribute() - Method in class org.sbml.libsbml.SBase
-
Predicate returning true if this object's 'id' attribute is set.
- isSetIdentifyingParent() - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- isSetIdRef() - Method in class org.sbml.libsbml.Member
-
Predicate returning
true if this
Member's 'idRef' attribute is set.
- isSetIdRef() - Method in class org.sbml.libsbml.SBaseRef
-
Predicate returning
true or
false depending on whether this
SBaseRef's 'idRef' attribute has been set.
- isSetImageReference() - Method in class org.sbml.libsbml.Image
-
Returns true if the image reference has been set.
- 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.
- isSetInitialLevel() - Method in class org.sbml.libsbml.QualitativeSpecies
-
Predicate returning
true or
false depending on whether this
QualitativeSpecies's 'initialLevel' attribute has been 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.
- isSetIsType() - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
Returns true if this compartment's 'isType' attribute has been set.
- isSetKind() - Method in class org.sbml.libsbml.Group
-
Predicate returning
true if this
Group's 'kind' attribute 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.
- isSetLabel() - Method in class org.sbml.libsbml.GeneProduct
-
Predicate returning
true if this
GeneProduct's 'label' attribute is
set.
- isSetLengthUnits() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true if this
Model's 'lengthUnits' attribute is set.
- isSetLinearGradient_x1() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'linearGradient_x1' attribute is set.
- isSetLinearGradient_x2() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'linearGradient_x2' attribute is set.
- isSetLinearGradient_y1() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'linearGradient_y1' attribute is set.
- isSetLinearGradient_y2() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'linearGradient_y2' attribute is set.
- isSetLinearGradient_z1() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'linearGradient_z1' attribute is set.
- isSetLinearGradient_z2() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'linearGradient_z2' attribute is set.
- isSetLowerFluxBound() - Method in class org.sbml.libsbml.FbcReactionPlugin
-
Predicate returning
true if this
FbcReactionPlugin's 'lowerFluxBound'
attribute is set.
- isSetMajorVersion() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- isSetMajorVersion() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- 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.FunctionTerm
-
Predicate returning
true or
false depending on whether this
FunctionTerm's 'math' element has been set.
- 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.
- isSetMatrix() - Method in class org.sbml.libsbml.Transformation
-
Returns true if the matrix has been set or false otherwise.
- isSetMaxLevel() - Method in class org.sbml.libsbml.QualitativeSpecies
-
Predicate returning
true or
false depending on whether this
QualitativeSpecies's 'maxLevel' attribute has been set.
- isSetMd5() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
Predicate returning
true or
false depending on whether this
ExternalModelDefinition's 'md5' attribute has been set.
- 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
-
Predicate returning
true or
false depending on whether this
GraphicalObject's 'metaidRef' attribute has been set.
- isSetMetaIdRef() - Method in class org.sbml.libsbml.Member
-
Predicate returning
true if this
Member's 'metaIdRef' attribute is set.
- isSetMetaIdRef() - Method in class org.sbml.libsbml.SBaseRef
-
Predicate returning
true or
false depending on whether this
SBaseRef's 'metaIdRef' attribute has been set.
- isSetMinorVersion() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- isSetMinorVersion() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- isSetModel() - Method in class org.sbml.libsbml.SBMLDocument
-
Returns
true if the
Model object has been set, otherwise
returns
false.
- 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
-
Predicate returning
true or
false depending on whether this
ExternalModelDefinition's 'modelRef' attribute has been set.
- isSetModelRef() - Method in class org.sbml.libsbml.Submodel
-
Predicate returning
true or
false depending on whether this
Submodel's 'modelRef' attribute has been set.
- 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.ColorDefinition
-
Predicate returning
true if this
ColorDefinition's 'name' attribute is
set.
- isSetName() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true if this
Compartment object's 'name'
attribute is set.
- isSetName() - Method in class org.sbml.libsbml.CompartmentReference
-
- isSetName() - Method in class org.sbml.libsbml.CompartmentType
-
Predicate returning
true if this
CompartmentType object's 'name'
attribute is set.
- isSetName() - Method in class org.sbml.libsbml.Deletion
-
Predicate returning true or false depending on whether this
object's 'name' attribute has been 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.ExternalModelDefinition
-
Predicate returning true or false depending on whether this
object's 'name' attribute has been set.
- isSetName() - Method in class org.sbml.libsbml.FluxBound
-
Predicate returning
true if this
FluxBound's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.FluxObjective
-
Predicate returning
true if this
FluxObjective's 'name' attribute is
set.
- isSetName() - Method in class org.sbml.libsbml.FunctionDefinition
-
- isSetName() - Method in class org.sbml.libsbml.GeneProduct
-
Predicate returning
true if this
GeneProduct's 'name' attribute is
set.
- isSetName() - Method in class org.sbml.libsbml.GeneProductAssociation
-
- isSetName() - Method in class org.sbml.libsbml.GeneProductRef
-
Predicate returning
true if this
GeneProductRef's 'name' attribute is
set.
- isSetName() - Method in class org.sbml.libsbml.GradientBase
-
Predicate returning
true if this
GradientBase's 'name' attribute is
set.
- isSetName() - Method in class org.sbml.libsbml.Group
-
Predicate returning
true if this
Group's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.Input
-
Predicate returning
true or
false depending on whether this
Input's 'name' attribute has been set.
- isSetName() - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- isSetName() - Method in class org.sbml.libsbml.Layout
-
Predicate returning
true or
false depending on whether this
Layout's 'name' attribute has been set.
- isSetName() - Method in class org.sbml.libsbml.ListOfMembers
-
Predicate returning
true if this
ListOfMembers's 'name' attribute is
set.
- isSetName() - Method in class org.sbml.libsbml.Member
-
Predicate returning
true if this
Member's 'name' attribute is set.
- 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.ModelCreator
-
Predicate returning
true or
false depending on whether this
ModelCreator's 'fn' part is set (when using vCard4).
- isSetName() - Method in class org.sbml.libsbml.MultiSpeciesType
-
- isSetName() - Method in class org.sbml.libsbml.Objective
-
Predicate returning
true if this
Objective's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.Output
-
Predicate returning
true or
false depending on whether this
Output's 'name' attribute has been set.
- isSetName() - Method in class org.sbml.libsbml.OutwardBindingSite
-
- 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.Port
-
Predicate returning
true or
false depending on whether this
Port's 'name' attribute has been set.
- isSetName() - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
- isSetName() - Method in class org.sbml.libsbml.QualitativeSpecies
-
Predicate returning
true or
false depending on whether this
QualitativeSpecies's 'name' attribute has been 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.RenderInformationBase
-
- isSetName() - Method in class org.sbml.libsbml.SBase
-
Predicate returning true if this
object'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.SpeciesFeature
-
- isSetName() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- 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.SpeciesTypeComponentIndex
-
- isSetName() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- isSetName() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- isSetName() - Method in class org.sbml.libsbml.Style
-
Predicate returning
true if this
Style's 'name' attribute is set.
- isSetName() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- isSetName() - Method in class org.sbml.libsbml.Submodel
-
Predicate returning
true or
false depending on whether this
Submodel's 'name' attribute has been set.
- isSetName() - Method in class org.sbml.libsbml.Transformation
-
Predicate returning
true if this
Transformation's 'name' attribute is
set.
- isSetName() - Method in class org.sbml.libsbml.Transition
-
Predicate returning
true or
false depending on whether this
Transition's 'name' attribute has been 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.
- isSetNumericValue() - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
- isSetObjectRole() - Method in class org.sbml.libsbml.RenderGraphicalObjectPlugin
-
Returns whether the object role has been set or not.
- isSetOccur() - Method in class org.sbml.libsbml.SpeciesFeature
-
- isSetOccur() - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- isSetOffset() - Method in class org.sbml.libsbml.GradientStop
-
Predicate returning
true if this
GradientStop's 'offset' element is
set.
- isSetOffset() - Method in class org.sbml.libsbml.Unit
-
Predicate to test whether the 'offset' attribute of this
Unit
is set.
- isSetOperation() - Method in class org.sbml.libsbml.FluxBound
-
Predicate returning
true if this
FluxBound's 'operation' attribute is
set.
- isSetOrder() - Method in class org.sbml.libsbml.CompartmentGlyph
-
Returns true if the compartment order has been set.
- 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
-
Returns true if the id of the origin of text is not the empty string.
- isSetOutputLevel() - Method in class org.sbml.libsbml.Output
-
Predicate returning
true or
false depending on whether this
Output's 'outputLevel' attribute has been set.
- isSetOutside() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true if this
Compartment object'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.
- isSetParentSBMLObject() - Method in class org.sbml.libsbml.ASTNode
-
Returns true if this node has a value for the parent SBML
object.
- isSetPersistent() - Method in class org.sbml.libsbml.Trigger
-
(SBML Level 3 only) Predicate to test whether the 'persistent'
attribute for this trigger is set.
- isSetPkgRequired(String) - Method in class org.sbml.libsbml.SBMLDocument
-
- isSetPortRef() - Method in class org.sbml.libsbml.SBaseRef
-
Predicate returning
true or
false depending on whether this
SBaseRef's 'portRef' attribute has been set.
- isSetPriority() - Method in class org.sbml.libsbml.Event
-
(SBML Level 3 only) Predicate for testing whether the priority
for this
Event is set.
- isSetProductComponent() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- isSetProgramName() - Method in class org.sbml.libsbml.RenderInformationBase
-
- isSetProgramVersion() - Method in class org.sbml.libsbml.RenderInformationBase
-
- isSetQualitativeSpecies() - Method in class org.sbml.libsbml.Input
-
Predicate returning
true or
false depending on whether this
Input's 'qualitativeSpecies' attribute has been set.
- isSetQualitativeSpecies() - Method in class org.sbml.libsbml.Output
-
Predicate returning
true or
false depending on whether this
Output's 'qualitativeSpecies' attribute has been set.
- isSetR() - Method in class org.sbml.libsbml.RadialGradient
-
- isSetRadialGradient_cx() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'radialGradient_cx' attribute is set.
- isSetRadialGradient_cy() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'radialGradient_cy' attribute is set.
- isSetRadialGradient_cz() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'radialGradient_cz' attribute is set.
- isSetRadialGradient_fx() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'radialGradient_fx' attribute is set.
- isSetRadialGradient_fy() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'radialGradient_fy' attribute is set.
- isSetRadialGradient_fz() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'radialGradient_fz' attribute is set.
- isSetRadialGradient_r() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'radialGradient_r' attribute is set.
- isSetRadiusX() - Method in class org.sbml.libsbml.Rectangle
-
Predicate returning
true if this
Rectangle's 'rX' attribute is set.
- isSetRadiusY() - Method in class org.sbml.libsbml.Rectangle
-
Predicate returning
true if this
Rectangle's 'rY' attribute is set.
- isSetRatio() - Method in class org.sbml.libsbml.Ellipse
-
Predicate returning
true if this
Ellipse's 'ratio' attribute is set.
- isSetRatio() - Method in class org.sbml.libsbml.Rectangle
-
Predicate returning
true if this
Rectangle's 'ratio' attribute is set.
- isSetReactant() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- isSetReactantComponent() - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- isSetReaction() - Method in class org.sbml.libsbml.FluxBound
-
Predicate returning
true if this
FluxBound's 'reaction' attribute is
set.
- isSetReaction() - Method in class org.sbml.libsbml.FluxObjective
-
Predicate returning
true if this
FluxObjective's 'reaction' attribute
is set.
- isSetReaction() - Method in class org.sbml.libsbml.GeneAssociation
-
Predicate returning
true if this
GeneAssociation's 'reaction'
attribute is set.
- isSetReactionId() - Method in class org.sbml.libsbml.ReactionGlyph
-
Returns true if the id of the associated reaction is not the empty
string.
- isSetReference() - Method in class org.sbml.libsbml.Association
-
Predicate returning
true if this
Association's 'reference' attribute
has been set.
- isSetReferenceId() - Method in class org.sbml.libsbml.GeneralGlyph
-
Returns true if the id of the associated element is not the empty
string.
- isSetReferenceId() - Method in class org.sbml.libsbml.ReferenceGlyph
-
Returns true if the id of the associated reference is not the
empty string.
- isSetReferenceRenderInformation() - Method in class org.sbml.libsbml.RenderInformationBase
-
- isSetRelation() - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- isSetRelativeValue() - Method in class org.sbml.libsbml.RelAbsVector
-
Predicate returning
true if this
RelAbsVector's 'rel' attribute is set.
- isSetReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
-
- isSetRepresentationType() - Method in class org.sbml.libsbml.MultiASTPlugin
-
Predicate returning
true if this
MultiASTPlugin's 'representationType' attribute is set.
- isSetRequired() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
-
Returns the value of the 'required' attribute.
- isSetResultLevel() - Method in class org.sbml.libsbml.DefaultTerm
-
Predicate returning
true or
false depending on whether this
DefaultTerm's 'resultLevel' attribute has been set.
- isSetResultLevel() - Method in class org.sbml.libsbml.FunctionTerm
-
Predicate returning
true or
false depending on whether this
FunctionTerm's 'resultLevel' 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
-
Returns true of role is different from the empty string.
- isSetRole() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
- isSetRX() - Method in class org.sbml.libsbml.Ellipse
-
Predicate returning
true if this
Ellipse's 'rx' element is set.
- isSetRX() - Method in class org.sbml.libsbml.Rectangle
-
Predicate returning
true if this
Rectangle's 'rX' attribute is set.
- isSetRY() - Method in class org.sbml.libsbml.Ellipse
-
Predicate returning
true if this
Ellipse's 'ry' element is set.
- isSetRY() - Method in class org.sbml.libsbml.Rectangle
-
Predicate returning
true if this
Rectangle's 'rY' attribute is set.
- isSetSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
-
Predicate for testing whether the sBaseRef for this
SBaseRef is set.
- 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.
- isSetSign() - Method in class org.sbml.libsbml.Input
-
Predicate returning
true or
false depending on whether this
Input's 'sign' attribute has been set.
- isSetSize() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true if this
Compartment object's 'size'
attribute is set.
- isSetSource() - Method in class org.sbml.libsbml.ExternalModelDefinition
-
Predicate returning
true or
false depending on whether this
ExternalModelDefinition's 'source' attribute has been set.
- isSetSpatialDimensions() - Method in class org.sbml.libsbml.Compartment
-
Predicate returning
true if this
Compartment object'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
-
- isSetSpeciesFeatureType() - Method in class org.sbml.libsbml.SpeciesFeature
-
Returns
true if this
SpeciesFeature's 'speciesFeatureType' attribute
has been set.
- isSetSpeciesGlyphId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Returns true if the id of the associated species glyph is not the
empty string.
- isSetSpeciesId() - Method in class org.sbml.libsbml.SpeciesGlyph
-
Returns true if the id of the associated species object is not the
empty string.
- isSetSpeciesReference() - Method in class org.sbml.libsbml.MultiASTPlugin
-
Predicate returning
true if this
MultiASTPlugin's 'speciesReference' attribute is set.
- isSetSpeciesReferenceId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Returns true if the id of the associated species reference is not the
empty string.
- isSetSpeciesType() - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
Returns
true if the 'speciesType' attribute of this 'multi'
Species
has been set.
- isSetSpeciesType() - Method in class org.sbml.libsbml.Species
-
Predicate returning
true if this
Species object's
'speciesType' attribute is set.
- isSetSpeciesType() - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- isSetSpreadMethod() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'spreadMethod' attribute is set.
- isSetSpreadMethod() - Method in class org.sbml.libsbml.GradientBase
-
Predicate returning
true if this
GradientBase's 'spreadMethod'
attribute is set.
- isSetStartHead() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'startHead'
attribute is set.
- isSetStartHead() - Method in class org.sbml.libsbml.RenderCurve
-
Predicate returning
true if this
RenderCurve's 'startHead' attribute is
set.
- isSetStartHead() - Method in class org.sbml.libsbml.RenderGroup
-
Predicate returning
true if this
RenderGroup's 'startHead' 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
- isSetStopColor() - Method in class org.sbml.libsbml.GradientStop
-
Predicate returning
true if this
GradientStop's 'stop-color' attribute
is set.
- isSetStrict() - Method in class org.sbml.libsbml.FbcModelPlugin
-
Predicate returning
true if this
FbcModelPlugin's 'strict' attribute
is set.
- isSetStroke() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'stroke'
attribute is set.
- isSetStroke() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- isSetStrokeDashArray() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- isSetStrokeWidth() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'stroke-width'
attribute is set.
- isSetStrokeWidth() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- isSetStyle() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node has a value for the MathML
attribute 'style'.
- isSetSubmodelRef() - Method in class org.sbml.libsbml.Replacing
-
Predicate returning
true or
false depending on whether this
SBaseRef's 'submodelRef' attribute has been set.
- isSetSubstanceConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
Returns false, since 'substanceConversionFactor' is not a part of the comp spec.
- 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.Text
-
Returns true if the text is set to something else than the empty string.
- isSetText() - Method in class org.sbml.libsbml.TextGlyph
-
Returns true if the text is not the empty string.
- isSetTextAnchor() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's 'text-anchor'
attribute is set.
- isSetTextAnchor() - Method in class org.sbml.libsbml.RenderGroup
-
Predicate returning
true if this
RenderGroup's 'text-anchor' attribute
is set.
- isSetTextAnchor() - Method in class org.sbml.libsbml.Text
-
Predicate returning
true if this
Text's 'text-anchor' attribute is set.
- isSetThresholdLevel() - Method in class org.sbml.libsbml.Input
-
Predicate returning
true or
false depending on whether this
Input's 'thresholdLevel' attribute has been set.
- isSetTimeConversionFactor() - Method in class org.sbml.libsbml.Submodel
-
Predicate returning
true or
false depending on whether this
Submodel's 'timeConversionFactor' attribute has been set.
- 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.
- isSetTransform() - Method in class org.sbml.libsbml.Transformation
-
Predicate returning
true if this
Transformation's 'transform' attribute
is set.
- isSetTransformer() - Method in class org.sbml.libsbml.CompModelPlugin
-
- isSetTransitionEffect() - Method in class org.sbml.libsbml.Input
-
Predicate returning
true or
false depending on whether this
Input's 'transitionEffect' attribute has been set.
- isSetTransitionEffect() - Method in class org.sbml.libsbml.Output
-
Predicate returning
true or
false depending on whether this
Output's 'transitionEffect' attribute has been 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
-
Predicate returning
true if this
Association's 'type' attribute is
set.
- isSetType() - Method in class org.sbml.libsbml.Objective
-
Predicate returning
true if this
Objective's 'type' attribute is set.
- isSetUnitRef() - Method in class org.sbml.libsbml.SBaseRef
-
Predicate returning
true or
false depending on whether this
SBaseRef's 'unitRef' attribute has been set.
- isSetUnits() - Method in class org.sbml.libsbml.ASTNode
-
Returns 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 object'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.
- isSetUpperFluxBound() - Method in class org.sbml.libsbml.FbcReactionPlugin
-
Predicate returning
true if this
FbcReactionPlugin's 'upperFluxBound'
attribute is set.
- isSetUserData() - Method in class org.sbml.libsbml.ASTNode
-
Returns true if this node has a user data object.
- isSetUserData() - Method in class org.sbml.libsbml.SBase
-
Predicate returning true or false depending on whether
the user data of this element has been 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.ColorDefinition
-
Predicate returning
true if this
ColorDefinition's 'value' attribute is
set.
- isSetValue() - Method in class org.sbml.libsbml.FluxBound
-
Predicate returning
true if this
FluxBound's 'value' attribute is
set.
- isSetValue() - Method in class org.sbml.libsbml.Parameter
-
Predicate returning
true if the
'value' attribute of this
Parameter is set.
- isSetValue() - Method in class org.sbml.libsbml.SpeciesFeatureValue
-
- 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 object's 'volume'
attribute is set.
- isSetVolumeUnits() - Method in class org.sbml.libsbml.Model
-
Predicate returning
true if this
Model's 'volumeUnits' attribute is set.
- isSetVTextAnchor() - Method in class org.sbml.libsbml.DefaultValues
-
Predicate returning
true if this
DefaultValues object's
'vtext-anchor' attribute is set.
- isSetVTextAnchor() - Method in class org.sbml.libsbml.RenderGroup
-
Predicate returning
true if this
RenderGroup's 'vtext-anchor' attribute
is set.
- isSetVTextAnchor() - Method in class org.sbml.libsbml.Text
-
Predicate returning
true if this
Text's 'vtext-anchor' attribute is
set.
- isSetWidth() - Method in class org.sbml.libsbml.Image
-
Predicate returning
true if this
Image's 'width' element is set.
- isSetWidth() - Method in class org.sbml.libsbml.Rectangle
-
Predicate returning
true if this
Rectangle's 'width' attribute is set.
- isSetX() - Method in class org.sbml.libsbml.Image
-
Predicate returning
true if this
Image's 'x' element is set.
- isSetX() - Method in class org.sbml.libsbml.Rectangle
-
Predicate returning
true if this
Rectangle's 'x' attribute is set.
- isSetX() - Method in class org.sbml.libsbml.RenderPoint
-
Predicate returning
true if this
RenderPoint's 'x' element is set.
- isSetX() - Method in class org.sbml.libsbml.Text
-
Predicate returning
true if this
Text's 'x' element is set.
- isSetX1() - Method in class org.sbml.libsbml.LinearGradient
-
Predicate returning
true if this
LinearGradient's 'x1' element is set.
- isSetX2() - Method in class org.sbml.libsbml.LinearGradient
-
Predicate returning
true if this
LinearGradient's 'x2' element is set.
- isSetY() - Method in class org.sbml.libsbml.Image
-
Predicate returning
true if this
Image's 'y' element is set.
- isSetY() - Method in class org.sbml.libsbml.Rectangle
-
Predicate returning
true if this
Rectangle's 'y' attribute is set.
- isSetY() - Method in class org.sbml.libsbml.RenderPoint
-
Predicate returning
true if this
RenderPoint's 'y' element is set.
- isSetY() - Method in class org.sbml.libsbml.Text
-
Predicate returning
true if this
Text's 'y' element is set.
- isSetY1() - Method in class org.sbml.libsbml.LinearGradient
-
Predicate returning
true if this
LinearGradient's 'y1' element is set.
- isSetY2() - Method in class org.sbml.libsbml.LinearGradient
-
Predicate returning
true if this
LinearGradient's 'y2' element is set.
