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

F

factorial(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

factorial(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

factorial(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

factorial(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

factorial(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

factorial(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

factorial(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

factorial(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler

factorial(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

factorial(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML

factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler

factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

factorial(int) - Static method in class org.sbml.jsbml.util.Maths

This method computes the factorial!

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

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

fatal(String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger

FBCConstants - Class in org.sbml.jsbml.ext.fbc

Contains constants related to the FBC package.

FBCConstants() - Constructor for class org.sbml.jsbml.ext.fbc.FBCConstants

FBCList - Enum in org.sbml.jsbml.ext.fbc

Lists used in the FBC package.

FBCModelPlugin - Class in org.sbml.jsbml.ext.fbc

FBCModelPlugin is the extended Model class for the FBC package.

FBCModelPlugin(FBCModelPlugin) - Constructor for class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Clone constructor

FBCModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.fbc.FBCModelPlugin

FBCParser - Class in org.sbml.jsbml.xml.parsers

This class is used to parse the fbc extension package elements and attributes.

FBCParser() - Constructor for class org.sbml.jsbml.xml.parsers.FBCParser

FBCReactionPlugin - Class in org.sbml.jsbml.ext.fbc

Introduced to FBC in version 2.

FBCReactionPlugin() - Constructor for class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

FBCReactionPlugin(FBCReactionPlugin) - Constructor for class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

FBCReactionPlugin(Reaction) - Constructor for class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

FBCSpeciesPlugin - Class in org.sbml.jsbml.ext.fbc

FBCSpeciesPlugin is the extended Species class with the additional attributes charge and chemicalFormula

FBCSpeciesPlugin(FBCSpeciesPlugin) - Constructor for class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

Clone constructor

FBCSpeciesPlugin(Species) - Constructor for class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

Creates an FBCSpeciesPlugin instance

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

fill(int, char, String) - Static method in class org.sbml.jsbml.util.StringTools

fill(int, char) - Static method in class org.sbml.jsbml.util.StringTools

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

filter(Filter) - Method in class org.sbml.jsbml.AbstractTreeNode

filter(Filter, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode

filter(Filter, boolean, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode

filter(Filter) - Method in class org.sbml.jsbml.math.ASTUnknown

filter(Filter, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown

filter(Filter, boolean, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown

Filter - Interface in org.sbml.jsbml.util.filters

A filter is a general interface that allows to check an object for a certain property.

filter(Filter) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Filters this tree data structure recursively and returns a list of all TreeNodes that are accepted by the Filter.

filter(Filter, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Filters this tree data structure recursively and returns a list of all TreeNodes that are accepted by the Filter.

filter(Filter, boolean, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Filters this tree data structure recursively and returns a list of all TreeNodes that are accepted by the Filter.

filterCVTerms(CVTerm.Qualifier) - Method in class org.sbml.jsbml.AbstractSBase

filterCVTerms(CVTerm.Qualifier, boolean, String...) - Method in class org.sbml.jsbml.AbstractSBase

filterCVTerms(CVTerm.Qualifier, String) - Method in class org.sbml.jsbml.AbstractSBase

filterCVTerms(CVTerm.Qualifier, String, boolean) - Method in class org.sbml.jsbml.AbstractSBase

filterCVTerms(CVTerm.Qualifier) - Method in class org.sbml.jsbml.Annotation

Returns a list of CVTerm having the given qualifier.

filterCVTerms(CVTerm.Qualifier, String) - Method in class org.sbml.jsbml.Annotation

Returns a list of CVTerm having the given qualifier and where the URI contains the given pattern.

filterCVTerms(CVTerm.Qualifier) - Method in interface org.sbml.jsbml.SBase

Returns a list of all the CVTerm with the given CVTerm.Qualifier.

filterCVTerms(CVTerm.Qualifier, String) - Method in interface org.sbml.jsbml.SBase

Queries the list of controlled vocabulary terms (CVTerm) for those terms whose CVTerm.Qualifier is of the given type and selects only those resources from these terms that contain the given pattern.

filterCVTerms(CVTerm.Qualifier, String, boolean) - Method in interface org.sbml.jsbml.SBase

Returns a list of resource URIs for the given CVTerm.Qualifier that match the given pattern.

