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B

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

backup(int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Backup a number of characters.

backup(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Backup a number of characters.

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

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

The suffix used in UnitDefinition objects that represent a base Unit.Kind with offset = 0, multiplier = 1, scale = 0, and exponent = 1.

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

basePoint1 - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

basePoint2 - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

beginColumn - Variable in class org.sbml.jsbml.math.parser.Token

The column number of the first character of this Token.

beginColumn - Variable in class org.sbml.jsbml.text.parser.Token

The column number of the first character of this Token.

beginLine - Variable in class org.sbml.jsbml.math.parser.Token

The line number of the first character of this Token.

beginLine - Variable in class org.sbml.jsbml.text.parser.Token

The line number of the first character of this Token.

BeginToken() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Start.

BeginToken() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Start.

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

bindingSite1 - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

bindingSite2 - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

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

BindingSiteSpeciesType - Class in org.sbml.jsbml.ext.multi

BindingSiteSpeciesType() - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingSiteSpeciesType(int, int) - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingSiteSpeciesType(BindingSiteSpeciesType) - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingSiteSpeciesType(String) - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingSiteSpeciesType(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingSiteSpeciesType(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingStatus - Enum in org.sbml.jsbml.ext.multi

The BindingStatus enumeration is used in the definition of the OutwardBindingSite class.

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

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

BOOLEAN_LOGIC - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants

RegularExpression Id.

BOOLEAN_LOGIC - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants

RegularExpression Id.

BOOLEAN_LOGIC - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

BOOLEAN_LOGIC - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants

RegularExpression Id.

BOOLEAN_LOGIC - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants

RegularExpression Id.

BOOLEAN_LOGIC - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants

RegularExpression Id.

BOOLEAN_LOGIC - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants

RegularExpression Id.

BOOLEAN_LOGIC - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

BOOLEAN_LOGIC - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants

RegularExpression Id.

bottomrule - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler

Requires LaTeX package booktabs.

bottomrule - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler

Requires LaTeX package booktabs.

Boundary - Class in org.sbml.jsbml.ext.spatial

Boundary() - Constructor for class org.sbml.jsbml.ext.spatial.Boundary

Boundary(Boundary) - Constructor for class org.sbml.jsbml.ext.spatial.Boundary

BoundaryCondition - Class in org.sbml.jsbml.ext.spatial

BoundaryCondition() - Constructor for class org.sbml.jsbml.ext.spatial.BoundaryCondition

BoundaryCondition(BoundaryCondition) - Constructor for class org.sbml.jsbml.ext.spatial.BoundaryCondition

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

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

BoundaryConditionFilter - Class in org.sbml.jsbml.util.filters

This filter accepts species whose boundary condition is set to true.

BoundaryConditionFilter() - Constructor for class org.sbml.jsbml.util.filters.BoundaryConditionFilter

Constructs a new boundary condition filter.

BoundaryConditionKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

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

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

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

BoundingBox - Class in org.sbml.jsbml.ext.layout

The BoundingBox class specifies the required elements position and dimension.

BoundingBox() - Constructor for class org.sbml.jsbml.ext.layout.BoundingBox

BoundingBox(BoundingBox) - Constructor for class org.sbml.jsbml.ext.layout.BoundingBox

BoundingBox(int, int) - Constructor for class org.sbml.jsbml.ext.layout.BoundingBox

BoundingBox(String) - Constructor for class org.sbml.jsbml.ext.layout.BoundingBox

BoundingBox(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.BoundingBox

boundingBox - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

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

brackets(Object) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler

brackets(Object) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

Encloses the given formula in brackets.

brackets(Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler

brackets(Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

Encloses the given formula in brackets.

bufpos - Variable in class org.sbml.jsbml.math.parser.SimpleCharStream

Position in buffer.

bufpos - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream

Position in buffer.

buildCompartment(String, boolean, String, double, double, String) - Method in class org.sbml.jsbml.util.ModelBuilder

buildCompartment(String, boolean, String, double, double, Unit.Kind) - Method in class org.sbml.jsbml.util.ModelBuilder

buildCompartment(String, boolean, String, double, double, UnitDefinition) - Method in class org.sbml.jsbml.util.ModelBuilder

buildKineticLaw(Reaction, String, Pair<String, Double>...) - Static method in class org.sbml.jsbml.util.ModelBuilder

buildModel(String, String) - Method in class org.sbml.jsbml.util.ModelBuilder

buildModifiers(Reaction, Pair<Species, Integer>...) - Static method in class org.sbml.jsbml.util.ModelBuilder

A convenient method to create multiple modifiers in one single step by passing the Species along with its role (SBO term) to this method.

buildParameter(String, String, double, boolean, String) - Method in class org.sbml.jsbml.util.ModelBuilder

buildParameter(String, String, double, boolean, Unit.Kind) - Method in class org.sbml.jsbml.util.ModelBuilder

buildParameter(String, String, double, boolean, UnitDefinition) - Method in class org.sbml.jsbml.util.ModelBuilder

buildProducts(Reaction, Pair<Double, Species>...) - Static method in class org.sbml.jsbml.util.ModelBuilder

Convenient method to build multiple products together with their stoichiometry in one step.

buildReactants(Reaction, Pair<Double, Species>...) - Static method in class org.sbml.jsbml.util.ModelBuilder

Convenient method to build multiple reactants together with their stoichiometry in one step.

buildReaction(String, String, Compartment, boolean, boolean) - Method in class org.sbml.jsbml.util.ModelBuilder

buildReaction(String, String, String, boolean, boolean) - Method in class org.sbml.jsbml.util.ModelBuilder

buildSpecies(String, String, Compartment, boolean, boolean, boolean, double, String) - Method in class org.sbml.jsbml.util.ModelBuilder

buildSpecies(String, String, Compartment, boolean, boolean, boolean, double, Unit.Kind) - Method in class org.sbml.jsbml.util.ModelBuilder

buildSpecies(String, String, Compartment, boolean, boolean, boolean, double, UnitDefinition) - Method in class org.sbml.jsbml.util.ModelBuilder

buildSpecies(String, String, String, boolean, boolean, boolean, double, String) - Method in class org.sbml.jsbml.util.ModelBuilder

buildUnit(UnitDefinition, double, int, Unit.Kind, double) - Static method in class org.sbml.jsbml.util.ModelBuilder

buildUnitDefinition(String, String) - Method in class org.sbml.jsbml.util.ModelBuilder

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

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

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