- isSetZ() - Method in class org.sbml.libsbml.Image
-
Predicate returning
true if this
Image's 'z' element is set.
- isSetZ() - Method in class org.sbml.libsbml.Rectangle
-
Predicate returning
true if this
Rectangle's 'z' attribute is set.
- isSetZ() - Method in class org.sbml.libsbml.RenderPoint
-
Predicate returning
true if this
RenderPoint's 'z' element is set.
- isSetZ() - Method in class org.sbml.libsbml.Text
-
Predicate returning
true if this
Text's 'z' element is set.
- isSetZ1() - Method in class org.sbml.libsbml.LinearGradient
-
Predicate returning
true if this
LinearGradient's 'z1' element is set.
- isSetZ2() - Method in class org.sbml.libsbml.LinearGradient
-
Predicate returning
true if this
LinearGradient's 'z2' element is set.
- isSeverityOverridden() - Method in class org.sbml.libsbml.XMLErrorLog
-
Returns a boolean indicating whether or not the severity has been
overridden.
- 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
-
Returns true (non-zero) if this node represents a
square root function, false (zero) otherwise.
- isStart() - Method in class org.sbml.libsbml.XMLToken
-
Returns true if this token represents 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
- isStripAllUnrecognizedPackages() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
-
- isSupported(String) - Method in class org.sbml.libsbml.SBMLExtension
-
Returns true if the given XML namespace URI is supported by this
package extension.
- 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.GraphicalPrimitive1D
-
- isText() - Method in class org.sbml.libsbml.Transformation
-
- isText() - Method in class org.sbml.libsbml.Transformation2D
-
- isText() - Method in class org.sbml.libsbml.XMLToken
-
Returns true if this token represents an XML text element.
- isUMinus() - Method in class org.sbml.libsbml.ASTNode
-
Returns 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
-
Returns true (non-zero) if this node has an unknown type.
- isUPlus() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node is a unary plus
operator, false (zero) otherwise.
- isUserFunction() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node represents a
MathML user-defined function.
- 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 or false depending on whether the argument
string conforms to the syntax of SBML identifiers.
- isValidTypeForList(SBase) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- isValidTypeForList(SBase) - Method in class org.sbml.libsbml.SBasePlugin
-
- 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.
- isValidXMLanyURI(String) - Static method in class org.sbml.libsbml.SyntaxChecker
-
Returns true or false depending on whether the uri argument string
conforms to the XML data type anyURI.
- 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(boolean) - 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'.
- 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(boolean) - Method in class org.sbml.libsbml.UnitDefinition
-
Convenience function for testing if a given unit definition is a
variant of the unit 'dimensionless'.
- 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(boolean) - 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'.
- 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(boolean) - 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'.
- 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(boolean) - 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'.
- 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(boolean) - 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'.
- 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(boolean) - 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'.
- 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(boolean) - 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'.
- 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
-
Returns
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).
- RadialGradient - Class in org.sbml.libsbml
-
render
Representation of a radial gradient.
- RadialGradient(long, long, long) - Constructor for class org.sbml.libsbml.RadialGradient
-
Creates a new
RadialGradient using the given SBML Level, Version and
“render” package version.
- RadialGradient(long, long) - Constructor for class org.sbml.libsbml.RadialGradient
-
Creates a new
RadialGradient using the given SBML Level, Version and
“render” package version.
- RadialGradient(long) - Constructor for class org.sbml.libsbml.RadialGradient
-
Creates a new
RadialGradient using the given SBML Level, Version and
“render” package version.
- RadialGradient() - Constructor for class org.sbml.libsbml.RadialGradient
-
Creates a new
RadialGradient using the given SBML Level, Version and
“render” package version.
- RadialGradient(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RadialGradient
-
- RadialGradient(XMLNode, long) - Constructor for class org.sbml.libsbml.RadialGradient
-
- RadialGradient(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.RadialGradient
-
- RadialGradient(RadialGradient) - Constructor for class org.sbml.libsbml.RadialGradient
-
- RateOfSpeciesTargetCompartmentNot - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RateOfTargetCannotBeAssigned - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RateOfTargetMustBeCi - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RateRule - Class in org.sbml.libsbml
-
An SBML rate rule representing dx/dt = f(Y).
- RateRule(long, long) - Constructor for class org.sbml.libsbml.RateRule
-
Creates a new
RateRule using the given SBML
level and
version
values.
- RateRule(SBMLNamespaces) - Constructor for class org.sbml.libsbml.RateRule
-
- RateRuleCompartmentMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RateRuleForConstantEntity - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RateRuleParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RateRuleSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RateRuleStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RDFAboutTagNotMetaid - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RDFAnnotationParser - Class in org.sbml.libsbml
-
MIRIAM-compliant RDF annotation reader/writer.
- RDFAnnotationParser() - Constructor for class org.sbml.libsbml.RDFAnnotationParser
-
- RDFEmptyAboutTag - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RDFMissingAboutTag - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RDFNotCompleteModelHistory - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RDFNotModelHistory - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- Reaction - Class in org.sbml.libsbml
-
An SBML reaction between species in an SBML model.
- Reaction(long, long) - Constructor for class org.sbml.libsbml.Reaction
-
Creates a new
Reaction using the given SBML
level and
version
values.
- Reaction(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Reaction
-
- Reaction(Reaction) - Constructor for class org.sbml.libsbml.Reaction
-
Copy constructor; creates a copy of this
Reaction.
- ReactionGlyph - Class in org.sbml.libsbml
-
layout
A glyph for an SBML reaction.
- ReactionGlyph(long, long, long) - Constructor for class org.sbml.libsbml.ReactionGlyph
-
- ReactionGlyph(long, long) - Constructor for class org.sbml.libsbml.ReactionGlyph
-
- ReactionGlyph(long) - Constructor for class org.sbml.libsbml.ReactionGlyph
-
- ReactionGlyph() - Constructor for class org.sbml.libsbml.ReactionGlyph
-
- ReactionGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ReactionGlyph
-
- ReactionGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.ReactionGlyph
-
- ReactionGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.ReactionGlyph
-
Creates a ResctionGlyph with the given
LayoutPkgNamespaces, id and set the id of the
associated reaction to the second argument.
- ReactionGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.ReactionGlyph
-
- ReactionGlyph(XMLNode) - Constructor for class org.sbml.libsbml.ReactionGlyph
-
- ReactionGlyph(ReactionGlyph) - Constructor for class org.sbml.libsbml.ReactionGlyph
-
Copy constructor.
- readMathMLFromString(String) - Static method in class org.sbml.libsbml.libsbml
-
Reads the MathML from the given XML string, constructs a corresponding
abstract syntax tree, and returns a pointer to the root of the tree.
- readMathMLFromStringWithNamespaces(String, XMLNamespaces) - Static method in class org.sbml.libsbml.libsbml
-
Reads the MathML from the given XML string, constructs a corresponding
abstract syntax tree, and returns a pointer to the root of the tree.
- readSBML(String) - Static method in class org.sbml.libsbml.libsbml
-
Reads an SBML document from the given file.
- readSBML(String) - Method in class org.sbml.libsbml.SBMLReader
-
Reads an SBML document from the given file.
- readSBMLFromFile(String) - Static method in class org.sbml.libsbml.libsbml
-
Reads an SBML document from the given file.
- readSBMLFromFile(String) - Method in class org.sbml.libsbml.SBMLReader
-
Reads an SBML document from the given file.
- readSBMLFromString(String) - Static method in class org.sbml.libsbml.libsbml
-
Reads an SBML document from a text string.
- readSBMLFromString(String) - Method in class org.sbml.libsbml.SBMLReader
-
Reads an SBML document from a text string.
- Rectangle - Class in org.sbml.libsbml
-
render
Representation of a rectangle.
- Rectangle(long, long, long) - Constructor for class org.sbml.libsbml.Rectangle
-
Creates a new
Rectangle using the given SBML Level, Version and
“render” package version.
- Rectangle(long, long) - Constructor for class org.sbml.libsbml.Rectangle
-
Creates a new
Rectangle using the given SBML Level, Version and
“render” package version.
- Rectangle(long) - Constructor for class org.sbml.libsbml.Rectangle
-
Creates a new
Rectangle using the given SBML Level, Version and
“render” package version.
- Rectangle() - Constructor for class org.sbml.libsbml.Rectangle
-
Creates a new
Rectangle using the given SBML Level, Version and
“render” package version.
- Rectangle(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.Rectangle
-
- Rectangle(XMLNode, long) - Constructor for class org.sbml.libsbml.Rectangle
-
- Rectangle(XMLNode) - Constructor for class org.sbml.libsbml.Rectangle
-
- Rectangle(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.Rectangle
-
- Rectangle(RenderPkgNamespaces, String, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Rectangle
-
- Rectangle(RenderPkgNamespaces, String, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Rectangle
-
- Rectangle(Rectangle) - Constructor for class org.sbml.libsbml.Rectangle
-
- RecursiveCompartmentContainment - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RecursiveFunctionDefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- reduceToBinary() - Method in class org.sbml.libsbml.ASTNode
-
Reduces this
ASTNode to a binary tree.
- ReferenceGlyph - Class in org.sbml.libsbml
-
layout
Connection between an object and a glyph.
- ReferenceGlyph(long, long, long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
-
Creates a new
ReferenceGlyph with the given SBML level, version and
package version.
- ReferenceGlyph(long, long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
-
Creates a new
ReferenceGlyph with the given SBML level, version and
package version.
- ReferenceGlyph(long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
-
Creates a new
ReferenceGlyph with the given SBML level, version and
package version.
- ReferenceGlyph() - Constructor for class org.sbml.libsbml.ReferenceGlyph
-
Creates a new
ReferenceGlyph with the given SBML level, version and
package version.
- ReferenceGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ReferenceGlyph
-
Constructor.
- ReferenceGlyph(LayoutPkgNamespaces, String, String, String, String) - Constructor for class org.sbml.libsbml.ReferenceGlyph
-
- ReferenceGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
-
- ReferenceGlyph(XMLNode) - Constructor for class org.sbml.libsbml.ReferenceGlyph
-
- ReferenceGlyph(ReferenceGlyph) - Constructor for class org.sbml.libsbml.ReferenceGlyph
-
Copy constructor.
- REFLECT - Static variable in class org.sbml.libsbml.GradientBase
-
- RelAbsVector - Class in org.sbml.libsbml
-
render
Vectors with an absolute value and a relative value.
- RelAbsVector(double, double) - Constructor for class org.sbml.libsbml.RelAbsVector
-
Constructor with two values.
- RelAbsVector(double) - Constructor for class org.sbml.libsbml.RelAbsVector
-
Constructor with two values.
- RelAbsVector() - Constructor for class org.sbml.libsbml.RelAbsVector
-
Constructor with two values.
- RelAbsVector(String) - Constructor for class org.sbml.libsbml.RelAbsVector
-
Constructor with a value string.
- RelAbsVector(RelAbsVector) - Constructor for class org.sbml.libsbml.RelAbsVector
-
- Relation_fromString(String) - Static method in class org.sbml.libsbml.libsbml
-
Returns the
Relation_t enumeration corresponding to the given string or
MULTI_RELATION_UNKNOWN if there is no such match.
- Relation_toString(int) - Static method in class org.sbml.libsbml.libsbml
-
Returns the string version of the provided Relation_t enumeration.
- relativeTo(String) - Method in class org.sbml.libsbml.SBMLUri
-
Constructs a new URI relative to this object and the given URI.
- remove(long) - Method in class org.sbml.libsbml.ASTNodeList
-
Removes the
nth
ASTNode object from this list and
returns it.
- remove(long) - Method in class org.sbml.libsbml.CVTermList
-
Removes the
nth
CVTerm object from this list and
returns it.
- remove(long) - Method in class org.sbml.libsbml.DateList
-
Removes the
nth
Date object from this list and
returns it.
- remove(long) - Method in class org.sbml.libsbml.ListOf
-
Removes the
nth item from this
ListOf list of items and returns
it.
- remove(long) - Method in class org.sbml.libsbml.ListOfColorDefinitions
-
- remove(String) - Method in class org.sbml.libsbml.ListOfColorDefinitions
-
- remove(long) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
- remove(String) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
-
- remove(long) - Method in class org.sbml.libsbml.ListOfCompartmentReferences
-
- remove(String) - Method in class org.sbml.libsbml.ListOfCompartmentReferences
-
- remove(long) - Method in class org.sbml.libsbml.ListOfCompartments
-
- remove(String) - Method in class org.sbml.libsbml.ListOfCompartments
-
- remove(long) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
-
- remove(String) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
-
- remove(long) - Method in class org.sbml.libsbml.ListOfConstraints
-
- remove(long) - Method in class org.sbml.libsbml.ListOfCurveElements
-
- remove(String) - Method in class org.sbml.libsbml.ListOfCurveElements
-
- remove(long) - Method in class org.sbml.libsbml.ListOfDeletions
-
Removes the nth item from this
ListOfDeletions items and returns a
pointer to it.
- remove(String) - Method in class org.sbml.libsbml.ListOfDeletions
-
Removes an item from this
ListOfDeletions items based on its identifier
and returns a pointer to it.
- remove(long) - Method in class org.sbml.libsbml.ListOfDrawables
-
- remove(String) - Method in class org.sbml.libsbml.ListOfDrawables
-
- remove(long) - Method in class org.sbml.libsbml.ListOfEventAssignments
-
- remove(String) - Method in class org.sbml.libsbml.ListOfEventAssignments
-
- remove(long) - Method in class org.sbml.libsbml.ListOfEvents
-
Removes the nth item from this
ListOfEvents items and returns a pointer to
it.
- remove(String) - Method in class org.sbml.libsbml.ListOfEvents
-
Removes item in this
ListOfEvents items with the given identifier.
- remove(long) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
-
- remove(String) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
-
- remove(long) - Method in class org.sbml.libsbml.ListOfFbcAssociations
-
- remove(String) - Method in class org.sbml.libsbml.ListOfFbcAssociations
-
- remove(long) - Method in class org.sbml.libsbml.ListOfFluxBounds
-
Removes the nth item from this
ListOfFluxBounds items and returns a pointer to
it.
- remove(String) - Method in class org.sbml.libsbml.ListOfFluxBounds
-
- remove(long) - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
- remove(String) - Method in class org.sbml.libsbml.ListOfFluxObjectives
-
- remove(long) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
-
- remove(String) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
-
- remove(long) - Method in class org.sbml.libsbml.ListOfFunctionTerms
-
- remove(String) - Method in class org.sbml.libsbml.ListOfFunctionTerms
-
- remove(long) - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
- remove(String) - Method in class org.sbml.libsbml.ListOfGeneAssociations
-
- remove(long) - Method in class org.sbml.libsbml.ListOfGeneProducts
-
- remove(String) - Method in class org.sbml.libsbml.ListOfGeneProducts
-
- remove(long) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- remove(String) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- remove(long) - Method in class org.sbml.libsbml.ListOfGlobalStyles
-
- remove(String) - Method in class org.sbml.libsbml.ListOfGlobalStyles
-
- remove(long) - Method in class org.sbml.libsbml.ListOfGradientDefinitions
-
- remove(String) - Method in class org.sbml.libsbml.ListOfGradientDefinitions
-
- remove(long) - Method in class org.sbml.libsbml.ListOfGradientStops
-
- remove(String) - Method in class org.sbml.libsbml.ListOfGradientStops
-
- remove(long) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
- remove(String) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
-
- remove(long) - Method in class org.sbml.libsbml.ListOfGroups
-
- remove(String) - Method in class org.sbml.libsbml.ListOfGroups
-
Removes the
Group from this
ListOfGroups based on its identifier and
returns a pointer to it.
- remove(long) - Method in class org.sbml.libsbml.ListOfInitialAssignments
-
- remove(String) - Method in class org.sbml.libsbml.ListOfInitialAssignments
-
- remove(long) - Method in class org.sbml.libsbml.ListOfInputs
-
- remove(String) - Method in class org.sbml.libsbml.ListOfInputs
-
Removes the
Input from this
ListOfInputs with the given identifier
and returns a pointer to it.
- remove(long) - Method in class org.sbml.libsbml.ListOfInSpeciesTypeBonds
-
- remove(String) - Method in class org.sbml.libsbml.ListOfInSpeciesTypeBonds
-
- remove(long) - Method in class org.sbml.libsbml.ListOfLayouts
-
Removes the nth item from this
ListOfLayouts items and returns a pointer to
it.
- remove(String) - Method in class org.sbml.libsbml.ListOfLayouts
-
Removes item in this
ListOfLayouts items with the given identifier.
- remove(long) - Method in class org.sbml.libsbml.ListOfLineEndings
-
- remove(String) - Method in class org.sbml.libsbml.ListOfLineEndings
-
- remove(long) - Method in class org.sbml.libsbml.ListOfLineSegments
-
- remove(long) - Method in class org.sbml.libsbml.ListOfLocalParameters
-
- remove(String) - Method in class org.sbml.libsbml.ListOfLocalParameters
-
- remove(long) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- remove(String) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- remove(long) - Method in class org.sbml.libsbml.ListOfLocalStyles
-
- remove(String) - Method in class org.sbml.libsbml.ListOfLocalStyles
-
- remove(long) - Method in class org.sbml.libsbml.ListOfMembers
-
- remove(String) - Method in class org.sbml.libsbml.ListOfMembers
-
Removes the
Member from this
ListOfMembers based on its identifier and
returns a pointer to it.
- remove(long) - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
- remove(String) - Method in class org.sbml.libsbml.ListOfModelDefinitions
-
- remove(long) - Method in class org.sbml.libsbml.ListOfMultiSpeciesTypes
-
- remove(String) - Method in class org.sbml.libsbml.ListOfMultiSpeciesTypes
-
- remove(long) - Method in class org.sbml.libsbml.ListOfObjectives
-
- remove(String) - Method in class org.sbml.libsbml.ListOfObjectives
-
- remove(long) - Method in class org.sbml.libsbml.ListOfOutputs
-
- remove(String) - Method in class org.sbml.libsbml.ListOfOutputs
-
Removes the
Output from this
ListOfOutputs with the given identifier
and returns a pointer to it.
- remove(long) - Method in class org.sbml.libsbml.ListOfOutwardBindingSites
-
- remove(String) - Method in class org.sbml.libsbml.ListOfOutwardBindingSites
-
- remove(long) - Method in class org.sbml.libsbml.ListOfParameters
-
- remove(String) - Method in class org.sbml.libsbml.ListOfParameters
-
- remove(String) - Method in class org.sbml.libsbml.ListOfPorts
-
Removes an item from this
ListOfPorts items based on the identifier and
returns a pointer to it.
- remove(long) - Method in class org.sbml.libsbml.ListOfPorts
-
Removes the nth item from this
ListOfPorts items and returns a pointer
to it.
- remove(long) - Method in class org.sbml.libsbml.ListOfPossibleSpeciesFeatureValues
-
- remove(String) - Method in class org.sbml.libsbml.ListOfPossibleSpeciesFeatureValues
-
- remove(long) - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
-
- remove(String) - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
-
- remove(long) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
- remove(String) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
-
- remove(long) - Method in class org.sbml.libsbml.ListOfReactions
-
Removes the nth item from this
ListOfReactions items and returns a
pointer to it.
- remove(String) - Method in class org.sbml.libsbml.ListOfReactions
-
- remove(long) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
-
- remove(String) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
-
- remove(long) - Method in class org.sbml.libsbml.ListOfReplacedElements
-
- remove(long) - Method in class org.sbml.libsbml.ListOfRules
-
Removes the nth item from this
ListOfRules items and returns a pointer to
it.
- remove(String) - Method in class org.sbml.libsbml.ListOfRules
-
Removes item in this
ListOfRules items with the given identifier.
- remove(long) - Method in class org.sbml.libsbml.ListOfSpecies
-
Removes the nth item from this ListOfSpeciess items and returns a pointer to
it.
- remove(String) - Method in class org.sbml.libsbml.ListOfSpecies
-
Removes item in this ListOfSpeciess items with the given identifier.
- remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
- remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
- remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesFeatureTypes
-
- remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesFeatureTypes
-
- remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesFeatureValues
-
- remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesFeatureValues
-
- remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
-
- remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
-
- remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
- remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
-
- remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
-
- remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
-
- remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentIndexes
-
- remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentIndexes
-
- remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentMapInProducts
-
- remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypeComponentMapInProducts
-
- remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypeInstances
-
- remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypeInstances
-
- remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
-
- remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
-
- remove(long) - Method in class org.sbml.libsbml.ListOfSubmodels
-
Removes the nth item from this
ListOfSubmodels items and returns a
pointer to it.
- remove(String) - Method in class org.sbml.libsbml.ListOfSubmodels
-
Removes an item from this
ListOfSubmodels items based on its identifier
and returns a pointer to it.
- remove(long) - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
Removes the nth item from this
ListOfTextGlyphs items and returns a pointer to
it.
- remove(String) - Method in class org.sbml.libsbml.ListOfTextGlyphs
-
- remove(long) - Method in class org.sbml.libsbml.ListOfTransitions
-
- remove(String) - Method in class org.sbml.libsbml.ListOfTransitions
-
- remove(long) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
-
- remove(String) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
-
- remove(long) - Method in class org.sbml.libsbml.ListOfUnits
-
Removes the nth item from this
ListOfUnits items and returns a pointer to
it.
- remove(long) - Method in class org.sbml.libsbml.ModelCreatorList
-
Removes the
nth
ModelCreator object from this list and
returns it.
- remove(long) - Method in class org.sbml.libsbml.SBaseList
-
Removes the
nth
SBase object from this list and
returns it.
- remove(long) - Method in class org.sbml.libsbml.SBMLErrorLog
-
Removes an error having errorId from the
SBMLError list.
- remove(long) - Method in class org.sbml.libsbml.SBMLNamespacesList
-
- remove(long) - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- remove(String) - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- remove(int) - Method in class org.sbml.libsbml.XMLAttributes
-
Removes the nth attribute from this list of attributes.
- remove(String, String) - Method in class org.sbml.libsbml.XMLAttributes
-
Removes a named attribute from this list of attributes.
- remove(String) - Method in class org.sbml.libsbml.XMLAttributes
-
Removes a named attribute from this list of attributes.