filterCVTerms(CVTerm.Qualifier, boolean, String...) - Method in interface org.sbml.jsbml.SBase

Returns a list of resource URIs for the given CVTerm.Qualifier that match the given patterns.

filterList(Filter) - Method in class org.sbml.jsbml.ListOf

Returns a new List that contains only those elements that satisfy a certain filter criterion.

filterResources(Pattern...) - Method in class org.sbml.jsbml.CVTerm

Returns a list of resource URIs that contain the given Pattern(s).

filterResources(String...) - Method in class org.sbml.jsbml.CVTerm

Returns a list of resource URIs that contain the given pattern(s).

findCallableSBase(String) - Method in class org.sbml.jsbml.Model

Returns a CallableSBase element of the Model that has the given 'id' as identifier or null if no element is found.

findCompartmentGlyphs(String) - Method in class org.sbml.jsbml.ext.layout.Layout

Searches all instances of CompartmentGlyph within this Layout that refer to the Compartment with the given id.

findIdentical(UnitDefinition) - Method in class org.sbml.jsbml.Model

Searches the first UnitDefinition within this Model's Model.listOfUnitDefinitions that is identical to the given UnitDefinition.

findLocalParameters(String) - Method in class org.sbml.jsbml.Model

Finds all instances of LocalParameter in this Model and adds them to a List.

findModifierSpeciesReference(String) - Method in class org.sbml.jsbml.Model

Returns the ModifierSpeciesReference with all Reactions of this Model that has 'id' as id.

findNamedSBase(String) - Method in class org.sbml.jsbml.Model

Returns a NamedSBase element of the model that has the given 'id' as id or null if no element is found.

findNamedSBaseWithDerivedUnit(String) - Method in class org.sbml.jsbml.Model

Returns a NamedSBaseWithDerivedUnit element of the Model that has the given 'id' as id or null if no element is found.

findPort(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns a Port element that has the given 'id' within this Model or null if no such element can be found.

findQuantity(String) - Method in class org.sbml.jsbml.Model

Searches for an instance of Quantity within all of this Model's components that has the given identifier or name attribute and returns it.

findQuantityWithUnit(String) - Method in class org.sbml.jsbml.Model

Searches for an instance of QuantityWithUnit within all of this Model's components that has the given identifier or name attribute and returns it.

findReactionGlyphs(String) - Method in class org.sbml.jsbml.ext.layout.Layout

Searches all instances of ReactionGlyph within this Layout that refer to the Reaction with the given id.

findReactionsForLocalParameter(String) - Method in class org.sbml.jsbml.Model

Returns a SortedSet of identifiers of all Reaction elements within this Model whose KineticLaws contain a LocalParameter that has the given 'id' or null if no element cannot be found.

findReferencedCallableSBases() - Method in class org.sbml.jsbml.math.ASTFunction

Goes through the formula and identifies all global parameters that are referenced by this rate rule.

findReferencedGlobalParameters() - Method in class org.sbml.jsbml.ASTNode

Goes through the formula and identifies all global parameters that are referenced by this rate equation.

findSBase(String) - Method in class org.sbml.jsbml.SBMLDocument

Looks up the SBase registered in this SBMLDocument for the given metaId.

findSimpleSpeciesReference(String) - Method in class org.sbml.jsbml.Model

Returns the SimpleSpeciesReference within all Reactions of this Model that has 'id' as id.

findSpeciesGlyphs(String) - Method in class org.sbml.jsbml.ext.layout.Layout

Searches all instances of SpeciesGlyph within this Layout that refer to the Species with the given id.

findSpeciesReference(String) - Method in class org.sbml.jsbml.Model

Returns the SpeciesReference with all Reactions of this Model that has 'id' as id.

findSymbol(String) - Method in class org.sbml.jsbml.Model

Searches in the list of Compartments, Species, and Parameters for the element with the given identifier.

findTextGlyphs(String) - Method in class org.sbml.jsbml.ext.layout.Layout

Searches within the Layout.listOfTextGlyphs for TextGlyphs whose TextGlyph.getOriginOfText() points to the given id.

findUniqueNamedSBase(String) - Method in class org.sbml.jsbml.Model

Returns a UniqueNamedSBase element that has the given 'id' within this Model or null if no such element can be found.

findUnitDefinition(String) - Method in class org.sbml.jsbml.Model

Returns a UnitDefinition element that has the given 'id' within this Model or null if no such element can be found.

