A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

V

validate(Object) - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Validates the object against the loaded constraints.

validate(Object, boolean) - Method in class org.sbml.jsbml.validator.offline.LoggingValidationContext

validate(Object, boolean) - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Validates the object with the loaded constraints and clears the HashMap afterwards if the clearMap is set to true.

validate(Model, Dimension) - Static method in class org.sbml.jsbml.ext.arrays.validator.DimensionValidator

Validates the given SBase object.

validate(Model, Index) - Static method in class org.sbml.jsbml.ext.arrays.validator.IndexValidator

Validates the given SBase object.

validate(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.validator.ArraysMathValidator

Validates the given SBase object.

validate(Model, SBase) - Static method in class org.sbml.jsbml.ext.arrays.validator.ExtendedSBaseValidator

Validates the given SBase object.

validate(SBMLDocument) - Static method in class org.sbml.jsbml.ext.arrays.validator.ArraysValidator

Validates the given SBMLDocument

validate(SBMLDocument, boolean) - Static method in class org.sbml.jsbml.ext.arrays.validator.ArraysValidator

Validates the given SBMLDocument

VALIDATION_CONSISTENCY - org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY

Checks for validationsupport level.

ValidationConstraint<T> - Class in org.sbml.jsbml.validator.offline.constraints

The basic constraint which uses a ValidationFunction object to perform validation.

ValidationConstraint(int, ValidationFunction<T>) - Constructor for class org.sbml.jsbml.validator.offline.constraints.ValidationConstraint

Creates a new ValidationConstraint instance.

ValidationContext - Class in org.sbml.jsbml.validator.offline

A ValidationContext object is used to perform offline validation.

ValidationContext(int, int) - Constructor for class org.sbml.jsbml.validator.offline.ValidationContext

Creates a new ValidationContext for the given SBML level and version.

ValidationContext(int, int, AnyConstraint<Object>, Set<SBMLValidator.CHECK_CATEGORY>) - Constructor for class org.sbml.jsbml.validator.offline.ValidationContext

Creates a new ValidationContext for the given SBML level and version.

ValidationFunction<T> - Interface in org.sbml.jsbml.validator.offline.constraints

Basic functional interface for a ValidationFunction.

ValidationListener - Interface in org.sbml.jsbml.validator.offline

Tracks the progress of a the validation.

ValidationTools - Class in org.sbml.jsbml.validator.offline.constraints.helper

Collection of helpful functions and variables for validation.

ValidationTools() - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

ValidationUnitsCompiler - Class in org.sbml.jsbml.validator.offline.constraints.helper

A units compiler which is also doing validation and reporting validation errors.

ValidationUnitsCompiler() - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.ValidationUnitsCompiler

value - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

value - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

value - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

value - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

value - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

value - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

valueLower - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

valueOf(int) - Static method in enum org.sbml.jsbml.ext.layout.SpeciesReferenceRole

valueOf(Class<? extends SBase>) - Static method in enum org.sbml.jsbml.ListOf.Type

Gives the corresponding ListOf.Type for the given Class object.

valueOf(String) - Static method in enum org.sbml.jsbml.ASTNode.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.CVTerm.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.distrib.UncertParameter.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.dyn.SpatialKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.fbc.FBCList

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.fbc.FluxBound.Operation

Deprecated.

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.fbc.Objective.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.groups.Group.Kind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.layout.CurveSegment.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.layout.SpeciesReferenceRole

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.multi.BindingStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.multi.Relation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.multi.RepresentationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.qual.InputTransitionEffect

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.qual.OutputTransitionEffect

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.qual.QualList

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.qual.Sign

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm.RelativePosition

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.FontFamily

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.GradientBase.Spread

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.GraphicalPrimitive2D.FillRule

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.HTextAnchor

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.RenderCurveSegment.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.Style.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.VTextAnchor

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.BoundaryConditionKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.CompressionKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.CoordinateKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.DataKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.DiffusionKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.FunctionKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.GeometryKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.InterpolationKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.PolygonKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.PrimitiveKind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.spatial.SetOperation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ListOf.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.SBMLError.SEVERITY

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.SBMLException.Category

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.SBMLException.Code

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.SBMLException.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.text.parser.FormulaParserLL3.LOG_BEHAVIOR

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.Unit.Kind

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY

Returns the enum constant of this type with the specified name.

ValuePair<L extends java.lang.Comparable<? super L>,V extends java.lang.Comparable<? super V>> - Class in org.sbml.jsbml.util

A pair of two values with type parameters.