- remove(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
-
Removes a specific attribute from this list of attributes.
- remove(int) - Method in class org.sbml.libsbml.XMLNamespaces
-
Removes an XML Namespace stored in the given position of this list.
- remove(String) - Method in class org.sbml.libsbml.XMLNamespaces
-
Removes an XML Namespace with the given prefix.
- removeAdditionalGraphicalObject(long) - Method in class org.sbml.libsbml.Layout
-
Removes the graphical object with the given index from the layout.
- removeAdditionalGraphicalObject(String) - Method in class org.sbml.libsbml.Layout
-
Remove the graphical object with the given id.
- removeAll(long) - Method in class org.sbml.libsbml.SBMLErrorLog
-
Removes all errors having errorId from the
SBMLError list.
- removeAssociation(int) - Method in class org.sbml.libsbml.Association
-
Removes the child Associations with the given
index from this
Association object.
- removeAssociation(long) - Method in class org.sbml.libsbml.FbcAnd
-
- removeAssociation(String) - Method in class org.sbml.libsbml.FbcAnd
-
- removeAssociation(long) - Method in class org.sbml.libsbml.FbcOr
-
- removeAssociation(String) - Method in class org.sbml.libsbml.FbcOr
-
- removeAttr(int) - Method in class org.sbml.libsbml.XMLToken
-
Removes the nth attribute from the XML element represented by
this token.
- removeAttr(String, String) - Method in class org.sbml.libsbml.XMLToken
-
Removes an attribute from the XML element represented by this token.
- removeAttr(String) - Method in class org.sbml.libsbml.XMLToken
-
Removes an attribute from the XML element represented by this token.
- removeAttr(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
-
Removes an attribute from the XML element represented by this token.
- removeChild(long) - Method in class org.sbml.libsbml.ASTNode
-
Removes the nth child of this
ASTNode object.
- removeChild(long) - Method in class org.sbml.libsbml.XMLNode
-
Removes the
nth child of this
XMLNode and returns the
removed node.
- removeChildren() - Method in class org.sbml.libsbml.XMLNode
-
Removes all children from this node.
- removeColorDefinition(long) - Method in class org.sbml.libsbml.RenderInformationBase
-
- removeColorDefinition(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- removeCompartment(long) - Method in class org.sbml.libsbml.Model
-
Removes the nth
Compartment object from this
Model object and
returns a pointer to it.
- removeCompartment(String) - Method in class org.sbml.libsbml.Model
-
Removes the
Compartment object with the given identifier from this
Model
object and returns a pointer to it.
- removeCompartmentGlyph(long) - Method in class org.sbml.libsbml.Layout
-
Removes the compartment glyph with the given index from the layout.
- removeCompartmentGlyph(String) - Method in class org.sbml.libsbml.Layout
-
Remove the compartment glyph with the given id.
- removeCompartmentReference(long) - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
- removeCompartmentReference(String) - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
- removeCompartmentType(long) - Method in class org.sbml.libsbml.Model
-
- removeCompartmentType(String) - Method in class org.sbml.libsbml.Model
-
Removes the
CompartmentType object with the given identifier from this
Model
object and returns a pointer to it.
- removeConstraint(long) - Method in class org.sbml.libsbml.Model
-
Removes the nth
Constraint object from this
Model object and
returns a pointer to it.
- removeDash(long) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
Removes the dash length at the given index.
- removeDeletion(long) - Method in class org.sbml.libsbml.Submodel
-
Removes the deletion with the given
index from the
Submodel.
- removeDeletion(String) - Method in class org.sbml.libsbml.Submodel
-
Removes the deletion with the given identifier from the
Submodel.
- removeElement(long) - Method in class org.sbml.libsbml.Polygon
-
- removeElement(String) - Method in class org.sbml.libsbml.Polygon
-
- removeElement(long) - Method in class org.sbml.libsbml.RenderCurve
-
- removeElement(long) - Method in class org.sbml.libsbml.RenderGroup
-
- removeElement(String) - Method in class org.sbml.libsbml.RenderGroup
-
- removeEvent(long) - Method in class org.sbml.libsbml.Model
-
Removes the nth
Event object from this
Model object and
returns a pointer to it.
- removeEvent(String) - Method in class org.sbml.libsbml.Model
-
Removes the
Event object with the given identifier from this
Model
object and returns a pointer to it.
- removeEventAssignment(long) - Method in class org.sbml.libsbml.Event
-
- removeEventAssignment(String) - Method in class org.sbml.libsbml.Event
-
Removes the
EventAssignment object with the given 'variable' attribute
from this
Event object and returns a pointer to it.
- removeExternalModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- removeExternalModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- removeFluxBound(long) - Method in class org.sbml.libsbml.FbcModelPlugin
-
Removes the nth
FluxBound object from this plugin object and
returns a pointer to it.
- removeFluxBound(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
Removes the
FluxBound object with the given
sid attribute from
this plugin object and returns a pointer to it.
- removeFluxObjective(long) - Method in class org.sbml.libsbml.Objective
-
- removeFluxObjective(String) - Method in class org.sbml.libsbml.Objective
-
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.Delay
-
Finds this
Delay's
Event parent and calls unsetDelay() on it, indirectly
deleting itself.
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.KineticLaw
-
Finds this
KineticLaw's
Reaction parent and calls unsetKineticLaw() on
it, indirectly deleting itself.
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.ListOf
-
Removes all items in this
ListOf object and deletes its properties too.
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.Model
-
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.ModelDefinition
-
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.Priority
-
Finds this
Priority's
Event parent and calls unsetPriority() on it,
indirectly deleting itself.
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.ReplacedBy
-
Finds this
ReplacedBy's
SBase parent, gets the “comp” plugin from it,
and tells that to remove this.
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.SBase
-
Removes this object from its parent.
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.SBaseRef
-
Finds this
SBaseRef's parent, which can either be a List or can be
another
SBaseRef, and tells it to remove this.
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.StoichiometryMath
-
- removeFromParentAndDelete() - Method in class org.sbml.libsbml.Trigger
-
Finds this
Trigger's
Event parent and calls unsetTrigger() on it, indirectly deleting itself.
- removeFunctionDefinition(long) - Method in class org.sbml.libsbml.Model
-
- removeFunctionDefinition(String) - Method in class org.sbml.libsbml.Model
-
Removes the
FunctionDefinition object with the given identifier from this
Model
object and returns a pointer to it.
- removeFunctionTerm(long) - Method in class org.sbml.libsbml.Transition
-
- removeFunctionTerm(String) - Method in class org.sbml.libsbml.Transition
-
- removeGeneAssociation(long) - Method in class org.sbml.libsbml.FbcModelPlugin
-
Removes the nth
GeneAssociation annotation object from this plugin object and
returns a pointer to it.
- removeGeneAssociation(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
Removes the
GeneAssociation annotation object with the given
sid attribute from
this plugin object and returns a pointer to it.
- removeGeneProduct(long) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- removeGeneProduct(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- removeGlobalRenderInformation(long) - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
-
Removed the render information with the given index from the list.
- removeGlobalRenderInformation(String) - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
-
Removed the render information with the given id from the list.
- removeGlobalStyle(long) - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- removeGlobalStyle(String) - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- removeGradientDefinition(long) - Method in class org.sbml.libsbml.RenderInformationBase
-
- removeGradientDefinition(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- removeGradientStop(long) - Method in class org.sbml.libsbml.GradientBase
-
- removeGradientStop(String) - Method in class org.sbml.libsbml.GradientBase
-
- removeGroup(long) - Method in class org.sbml.libsbml.GroupsModelPlugin
-
- removeGroup(String) - Method in class org.sbml.libsbml.GroupsModelPlugin
-
- removeId(String) - Method in class org.sbml.libsbml.LocalStyle
-
Removes an id from the set.
- removeInitialAssignment(long) - Method in class org.sbml.libsbml.Model
-
- removeInitialAssignment(String) - Method in class org.sbml.libsbml.Model
-
Removes the
InitialAssignment object with the given 'symbol' attribute
from this
Model object and returns a pointer to it.
- removeInput(long) - Method in class org.sbml.libsbml.Transition
-
- removeInput(String) - Method in class org.sbml.libsbml.Transition
-
- removeInSpeciesTypeBond(long) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- removeInSpeciesTypeBond(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- removeL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.LayoutExtension
-
Removes the L2 Namespace from a document.
- removeL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.RenderExtension
-
Removes the L2 Namespace from a document.
- removeL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Removes SBML Level 2 namespaces from the namespace list.
- removeLayout(long) - Method in class org.sbml.libsbml.LayoutModelPlugin
-
Removes the nth
Layout object from this
Model object and
returns a pointer to it.
- removeLineEnding(long) - Method in class org.sbml.libsbml.RenderInformationBase
-
- removeLineEnding(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- removeLocalParameter(long) - Method in class org.sbml.libsbml.KineticLaw
-
Removes the nth
LocalParameter object in the list of local parameters
in this
KineticLaw instance and returns a pointer to it.
- removeLocalParameter(String) - Method in class org.sbml.libsbml.KineticLaw
-
Removes a
LocalParameter object with the given identifier in the list of
local parameters in this
KineticLaw instance and returns a pointer to it.
- removeLocalRenderInformation(long) - Method in class org.sbml.libsbml.RenderLayoutPlugin
-
Removed the render information with the given index from the list.
- removeLocalRenderInformation(String) - Method in class org.sbml.libsbml.RenderLayoutPlugin
-
Removed the render information with the given id from the list.
- removeLocalStyle(long) - Method in class org.sbml.libsbml.LocalRenderInformation
-
- removeLocalStyle(String) - Method in class org.sbml.libsbml.LocalRenderInformation
-
- removeMember(long) - Method in class org.sbml.libsbml.Group
-
Removes the nth
Member from this
Group and returns a pointer to it.
- removeMember(String) - Method in class org.sbml.libsbml.Group
-
Removes the
Member from this
Group based on its identifier and returns a
pointer to it.
- removeModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- removeModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
- removeModifier(long) - Method in class org.sbml.libsbml.Reaction
-
Removes the nth modifier species (ModifierSpeciesReference object) in
the list of modifiers in this
Reaction and returns a pointer to it.
- removeModifier(String) - Method in class org.sbml.libsbml.Reaction
-
Removes the modifier species (ModifierSpeciesReference object) having
the given 'species' attribute in this
Reaction and returns a pointer to it.
- removeMultiSpeciesType(long) - Method in class org.sbml.libsbml.MultiModelPlugin
-
Removes the nth
MultiSpeciesType object from this plugin object
and returns a pointer to it.
- removeMultiSpeciesType(String) - Method in class org.sbml.libsbml.MultiModelPlugin
-
Removes the
MultiSpeciesType object with the given id from this plugin object
and returns a pointer to it.
- removeNamespace(String) - Method in class org.sbml.libsbml.SBMLNamespaces
-
Removes an XML namespace from the set of namespaces within this
SBMLNamespaces object.
- removeNamespace(int) - Method in class org.sbml.libsbml.XMLToken
-
Removes the nth XML namespace declaration.
- removeNamespace(String) - Method in class org.sbml.libsbml.XMLToken
-
Removes an XML namespace declaration having a given prefix.
- removeNestedCVTerm(long) - Method in class org.sbml.libsbml.CVTerm
-
Removes the nth
CVTerm in the list of CVTerms of this
CVTerm
object and returns a pointer to it.
- removeObjective(long) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- removeObjective(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- removeOption(String) - Method in class org.sbml.libsbml.ConversionProperties
-
Removes the option with the given key from this properties object.
- removeOutput(long) - Method in class org.sbml.libsbml.Transition
-
- removeOutput(String) - Method in class org.sbml.libsbml.Transition
-
- removeOutwardBindingSite(long) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- removeOutwardBindingSite(String) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- removePackageNamespace(long, long, String, long) - Method in class org.sbml.libsbml.SBMLNamespaces
-
Removes an XML namespace of a package extension from the set of namespaces
within this
SBMLNamespaces object.
- removeParameter(long) - Method in class org.sbml.libsbml.KineticLaw
-
Removes the nth
Parameter object in the list of parameters
in this
KineticLaw instance and returns a pointer to it.
- removeParameter(String) - Method in class org.sbml.libsbml.KineticLaw
-
Removes a
Parameter object with the given identifier in the list of
parameters in this
KineticLaw instance and returns a pointer to it.
- removeParameter(long) - Method in class org.sbml.libsbml.Model
-
Removes the nth
Parameter object from this
Model object and
returns a pointer to it.
- removeParameter(String) - Method in class org.sbml.libsbml.Model
-
Removes the
Parameter object with the given identifier from this
Model
object and returns a pointer to it.
- removePort(long) - Method in class org.sbml.libsbml.CompModelPlugin
-
Removes the port with the given index.
- removePossibleSpeciesFeatureValue(long) - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- removePossibleSpeciesFeatureValue(String) - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- removeProduct(long) - Method in class org.sbml.libsbml.Reaction
-
Removes the nth product species (SpeciesReference object) in the list of
products in this
Reaction and returns a pointer to it.
- removeProduct(String) - Method in class org.sbml.libsbml.Reaction
-
Removes the product species (SpeciesReference object) having the given
'species' attribute in this
Reaction and returns a pointer to it.
- removeQualitativeSpecies(long) - Method in class org.sbml.libsbml.QualModelPlugin
-
Removes the nth
QualitativeSpecies object from this plugin object and
returns a pointer to it.
- removeQualitativeSpecies(String) - Method in class org.sbml.libsbml.QualModelPlugin
-
Removes the
QualitativeSpecies object with the given id attribute from
this plugin object and returns a pointer to it.
- removeReactant(long) - Method in class org.sbml.libsbml.Reaction
-
Removes the nth reactant species (SpeciesReference object) in the list of
reactants in this
Reaction and returns a pointer to it.
- removeReactant(String) - Method in class org.sbml.libsbml.Reaction
-
Removes the reactant species (SpeciesReference object) having the given
'species' attribute in this
Reaction and returns a pointer to it.
- removeReaction(long) - Method in class org.sbml.libsbml.Model
-
Removes the nth
Reaction object from this
Model object and
returns a pointer to it.
- removeReaction(String) - Method in class org.sbml.libsbml.Model
-
Removes the
Reaction object with the given identifier from this
Model
object and returns a pointer to it.
- removeReactionGlyph(long) - Method in class org.sbml.libsbml.Layout
-
Removes the reaction glyph with the given index from the layout.
- removeReactionGlyph(String) - Method in class org.sbml.libsbml.Layout
-
Remove the reaction glyph with the given id.
- removeReferenceGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
-
Remove the reference glyph with the given index.
- removeReferenceGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
-
Remove the reference glyph with the given id.
- removeReplacedElement(long) - Method in class org.sbml.libsbml.CompSBasePlugin
-
- removeResolver(int) - Method in class org.sbml.libsbml.SBMLResolverRegistry
-
Removes the resolver with the given index.
- removeResource(String) - Method in class org.sbml.libsbml.CVTerm
-
Removes a resource URI from the set of resources stored in this
CVTerm
object.
- removeRole(String) - Method in class org.sbml.libsbml.Style
-
Removes the given role from the role list.
- removeRule(long) - Method in class org.sbml.libsbml.Model
-
Removes the nth
Rule object from this
Model object and
returns a pointer to it.
- removeRule(String) - Method in class org.sbml.libsbml.Model
-
Removes the
Rule object with the given 'variable' attribute from this
Model
object and returns a pointer to it.
- removeRuleByVariable(String) - Method in class org.sbml.libsbml.Model
-
Removes the
Rule object with the given 'variable' attribute from this
Model
object and returns a pointer to it.
- removeScale(Unit) - Static method in class org.sbml.libsbml.Unit
-
Manipulates the attributes of the
Unit to express the unit with the
value of the scale attribute reduced to zero.
- removeSpecies(long) - Method in class org.sbml.libsbml.Model
-
Removes the nth
Species object from this
Model object and
returns a pointer to it.
- removeSpecies(String) - Method in class org.sbml.libsbml.Model
-
Removes the
Species object with the given identifier from this
Model
object and returns a pointer to it.
- removeSpeciesFeature(long) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- removeSpeciesFeature(String) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
- removeSpeciesFeatureType(long) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- removeSpeciesFeatureType(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- removeSpeciesFeatureValue(long) - Method in class org.sbml.libsbml.SpeciesFeature
-
- removeSpeciesFeatureValue(String) - Method in class org.sbml.libsbml.SpeciesFeature
-
- removeSpeciesGlyph(long) - Method in class org.sbml.libsbml.Layout
-
Removes the species glyph with the given index from the layout.
- removeSpeciesGlyph(String) - Method in class org.sbml.libsbml.Layout
-
Remove the species glyph with the given id.
- removeSpeciesReferenceGlyph(String) - Method in class org.sbml.libsbml.Layout
-
Remove the species reference glyph with the given id.
- removeSpeciesReferenceGlyph(long) - Method in class org.sbml.libsbml.ReactionGlyph
-
Remove the species reference glyph with the given index.
- removeSpeciesReferenceGlyph(String) - Method in class org.sbml.libsbml.ReactionGlyph
-
Remove the species reference glyph with the given id.
- removeSpeciesType(long) - Method in class org.sbml.libsbml.Model
-
Removes the nth
SpeciesType object from this
Model object and
returns a pointer to it.
- removeSpeciesType(String) - Method in class org.sbml.libsbml.Model
-
Removes the
SpeciesType object with the given identifier from this
Model
object and returns a pointer to it.
- removeSpeciesTypeComponentIndex(long) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- removeSpeciesTypeComponentIndex(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- removeSpeciesTypeComponentMapInProduct(long) - Method in class org.sbml.libsbml.MultiSpeciesReferencePlugin
-
- removeSpeciesTypeComponentMapInProduct(String) - Method in class org.sbml.libsbml.MultiSpeciesReferencePlugin
-
- removeSpeciesTypeInstance(long) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- removeSpeciesTypeInstance(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- removeStyle(long) - Method in class org.sbml.libsbml.GlobalRenderInformation
-
- removeStyle(long) - Method in class org.sbml.libsbml.LocalRenderInformation
-
- removeStyle(String) - Method in class org.sbml.libsbml.LocalRenderInformation
-
- removeSubGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
-
Remove the subglyph with the given index.
- removeSubGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
-
Remove the subglyph with the given id.
- removeSubListOfSpeciesFeatures(long) - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
- removeSubListOfSpeciesFeatures(String) - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
- removeSubmodel(long) - Method in class org.sbml.libsbml.CompModelPlugin
-
Removes the submodel with the given index.
- removeTextGlyph(long) - Method in class org.sbml.libsbml.Layout
-
Removes the text glyph with the given index from the layout.
- removeTextGlyph(String) - Method in class org.sbml.libsbml.Layout
-
Remove the text glyph with the given id.
- removeTopLevelAnnotationElement(String, String, boolean) - Method in class org.sbml.libsbml.SBase
-
Removes the top-level element within the 'annotation' subelement of this
SBML object with the given name and optional URI.
- removeTopLevelAnnotationElement(String, String) - Method in class org.sbml.libsbml.SBase
-
Removes the top-level element within the 'annotation' subelement of this
SBML object with the given name and optional URI.
- removeTopLevelAnnotationElement(String) - Method in class org.sbml.libsbml.SBase
-
Removes the top-level element within the 'annotation' subelement of this
SBML object with the given name and optional URI.
- removeTransition(long) - Method in class org.sbml.libsbml.QualModelPlugin
-
Removes the nth
Transition object from this plugin object and
returns a pointer to it.
- removeTransition(String) - Method in class org.sbml.libsbml.QualModelPlugin
-
Removes the
Transition object with the given id attribute from
this plugin object and returns a pointer to it.
- removeType(String) - Method in class org.sbml.libsbml.Style
-
Removes a type string from the type list.
- removeUnit(long) - Method in class org.sbml.libsbml.UnitDefinition
-
- removeUnitDefinition(long) - Method in class org.sbml.libsbml.Model
-
- removeUnitDefinition(String) - Method in class org.sbml.libsbml.Model
-
Removes the
UnitDefinition object with the given identifier from this
Model
object and returns a pointer to it.
- renameIDs(SBaseList, IdentifierTransformer) - Method in class org.sbml.libsbml.Model
-
- renameMetaIdRefs(String, String) - Method in class org.sbml.libsbml.GraphicalObject
-
Renames all the MetaIdRef attributes on this element.
- renameMetaIdRefs(String, String) - Method in class org.sbml.libsbml.Port
-
Replaces all uses of a given meta identifier attribute value with
another value.
- renameMetaIdRefs(String, String) - Method in class org.sbml.libsbml.SBase
-
Replaces all uses of a given meta identifier attribute value with
another value.
- renameMetaIdRefs(String, String) - Method in class org.sbml.libsbml.SBasePlugin
-
Replaces all uses of a given meta identifier attribute value with
another value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.AssignmentRule
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ASTNode
-
Renames all the SIdRef attributes on this node and any child node
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Compartment
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.CompartmentGlyph
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.CompartmentReference
-
Renames all the SIdRef attributes on this element, including any
found in MathML content (if such exists).
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Constraint
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.DefaultValues
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Delay
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.EventAssignment
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.FbcReactionPlugin
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.FluxBound
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.FluxObjective
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.FunctionTerm
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.GeneProduct
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.GeneProductRef
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.GeneralGlyph
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.InitialAssignment
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Input
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
Renames all the SIdRef attributes on this element, including any
found in MathML content (if such exists).
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.KineticLaw
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ListOfObjectives
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Member
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Model
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.MultiASTPlugin
-
Renames the speciesReference SIdRef attribute on this node.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
Renames all the SIdRef attributes on this element, including any
found in MathML content (if such exists).
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Output
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.OutwardBindingSite
-
Renames all the SIdRef attributes on this element, including any
found in MathML content (if such exists).
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Port
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
Renames all the SIdRef attributes on this element, including any
found in MathML content (if such exists).
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Priority
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.QualitativeSpecies
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.RateRule
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Reaction
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ReactionGlyph
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ReferenceGlyph
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.RenderCurve
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.RenderGroup
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.RenderInformationBase
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ReplacedElement
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Replacing
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Rule
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SBase
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SBasePlugin
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SBaseRef
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Species
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SpeciesFeature
-
Renames all the SIdRef attributes on this element, including any
found in MathML content (if such exists).
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SpeciesFeatureValue
-
Renames all the SIdRef attributes on this element, including any
found in MathML content (if such exists).
