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

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.

BadCsymbolDefinitionURLValue - org.sbml.jsbml.SBMLException.Code

Invalid <csymbol> definitionURL attribute value

BadMathML - org.sbml.jsbml.SBMLException.Code

Invalid MathML expression

BadMathMLNodeType - org.sbml.jsbml.SBMLException.Code

Invalid MathML element

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.

base64 - org.sbml.jsbml.ext.spatial.CompressionKind

If the base 64 algorithm was used to transform the binary form of the actual members into text

BASELINE - org.sbml.jsbml.ext.render.VTextAnchor

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

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

basepoint1_x - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

basepoint1_y - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

basepoint1_z - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

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

basepoint2_x - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

basepoint2_y - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

basepoint2_z - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

BECQUEREL - org.sbml.jsbml.Unit.Kind

The becquerel unit.

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.

BELOW - org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm.RelativePosition

beta - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to elemental rotation of an object about the Y coordinate axis

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

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

A BindingSiteSpeciesType object is a binding site, and therefore its instance can further define the bindingStatus attribute and can participate a binding internally and explicitly in an InSpeciesTypeBond object, or externally and implicitly defined by an OutwardBindingSite object.

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

Creates a new BindingSiteSpeciesType instance.

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

Creates a new BindingSiteSpeciesType instance.

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

Creates a new BindingSiteSpeciesType instance.

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

Creates a new BindingSiteSpeciesType instance.

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

Creates a new BindingSiteSpeciesType instance.

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

Creates a new BindingSiteSpeciesType instance, cloned from the given object.

BindingSiteSpeciesTypeConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

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

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

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

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

BIOLOGICAL_QUALIFIER - org.sbml.jsbml.CVTerm.Type

If the MIRIAM qualifier is a biological qualifier.

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.

BooleanOpsNeedBooleanArgs - org.sbml.jsbml.SBMLException.Code

Non-boolean argument given to boolean operator

BothAmountAndConcentrationSet - org.sbml.jsbml.SBMLException.Code

Cannot set both initialConcentration and initialAmount

BothStoichiometryAndMath - org.sbml.jsbml.SBMLException.Code

Cannot use both stoichiometry and <stoichiometryMath> simultaneously

BOTTOM - org.sbml.jsbml.ext.render.VTextAnchor

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.

bound - org.sbml.jsbml.ext.multi.BindingStatus

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

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

Creates a new Boundary instance.

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

Creates a new Boundary instance cloned from the given boundary.

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

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

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

BoundaryConditionConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the BoundaryCondition class.

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

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.

BoundaryConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the Boundary class.

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

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

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

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

Creates a new instance of BoundingBox.

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

Creates a new instance of BoundingBox.

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

Creates a new instance of BoundingBox.

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

Creates a new instance of BoundingBox.

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

Creates a new instance of BoundingBox.

BoundingBoxConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the BoundingBox class.

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

BQB_ENCODES - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'encodes': the biological entity represented by the model element encodes, directly or transitively, the subject of the referenced resource (biological entity B).

BQB_HAS_PART - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'hasPart': the biological entity represented by the model element includes the subject of the referenced resource (biological entity B), either physically or logically.

BQB_HAS_PROPERTY - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'hasProperty': the subject of the referenced resource (biological entity B) is a property of the biological entity represented by the model element.

BQB_HAS_TAXON - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'hasTaxon': the biological entity represented by the model element is taxonomically restricted, where the restriction is the subject of the referenced resource (biological entity B).

BQB_HAS_VERSION - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'hasVersion': the subject of the referenced resource (biological entity B) is a version or an instance of the biological entity represented by the model element.

BQB_IS - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'is': the biological entity represented by the model element has identity with the subject of the referenced resource (biological entity B).

BQB_IS_DESCRIBED_BY - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'isDescribedBy': the biological entity represented by the model element is described by the subject of the referenced resource (biological entity B).

BQB_IS_ENCODED_BY - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'isEncodedBy': the biological entity represented by the model element is encoded, directly or transitively, by the subject of the referenced resource (biological entity B).

BQB_IS_HOMOLOG_TO - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'isHomologTo': the biological entity represented by the model element is homologous to the subject of the referenced resource (biological entity B).

BQB_IS_PART_OF - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'isPartOf': the biological entity represented by the model element is a physical or logical part of the subject of the referenced resource (biological entity B).

BQB_IS_PROPERTY_OF - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'isPropertyOf': the biological entity represented by the model element is a property of the referenced resource (biological entity B).

BQB_IS_RELATED_TO - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'isRelatedTo': the biological entity represented by the model element is somehow associated, directly or transitively, with the subject of the referenced resource (biological entity B).

BQB_IS_VERSION_OF - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'isVersionOf': the biological entity represented by the model element is a version or an instance of the subject of the referenced resource (biological entity B).

BQB_OCCURS_IN - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM biological qualifier 'occursIn': the biological entity represented by the model element is physically limited to a location, which is the subject of the referenced resource (biological entity B).

BQB_UNKNOWN - org.sbml.jsbml.CVTerm.Qualifier

Represents an unknown MIRIAM biological qualifier, equivalent to CVTerm.Qualifier.BQB_IS_RELATED_TO.

BQM_HAS_INSTANCE - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM model qualifier 'hasInstance': the modelling object represented by the model element has for instance (is a class of) the subject of the referenced resource (modelling object B).

BQM_IS - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM model qualifier 'is': the modeling object represented by the model element is identical with the subject of the referenced resource (modeling object B).

BQM_IS_DERIVED_FROM - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM model qualifier 'isDerivedFrom': the modeling object represented by the model element is derived from the modeling object represented by the referenced resource (modeling object B).

BQM_IS_DESCRIBED_BY - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM model qualifier 'isDescribedBy': the modeling object represented by the model element is described by the subject of the referenced resource (modeling object B).

BQM_IS_INSTANCE_OF - org.sbml.jsbml.CVTerm.Qualifier

Represents the MIRIAM model qualifier 'isInstanceOf': the modelling object represented by the model element is an instance of the subject of the referenced resource (modelling object B).

BQM_UNKNOWN - org.sbml.jsbml.CVTerm.Qualifier

Represents an unknown MIRIAM model qualifier.

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.

buildCBMunits() - Method in class org.sbml.jsbml.util.ModelBuilder

Creates the default units needed in a constraint-based modeling context

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

buildCompartment(CompartmentGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for the drawing of a compartment with the size and position of the BoundingBox of the given CompartmentGlyph

buildConnectingArc(SpeciesReferenceGlyph, ReactionGlyph, double) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for the drawing of a connecting arc or line with the size and position specified by the given SpeciesReferenceGlyph

buildCubicBezier(CubicBezier, double) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method to draw an arc between the two base points of the given CubicBezier.

buildEntityPoolNode(SpeciesGlyph, boolean) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for the drawing of an entity pool node with the given size and position of the BoundingBox of the given SpeciesGlyph

builderEnd() - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for actions that have to be done at the end of the builder e.g.

builderStart(Layout) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for preparations that have to be done at the beginning of the builder, e.g., the commands at the beginning of a LaTeX document

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

buildProcessNode(ReactionGlyph, double, double) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for the drawing of a process node with the size and position of the BoundingBox of the given ReactionGlyph

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

buildReaction(String, String, Compartment, boolean, boolean) - 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

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

buildTextGlyph(TextGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for drawing/writing the given TextGlyph

buildUnit(double, int, Unit.Kind, double) - 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, Unit...) - 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

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