ValuePair() - Constructor for class org.sbml.jsbml.util.ValuePair

Creates a new ValuePair with both attributes set to null.

ValuePair(L, V) - Constructor for class org.sbml.jsbml.util.ValuePair

ValuePair(ValuePair<L, V>) - Constructor for class org.sbml.jsbml.util.ValuePair

valuePairOf(L, V) - Static method in class org.sbml.jsbml.util.ValuePair

Can be used for static import, i.e. use

values() - Static method in enum org.sbml.jsbml.ASTNode.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.CVTerm.Qualifier

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.CVTerm.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.distrib.UncertParameter.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.dyn.SpatialKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.fbc.FBCList

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.fbc.FluxBound.Operation

Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.fbc.Objective.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.groups.Group.Kind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.layout.CurveSegment.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.layout.SpeciesReferenceRole

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.multi.BindingStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.multi.Relation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.multi.RepresentationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.qual.InputTransitionEffect

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.qual.OutputTransitionEffect

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.qual.QualList

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.qual.Sign

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm.RelativePosition

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.FontFamily

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.GradientBase.Spread

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.GraphicalPrimitive2D.FillRule

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.HTextAnchor

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.RenderCurveSegment.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.Style.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.VTextAnchor

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.BoundaryConditionKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.CompressionKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.CoordinateKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.DataKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.DiffusionKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.FunctionKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.GeometryKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.InterpolationKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.PolygonKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.PrimitiveKind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.spatial.SetOperation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ListOf.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.SBMLError.SEVERITY

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.SBMLException.Category

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.SBMLException.Code

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.SBMLException.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.text.parser.FormulaParserLL3.LOG_BEHAVIOR

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.Unit.Kind

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY

Returns an array containing the constants of this enum type, in the order they are declared.

ValuesFromTriggerTimeNeedDelay - org.sbml.jsbml.SBMLException.Code

useValuesFromTriggerTime=false, but no delay defined in event

valueUpper - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

var - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

variable - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

variable - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

variable - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

Variable - Interface in org.sbml.jsbml

A variable of the system is a Quantity whose value may change during a simulation.

VariableNotValidAttribute - org.sbml.jsbml.SBMLException.Code

Attribute variable not valid

variance - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The variance of a random quantity (or distribution) is the average value of the square of the deviation of that variable from its mean.

variance - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

varLower - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

varUpper - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

vector(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

vector(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

vector(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

vector(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

Dealing with a vector.

vector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

vector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

vector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

vector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

vector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

vector(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

Dealing with a vector.

vector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

vector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

vector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

vector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

VECTOR - org.sbml.jsbml.ASTNode.Type

VectorCompiler - Class in org.sbml.jsbml.ext.arrays.compiler

VectorCompiler(Model) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

VectorCompiler(Model, boolean) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

VectorCompiler(Model, boolean, Map<String, ASTNode>) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

VectorCompiler(Model, NamedSBase, boolean) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

version - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

VERSION_MISMATCH - Static variable in class org.sbml.jsbml.JSBML

VERSION_MISMATCH_MSG - Static variable in exception org.sbml.jsbml.LevelVersionError

Message to display in cases that two objects do not have identical version attributes.

versionMajor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

versionMinor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

versionMismatchMessage(SBase, SBase) - Static method in exception org.sbml.jsbml.LevelVersionError

Creates an error message if the version fields of both elements are not identical, or an empty String otherwise.

viableWithoutChange - Static variable in class org.sbml.jsbml.ext.req.ReqConstants

VOLT - org.sbml.jsbml.Unit.Kind

The volt unit.

volume - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

volume(int, int) - Static method in class org.sbml.jsbml.UnitDefinition

Returns the predefined unit for volume.

VOLUME - Static variable in class org.sbml.jsbml.UnitDefinition

Identifier of the (for some SBML Levels 1 and 2) predefined UnitDefinition volume.

VolumeLitreDefExponentNotOne - org.sbml.jsbml.SBMLException.Code

Must use exponent=1 when defining volume in terms of litres

VolumeMetreDefExponentNot3 - org.sbml.jsbml.SBMLException.Code

Must use exponent=3 when defining volume in terms of metres

volumeUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

vTextAnchor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

VTextAnchor - Enum in org.sbml.jsbml.ext.render

The VTextAnchor enumeration allows models to specify how text elements are to be vertically aligned within their BoundingBox.

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