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SpeciesGlyph
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
Renames all the SIdRef attributes on this element, including any
found in MathML content (if such exists).
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
Renames all the SIdRef attributes on this element, including any
found in MathML content (if such exists).
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
Renames all the SIdRef attributes on this element, including any
found in MathML content (if such exists).
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.StoichiometryMath
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Submodel
-
Renames the conversion factor attributes on this element if oldid matches.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.TextGlyph
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Trigger
-
Replaces all uses of a given SIdRef type attribute value with another
value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.ASTNode
-
Renames all the UnitSIdRef attributes on this node and any child node.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Compartment
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Constraint
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Delay
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.EventAssignment
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.FunctionDefinition
-
Renames all the UnitSIdRef attributes on this element.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.InitialAssignment
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.KineticLaw
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Model
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Parameter
-
Renames all the UnitSIdRef attributes on this element.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Port
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Priority
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Rule
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.SBase
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.SBasePlugin
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Species
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.StoichiometryMath
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Trigger
-
Replaces all uses of a given UnitSIdRef type attribute value with
another value.
- RenderCubicBezier - Class in org.sbml.libsbml
-
render
Representation of cubic Bezier curves.
- RenderCubicBezier(long, long, long) - Constructor for class org.sbml.libsbml.RenderCubicBezier
-
Creates a new
RenderCubicBezier using the given SBML Level, Version and
“render” package version.
- RenderCubicBezier(long, long) - Constructor for class org.sbml.libsbml.RenderCubicBezier
-
Creates a new
RenderCubicBezier using the given SBML Level, Version and
“render” package version.
- RenderCubicBezier(long) - Constructor for class org.sbml.libsbml.RenderCubicBezier
-
Creates a new
RenderCubicBezier using the given SBML Level, Version and
“render” package version.
- RenderCubicBezier() - Constructor for class org.sbml.libsbml.RenderCubicBezier
-
Creates a new
RenderCubicBezier using the given SBML Level, Version and
“render” package version.
- RenderCubicBezier(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderCubicBezier
-
- RenderCubicBezier(RenderPkgNamespaces, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.RenderCubicBezier
-
- RenderCubicBezier(XMLNode, long) - Constructor for class org.sbml.libsbml.RenderCubicBezier
-
- RenderCubicBezier(XMLNode) - Constructor for class org.sbml.libsbml.RenderCubicBezier
-
- RenderCubicBezier(RenderCubicBezier) - Constructor for class org.sbml.libsbml.RenderCubicBezier
-
- RenderCurve - Class in org.sbml.libsbml
-
render
Representation of curves.
- RenderCurve(long, long, long) - Constructor for class org.sbml.libsbml.RenderCurve
-
Creates a new
RenderCurve using the given SBML Level, Version and
“render” package version.
- RenderCurve(long, long) - Constructor for class org.sbml.libsbml.RenderCurve
-
Creates a new
RenderCurve using the given SBML Level, Version and
“render” package version.
- RenderCurve(long) - Constructor for class org.sbml.libsbml.RenderCurve
-
Creates a new
RenderCurve using the given SBML Level, Version and
“render” package version.
- RenderCurve() - Constructor for class org.sbml.libsbml.RenderCurve
-
Creates a new
RenderCurve using the given SBML Level, Version and
“render” package version.
- RenderCurve(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderCurve
-
- RenderCurve(XMLNode, long) - Constructor for class org.sbml.libsbml.RenderCurve
-
- RenderCurve(XMLNode) - Constructor for class org.sbml.libsbml.RenderCurve
-
- RenderCurve(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.RenderCurve
-
Instantiates an empty curve object with the given id.
- RenderCurve(RenderCurve) - Constructor for class org.sbml.libsbml.RenderCurve
-
- RenderExtension - Class in org.sbml.libsbml
-
render
Base extension class for the package.
- RenderExtension() - Constructor for class org.sbml.libsbml.RenderExtension
-
Constructor
- RenderExtension(RenderExtension) - Constructor for class org.sbml.libsbml.RenderExtension
-
Copy constructor.
- RenderGraphicalObjectPlugin - Class in org.sbml.libsbml
-
- RenderGraphicalObjectPlugin(String, String, RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderGraphicalObjectPlugin
-
Constructor
- RenderGraphicalObjectPlugin(RenderGraphicalObjectPlugin) - Constructor for class org.sbml.libsbml.RenderGraphicalObjectPlugin
-
Copy constructor.
- RenderGroup - Class in org.sbml.libsbml
-
render
A group of graphical primitives creating a composite.
- RenderGroup(long, long, long) - Constructor for class org.sbml.libsbml.RenderGroup
-
Creates a new
RenderGroup using the given SBML Level, Version and
“render” package version.
- RenderGroup(long, long) - Constructor for class org.sbml.libsbml.RenderGroup
-
Creates a new
RenderGroup using the given SBML Level, Version and
“render” package version.
- RenderGroup(long) - Constructor for class org.sbml.libsbml.RenderGroup
-
Creates a new
RenderGroup using the given SBML Level, Version and
“render” package version.
- RenderGroup() - Constructor for class org.sbml.libsbml.RenderGroup
-
Creates a new
RenderGroup using the given SBML Level, Version and
“render” package version.
- RenderGroup(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderGroup
-
- RenderGroup(XMLNode, long) - Constructor for class org.sbml.libsbml.RenderGroup
-
- RenderGroup(XMLNode) - Constructor for class org.sbml.libsbml.RenderGroup
-
- RenderGroup(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.RenderGroup
-
- RenderGroup(RenderGroup) - Constructor for class org.sbml.libsbml.RenderGroup
-
- RenderInformationBase - Class in org.sbml.libsbml
-
render
Abstract base class for local and global rendering information.
- RenderInformationBase(long, long, long) - Constructor for class org.sbml.libsbml.RenderInformationBase
-
- RenderInformationBase(long, long) - Constructor for class org.sbml.libsbml.RenderInformationBase
-
- RenderInformationBase(long) - Constructor for class org.sbml.libsbml.RenderInformationBase
-
- RenderInformationBase() - Constructor for class org.sbml.libsbml.RenderInformationBase
-
- RenderInformationBase(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderInformationBase
-
- RenderInformationBase(RenderInformationBase) - Constructor for class org.sbml.libsbml.RenderInformationBase
-
- RenderInformationBase(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.RenderInformationBase
-
Constructor which creates a
RenderInformationBase object
empty color definition, gradient definition
and line endings set.
- RenderLayoutPlugin - Class in org.sbml.libsbml
-
render
LibSBML implementation for the extension to the
Layout class by the Render extension.
- RenderLayoutPlugin(String, String, RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderLayoutPlugin
-
Constructor
- RenderLayoutPlugin(RenderLayoutPlugin) - Constructor for class org.sbml.libsbml.RenderLayoutPlugin
-
Copy constructor.
- RenderListOfLayoutsPlugin - Class in org.sbml.libsbml
-
render
A list of layout objects used by the 'render' extension.
- RenderListOfLayoutsPlugin(String, String, RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderListOfLayoutsPlugin
-
Constructor
- RenderListOfLayoutsPlugin(RenderListOfLayoutsPlugin) - Constructor for class org.sbml.libsbml.RenderListOfLayoutsPlugin
-
Copy constructor.
- RenderPkgNamespaces - Class in org.sbml.libsbml
-
Set of SBML Level + Version + namespace triples.
- RenderPkgNamespaces(long, long, long, String) - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
-
- RenderPkgNamespaces(long, long, long) - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
-
- RenderPkgNamespaces(long, long) - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
-
- RenderPkgNamespaces(long) - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
-
- RenderPkgNamespaces() - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
-
- RenderPkgNamespaces(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
-
- RenderPoint - Class in org.sbml.libsbml
-
render
A point with both absolute and relative values
- RenderPoint(long, long, long) - Constructor for class org.sbml.libsbml.RenderPoint
-
Creates a new
RenderPoint using the given SBML Level, Version and
“render” package version.
- RenderPoint(long, long) - Constructor for class org.sbml.libsbml.RenderPoint
-
Creates a new
RenderPoint using the given SBML Level, Version and
“render” package version.
- RenderPoint(long) - Constructor for class org.sbml.libsbml.RenderPoint
-
Creates a new
RenderPoint using the given SBML Level, Version and
“render” package version.
- RenderPoint() - Constructor for class org.sbml.libsbml.RenderPoint
-
Creates a new
RenderPoint using the given SBML Level, Version and
“render” package version.
- RenderPoint(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderPoint
-
- RenderPoint(RenderPkgNamespaces, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.RenderPoint
-
Creates a new point with the given coordinates.
- RenderPoint(RenderPkgNamespaces, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.RenderPoint
-
Creates a new point with the given coordinates.
- RenderPoint(XMLNode, long) - Constructor for class org.sbml.libsbml.RenderPoint
-
- RenderPoint(XMLNode) - Constructor for class org.sbml.libsbml.RenderPoint
-
- RenderPoint(RenderPoint) - Constructor for class org.sbml.libsbml.RenderPoint
-
- reorder(UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
-
- REPEAT - Static variable in class org.sbml.libsbml.GradientBase
-
- RepeatedRule10304 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- RepeatedRule20611 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- replaceArgument(String, ASTNode) - Method in class org.sbml.libsbml.ASTNode
-
Replaces occurences of a given name within this
ASTNode with the
name/value/formula represented by
arg.
- replaceChild(long, ASTNode, boolean) - Method in class org.sbml.libsbml.ASTNode
-
Replaces and optionally deletes the nth child of this
ASTNode with the given
ASTNode.
- replaceChild(long, ASTNode) - Method in class org.sbml.libsbml.ASTNode
-
Replaces and optionally deletes the nth child of this
ASTNode with the given
ASTNode.
- ReplacedBy - Class in org.sbml.libsbml
-
comp
Indicates an object replaced by another.
- ReplacedBy(long, long, long) - Constructor for class org.sbml.libsbml.ReplacedBy
-
Creates a new
ReplacedBy with the given level, version, and package
version.
- ReplacedBy(long, long) - Constructor for class org.sbml.libsbml.ReplacedBy
-
Creates a new
ReplacedBy with the given level, version, and package
version.
- ReplacedBy(long) - Constructor for class org.sbml.libsbml.ReplacedBy
-
Creates a new
ReplacedBy with the given level, version, and package
version.
- ReplacedBy() - Constructor for class org.sbml.libsbml.ReplacedBy
-
Creates a new
ReplacedBy with the given level, version, and package
version.
- ReplacedBy(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ReplacedBy
-
- ReplacedBy(ReplacedBy) - Constructor for class org.sbml.libsbml.ReplacedBy
-
Copy constructor.
- ReplacedElement - Class in org.sbml.libsbml
-
comp
Indicates an object replaces another.
- ReplacedElement(long, long, long) - Constructor for class org.sbml.libsbml.ReplacedElement
-
Creates a new
ReplacedElement with the given level, version, and package
version.
- ReplacedElement(long, long) - Constructor for class org.sbml.libsbml.ReplacedElement
-
Creates a new
ReplacedElement with the given level, version, and package
version.
- ReplacedElement(long) - Constructor for class org.sbml.libsbml.ReplacedElement
-
Creates a new
ReplacedElement with the given level, version, and package
version.
- ReplacedElement() - Constructor for class org.sbml.libsbml.ReplacedElement
-
Creates a new
ReplacedElement with the given level, version, and package
version.
- ReplacedElement(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ReplacedElement
-
- ReplacedElement(ReplacedElement) - Constructor for class org.sbml.libsbml.ReplacedElement
-
Copy constructor.
- replaceElement(SBase, SBase) - Method in class org.sbml.libsbml.Submodel
-
Delete the element in question from the stored instantiated
Model, and
replace all references to it with references to the replacement object.
- replaceTopLevelAnnotationElement(XMLNode) - Method in class org.sbml.libsbml.SBase
-
Replaces the given top-level element within the 'annotation'
subelement of this SBML object and with the annotation element supplied.
- replaceTopLevelAnnotationElement(String) - Method in class org.sbml.libsbml.SBase
-
Replaces the given top-level element within the 'annotation'
subelement of this SBML object and with the annotation element supplied.
- Replacing - Class in org.sbml.libsbml
-
- representsValidDate() - Method in class org.sbml.libsbml.Date
-
Returns true or false depending on whether this date object represents
a valid date and time value.
- RequiredPackagePresent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- resetElementNamespace(String) - Method in class org.sbml.libsbml.ListOfLayouts
-
- resolve(String, String) - Method in class org.sbml.libsbml.SBMLFileResolver
-
Resolves the document for the given URI.
- resolve(String) - Method in class org.sbml.libsbml.SBMLFileResolver
-
Resolves the document for the given URI.
- resolve(String, String) - Method in class org.sbml.libsbml.SBMLResolver
-
Resolves the document for the given URI.
- resolve(String) - Method in class org.sbml.libsbml.SBMLResolver
-
Resolves the document for the given URI.
- resolve(String, String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
-
Resolves the document for the given URI.
- resolve(String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
-
Resolves the document for the given URI.
- resolveUri(String, String) - Method in class org.sbml.libsbml.SBMLFileResolver
-
Resolves the full URI for a given URI without actually reading the
document.
- resolveUri(String) - Method in class org.sbml.libsbml.SBMLFileResolver
-
Resolves the full URI for a given URI without actually reading the
document.
- resolveUri(String, String) - Method in class org.sbml.libsbml.SBMLResolver
-
Resolves the full URI for the given URI without actually reading the
document.
- resolveUri(String) - Method in class org.sbml.libsbml.SBMLResolver
-
Resolves the full URI for the given URI without actually reading the
document.
- resolveUri(String, String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
-
Resolves the full URI for the given URI without actually reading the
document.
- resolveUri(String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
-
Resolves the full URI for the given URI without actually reading the
document.
- returnsBoolean(Model) - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node returns a boolean type
or false (zero) otherwise.
- returnsBoolean() - Method in class org.sbml.libsbml.ASTNode
-
Returns true (non-zero) if this node returns a boolean type
or false (zero) otherwise.
- Rule - Class in org.sbml.libsbml
-
Parent class for SBML rules in libSBML.
- Rule(Rule) - Constructor for class org.sbml.libsbml.Rule
-
Copy constructor; creates a copy of this
Rule.
- RULE_TYPE_INVALID - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML
Rule object types.
- RULE_TYPE_RATE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML
Rule object types.
- RULE_TYPE_SCALAR - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML
Rule object types.
- RuleCannotRef0DComp - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- saveReferencedElement() - Method in class org.sbml.libsbml.Deletion
-
Finds and stores the referenced object.
- saveReferencedElement() - Method in class org.sbml.libsbml.Port
-
Finds and stores the referenced object by finding its
Model parent,
calling 'getReferencedElementFrom()' on that model, and storing the
result.
- saveReferencedElement() - Method in class org.sbml.libsbml.Replacing
-
Finds and stores the referenced object.
- saveReferencedElement() - Method in class org.sbml.libsbml.SBaseRef
-
Finds and stores the referenced object by finding the
Model it needs to
point to, calling 'saveReferencedElement' on its parent (which will also
be a
SBaseRef or one of its subclasses), and the storing the result.
- SBase - Class in org.sbml.libsbml
-
SBML's SBase class, base class of most SBML objects.
- SBaseList - Class in org.sbml.libsbml
-
Class for managing lists of
SBase objects.
- SBaseList() - Constructor for class org.sbml.libsbml.SBaseList
-
Explicit constructor for this list.
- SBasePlugin - Class in org.sbml.libsbml
-
Base class for extending SBML objects in packages.
- SBaseRef - Class in org.sbml.libsbml
-
comp
Base class for references to objects.
- SBaseRef(long, long, long) - Constructor for class org.sbml.libsbml.SBaseRef
-
Creates a new
SBaseRef with the given level, version, and package version.
- SBaseRef(long, long) - Constructor for class org.sbml.libsbml.SBaseRef
-
Creates a new
SBaseRef with the given level, version, and package version.
- SBaseRef(long) - Constructor for class org.sbml.libsbml.SBaseRef
-
Creates a new
SBaseRef with the given level, version, and package version.
- SBaseRef() - Constructor for class org.sbml.libsbml.SBaseRef
-
Creates a new
SBaseRef with the given level, version, and package version.
- SBaseRef(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.SBaseRef
-
- SBaseRef(SBaseRef) - Constructor for class org.sbml.libsbml.SBaseRef
-
Copy constructor.
- SBML_ALGEBRAIC_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_ASSIGNMENT_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_COMP_DELETION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
comp One of the
possible SBML component type codes.
- SBML_COMP_EXTERNALMODELDEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
comp One of the
possible SBML component type codes.
- SBML_COMP_MODELDEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
comp One of the
possible SBML component type codes.
- SBML_COMP_PORT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
comp One of the
possible SBML component type codes.
- SBML_COMP_REPLACEDBY - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
comp One of the
possible SBML component type codes.
- SBML_COMP_REPLACEDELEMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
comp One of the
possible SBML component type codes.
- SBML_COMP_SBASEREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
comp One of the
possible SBML component type codes.
- SBML_COMP_SUBMODEL - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
comp One of the
possible SBML component type codes.
- SBML_COMPARTMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_COMPARTMENT_TYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_COMPARTMENT_VOLUME_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_CONSTRAINT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_DELAY - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_DOCUMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_EVENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_EVENT_ASSIGNMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_FBC_AND - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FBC_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FBC_FLUXBOUND - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FBC_FLUXOBJECTIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FBC_GENEASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FBC_GENEPRODUCT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FBC_GENEPRODUCTASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FBC_GENEPRODUCTREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FBC_OBJECTIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FBC_OR - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FBC_V1ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
fbc One of the
possible SBML component type codes.
- SBML_FUNCTION_DEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_GENERIC_SBASE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_GROUPS_GROUP - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups One of the
possible SBML component type codes.
- SBML_GROUPS_MEMBER - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
groups One of the
possible SBML component type codes.
- SBML_INITIAL_ASSIGNMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_KINETIC_LAW - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_LAYOUT_BOUNDINGBOX - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_COMPARTMENTGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_CUBICBEZIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_CURVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_DIMENSIONS - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_GENERALGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_GRAPHICALOBJECT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_LAYOUT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_LINESEGMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_POINT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_REACTIONGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_REFERENCEGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_SPECIESGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_SPECIESREFERENCEGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LAYOUT_TEXTGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible SBML component type codes.
- SBML_LIST_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_LOCAL_PARAMETER - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_MODEL - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_MODIFIER_SPECIES_REFERENCE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_MULTI_BINDING_SITE_SPECIES_TYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_COMPARTMENT_REFERENCE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_IN_SPECIES_TYPE_BOND - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_INTRA_SPECIES_REACTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_OUTWARD_BINDING_SITE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_POSSIBLE_SPECIES_FEATURE_VALUE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_SPECIES_FEATURE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_SPECIES_FEATURE_TYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_SPECIES_FEATURE_VALUE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_SPECIES_TYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_SPECIES_TYPE_COMPONENT_INDEX - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_SPECIES_TYPE_COMPONENT_MAP_IN_PRODUCT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_SPECIES_TYPE_INSTANCE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_MULTI_SUBLIST_OF_SPECIES_FEATURES - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
multi A value in an
enumeration defined by the libSBML “multi” extension
for objects in the SBML Level 3 Multistate, Multicomponent
and Multicompartment Species package.
- SBML_PARAMETER - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_PARAMETER_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_PRIORITY - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_QUAL_DEFAULT_TERM - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible SBML component type codes.
- SBML_QUAL_FUNCTION_TERM - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible SBML component type codes.
- SBML_QUAL_INPUT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible SBML component type codes.
- SBML_QUAL_OUTPUT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible SBML component type codes.
- SBML_QUAL_QUALITATIVE_SPECIES - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible SBML component type codes.
- SBML_QUAL_TRANSITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
qual One of the
possible SBML component type codes.
- SBML_RATE_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_REACTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_RENDER_COLORDEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_CUBICBEZIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_CURVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_DEFAULTS - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_ELLIPSE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_GLOBALRENDERINFORMATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_GLOBALSTYLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_GRADIENT_STOP - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_GRADIENTDEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_GRAPHICALPRIMITIVE1D - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_GRAPHICALPRIMITIVE2D - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_GROUP - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_IMAGE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_LINEARGRADIENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_LINEENDING - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_LINESEGMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_LISTOFGLOBALSTYLES - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_LISTOFLOCALSTYLES - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_LOCALRENDERINFORMATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_LOCALSTYLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_POINT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_POLYGON - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_RADIALGRADIENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_RECTANGLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_RELABSVECTOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_RENDERINFORMATION_BASE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_STYLE_BASE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_TEXT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_TRANSFORMATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RENDER_TRANSFORMATION2D - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
render A value in an
enumeration defined by the libSBML “render” extension
for objects in the SBML Level 3 Rendering package.
- SBML_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_SPECIES - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_SPECIES_CONCENTRATION_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_SPECIES_REFERENCE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_SPECIES_TYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_STOICHIOMETRY_MATH - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_TRIGGER - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_UNIT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_UNIT_DEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBML_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
One of the possible SBML component type codes.
- SBMLCodesUpperBound - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SBMLConstructorException - Exception in org.sbml.libsbml
-
Exceptions class for libSBML object constructors.
- SBMLConstructorException(String) - Constructor for exception org.sbml.libsbml.SBMLConstructorException
-
Constructor; version taking a message argument.
- SBMLConstructorException() - Constructor for exception org.sbml.libsbml.SBMLConstructorException
-
Constructor; version taking no arguments.
- SBMLConverter - Class in org.sbml.libsbml
-
Base class for SBML converters.
- SBMLConverter() - Constructor for class org.sbml.libsbml.SBMLConverter
-
- SBMLConverter(String) - Constructor for class org.sbml.libsbml.SBMLConverter
-
- SBMLConverter(SBMLConverter) - Constructor for class org.sbml.libsbml.SBMLConverter
-
Copy constructor.
- SBMLConverterRegistry - Class in org.sbml.libsbml
-
Registry of all libSBML SBML converters.
- SBMLDocument - Class in org.sbml.libsbml
-
Overall SBML container object.
- SBMLDocument(long, long) - Constructor for class org.sbml.libsbml.SBMLDocument
-
Creates a new
SBMLDocument, optionally with given values for the SBML
Level and Version.
- SBMLDocument(long) - Constructor for class org.sbml.libsbml.SBMLDocument
-
Creates a new
SBMLDocument, optionally with given values for the SBML
Level and Version.
- SBMLDocument() - Constructor for class org.sbml.libsbml.SBMLDocument
-
Creates a new
SBMLDocument, optionally with given values for the SBML
Level and Version.
- SBMLDocument(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SBMLDocument
-
- SBMLDocument(SBMLDocument) - Constructor for class org.sbml.libsbml.SBMLDocument
-
- SBMLDocumentPlugin - Class in org.sbml.libsbml
-
- SBMLDocumentPlugin(String, String, SBMLNamespaces) - Constructor for class org.sbml.libsbml.SBMLDocumentPlugin
-
- SBMLDocumentPlugin(SBMLDocumentPlugin) - Constructor for class org.sbml.libsbml.SBMLDocumentPlugin
-
Copy constructor.
- SBMLError - Class in org.sbml.libsbml
-
An error, warning or other diagnostic.
- SBMLError(long, long, long, String, long, long, long, long, String, long) - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError(long, long, long, String, long, long, long, long, String) - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError(long, long, long, String, long, long, long, long) - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError(long, long, long, String, long, long, long) - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError(long, long, long, String, long, long) - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError(long, long, long, String, long) - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError(long, long, long, String) - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError(long, long, long) - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError(long, long) - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError(long) - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError() - Constructor for class org.sbml.libsbml.SBMLError
-
Creates a new
SBMLError to report that something occurred during SBML
processing.
- SBMLError(SBMLError) - Constructor for class org.sbml.libsbml.SBMLError
-
Copy constructor; creates a copy of this
SBMLError.
- SBMLErrorLog - Class in org.sbml.libsbml
-
Log of diagnostics reported during processing.
- SBMLExtension - Class in org.sbml.libsbml
-
Base class for SBML Level 3 package plug-ins.
- SBMLExtensionException - Class in org.sbml.libsbml
-
Exception used by package extensions
- SBMLExtensionException(String) - Constructor for class org.sbml.libsbml.SBMLExtensionException
-
- SBMLExtensionRegistry - Class in org.sbml.libsbml
-
Registry where package extensions are registered.
- SBMLFileResolver - Class in org.sbml.libsbml
-
comp
Resolves documents stored on a file system.
- SBMLFileResolver() - Constructor for class org.sbml.libsbml.SBMLFileResolver
-
- SBMLFileResolver(SBMLFileResolver) - Constructor for class org.sbml.libsbml.SBMLFileResolver
-
Copy constructor.
- SBMLFunctionDefinitionConverter - Class in org.sbml.libsbml
-
Converter to expand user-defined functions in-line.
- SBMLFunctionDefinitionConverter() - Constructor for class org.sbml.libsbml.SBMLFunctionDefinitionConverter
-
- SBMLFunctionDefinitionConverter(SBMLFunctionDefinitionConverter) - Constructor for class org.sbml.libsbml.SBMLFunctionDefinitionConverter
-
- SBMLIdConverter - Class in org.sbml.libsbml
-
Converter for replacing object identifiers.
- SBMLIdConverter() - Constructor for class org.sbml.libsbml.SBMLIdConverter
-
- SBMLIdConverter(SBMLIdConverter) - Constructor for class org.sbml.libsbml.SBMLIdConverter
-
- SBMLInferUnitsConverter - Class in org.sbml.libsbml
-
Converter for inferring and setting parameter units.
- SBMLInferUnitsConverter() - Constructor for class org.sbml.libsbml.SBMLInferUnitsConverter
-
- SBMLInferUnitsConverter(SBMLInferUnitsConverter) - Constructor for class org.sbml.libsbml.SBMLInferUnitsConverter
-
- SBMLInitialAssignmentConverter - Class in org.sbml.libsbml
-
Converter that removes SBML initial assignments.
- SBMLInitialAssignmentConverter() - Constructor for class org.sbml.libsbml.SBMLInitialAssignmentConverter
-
- SBMLInitialAssignmentConverter(SBMLInitialAssignmentConverter) - Constructor for class org.sbml.libsbml.SBMLInitialAssignmentConverter
-
- SBMLLevel1Version1Converter - Class in org.sbml.libsbml
-
Whole-document SBML Level/Version converter.
- SBMLLevel1Version1Converter() - Constructor for class org.sbml.libsbml.SBMLLevel1Version1Converter
-
- SBMLLevel1Version1Converter(SBMLLevel1Version1Converter) - Constructor for class org.sbml.libsbml.SBMLLevel1Version1Converter
-
- SBMLLevelVersionConverter - Class in org.sbml.libsbml
-
Whole-document SBML Level/Version converter.
- SBMLLevelVersionConverter() - Constructor for class org.sbml.libsbml.SBMLLevelVersionConverter
-
- SBMLLevelVersionConverter(SBMLLevelVersionConverter) - Constructor for class org.sbml.libsbml.SBMLLevelVersionConverter
-
- SBMLLocalParameterConverter - Class in org.sbml.libsbml
-
Converter to turn local parameters into global ones.
- SBMLLocalParameterConverter() - Constructor for class org.sbml.libsbml.SBMLLocalParameterConverter
-
- SBMLLocalParameterConverter(SBMLLocalParameterConverter) - Constructor for class org.sbml.libsbml.SBMLLocalParameterConverter
-
- SBMLNamespaceInAnnotation - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SBMLNamespaces - Class in org.sbml.libsbml
-
Set of SBML Level + Version + namespace triples.
- SBMLNamespaces(long, long) - Constructor for class org.sbml.libsbml.SBMLNamespaces
-
Creates a new
SBMLNamespaces object corresponding to the given SBML
level and
version.
- SBMLNamespaces(long) - Constructor for class org.sbml.libsbml.SBMLNamespaces
-
Creates a new
SBMLNamespaces object corresponding to the given SBML
level and
version.
- SBMLNamespaces() - Constructor for class org.sbml.libsbml.SBMLNamespaces
-
Creates a new
SBMLNamespaces object corresponding to the given SBML
level and
version.
- SBMLNamespaces(long, long, String, long, String) - Constructor for class org.sbml.libsbml.SBMLNamespaces
-
(For extensions) Creates a new
SBMLNamespaces object corresponding to
the combination of (1) the given SBML
level and
version, and (2)
the given
package with the
package version.
- SBMLNamespaces(long, long, String, long) - Constructor for class org.sbml.libsbml.SBMLNamespaces
-
(For extensions) Creates a new
SBMLNamespaces object corresponding to
the combination of (1) the given SBML
level and
version, and (2)
the given
package with the
package version.
- SBMLNamespaces(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SBMLNamespaces
-
- SBMLNamespacesList - Class in org.sbml.libsbml
-
- SBMLNamespacesList() - Constructor for class org.sbml.libsbml.SBMLNamespacesList
-
Explicit constructor for this list.
- SBMLReactionConverter - Class in org.sbml.libsbml
-
Converter to replace reactions with SBML rate rules.
- SBMLReactionConverter() - Constructor for class org.sbml.libsbml.SBMLReactionConverter
-
- SBMLReactionConverter(SBMLReactionConverter) - Constructor for class org.sbml.libsbml.SBMLReactionConverter
-
- SBMLReader - Class in org.sbml.libsbml
-
File and text-string SBML reader.
- SBMLReader() - Constructor for class org.sbml.libsbml.SBMLReader
-
- SBMLResolver - Class in org.sbml.libsbml
-
comp
Base class for SBML resolvers.
- SBMLResolver() - Constructor for class org.sbml.libsbml.SBMLResolver
-
- SBMLResolver(SBMLResolver) - Constructor for class org.sbml.libsbml.SBMLResolver
-
Copy constructor.
- SBMLResolverRegistry - Class in org.sbml.libsbml
-
comp
Registry of all SBML resolvers.
- SBMLRuleConverter - Class in org.sbml.libsbml
-
Converter that sorts SBML rules and assignments.
- SBMLRuleConverter() - Constructor for class org.sbml.libsbml.SBMLRuleConverter
-
- SBMLRuleConverter(SBMLRuleConverter) - Constructor for class org.sbml.libsbml.SBMLRuleConverter
-
- SBMLStripPackageConverter - Class in org.sbml.libsbml
-
Converter that removes SBML Level 3 packages.
- SBMLStripPackageConverter() - Constructor for class org.sbml.libsbml.SBMLStripPackageConverter
-
- SBMLStripPackageConverter(SBMLStripPackageConverter) - Constructor for class org.sbml.libsbml.SBMLStripPackageConverter
-
- SBMLTypeCode_toString(int, String) - Static method in class org.sbml.libsbml.libsbml
-
This method takes an SBML type code and returns a string representing
the code.
- SBMLUnitsConverter - Class in org.sbml.libsbml
-
Converts a model's existing units to SI units.
- SBMLUnitsConverter() - Constructor for class org.sbml.libsbml.SBMLUnitsConverter
-
- SBMLUnitsConverter(SBMLUnitsConverter) - Constructor for class org.sbml.libsbml.SBMLUnitsConverter
-
- SBMLUri - Class in org.sbml.libsbml
-
comp
Utility class for handling URIs.
- SBMLUri(String) - Constructor for class org.sbml.libsbml.SBMLUri
-
Creates a new
SBMLUri from the given string URI.
- SBMLUri(SBMLUri) - Constructor for class org.sbml.libsbml.SBMLUri
-
Copy constructor.
- SBMLValidator - Class in org.sbml.libsbml
-
Base class for SBML validators.
- SBMLValidator() - Constructor for class org.sbml.libsbml.SBMLValidator
-
- SBMLValidator(SBMLValidator) - Constructor for class org.sbml.libsbml.SBMLValidator
-
- SBMLWriter - Class in org.sbml.libsbml
-
File and text-string SBML writer.
- SBMLWriter() - Constructor for class org.sbml.libsbml.SBMLWriter
-
- SBO - Class in org.sbml.libsbml
-
Facilities for using the Systems Biology Ontology.
- SBO() - Constructor for class org.sbml.libsbml.SBO
-
- SBOTermNotUniversalInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SBOTermNotValidAttributeBeforeL2V2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SBOTermNotValidAttributeBeforeL2V3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- setAbsoluteValue(double) - Method in class org.sbml.libsbml.RelAbsVector
-
Sets the absolute coordinate value.
- setActiveObjective(String) - Method in class org.sbml.libsbml.ListOfObjectives
-
- setActiveObjectiveId(String) - Method in class org.sbml.libsbml.FbcModelPlugin
-
Sets the id of the active objective.
- setAllowedChildrenType(int) - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- setAlpha(short) - Method in class org.sbml.libsbml.ColorDefinition
-
Sets alpha red color component.
- setAnnotation(XMLNode) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'annotation' subelement of this SBML object to a
copy of annotation.
- setAnnotation(String) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'annotation' subelement of this SBML object to a
copy of annotation.
- setAnnotation(XMLNode) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the 'annotation' subelement of this SBML object.
- setAnnotation(String) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the 'annotation' subelement of this SBML object.
- setAnnotation(XMLNode) - Method in class org.sbml.libsbml.SpeciesReference
-
Sets the value of the 'annotation' subelement of this SBML object to a
copy of annotation.
- setAnnotation(String) - Method in class org.sbml.libsbml.SpeciesReference
-
Sets the value of the 'annotation' subelement of this SBML object to a
copy of annotation.
- setAreaUnits(String) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'areaUnits' attribute of this
Model.
- setAssociatedSpecies(String) - Method in class org.sbml.libsbml.GeneProduct
-
Sets the value of the 'associatedSpecies' attribute of this
GeneProduct.
- setAssociation(Association) - Method in class org.sbml.libsbml.GeneAssociation
-
- setAssociation(FbcAssociation) - Method in class org.sbml.libsbml.GeneProductAssociation
-
- setAssociation(String, boolean, boolean) - Method in class org.sbml.libsbml.GeneProductAssociation
-
- setAssociation(String, boolean) - Method in class org.sbml.libsbml.GeneProductAssociation
-
- setAssociation(String) - Method in class org.sbml.libsbml.GeneProductAssociation
-
- setAttributes(XMLAttributes) - Method in class org.sbml.libsbml.XMLToken
-
Sets the attributes on the XML element represented by this token.
- setAutoIndent(boolean) - Method in class org.sbml.libsbml.XMLOutputStream
-
- setBackgroundColor(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'backgroundColor' attribute of this
DefaultValues
object.
- setBackgroundColor(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- setBasePoint1(Point) - Method in class org.sbml.libsbml.CubicBezier
-
Initializes first base point with a copy of the given point.
- setBasePoint1(double, double, double) - Method in class org.sbml.libsbml.CubicBezier
-
Initializes first base point with the given coordinates.
- setBasePoint1(double, double) - Method in class org.sbml.libsbml.CubicBezier
-
Initializes first base point with the given coordinates.
- setBasePoint1(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
Sets the first basepoint to the given coordinatees.
- setBasePoint1(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
Sets the first basepoint to the given coordinatees.
- setBasePoint1_x(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
- setBasePoint1_X(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
Sets the x value of the first base point of the curve (the one closer to the
starting point).
- setBasePoint1_y(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
- setBasePoint1_Y(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
- setBasePoint1_z(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
- setBasePoint1_Z(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
- setBasePoint2(Point) - Method in class org.sbml.libsbml.CubicBezier
-
Initializes second base point with a copy of the given point.
- setBasePoint2(double, double, double) - Method in class org.sbml.libsbml.CubicBezier
-
Initializes second base point with the given coordinates.
- setBasePoint2(double, double) - Method in class org.sbml.libsbml.CubicBezier
-
Initializes second base point with the given coordinates.
- setBasePoint2(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
Sets the second basepoint to the given coordinatees.
- setBasePoint2(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
Sets the second basepoint to the given coordinatees.
- setBasePoint2_x(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
- setBasePoint2_X(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
Sets the x value of the second base point of the curve (the one further from the
starting point).
- setBasePoint2_y(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
- setBasePoint2_Y(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
Sets the y value of the second base point of the curve (the one further from the
starting point).
- setBasePoint2_z(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
- setBasePoint2_Z(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
-
Sets the z value of the second base point of the curve (the one further from the
starting point).
- setBindingSite1(String) - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- setBindingSite2(String) - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- setBindingStatus(int) - Method in class org.sbml.libsbml.OutwardBindingSite
-
- setBindingStatus(String) - Method in class org.sbml.libsbml.OutwardBindingSite
-
- setBiologicalQualifierType(int) - Method in class org.sbml.libsbml.CVTerm
-
Sets the biology qualifier
type of this
CVTerm object.
- setBiologicalQualifierType(String) - Method in class org.sbml.libsbml.CVTerm
-
Sets the biology qualifier
type code of this
CVTerm object.
- setBlue(short) - Method in class org.sbml.libsbml.ColorDefinition
-
Sets the blue color component.
- setBoolValue(boolean) - Method in class org.sbml.libsbml.ConversionOption
-
Set the value of this option to a given Boolean value.
- setBoolValue(String, boolean) - Method in class org.sbml.libsbml.ConversionProperties
-
Sets the value of the given option to a Boolean.
- setBoundaryCondition(boolean) - Method in class org.sbml.libsbml.Species
-
Sets the 'boundaryCondition' attribute of this
Species object.
- setBoundingBox(BoundingBox) - Method in class org.sbml.libsbml.GraphicalObject
-
- setBoundingBox(BoundingBox) - Method in class org.sbml.libsbml.LineEnding
-
Sets the value of the 'boundingBox' element of this
LineEnding.
- setBounds(double, double, double) - Method in class org.sbml.libsbml.Dimensions
-
Sets all sizes of the
Dimensions object to the given values.
- setBounds(double, double) - Method in class org.sbml.libsbml.Dimensions
-
Sets all sizes of the
Dimensions object to the given values.
- setCenter(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
Sets the coordinates for the center point.
- setCenter(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
Sets the coordinates for the center point.
- setCenter2D(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
-
Sets the 2D coordinates for the center point.
- setCenter3D(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
-
Sets the 3D coordinates for the center point.
- setCharacter(char) - Method in class org.sbml.libsbml.ASTNode
-
Sets the value of this
ASTNode to the given character.
- setCharacters(String) - Method in class org.sbml.libsbml.XMLToken
-
- setCharge(int) - Method in class org.sbml.libsbml.FbcSpeciesPlugin
-
- setCharge(int) - Method in class org.sbml.libsbml.Species
-
Sets the 'charge' attribute of this
Species object.
- setChemicalFormula(String) - Method in class org.sbml.libsbml.FbcSpeciesPlugin
-
- setClassName(String) - Method in class org.sbml.libsbml.ASTNode
-
Sets the MathML class of this
ASTNode to className.
- setCoefficient(double) - Method in class org.sbml.libsbml.FluxObjective
-
Sets the value of the 'coefficient' attribute of this
FluxObjective.
- setColorValue(String) - Method in class org.sbml.libsbml.ColorDefinition
-
Sets the color value from a given value string.
- setColumn(long) - Method in class org.sbml.libsbml.XMLError
-
Sets the column number where this error occurred.
- setComparisonCaseSensitivity(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
-
Sets the parser's behavior with respect to case sensitivity for
recognizing predefined symbols.
- setCompartment(String) - Method in class org.sbml.libsbml.CompartmentReference
-
- setCompartment(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- setCompartment(String) - Method in class org.sbml.libsbml.QualitativeSpecies
-
- setCompartment(String) - Method in class org.sbml.libsbml.Reaction
-
Sets the value of the 'compartment' attribute of this
Reaction.
- setCompartment(String) - Method in class org.sbml.libsbml.Species
-
Sets the 'compartment' attribute of this
Species object.
- setCompartmentId(String) - Method in class org.sbml.libsbml.CompartmentGlyph
-
Sets the id of the associated compartment.
- setCompartmentReference(String) - Method in class org.sbml.libsbml.MultiSimpleSpeciesReferencePlugin
-
- setCompartmentReference(String) - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- setCompartmentType(String) - Method in class org.sbml.libsbml.Compartment
-
Sets the 'compartmentType' attribute of this
Compartment object.
- setCompartmentType(String) - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
Sets the value of the 'compartmentType' attribute on this compartment.
- setComponent(String) - Method in class org.sbml.libsbml.OutwardBindingSite
-
- setComponent(String) - Method in class org.sbml.libsbml.SpeciesFeature
-
- setComponent(String) - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- setComponent(String) - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- setConsistencyChecks(int, boolean) - Method in class org.sbml.libsbml.SBMLDocument
-
- setConsistencyChecksForConversion(int, boolean) - Method in class org.sbml.libsbml.SBMLDocument
-
- setConstant(boolean) - Method in class org.sbml.libsbml.Compartment
-
Sets the value of the 'constant' attribute of this
Compartment object.
- setConstant(boolean) - Method in class org.sbml.libsbml.Parameter
-
Sets the 'constant' attribute of this
Parameter to the given boolean
flag.
- setConstant(boolean) - Method in class org.sbml.libsbml.QualitativeSpecies
-
- setConstant(boolean) - Method in class org.sbml.libsbml.Species
-
Sets the 'constant' attribute of this
Species object.
- setConstant(boolean) - Method in class org.sbml.libsbml.SpeciesReference
-
Sets the 'constant' attribute of this
SpeciesReference to the given boolean
flag.
- setConversionFactor(String) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'conversionFactor' attribute of this
Model.
- setConversionFactor(String) - Method in class org.sbml.libsbml.ReplacedElement
-
Sets the value of the 'conversionFactor' attribute of this
ReplacedElement.
- setConversionFactor(String) - Method in class org.sbml.libsbml.Species
-
Sets the value of the 'conversionFactor' attribute of this
Species object.
- setCoordinate(double, double) - Method in class org.sbml.libsbml.RelAbsVector
-
Sets the relative and absolute value.
- setCoordinate(double) - Method in class org.sbml.libsbml.RelAbsVector
-
Sets the relative and absolute value.
- setCoordinate(String) - Method in class org.sbml.libsbml.RelAbsVector
-
Sets the coordinates from the given string.
- setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Image
-
Sets the position of the image relative to its viewport.
- setCoordinates(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Image
-
Sets the position of the image relative to its viewport.
- setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
Sets the 3D coordinates for the start and the end point of the linear gradient vector.
- setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
Sets the 2D coordinates for the start and the end point of the linear gradient vector.
- setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
Sets the 3D coordinates for the center and the focal
point as well as the radius.
- setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
Sets the 2D coordinates for the center and the focal
point as well as the radius.
- setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
Sets the position of the
Rectangle within the viewport.
- setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
-
Sets the coordinates of the
RenderPoint to the given values.
- setCoordinates(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
-
Sets the coordinates of the
RenderPoint to the given values.
- setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Text
-
Sets the position of the text within the viewport.
- setCoordinates(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Text
-
Sets the position of the text within the viewport.
- setCoordinatesAndSize(RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
Sets the position and the size of the
Rectangle within the viewport.
- setCreatedDate(Date) - Method in class org.sbml.libsbml.ModelHistory
-
- setCsymbolURL(String) - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- setCurve(Curve) - Method in class org.sbml.libsbml.GeneralGlyph
-
Sets the curve object for the reaction glyph.
- setCurve(Curve) - Method in class org.sbml.libsbml.ReactionGlyph
-
Sets the curve object for the reaction glyph.
- setCurve(Curve) - Method in class org.sbml.libsbml.ReferenceGlyph
-
Sets the curve object for the reference glyph.
- setCurve(Curve) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Sets the curve object for the species reference glyph.
- setCX(RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
-
Sets the x coordinates for the center point.
- setCx(RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
- setCY(RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
-
Sets the y coordinates for the center point.
- setCy(RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
- setCZ(RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
-
Sets the z coordinates for the center point.
- setCz(RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
- setDashByIndex(long, long) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
Sets the integer value of the dash at the given position.
- setDateAsString(String) - Method in class org.sbml.libsbml.Date
-
Sets the value of this
Date object using a date and time value
expressed as a text string.
- setDay(long) - Method in class org.sbml.libsbml.Date
-
Sets the value of the day of this
Date object.
- setDefault_z(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'default_z' attribute of this
DefaultValues
object.
- setDefaultTerm(DefaultTerm) - Method in class org.sbml.libsbml.ListOfFunctionTerms
-
- setDefaultTerm(DefaultTerm) - Method in class org.sbml.libsbml.Transition
-
- setDefaultValues(DefaultValues) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- setDefaultValues(DefaultValues) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- setDelay(Delay) - Method in class org.sbml.libsbml.Event
-
Sets the delay definition of this
Event to a copy of the given
Delay
object instance.
- setDeletion(String) - Method in class org.sbml.libsbml.ReplacedElement
-
- setDenominator(int) - Method in class org.sbml.libsbml.SpeciesReference
-
Set the value of the 'denominator' attribute, for the case of a
rational-numbered stoichiometry or a model in SBML Level 1.
- setDepth(double) - Method in class org.sbml.libsbml.BoundingBox
-
Set depth of the bounding box.
- setDepth(double) - Method in class org.sbml.libsbml.Dimensions
-
Sets the depth to the given value.
- setDescription(String) - Method in class org.sbml.libsbml.ConversionOption
-
Sets the description text for this option.
- setDimensions(Dimensions) - Method in class org.sbml.libsbml.BoundingBox
-
Sets the dimensions to a copy of the
Dimensions object given.
- setDimensions(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Image
-
Sets the dimensions of the image.
- setDimensions(Dimensions) - Method in class org.sbml.libsbml.Layout
-
Sets the dimensions of the layout.
- setDivider(String) - Method in class org.sbml.libsbml.CompModelPlugin
-
Set the string used as the divider between names when renaming and
flattening models.
- setDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLConverter
-
Sets the SBML document to be converted.
- setDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLReactionConverter
-
Sets the current SBML document to the given
SBMLDocument object.
- setDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLValidator
-
Sets the current SBML document to the given
SBMLDocument object.
- setDoubleValue(double) - Method in class org.sbml.libsbml.ConversionOption
-
Set the value of this option to a given double value.
- setDoubleValue(String, double) - Method in class org.sbml.libsbml.ConversionProperties
-
Sets the value of the given option to a double.
- setElementName(String) - Method in class org.sbml.libsbml.Point
-
Sets the element name to be returned by getElementName().
- setElementNamespace(String) - Method in class org.sbml.libsbml.SBasePlugin
-
Sets the XML namespace to which this object belongs.
- setEmail(String) - Method in class org.sbml.libsbml.ModelCreator
-
- setEnabled(boolean) - Method in class org.sbml.libsbml.SBMLExtension
-
Enable or disable this package.
- setEnabled(String, boolean) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
-
Enables or disable the package with the given URI.
- setEnableRotationalMapping(boolean) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'enableRotationalMapping' attribute of this
DefaultValues object.
- setEnableRotationalMapping(boolean) - Method in class org.sbml.libsbml.LineEnding
-
Sets the value of the 'enableRotationalMapping' attribute of this
LineEnding.
- setEnd(Point) - Method in class org.sbml.libsbml.LineSegment
-
Initializes the end point with a copy of the given
Point object.
- setEnd(double, double, double) - Method in class org.sbml.libsbml.LineSegment
-
Initializes the end point with the given coordinates.
- setEnd(double, double) - Method in class org.sbml.libsbml.LineSegment
-
Initializes the end point with the given coordinates.
- setEnd() - Method in class org.sbml.libsbml.XMLToken
-
Declares that this token represents an XML element end tag.
- setEndHead(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'endHead' attribute of this
DefaultValues object.
- setEndHead(String) - Method in class org.sbml.libsbml.RenderCurve
-
Sets the value of the 'endHead' attribute of this
RenderCurve.
- setEndHead(String) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'endHead' attribute of this
RenderGroup.
- setEOF() - Method in class org.sbml.libsbml.XMLToken
-
Declares that this token is an end-of-file/input marker.
- setErrorLog(XMLErrorLog) - Method in class org.sbml.libsbml.XMLInputStream
-
Sets the
XMLErrorLog this stream will use to log errors.
- setExponent(int) - Method in class org.sbml.libsbml.Unit
-
Sets the 'exponent' attribute value of this
Unit.
- setExponent(double) - Method in class org.sbml.libsbml.Unit
-
Sets the 'exponent' attribute value of this
Unit.
- setExtentConversionFactor(String) - Method in class org.sbml.libsbml.Submodel
-
Sets the value of the 'extentConversionFactor' attribute of this
Submodel.
- setExtentUnits(String) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'extentUnits' attribute of this
Model.
- setFamilyName(String) - Method in class org.sbml.libsbml.ModelCreator
-
- setFast(boolean) - Method in class org.sbml.libsbml.Reaction
-
Sets the value of the 'fast' attribute of this
Reaction.
- setFill(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'fill' attribute of this
DefaultValues object.
- setFill(String) - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- setFillColor(String) - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
Set fill color to the id of a color definition, the id of a gradient
definition or a color value string.
- setFillRule(int) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'fill-rule' attribute of this
DefaultValues
object.
- setFillRule(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'fill-rule' attribute of this
DefaultValues
object.
- setFillRule(int) - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- setFillRule(String) - Method in class org.sbml.libsbml.GraphicalPrimitive2D
-
- setFloatValue(float) - Method in class org.sbml.libsbml.ConversionOption
-
Set the value of this option to a given float value.
- setFloatValue(String, float) - Method in class org.sbml.libsbml.ConversionProperties
-
Sets the value of the given option to a float.
- setFocalPoint(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
Sets the coordinates for the focal point.
- setFocalPoint(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
Sets the coordinates for the focal point.
- setFontFamily(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'font-family' attribute of this
DefaultValues
object.
- setFontFamily(String) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'font-family' attribute of this
RenderGroup.
- setFontFamily(String) - Method in class org.sbml.libsbml.Text
-
Sets the value of the 'font-family' attribute of this
Text.
- setFontSize(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'font-size' attribute of this
DefaultValues
object.
- setFontSize(RelAbsVector) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the font size.
- setFontSize(RelAbsVector) - Method in class org.sbml.libsbml.Text
-
Sets the font size.
- setFontStyle(int) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'font-style' attribute of this
DefaultValues
object.
- setFontStyle(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'font-style' attribute of this
DefaultValues.
- setFontStyle(int) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'font-style' attribute of this
RenderGroup.
- setFontStyle(String) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'font-style' attribute of this
RenderGroup.
- setFontStyle(int) - Method in class org.sbml.libsbml.Text
-
Sets the value of the 'font-style' attribute of this
Text.
- setFontStyle(String) - Method in class org.sbml.libsbml.Text
-
Sets the value of the 'font-style' attribute of this
Text.
- setFontWeight(int) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'font-weight' attribute of this
DefaultValues
object.
- setFontWeight(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'font-weight' attribute of this
DefaultValues.
- setFontWeight(int) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'font-weight' attribute of this
RenderGroup.
- setFontWeight(String) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'font-weight' attribute of this
RenderGroup.
- setFontWeight(int) - Method in class org.sbml.libsbml.Text
-
Sets the value of the 'font-weight' attribute of this
Text.
- setFontWeight(String) - Method in class org.sbml.libsbml.Text
-
Sets the value of the 'font-weight' attribute of this
Text.
- setFormula(String) - Method in class org.sbml.libsbml.KineticLaw
-
Sets the mathematical expression of this
KineticLaw instance to the
given
formula.
- setFormula(String) - Method in class org.sbml.libsbml.Rule
-
Sets the 'math' subelement of this
Rule to an expression in text-string
form.
- setFx(RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
- setFy(RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
- setFz(RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
- setGeneProduct(String) - Method in class org.sbml.libsbml.GeneProductRef
-
- setGeneProductAssociation(GeneProductAssociation) - Method in class org.sbml.libsbml.FbcReactionPlugin
-
- setGivenName(String) - Method in class org.sbml.libsbml.ModelCreator
-
- setGlyphId(String) - Method in class org.sbml.libsbml.ReferenceGlyph
-
Sets the id of the associated glyph.
- setGraphicalObjectId(String) - Method in class org.sbml.libsbml.TextGlyph
-
Sets the id of the associated graphical object.
- setGreen(short) - Method in class org.sbml.libsbml.ColorDefinition
-
Sets the green color component.
- setGroup(RenderGroup) - Method in class org.sbml.libsbml.LineEnding
-
Sets the value of the 'group' element of this
LineEnding.
- setGroup(RenderGroup) - Method in class org.sbml.libsbml.Style
-
Sets the value of the 'group' element of this
Style.
- setHasOnlySubstanceUnits(boolean) - Method in class org.sbml.libsbml.Species
-
Sets the 'hasOnlySubstanceUnits' attribute of this
Species object.
- setHeight(double) - Method in class org.sbml.libsbml.BoundingBox
-
Set height of the bounding box.
- setHeight(double) - Method in class org.sbml.libsbml.Dimensions
-
Sets the height to the given value.
- setHeight(RelAbsVector) - Method in class org.sbml.libsbml.Image
-
Sets the height of the image when rendered.
- setHeight(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
- setHour(long) - Method in class org.sbml.libsbml.Date
-
Sets the value of the hour of this
Date object.
- setHoursOffset(long) - Method in class org.sbml.libsbml.Date
-
Sets the value of this
Date object's time zone hour offset.
- setHref(String) - Method in class org.sbml.libsbml.Image
-
Sets the value of the 'href' attribute of this
Image.
- setId(String) - Method in class org.sbml.libsbml.ASTNode
-
Sets the MathML id of this
ASTNode to id.
- setId(String) - Method in class org.sbml.libsbml.BoundingBox
-
Sets the value of the 'id' attribute of this
BoundingBox.
- setId(String) - Method in class org.sbml.libsbml.ColorDefinition
-
- setId(String) - Method in class org.sbml.libsbml.Compartment
-
Sets the value of the 'id' attribute of this
Compartment object.
- setId(String) - Method in class org.sbml.libsbml.CompartmentReference
-
- setId(String) - Method in class org.sbml.libsbml.CompartmentType
-
- setId(String) - Method in class org.sbml.libsbml.Deletion
-
Sets the value of the 'id' attribute of this
Deletion.
- setId(String) - Method in class org.sbml.libsbml.Dimensions
-
Sets the value of the 'id' attribute of this
Dimensions.
- setId(String) - Method in class org.sbml.libsbml.Event
-
Sets the value of the 'id' attribute of this
Event.
- setId(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- setId(String) - Method in class org.sbml.libsbml.FluxBound
-
Sets the value of the 'id' attribute of this
FluxBound.
- setId(String) - Method in class org.sbml.libsbml.FluxObjective
-
- setId(String) - Method in class org.sbml.libsbml.FunctionDefinition
-
- setId(String) - Method in class org.sbml.libsbml.GeneAssociation
-
- setId(String) - Method in class org.sbml.libsbml.GeneProduct
-
Sets the value of the 'id' attribute of this
GeneProduct.
- setId(String) - Method in class org.sbml.libsbml.GeneProductAssociation
-
- setId(String) - Method in class org.sbml.libsbml.GeneProductRef
-
- setId(String) - Method in class org.sbml.libsbml.GradientBase
-
- setId(String) - Method in class org.sbml.libsbml.GraphicalObject
-
- setId(String) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- setId(String) - Method in class org.sbml.libsbml.Group
-
Sets the value of the 'id' attribute of this
Group.
- setId(String) - Method in class org.sbml.libsbml.Image
-
Sets the value of the 'id' attribute of this
Image.
- setId(String) - Method in class org.sbml.libsbml.Input
-
Sets the value of the 'id' attribute of this obInputject.
- setId(String) - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- setId(String) - Method in class org.sbml.libsbml.Layout
-
Sets the value of the 'id' attribute of this
Layout.
- setId(String) - Method in class org.sbml.libsbml.LineEnding
-
Sets the value of the 'id' attribute of this
LineEnding.
- setId(String) - Method in class org.sbml.libsbml.ListOfMembers
-
- setId(String) - Method in class org.sbml.libsbml.Member
-
Sets the value of the 'id' attribute of this
Member.
- setId(String) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'id' attribute of this
Model.
- setId(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- setId(String) - Method in class org.sbml.libsbml.Objective
-
Sets the value of the 'id' attribute of this
Objective.
- setId(String) - Method in class org.sbml.libsbml.Output
-
Sets the value of the 'id' attribute of this
Output.
- setId(String) - Method in class org.sbml.libsbml.OutwardBindingSite
-
- setId(String) - Method in class org.sbml.libsbml.Parameter
-
Sets the value of the 'id' attribute of this
Parameter.
- setId(String) - Method in class org.sbml.libsbml.Point
-
Sets the value of the 'id' attribute of this
Point.
- setId(String) - Method in class org.sbml.libsbml.Port
-
Sets the value of the 'id' attribute of this
Port.
- setId(String) - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
- setId(String) - Method in class org.sbml.libsbml.QualitativeSpecies
-
- setId(String) - Method in class org.sbml.libsbml.Reaction
-
Sets the value of the 'id' attribute of this
Reaction.
- setId(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- setId(String) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the 'id' attribute of this SBML object.
- setId(String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
- setId(String) - Method in class org.sbml.libsbml.Species
-
Sets the value of the 'id' attribute of this
Species.
- setId(String) - Method in class org.sbml.libsbml.SpeciesFeature
-
- setId(String) - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- setId(String) - Method in class org.sbml.libsbml.SpeciesType
-
Sets the value of the 'id' attribute of this
SpeciesType.
- setId(String) - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- setId(String) - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- setId(String) - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- setId(String) - Method in class org.sbml.libsbml.Style
-
Sets the value of the 'id' attribute of this
Style.
- setId(String) - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- setId(String) - Method in class org.sbml.libsbml.Submodel
-
Sets the value of the 'id' attribute of this
Submodel.
- setId(String) - Method in class org.sbml.libsbml.Transition
-
Sets the value of the 'id' attribute of this
Transition.
- setId(String) - Method in class org.sbml.libsbml.UnitDefinition
-
- setIdAttribute(String) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the 'id' attribute of this SBML object.
- setIdentifyingParent(String) - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- setIdList(StringSet) - Method in class org.sbml.libsbml.LocalStyle
-
Sets the id list.
- setIdRef(String) - Method in class org.sbml.libsbml.Member
-
Sets the value of the 'idRef' attribute of this
Member.
- setIdRef(String) - Method in class org.sbml.libsbml.SBaseRef
-
Sets the value of the 'idRef' attribute of this
SBaseRef.
- setImageReference(String) - Method in class org.sbml.libsbml.Image
-
Sets the reference to the image location.
- setInitialAmount(double) - Method in class org.sbml.libsbml.Species
-
Sets the 'initialAmount' attribute of this
Species and marks the field
as set.
- setInitialConcentration(double) - Method in class org.sbml.libsbml.Species
-
Sets the 'initialConcentration' attribute of this
Species and marks
the field as set.
- setInitialLevel(int) - Method in class org.sbml.libsbml.QualitativeSpecies
-
- setInitialValue(boolean) - Method in class org.sbml.libsbml.Trigger
-
(SBML Level 3 only) Sets the 'initialValue' attribute of this
Trigger instance.
- setIntValue(int) - Method in class org.sbml.libsbml.ConversionOption
-
Set the value of this option to a given int value.
- setIntValue(String, int) - Method in class org.sbml.libsbml.ConversionProperties
-
Sets the value of the given option to an integer.
- setIsFunction(boolean) - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- setIsType(boolean) - Method in class org.sbml.libsbml.MultiCompartmentPlugin
-
Sets the value of the 'isType' attribute.
- setitem(int, double) - Method in class org.sbml.libsbml.double_array
-
- setitem(int, int) - Method in class org.sbml.libsbml.int_array
-
- setKey(String) - Method in class org.sbml.libsbml.ConversionOption
-
Sets the key for this option.
- setKind(int) - Method in class org.sbml.libsbml.Group
-
Sets the value of the 'kind' attribute of this
Group.
- setKind(String) - Method in class org.sbml.libsbml.Group
-
Sets the value of the 'kind' attribute of this
Group.
- setKind(int) - Method in class org.sbml.libsbml.Unit
-
Sets the 'kind' attribute value of this
Unit.
- setKineticLaw(KineticLaw) - Method in class org.sbml.libsbml.Reaction
-
Sets the 'kineticLaw' subelement of this
Reaction to a copy of the
given
KineticLaw object.
- setL1TypeCode(int) - Method in class org.sbml.libsbml.Rule
-
Sets the SBML Level 1 type code for this
Rule.
- setLabel(String) - Method in class org.sbml.libsbml.GeneProduct
-
Sets the value of the 'label' attribute of this
GeneProduct.
- setLengthUnits(String) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'lengthUnits' attribute of this
Model.
- setLevelAndVersion(long, long, boolean, boolean) - Method in class org.sbml.libsbml.SBMLDocument
-
Sets the SBML Level and Version of this
SBMLDocument instance,
attempting to convert the model as needed.
- setLevelAndVersion(long, long, boolean) - Method in class org.sbml.libsbml.SBMLDocument
-
Sets the SBML Level and Version of this
SBMLDocument instance,
attempting to convert the model as needed.
- setLevelAndVersion(long, long) - Method in class org.sbml.libsbml.SBMLDocument
-
Sets the SBML Level and Version of this
SBMLDocument instance,
attempting to convert the model as needed.
- setLibraryName(String) - Static method in class org.sbml.libsbml.XMLOutputStream
-
sets the name of the library writing the XML
- setLibraryVersion(String) - Static method in class org.sbml.libsbml.XMLOutputStream
-
sets the name of the library writing the output
- setLine(long) - Method in class org.sbml.libsbml.XMLError
-
Sets the line number where this error occurred.
- setLinearGradient_x1(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'linearGradient_x1' attribute of this
DefaultValues object.
- setLinearGradient_x2(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'linearGradient_x2' attribute of this
DefaultValues object.
- setLinearGradient_y1(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'linearGradient_y1' attribute of this
DefaultValues object.
- setLinearGradient_y2(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'linearGradient_y2' attribute of this
DefaultValues object.
- setLinearGradient_z1(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'linearGradient_z1' attribute of this
DefaultValues object.
- setLinearGradient_z2(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'linearGradient_z2' attribute of this
DefaultValues object.
- setLocationURI(String) - Method in class org.sbml.libsbml.SBMLDocument
-
- setLowerFluxBound(String) - Method in class org.sbml.libsbml.FbcReactionPlugin
-
- setMajorVersion(long) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- setMajorVersion(long) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- setMath(ASTNode) - Method in class org.sbml.libsbml.Constraint
-
Sets the mathematical expression of this
Constraint to a copy of the
AST given as
math.
- setMath(ASTNode) - Method in class org.sbml.libsbml.Delay
-
Sets the delay expression of this
Delay instance to a copy of the given
ASTNode.
- setMath(ASTNode) - Method in class org.sbml.libsbml.EventAssignment
-
- setMath(ASTNode) - Method in class org.sbml.libsbml.FunctionDefinition
-
Sets the 'math' subelement of this
FunctionDefinition to the Abstract
Syntax Tree given in
math.
- setMath(ASTNode) - Method in class org.sbml.libsbml.FunctionTerm
-
- setMath(ASTNode) - Method in class org.sbml.libsbml.InitialAssignment
-
- setMath(ASTNode) - Method in class org.sbml.libsbml.KineticLaw
-
Sets the mathematical expression of this
KineticLaw instance to a copy
of the given
ASTNode.
- setMath(ASTNode) - Method in class org.sbml.libsbml.Priority
-
Sets the math expression of this
Priority instance to a copy of the given
ASTNode.
- setMath(ASTNode) - Method in class org.sbml.libsbml.Rule
-
Sets the 'math' subelement of this
Rule to a copy of the given
ASTNode.
- setMath(ASTNode) - Method in class org.sbml.libsbml.StoichiometryMath
-
- setMath(ASTNode) - Method in class org.sbml.libsbml.Trigger
-
Sets the trigger expression of this
Trigger instance to a copy of the given
ASTNode.
- setMatrix(SWIGTYPE_p_double) - Method in class org.sbml.libsbml.Transformation
-
Sets the matrix to the values given in the array.
- setMatrix(SWIGTYPE_p_double) - Method in class org.sbml.libsbml.Transformation2D
-
Sets the 2D matrix to the values given in the array.
- setMatrix2D(SWIGTYPE_p_double) - Method in class org.sbml.libsbml.Transformation2D
-
Sets the 2D matrix to the values given in the array.
- setMaxLevel(int) - Method in class org.sbml.libsbml.QualitativeSpecies
-
- setMd5(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- setMessage(XMLNode) - Method in class org.sbml.libsbml.Constraint
-
- setMessage(String, boolean) - Method in class org.sbml.libsbml.Constraint
-
- setMessage(String) - Method in class org.sbml.libsbml.Constraint
-
- setMetaId(String) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the meta-identifier attribute of this SBML object.
- setMetaIdRef(String) - Method in class org.sbml.libsbml.GraphicalObject
-
- setMetaIdRef(String) - Method in class org.sbml.libsbml.Member
-
Sets the value of the 'metaIdRef' attribute of this
Member.
- setMetaIdRef(String) - Method in class org.sbml.libsbml.SBaseRef
-
Sets the value of the 'metaIdRef' attribute of this
SBaseRef.
- setMinorVersion(long) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
- setMinorVersion(long) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
- setMinute(long) - Method in class org.sbml.libsbml.Date
-
Sets the value of the minute of this
Date object.
- setMinutesOffset(long) - Method in class org.sbml.libsbml.Date
-
Sets the value of this
Date object's time zone minutes offset.
- setModel(Model) - Method in class org.sbml.libsbml.L3ParserSettings
-
- setModel(Model) - Method in class org.sbml.libsbml.SBMLDocument
-
- setModelHistory(ModelHistory) - Method in class org.sbml.libsbml.SBase
-
- setModelQualifierType(int) - Method in class org.sbml.libsbml.CVTerm
-
Sets the model qualifier type
of this
CVTerm object.
- setModelQualifierType(String) - Method in class org.sbml.libsbml.CVTerm
-
Sets the model qualifier
type value of this
CVTerm object.
- setModelRef(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- setModelRef(String) - Method in class org.sbml.libsbml.Submodel
-
Sets the value of the 'modelRef' attribute of this
Submodel.
- setModifiedDate(Date) - Method in class org.sbml.libsbml.ModelHistory
-
- setMonth(long) - Method in class org.sbml.libsbml.Date
-
Sets the value of the month of this
Date object.
- setMultiplier(double) - Method in class org.sbml.libsbml.Unit
-
Sets the 'multipler' attribute value of this
Unit.
- setName(String) - Method in class org.sbml.libsbml.ASTNode
-
Sets the value of this
ASTNode to the given name.
- setName(String) - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- setName(String) - Method in class org.sbml.libsbml.ColorDefinition
-
- setName(String) - Method in class org.sbml.libsbml.Compartment
-
Sets the value of the 'name' attribute of this
Compartment object.
- setName(String) - Method in class org.sbml.libsbml.CompartmentReference
-
- setName(String) - Method in class org.sbml.libsbml.CompartmentType
-
- setName(String) - Method in class org.sbml.libsbml.Deletion
-
Sets the value of the 'name' attribute of this
Deletion.
- setName(String) - Method in class org.sbml.libsbml.Event
-
Sets the value of the 'name' attribute of this
Event.
- setName(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- setName(String) - Method in class org.sbml.libsbml.FluxBound
-
Sets the value of the 'name' attribute of this
FluxBound.
- setName(String) - Method in class org.sbml.libsbml.FluxObjective
-
- setName(String) - Method in class org.sbml.libsbml.FunctionDefinition
-
- setName(String) - Method in class org.sbml.libsbml.GeneProduct
-
Sets the value of the 'name' attribute of this
GeneProduct.
- setName(String) - Method in class org.sbml.libsbml.GeneProductAssociation
-
- setName(String) - Method in class org.sbml.libsbml.GeneProductRef
-
- setName(String) - Method in class org.sbml.libsbml.GradientBase
-
Sets the value of the 'name' attribute of this
GradientBase.
- setName(String) - Method in class org.sbml.libsbml.Group
-
Sets the value of the 'name' attribute of this
Group.
- setName(String) - Method in class org.sbml.libsbml.Input
-
Sets the value of the 'name' attribute of this
Input.
- setName(String) - Method in class org.sbml.libsbml.InSpeciesTypeBond
-
- setName(String) - Method in class org.sbml.libsbml.Layout
-
Sets the value of the 'name' attribute of this
Layout.
- setName(String) - Method in class org.sbml.libsbml.ListOfMembers
-
- setName(String) - Method in class org.sbml.libsbml.Member
-
Sets the value of the 'name' attribute of this
Member.
- setName(String) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'name' attribute of this
Model.
- setName(String) - Method in class org.sbml.libsbml.ModelCreator
-
Sets the 'fn' portion of this
ModelCreator object (when using vCard4).
- setName(String) - Method in class org.sbml.libsbml.MultiSpeciesType
-
- setName(String) - Method in class org.sbml.libsbml.Objective
-
Sets the value of the 'name' attribute of this
Objective.
- setName(String) - Method in class org.sbml.libsbml.Output
-
Sets the value of the 'name' attribute of this
Output.
- setName(String) - Method in class org.sbml.libsbml.OutwardBindingSite
-
- setName(String) - Method in class org.sbml.libsbml.Parameter
-
Sets the value of the 'name' attribute of this
Parameter.
- setName(String) - Method in class org.sbml.libsbml.Port
-
Sets the value of the 'name' attribute of this
Port.
- setName(String) - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
- setName(String) - Method in class org.sbml.libsbml.QualitativeSpecies
-
- setName(String) - Method in class org.sbml.libsbml.Reaction
-
Sets the value of the 'name' attribute of this
Reaction.
- setName(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- setName(String) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the 'name' attribute of this SBML object.
- setName(String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
- setName(String) - Method in class org.sbml.libsbml.Species
-
Sets the value of the 'name' attribute of this
Species.
- setName(String) - Method in class org.sbml.libsbml.SpeciesFeature
-
- setName(String) - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- setName(String) - Method in class org.sbml.libsbml.SpeciesType
-
Sets the value of the 'name' attribute of this
SpeciesType.
- setName(String) - Method in class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- setName(String) - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- setName(String) - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- setName(String) - Method in class org.sbml.libsbml.Style
-
Sets the value of the 'name' attribute of this
Style.
- setName(String) - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- setName(String) - Method in class org.sbml.libsbml.Submodel
-
Sets the value of the 'name' attribute of this
Submodel.
- setName(String) - Method in class org.sbml.libsbml.Transformation
-
- setName(String) - Method in class org.sbml.libsbml.Transition
-
Sets the value of the 'name' attribute of this
Transition.
- setName(String) - Method in class org.sbml.libsbml.UnitDefinition
-
- setNamespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBase
-
Sets the namespaces relevant of this SBML object.
- setNamespaces(XMLNamespaces) - Method in class org.sbml.libsbml.XMLToken
-
Sets the XML namespaces on this XML element.
- setNotes(XMLNode) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the 'notes' subelement of this SBML object.
- setNotes(String, boolean) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the 'notes' subelement of this SBML object to a copy
of the string notes.
- setNotes(String) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the 'notes' subelement of this SBML object to a copy
of the string notes.
- setNumAllowedChildren(SWIGTYPE_p_std__vectorT_unsigned_int_t) - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- setNumericValue(String) - Method in class org.sbml.libsbml.PossibleSpeciesFeatureValue
-
- setObjectRole(String) - Method in class org.sbml.libsbml.RenderGraphicalObjectPlugin
-
Sets the object role string for the object.
- setOccur(long) - Method in class org.sbml.libsbml.SpeciesFeature
-
- setOccur(long) - Method in class org.sbml.libsbml.SpeciesFeatureType
-
- setOffset(RelAbsVector) - Method in class org.sbml.libsbml.GradientStop
-
Sets the value of the 'offset' element of this
GradientStop.
- setOffset(double, double) - Method in class org.sbml.libsbml.GradientStop
-
Sets the offset for the gradient stop.
- setOffset(String) - Method in class org.sbml.libsbml.GradientStop
-
Sets the offset to the value specified by the given string.
- setOffset(double) - Method in class org.sbml.libsbml.Unit
-
Sets the 'offset' attribute value of this
Unit.
- setOffsets(double, double, double) - Method in class org.sbml.libsbml.Point
-
Sets the coordinates to the given values.
- setOffsets(double, double) - Method in class org.sbml.libsbml.Point
-
Sets the coordinates to the given values.
- setOffsets(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
-
Sets the coordinates of the
RenderPoint to the given values.
- setOffsets(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
-
Sets the coordinates of the
RenderPoint to the given values.
- setOperation(String) - Method in class org.sbml.libsbml.FluxBound
-
Sets the value of the 'operation' attribute of this
FluxBound object.
- setOperation(int) - Method in class org.sbml.libsbml.FluxBound
-
Sets the value of the 'operation' attribute of this
FluxBound object.
- setOrder(double) - Method in class org.sbml.libsbml.CompartmentGlyph
-
Sets the compartment order.
- setOrganisation(String) - Method in class org.sbml.libsbml.ModelCreator
-
(Alternate spelling) Sets the 'organization' portion of this
ModelCreator object.
- setOrganization(String) - Method in class org.sbml.libsbml.ModelCreator
-
Sets the 'organization' portion of this
ModelCreator object.
- setOriginOfTextId(String) - Method in class org.sbml.libsbml.TextGlyph
-
Sets the id of the origin of text.
- setOutputLevel(int) - Method in class org.sbml.libsbml.Output
-
Sets the value of the 'outputLevel' attribute of this
Output.
- setOutside(String) - Method in class org.sbml.libsbml.Compartment
-
Sets the 'outside' attribute of this
Compartment object.
- setPackageRequired(String, boolean) - Method in class org.sbml.libsbml.SBMLDocument
-
Sets the required attribute value of the given package
extension.
- setParseAvogadroCsymbol(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
-
Sets the parser's behavior in handling the symbol avogadro in
mathematical formulas.
- setParseCollapseMinus(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
-
Sets the behavior for handling unary minuses appearing in mathematical
formulas.
- setParseL3v2Functions(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
-
Sets the behavior for handling functions added in SBML L3v2
- setParseLog(int) - Method in class org.sbml.libsbml.L3ParserSettings
-
Sets the behavior for handling log in mathematical formulas.
- setParseModuloL3v2(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
-
Sets the behavior for handling the '%' sumbol in mathematical
formulas.
- setParsePackageMath(int, boolean) - Method in class org.sbml.libsbml.L3ParserSettings
-
Sets the behavior for handling functions added in SBML packages
- setParseUnits(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
-
Sets the parser's behavior in handling units associated with numbers
in a mathematical formula.
- setPersistent(boolean) - Method in class org.sbml.libsbml.Trigger
-
(SBML Level 3 only) Sets the 'persistent' attribute of this
Trigger instance.
- setPkgRequired(String, boolean) - Method in class org.sbml.libsbml.SBMLDocument
-
- setPoint1(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
Sets the coordinates for the start point of the linear gradient vector.
- setPoint1(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
Sets the coordinates for the start point of the linear gradient vector.
- setPoint2(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
Sets the coordinates for the end point of the linear gradient vector.
- setPoint2(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
Sets the coordinates for the end point of the linear gradient vector.
- setPortRef(String) - Method in class org.sbml.libsbml.Port
-
Overrides SBaseRef.setPortRef to always fail, because
Port objects
themselves cannot refer to model elements by PortSId.
- setPortRef(String) - Method in class org.sbml.libsbml.SBaseRef
-
Sets the value of the 'portRef' attribute of this
SBaseRef.
- setPosition(Point) - Method in class org.sbml.libsbml.BoundingBox
-
Sets the position to a copy of the
Point object given.
- setPriority(Priority) - Method in class org.sbml.libsbml.Event
-
(SBML Level 3 only) Sets the priority definition of this
Event
to a copy of the given
Priority object instance.
- setProductComponent(String) - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- setProgramName(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- setProgramName(String) - Method in class org.sbml.libsbml.SBMLWriter
-
Sets the name of this program, i.e., the program that is about to
write out the
SBMLDocument.
- setProgramVersion(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- setProgramVersion(String) - Method in class org.sbml.libsbml.SBMLWriter
-
Sets the version of this program, i.e., the program that is about to
write out the
SBMLDocument.
- setProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLConverter
-
Sets the configuration properties to be used by this converter.
- setQualifierType(int) - Method in class org.sbml.libsbml.CVTerm
-
Sets the qualifier code of this
CVTerm object.
- setQualitativeSpecies(String) - Method in class org.sbml.libsbml.Input
-
Sets the value of the 'qualitativeSpecies' attribute of this
Input.
- setQualitativeSpecies(String) - Method in class org.sbml.libsbml.Output
-
Sets the value of the 'qualitativeSpecies' attribute of this
Output.
- setR(RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
- setRadialGradient_cx(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'radialGradient_cx' attribute of this
DefaultValues object.
- setRadialGradient_cy(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'radialGradient_cy' attribute of this
DefaultValues object.
- setRadialGradient_cz(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'radialGradient_cz' attribute of this
DefaultValues object.
- setRadialGradient_fx(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'radialGradient_fx' attribute of this
DefaultValues object.
- setRadialGradient_fy(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'radialGradient_fy' attribute of this
DefaultValues object.
- setRadialGradient_fz(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'radialGradient_fz' attribute of this
DefaultValues object.
- setRadialGradient_r(RelAbsVector) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'radialGradient_r' attribute of this
DefaultValues
object.
- setRadii(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
-
Sets the radii of the ellipse
- setRadii(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
Sets the two corner radii of the rectangle
- setRadius(RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
-
Sets the radius of the radial gradient.
- setRadiusX(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
Sets the corner radius along the x axis
- setRadiusY(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
Sets the corner radius along the y axis
- setRatio(double) - Method in class org.sbml.libsbml.Ellipse
-
Sets the value of the 'ratio' attribute of this
Ellipse.
- setRatio(double) - Method in class org.sbml.libsbml.Rectangle
-
Sets the value of the 'ratio' attribute of this
Rectangle.
- setReactant(String) - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- setReactantComponent(String) - Method in class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- setReaction(String) - Method in class org.sbml.libsbml.FluxBound
-
Sets the value of the 'reaction' attribute of this
FluxBound object.
- setReaction(String) - Method in class org.sbml.libsbml.FluxObjective
-
Sets the value of the 'reaction' attribute of this
FluxObjective.
- setReaction(String) - Method in class org.sbml.libsbml.GeneAssociation
-
Sets the SIdRef string of the 'reaction' attribute of this
GeneAssociation.
- setReactionId(String) - Method in class org.sbml.libsbml.ReactionGlyph
-
Sets the id of the associated reaction.
- setRed(short) - Method in class org.sbml.libsbml.ColorDefinition
-
Sets the red color component.
- setReference(String) - Method in class org.sbml.libsbml.Association
-
Sets the SIdRef string of the 'reference' attribute of this
Association object.
- setReferenceId(String) - Method in class org.sbml.libsbml.GeneralGlyph
-
Sets the id of the associated element.
- setReferenceId(String) - Method in class org.sbml.libsbml.ReferenceGlyph
-
Sets the id of the associated sbml reference.
- setReferenceRenderInformation(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- setReferenceRenderInformationId(String) - Method in class org.sbml.libsbml.RenderInformationBase
-
- setRelation(int) - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- setRelation(String) - Method in class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- setRelativeValue(double) - Method in class org.sbml.libsbml.RelAbsVector
-
Sets the relative coordinate value.
- setReplacedBy(ReplacedBy) - Method in class org.sbml.libsbml.CompSBasePlugin
-
- setRepresentationType(String) - Method in class org.sbml.libsbml.MultiASTPlugin
-
Sets the value of the 'representationType' attribute of this
MultiASTPlugin.
- setRequired(boolean) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
-
Sets the boolean value of 'required' attribute of corresponding package
in
SBMLDocument element.
- setRequired(boolean) - Method in class org.sbml.libsbml.SBMLDocumentPlugin
-
Sets the SBML 'required' attribute value.
- setResultLevel(int) - Method in class org.sbml.libsbml.DefaultTerm
-
Sets the value of the 'resultLevel' attribute of this
DefaultTerm.
- setResultLevel(int) - Method in class org.sbml.libsbml.FunctionTerm
-
Sets the value of the 'resultLevel' attribute of this
FunctionTerm.
- setReversible(boolean) - Method in class org.sbml.libsbml.Reaction
-
Sets the value of the 'reversible' attribute of this
Reaction.
- setRGBA(short, short, short, short) - Method in class org.sbml.libsbml.ColorDefinition
-
Sets the red green, blue and alpha color component.
- setRGBA(short, short, short) - Method in class org.sbml.libsbml.ColorDefinition
-
Sets the red green, blue and alpha color component.
- setRole(String) - Method in class org.sbml.libsbml.ReferenceGlyph
-
Sets the role.
- setRole(String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Sets the role based on a string.
- setRole(int) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Sets the role.
- setRoleList(StringSet) - Method in class org.sbml.libsbml.Style
-
Sets the complete role list to a copy of the given list.
- setRX(RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
-
Sets the radius along the x axis
- setRX(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
Sets the corner radius along the x axis
- setRY(RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
-
Sets the radius along the y axis
- setRY(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
Sets the corner radius along the y axis
- setSBaseRef(SBaseRef) - Method in class org.sbml.libsbml.SBaseRef
-
Sets the sBaseRef definition of this
SBaseRef to a copy of the given
SBaseRef object instance.
- setSBMLNamespaces(SBMLNamespaces) - Method in class org.sbml.libsbml.XMLInputStream
-
Sets the SBML namespaces associated with this XML input stream.
- setSBMLNamespaces(SBMLNamespaces) - Method in class org.sbml.libsbml.XMLOutputStream
-
- setSBOTerm(int) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the 'sboTerm' attribute.
- setSBOTerm(String) - Method in class org.sbml.libsbml.SBase
-
Sets the value of the 'sboTerm' attribute by string.
- setScale(int) - Method in class org.sbml.libsbml.Unit
-
Sets the 'scale' attribute value of this
Unit.
- setSecond(long) - Method in class org.sbml.libsbml.Date
-
Sets the value of the second of the
Date object.
- setSeverityOverride(int) - Method in class org.sbml.libsbml.XMLErrorLog
-
Set the severity override.
- setSign(int) - Method in class org.sbml.libsbml.Input
-
Sets the value of the 'sign' attribute of this
Input.
- setSignOffset(long) - Method in class org.sbml.libsbml.Date
-
Sets the value of the sign of the time zone offset of this
Date object.
- setSize(double) - Method in class org.sbml.libsbml.Compartment
-
Sets the 'size' attribute (or 'volume' in SBML Level 1) of this
Compartment object.
- setSize(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
- setSource(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
-
- setSpatialDimensions(long) - Method in class org.sbml.libsbml.Compartment
-
Sets the 'spatialDimensions' attribute of this
Compartment object.
- setSpatialDimensions(double) - Method in class org.sbml.libsbml.Compartment
-
Sets the 'spatialDimensions' attribute of this
Compartment object as a double.
- setSpatialSizeUnits(String) - Method in class org.sbml.libsbml.Species
-
(SBML Level 2 Versions 1–2) Sets the 'spatialSizeUnits' attribute of this
Species object.
- setSpecies(String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
-
- setSpeciesFeatureType(String) - Method in class org.sbml.libsbml.SpeciesFeature
-
Sets the value of the 'speciesFeatureType' attribute of this
SpeciesFeature.
- setSpeciesGlyphId(String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Sets the id of the associated species glyph.
- setSpeciesId(String) - Method in class org.sbml.libsbml.SpeciesGlyph
-
Sets the id of the associated species object.
- setSpeciesReference(String) - Method in class org.sbml.libsbml.MultiASTPlugin
-
Sets the value of the 'speciesReference' attribute of this
MultiASTPlugin.
- setSpeciesReferenceId(String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
-
Sets the id of the associated species reference.
- setSpeciesType(String) - Method in class org.sbml.libsbml.MultiSpeciesPlugin
-
Sets the value of the 'speciesType' attribute on this 'multi'
Species.
- setSpeciesType(String) - Method in class org.sbml.libsbml.Species
-
Sets the 'speciesType' attribute of this
Species object.
- setSpeciesType(String) - Method in class org.sbml.libsbml.SpeciesTypeInstance
-
- setSpreadMethod(int) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'spreadMethod' attribute of this
DefaultValues
object.
- setSpreadMethod(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'spreadMethod' attribute of this
DefaultValues object.
- setSpreadMethod(int) - Method in class org.sbml.libsbml.GradientBase
-
Sets the value of the 'spreadMethod' attribute of this
GradientBase.
- setSpreadMethod(String) - Method in class org.sbml.libsbml.GradientBase
-
Sets the value of the 'spreadMethod' attribute of this
GradientBase.
- setStart(Point) - Method in class org.sbml.libsbml.LineSegment
-
Initializes the start point with a copy of the given
Point object.
- setStart(double, double, double) - Method in class org.sbml.libsbml.LineSegment
-
Initializes the start point with the given coordinates.
- setStart(double, double) - Method in class org.sbml.libsbml.LineSegment
-
Initializes the start point with the given coordinates.
- setStartHead(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'startHead' attribute of this
DefaultValues
object.
- setStartHead(String) - Method in class org.sbml.libsbml.RenderCurve
-
Sets the value of the 'startHead' attribute of this
RenderCurve.
- setStartHead(String) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'startHead' attribute of this
RenderGroup.
- setStoichiometry(double) - Method in class org.sbml.libsbml.SpeciesReference
-
- setStoichiometryMath(StoichiometryMath) - Method in class org.sbml.libsbml.SpeciesReference
-
- setStopColor(String) - Method in class org.sbml.libsbml.GradientStop
-
Sets the value of the 'stop-color' attribute of this
GradientStop.
- setStrict(boolean) - Method in class org.sbml.libsbml.FbcModelPlugin
-
- setStroke(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'stroke' attribute of this
DefaultValues object.
- setStroke(String) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- setStrokeDashArray(SWIGTYPE_p_std__vectorT_unsigned_int_t) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- setStrokeWidth(double) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'stroke-width' attribute of this
DefaultValues
object.
- setStrokeWidth(double) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
-
- setStyle(String) - Method in class org.sbml.libsbml.ASTNode
-
Sets the MathML style of this
ASTNode to style.
- setSubmodelRef(String) - Method in class org.sbml.libsbml.Replacing
-
Sets the value of the 'submodelRef' attribute of this
SBaseRef.
- setSubstanceConversionFactor(String) - Method in class org.sbml.libsbml.Submodel
-
Automatically fails, since 'substanceConversionFactor' is not a part of the comp spec.
- setSubstanceUnits(String) - Method in class org.sbml.libsbml.KineticLaw
-
(SBML Level 2 Version 1 only) Sets the 'substanceUnits'
attribute of this
KineticLaw object to a copy of the identifier given
in
sid.
- setSubstanceUnits(String) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'substanceUnits' attribute of this
Model.
- setSubstanceUnits(String) - Method in class org.sbml.libsbml.Species
-
Sets the 'substanceUnits' attribute of this
Species object.
- setSymbol(String) - Method in class org.sbml.libsbml.InitialAssignment
-
- setTargetNamespaces(SBMLNamespaces) - Method in class org.sbml.libsbml.ConversionProperties
-
Sets the target namespace.
- setText(String) - Method in class org.sbml.libsbml.Text
-
Sets the text for the text element.
- setText(String) - Method in class org.sbml.libsbml.TextGlyph
-
Sets the text to be displayed by the text glyph.
- setTextAnchor(int) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'text-anchor' attribute of this
DefaultValues
object.
- setTextAnchor(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'text-anchor' attribute of this
DefaultValues.
- setTextAnchor(int) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'text-anchor' attribute of this
RenderGroup.
- setTextAnchor(String) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'text-anchor' attribute of this
RenderGroup.
- setTextAnchor(int) - Method in class org.sbml.libsbml.Text
-
Sets the value of the 'text-anchor' attribute of this
Text.
- setTextAnchor(String) - Method in class org.sbml.libsbml.Text
-
Sets the value of the 'text-anchor' attribute of this
Text.
- setThresholdLevel(int) - Method in class org.sbml.libsbml.Input
-
Sets the value of the 'thresholdLevel' attribute of this
Input.
- setTimeConversionFactor(String) - Method in class org.sbml.libsbml.Submodel
-
Sets the value of the 'timeConversionFactor' attribute of this
Submodel.
- setTimeUnits(String) - Method in class org.sbml.libsbml.Event
-
Sets the 'timeUnits' attribute of this
Event to a copy of
sid.
- setTimeUnits(String) - Method in class org.sbml.libsbml.KineticLaw
-
(SBML Level 2 Version 1 only) Sets the 'timeUnits' attribute
of this
KineticLaw object to a copy of the identifier in
sid.
- setTimeUnits(String) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'timeUnits' attribute of this
Model.
- setTransform(SWIGTYPE_p_double) - Method in class org.sbml.libsbml.Transformation
-
- setTransformer(SWIGTYPE_p_PrefixTransformer) - Method in class org.sbml.libsbml.CompModelPlugin
-
Sets the custom transformer that is to be used, instead of the standard
prefixing with the given divider.
- setTransitionEffect(int) - Method in class org.sbml.libsbml.Input
-
Sets the value of the 'transitionEffect' attribute of this
Input.
- setTransitionEffect(int) - Method in class org.sbml.libsbml.Output
-
Sets the value of the 'transitionEffect' attribute of this
Output.
- setTrigger(Trigger) - Method in class org.sbml.libsbml.Event
-
Sets the trigger definition of this
Event to a copy of the given
Trigger object instance.
- setTriple(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
-
Sets the name, namespace prefix and namespace URI of this token.
- setType(int) - Method in class org.sbml.libsbml.Association
-
Sets the SIdRef string of the 'type' attribute of this
Association object.
- setType(int) - Method in class org.sbml.libsbml.ASTNode
-
Sets the type of this
ASTNode to the given type code.
- setType(int) - Method in class org.sbml.libsbml.ASTNodeValues_t
-
- setType(int) - Method in class org.sbml.libsbml.ConversionOption
-
Sets the type of this option.
- setType(int) - Method in class org.sbml.libsbml.Objective
-
Sets the value of the 'type' attribute of this
Objective.
- setType(String) - Method in class org.sbml.libsbml.Objective
-
Sets the value of the 'type' attribute of this
Objective.
- setTypeList(StringSet) - Method in class org.sbml.libsbml.Style
-
Sets the complete type list to a copy of the given list.
- setUnitRef(String) - Method in class org.sbml.libsbml.SBaseRef
-
Sets the value of the 'unitRef' attribute of this
SBaseRef.
- setUnits(String) - Method in class org.sbml.libsbml.ASTNode
-
Sets the units of this
ASTNode to units.
- setUnits(String) - Method in class org.sbml.libsbml.Compartment
-
- setUnits(String) - Method in class org.sbml.libsbml.Parameter
-
Sets the 'units' attribute of this
Parameter to a copy of the given
units identifier
units.
- setUnits(String) - Method in class org.sbml.libsbml.Rule
-
Sets the units for this
Rule.
- setUnits(String) - Method in class org.sbml.libsbml.Species
-
(SBML Level 1 only) Sets the units of this
Species object.
- setUpperFluxBound(String) - Method in class org.sbml.libsbml.FbcReactionPlugin
-
- setUseValuesFromTriggerTime(boolean) - Method in class org.sbml.libsbml.Event
-
Sets the 'useValuesFromTriggerTime' attribute of this
Event to a
value.
- setValue(int) - Method in class org.sbml.libsbml.ASTNode
-
Sets the value of this
ASTNode to the given (
long) integer and sets
the node type to
AST_INTEGER.
- setValue(int, int) - Method in class org.sbml.libsbml.ASTNode
-
Sets the value of this
ASTNode to the given rational in two parts: the
numerator and denominator.
- setValue(double) - Method in class org.sbml.libsbml.ASTNode
-
Sets the value of this
ASTNode to the given real (
double) and sets
the node type to
AST_REAL.
- setValue(double, int) - Method in class org.sbml.libsbml.ASTNode
-
Sets the value of this
ASTNode to the given real (
double) in two
parts: the mantissa and the exponent.
- setValue(String) - Method in class org.sbml.libsbml.ColorDefinition
-
- setValue(String) - Method in class org.sbml.libsbml.ConversionOption
-
Sets the value for this option.
- setValue(String, String) - Method in class org.sbml.libsbml.ConversionProperties
-
Sets the value of the given option to a string.
- setValue(double) - Method in class org.sbml.libsbml.FluxBound
-
Sets the value of the 'value' attribute of this
FluxBound object.
- setValue(double) - Method in class org.sbml.libsbml.Parameter
-
Sets the 'value' attribute of this
Parameter to the given
double
value and marks the attribute as set.
- setValue(String) - Method in class org.sbml.libsbml.SpeciesFeatureValue
-
- setVariable(String) - Method in class org.sbml.libsbml.EventAssignment
-
Sets the attribute 'variable' of this
EventAssignment to a copy of
the given identifier string.
- setVariable(String) - Method in class org.sbml.libsbml.Rule
-
Sets the 'variable' attribute value of this
Rule object.
- setVersion(long, long) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
-
Sets the version of the render information list.
- setVersion(long, long) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
-
Sets the version of the render information list.
- setVolume(double) - Method in class org.sbml.libsbml.Compartment
-
Sets the 'volume' attribute (or 'size' in SBML Level 2) of this
Compartment object.
- setVolumeUnits(String) - Method in class org.sbml.libsbml.Model
-
Sets the value of the 'volumeUnits' attribute of this
Model.
- setVTextAnchor(int) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'vtext-anchor' attribute of this
DefaultValues
object.
- setVTextAnchor(String) - Method in class org.sbml.libsbml.DefaultValues
-
Sets the value of the 'vtext-anchor' attribute of this
DefaultValues.
- setVTextAnchor(int) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'vtext-anchor' attribute of this
RenderGroup.
- setVTextAnchor(String) - Method in class org.sbml.libsbml.RenderGroup
-
Sets the value of the 'vtext-anchor' attribute of this
RenderGroup.
- setVTextAnchor(int) - Method in class org.sbml.libsbml.Text
-
Sets the value of the 'vtext-anchor' attribute of this
Text.
- setVTextAnchor(String) - Method in class org.sbml.libsbml.Text
-
Sets the value of the 'vtext-anchor' attribute of this
Text.
- setWidth(double) - Method in class org.sbml.libsbml.BoundingBox
-
Set width of the bounding box.
- setWidth(double) - Method in class org.sbml.libsbml.Dimensions
-
Sets the width to the given value.
- setWidth(RelAbsVector) - Method in class org.sbml.libsbml.Image
-
Sets the width of the image when rendered.
- setWidth(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
- setWriteComment(boolean) - Static method in class org.sbml.libsbml.XMLOutputStream
-
sets a flag, whether the output stream will write an XML
comment at the top of the file.
- setWriteTimestamp(boolean) - Static method in class org.sbml.libsbml.XMLOutputStream
-
sets a flag, whether the output stream will write an XML
comment with a timestamp at the top of the file.
- setX(double) - Method in class org.sbml.libsbml.BoundingBox
-
Set x offset of the bounding box.
- setX(RelAbsVector) - Method in class org.sbml.libsbml.Image
-
Sets the x coordinate of the image position.
- setX(double) - Method in class org.sbml.libsbml.Point
-
Sets the x offset.
- setX(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
Sets the x position of the
Rectangle within the viewport.
- setX(RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
-
- setX(RelAbsVector) - Method in class org.sbml.libsbml.Text
-
Sets the x position of the text within the viewport.
- setX1(RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
- setX2(RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
- setXOffset(double) - Method in class org.sbml.libsbml.Point
-
Sets the x offset.
- setY(double) - Method in class org.sbml.libsbml.BoundingBox
-
Set y offset of the bounding box.
- setY(RelAbsVector) - Method in class org.sbml.libsbml.Image
-
Sets the y coordinate of the image position.
- setY(double) - Method in class org.sbml.libsbml.Point
-
Sets the y offset.
- setY(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
Sets the y position of the
Rectangle within the viewport.
- setY(RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
-
- setY(RelAbsVector) - Method in class org.sbml.libsbml.Text
-
Sets the y position of the text within the viewport.
- setY1(RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
- setY2(RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
- setYear(long) - Method in class org.sbml.libsbml.Date
-
Sets the value of the year of this
Date object.
- setYOffset(double) - Method in class org.sbml.libsbml.Point
-
Sets the y offset.
- setZ(double) - Method in class org.sbml.libsbml.BoundingBox
-
Set z offset of the bounding box.
- setZ(RelAbsVector) - Method in class org.sbml.libsbml.Image
-
Sets the z coordinate of the image position.
- setZ(double) - Method in class org.sbml.libsbml.Point
-
Sets the z offset.
- setZ(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
-
Sets the z position of the
Rectangle within the viewport.
- setZ(RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
-
- setZ(RelAbsVector) - Method in class org.sbml.libsbml.Text
-
Sets the z position of the text within the viewport.
- setZ1(RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
- setZ2(RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
-
- setZOffset(double) - Method in class org.sbml.libsbml.Point
-
Sets the z offset.
- SimpleSpeciesReference - Class in org.sbml.libsbml
-
Abstract class for references to species in reactions.
- simplify(UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
-
- size() - Method in class org.sbml.libsbml.ListOf
-
Returns number of items in this
ListOf list.
- size() - Method in class org.sbml.libsbml.ListOfSpeciesFeatures
-
- size() - Method in class org.sbml.libsbml.StringSet
-
- skipPastEnd(XMLToken) - Method in class org.sbml.libsbml.XMLInputStream
-
Consume zero or more tokens up to and including the corresponding end
element or EOF.
- skipText() - Method in class org.sbml.libsbml.XMLInputStream
-
Consume zero or more tokens up to but not including the next XML element
or EOF.
- SpatialSizeUnitsNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SpatialSizeUnitsRemoved - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SpatialUnitsInOneD - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SpatialUnitsInThreeD - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SpatialUnitsInTwoD - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- Species - Class in org.sbml.libsbml
-
An SBML species – a pool of entities.
- Species(long, long) - Constructor for class org.sbml.libsbml.Species
-
Creates a new
Species using the given SBML
level and
version
values.
- Species(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Species
-
- Species(Species) - Constructor for class org.sbml.libsbml.Species
-
Copy constructor; creates a copy of this
Species object.
- SPECIES_ROLE_ACTIVATOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible roles of a SpeciesReferenceGlyph.
- SPECIES_ROLE_INHIBITOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible roles of a SpeciesReferenceGlyph.
- SPECIES_ROLE_INVALID - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible roles of a SpeciesReferenceGlyph.
- SPECIES_ROLE_MODIFIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible roles of a SpeciesReferenceGlyph.
- SPECIES_ROLE_PRODUCT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible roles of a SpeciesReferenceGlyph.
- SPECIES_ROLE_SIDEPRODUCT - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible roles of a SpeciesReferenceGlyph.
- SPECIES_ROLE_SIDESUBSTRATE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible roles of a SpeciesReferenceGlyph.
- SPECIES_ROLE_SUBSTRATE - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible roles of a SpeciesReferenceGlyph.
- SPECIES_ROLE_UNDEFINED - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
layout One of the
possible roles of a SpeciesReferenceGlyph.
- SpeciesCompartmentRequiredInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SpeciesFeature - Class in org.sbml.libsbml
-
- SpeciesFeature(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesFeature
-
- SpeciesFeature(long, long) - Constructor for class org.sbml.libsbml.SpeciesFeature
-
- SpeciesFeature(long) - Constructor for class org.sbml.libsbml.SpeciesFeature
-
- SpeciesFeature() - Constructor for class org.sbml.libsbml.SpeciesFeature
-
- SpeciesFeature(MultiPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesFeature
-
- SpeciesFeature(SpeciesFeature) - Constructor for class org.sbml.libsbml.SpeciesFeature
-
- SpeciesFeatureType - Class in org.sbml.libsbml
-
- SpeciesFeatureType(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesFeatureType
-
- SpeciesFeatureType(long, long) - Constructor for class org.sbml.libsbml.SpeciesFeatureType
-
- SpeciesFeatureType(long) - Constructor for class org.sbml.libsbml.SpeciesFeatureType
-
- SpeciesFeatureType() - Constructor for class org.sbml.libsbml.SpeciesFeatureType
-
- SpeciesFeatureType(MultiPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesFeatureType
-
- SpeciesFeatureType(SpeciesFeatureType) - Constructor for class org.sbml.libsbml.SpeciesFeatureType
-
- SpeciesFeatureValue - Class in org.sbml.libsbml
-
- SpeciesFeatureValue(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesFeatureValue
-
- SpeciesFeatureValue(long, long) - Constructor for class org.sbml.libsbml.SpeciesFeatureValue
-
- SpeciesFeatureValue(long) - Constructor for class org.sbml.libsbml.SpeciesFeatureValue
-
- SpeciesFeatureValue() - Constructor for class org.sbml.libsbml.SpeciesFeatureValue
-
- SpeciesFeatureValue(MultiPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesFeatureValue
-
- SpeciesFeatureValue(SpeciesFeatureValue) - Constructor for class org.sbml.libsbml.SpeciesFeatureValue
-
- SpeciesGlyph - Class in org.sbml.libsbml
-
layout
A glyph for an SBML species.
- SpeciesGlyph(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
-
Creates a new
SpeciesGlyph with the given SBML level, version, and package version
and the id of the associated species set to the empty string.
- SpeciesGlyph(long, long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
-
Creates a new
SpeciesGlyph with the given SBML level, version, and package version
and the id of the associated species set to the empty string.
- SpeciesGlyph(long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
-
Creates a new
SpeciesGlyph with the given SBML level, version, and package version
and the id of the associated species set to the empty string.
- SpeciesGlyph() - Constructor for class org.sbml.libsbml.SpeciesGlyph
-
Creates a new
SpeciesGlyph with the given SBML level, version, and package version
and the id of the associated species set to the empty string.
- SpeciesGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesGlyph
-
Constructor.
- SpeciesGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.SpeciesGlyph
-
- SpeciesGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.SpeciesGlyph
-
Creates a new
SpeciesGlyph with the given
id and the id of the
associated species object set to the second argument.
- SpeciesGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
-
- SpeciesGlyph(XMLNode) - Constructor for class org.sbml.libsbml.SpeciesGlyph
-
- SpeciesGlyph(SpeciesGlyph) - Constructor for class org.sbml.libsbml.SpeciesGlyph
-
Copy constructor.
- SpeciesInvalidExtentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SpeciesReference - Class in org.sbml.libsbml
-
A reference to an SBML species in a reaction.
- SpeciesReference(long, long) - Constructor for class org.sbml.libsbml.SpeciesReference
-
- SpeciesReference(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SpeciesReference
-
- SpeciesReference(SpeciesReference) - Constructor for class org.sbml.libsbml.SpeciesReference
-
- SpeciesReferenceGlyph - Class in org.sbml.libsbml
-
layout
A glyph for an SBML
species reference.
- SpeciesReferenceGlyph(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
-
- SpeciesReferenceGlyph(long, long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
-
- SpeciesReferenceGlyph(long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
-
- SpeciesReferenceGlyph() - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
-
- SpeciesReferenceGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
-
Constructor.
- SpeciesReferenceGlyph(LayoutPkgNamespaces, String, String, String, int) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
-
- SpeciesReferenceGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
-
- SpeciesReferenceGlyph(XMLNode) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
-
- SpeciesReferenceGlyph(SpeciesReferenceGlyph) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
-
Copy constructor.
- SpeciesRefIdInMathMLNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SpeciesShouldHaveValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SpeciesType - Class in org.sbml.libsbml
-
A species type in SBML Level 2.
- SpeciesType(long, long) - Constructor for class org.sbml.libsbml.SpeciesType
-
Creates a new
SpeciesType using the given SBML
level and
version
values.
- SpeciesType(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SpeciesType
-
- SpeciesType(SpeciesType) - Constructor for class org.sbml.libsbml.SpeciesType
-
- SpeciesTypeComponentIndex - Class in org.sbml.libsbml
-
- SpeciesTypeComponentIndex(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- SpeciesTypeComponentIndex(long, long) - Constructor for class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- SpeciesTypeComponentIndex(long) - Constructor for class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- SpeciesTypeComponentIndex() - Constructor for class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- SpeciesTypeComponentIndex(MultiPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- SpeciesTypeComponentIndex(SpeciesTypeComponentIndex) - Constructor for class org.sbml.libsbml.SpeciesTypeComponentIndex
-
- SpeciesTypeComponentMapInProduct - Class in org.sbml.libsbml
-
multi
Distinguishes between components in reactants versus products.
- SpeciesTypeComponentMapInProduct(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- SpeciesTypeComponentMapInProduct(long, long) - Constructor for class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- SpeciesTypeComponentMapInProduct(long) - Constructor for class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- SpeciesTypeComponentMapInProduct() - Constructor for class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- SpeciesTypeComponentMapInProduct(MultiPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- SpeciesTypeComponentMapInProduct(SpeciesTypeComponentMapInProduct) - Constructor for class org.sbml.libsbml.SpeciesTypeComponentMapInProduct
-
- SpeciesTypeInstance - Class in org.sbml.libsbml
-
- SpeciesTypeInstance(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesTypeInstance
-
- SpeciesTypeInstance(long, long) - Constructor for class org.sbml.libsbml.SpeciesTypeInstance
-
- SpeciesTypeInstance(long) - Constructor for class org.sbml.libsbml.SpeciesTypeInstance
-
- SpeciesTypeInstance() - Constructor for class org.sbml.libsbml.SpeciesTypeInstance
-
- SpeciesTypeInstance(MultiPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesTypeInstance
-
- SpeciesTypeInstance(SpeciesTypeInstance) - Constructor for class org.sbml.libsbml.SpeciesTypeInstance
-
- SpeciesTypeNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SpeciesTypeNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SpreadMethod_fromString(String) - Static method in class org.sbml.libsbml.libsbml
-
- SpreadMethod_toString(int) - Static method in class org.sbml.libsbml.libsbml
-
- startElement(String, String) - Method in class org.sbml.libsbml.XMLOutputStream
-
- startElement(String) - Method in class org.sbml.libsbml.XMLOutputStream
-
- startElement(XMLTriple) - Method in class org.sbml.libsbml.XMLOutputStream
-
Writes the given XML start element
prefix:name on this output stream.
- startEndElement(String, String) - Method in class org.sbml.libsbml.XMLOutputStream
-
- startEndElement(String) - Method in class org.sbml.libsbml.XMLOutputStream
-
- startEndElement(XMLTriple) - Method in class org.sbml.libsbml.XMLOutputStream
-
Writes the given start element to this output stream.
- StoichiometryMath - Class in org.sbml.libsbml
-
Stochiometry expressions in SBML Level 2 reactions.
- StoichiometryMath(long, long) - Constructor for class org.sbml.libsbml.StoichiometryMath
-
- StoichiometryMath(SBMLNamespaces) - Constructor for class org.sbml.libsbml.StoichiometryMath
-
- StoichiometryMath(StoichiometryMath) - Constructor for class org.sbml.libsbml.StoichiometryMath
-
- StoichiometryMathMissingMath - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- StoichiometryMathNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- StoichiometryMathNotYetSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- str() - Method in class org.sbml.libsbml.OStringStream
-
Returns the copy of the string object currently assosiated
with this ostringstream buffer.
- str(String) - Method in class org.sbml.libsbml.OStringStream
-
Sets string s to the string object currently assosiated with
this stream buffer.
- straighten() - Method in class org.sbml.libsbml.CubicBezier
-
Turns the
CubicBezier into a line by setting both 'basepoint1' and
'basepoint2' children to the midpoint between the 'start' and the
'end' points.
- StrictSBORequiredInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- StrictSBORequiredInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- StrictUnitsRequiredInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- StrictUnitsRequiredInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- StrictUnitsRequiredInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- StrictUnitsRequiredInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- StringSet - Class in org.sbml.libsbml
-
- StringSet() - Constructor for class org.sbml.libsbml.StringSet
-
- StringSet(StringSet) - Constructor for class org.sbml.libsbml.StringSet
-
- stringToInt(String) - Static method in class org.sbml.libsbml.SBO
-
Returns the string as a correctly formatted SBO integer portion.
- Style - Class in org.sbml.libsbml
-
render
Abstract base class for local and global styles.
- Style(Style) - Constructor for class org.sbml.libsbml.Style
-
Copy constructor for
Style.
- STYLE_INVALID - Static variable in class org.sbml.libsbml.Text
-
- STYLE_ITALIC - Static variable in class org.sbml.libsbml.Text
-
- STYLE_NORMAL - Static variable in class org.sbml.libsbml.Text
-
- STYLE_UNSET - Static variable in class org.sbml.libsbml.Text
-
- SubListOfSpeciesFeatures - Class in org.sbml.libsbml
-
- SubListOfSpeciesFeatures(long, long, long) - Constructor for class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- SubListOfSpeciesFeatures(long, long) - Constructor for class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- SubListOfSpeciesFeatures(long) - Constructor for class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- SubListOfSpeciesFeatures() - Constructor for class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- SubListOfSpeciesFeatures(MultiPkgNamespaces) - Constructor for class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- SubListOfSpeciesFeatures(SubListOfSpeciesFeatures) - Constructor for class org.sbml.libsbml.SubListOfSpeciesFeatures
-
- Submodel - Class in org.sbml.libsbml
-
comp
A model instance inside another model.
- Submodel(long, long, long) - Constructor for class org.sbml.libsbml.Submodel
-
Creates a new
Submodel with the given level, version, and package
version.
- Submodel(long, long) - Constructor for class org.sbml.libsbml.Submodel
-
Creates a new
Submodel with the given level, version, and package
version.
- Submodel(long) - Constructor for class org.sbml.libsbml.Submodel
-
Creates a new
Submodel with the given level, version, and package
version.
- Submodel() - Constructor for class org.sbml.libsbml.Submodel
-
Creates a new
Submodel with the given level, version, and package
version.
- Submodel(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.Submodel
-
- Submodel(Submodel) - Constructor for class org.sbml.libsbml.Submodel
-
Copy constructor.
- SubstanceUnitsOnSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SubsUnitsAllowedInKL - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- SubsUnitsNoLongerValid - Static variable in interface org.sbml.libsbml.libsbmlConstants
-
A value in the enumeration of all the SBML error and warning codes
for objects of class
SBMLError.
- swapChildren(ASTNode) - Method in class org.sbml.libsbml.ASTNode
-
Swaps the children of this
ASTNode object with the children of the
given
ASTNode object.
- SyntaxChecker - Class in org.sbml.libsbml
-
Methods for checking the validity of SBML identifiers.
- SyntaxChecker() - Constructor for class org.sbml.libsbml.SyntaxChecker
-