FindUnitsCompiler - Class in org.sbml.jsbml.math.compiler

Finds if an ASTNode is using any units attribute.

FindUnitsCompiler() - Constructor for class org.sbml.jsbml.math.compiler.FindUnitsCompiler

FindUnitsCompiler - Class in org.sbml.jsbml.util.compilers

Finds if an ASTNode is using any units attribute.

FindUnitsCompiler() - Constructor for class org.sbml.jsbml.util.compilers.FindUnitsCompiler

findVariable(String) - Method in class org.sbml.jsbml.Model

Searches the Variable with the given identifier in this model.

fireNodeAddedEvent() - Method in class org.sbml.jsbml.AbstractTreeNode

fireNodeAddedEvent() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

fireNodeAddedEvent() - Method in class org.sbml.jsbml.math.ASTUnknown

fireNodeAddedEvent() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

All TreeNodeChangeListener instances linked to this TreeNode are informed about the adding of this Object to an owning parent Object.

fireNodeRemovedEvent() - Method in class org.sbml.jsbml.AbstractSBase

fireNodeRemovedEvent() - Method in class org.sbml.jsbml.AbstractTreeNode

fireNodeRemovedEvent() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

fireNodeRemovedEvent() - Method in class org.sbml.jsbml.math.ASTUnknown

fireNodeRemovedEvent() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

All TreeNodeChangeListener instances linked to this TreeNode are informed about the deletion of this TreeNode from a parent Object.

firePropertyChange(String, Object, Object) - Method in class org.sbml.jsbml.AbstractSBase

firePropertyChange(String, Object, Object) - Method in class org.sbml.jsbml.AbstractTreeNode

firePropertyChange(String, Object, Object) - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

firePropertyChange(String, Object, Object) - Method in class org.sbml.jsbml.math.ASTUnknown

firePropertyChange(String, Object, Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

All TreeNodeChangeListeners are informed about the change in this TreeNodeWithChangeSupport.

firstHit(Filter) - Method in class org.sbml.jsbml.ListOf

Returns the first element in this list that satisfies a certain filter criterion.

firstLetterLowerCase(String) - Static method in class org.sbml.jsbml.util.StringTools

Returns a String whose first letter is now in lower case.

firstLetterUpperCase(String) - Static method in class org.sbml.jsbml.util.StringTools

Returns a String who's first letter is now in upper case.

floor(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

floor(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

floor(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

floor(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

floor(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

floor(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

floor(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

floor(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

floor(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

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

FluxBound - Class in org.sbml.jsbml.ext.fbc

Deprecated.

Only defined in FBC Version 1.

FluxBound() - Constructor for class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

Only defined in FBC version 1.

FluxBound(FluxBound) - Constructor for class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

Only defined in FBC version 1.

FluxBound(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

Only defined in FBC version 1.

FluxBound(String) - Constructor for class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

Only defined in FBC version 1.

FluxBound(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

Only defined in FBC version 1.

FluxBound(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

Only defined in FBC version 1.

FluxBound.Operation - Enum in org.sbml.jsbml.ext.fbc

Deprecated.

Only defined in FBC version 1.

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

FluxObjective - Class in org.sbml.jsbml.ext.fbc

The FluxObjective class is a relatively simple container for a model variable weighted by a signed linear coefficient.

FluxObjective() - Constructor for class org.sbml.jsbml.ext.fbc.FluxObjective

Creates an FluxObjective instance

FluxObjective(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.FluxObjective

Creates a FluxObjective instance with a level and version.

FluxObjective(String) - Constructor for class org.sbml.jsbml.ext.fbc.FluxObjective

Creates a FluxObjective instance with an id.

FluxObjective(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.FluxObjective

Creates a FluxObjective instance with an id, level, and version.

FluxObjective(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.FluxObjective

Creates a FluxObjective instance with an id, name, level, and version.

FluxObjective(FluxObjective) - Constructor for class org.sbml.jsbml.ext.fbc.FluxObjective

Clone constructor

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

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

FontRenderStyle - Interface in org.sbml.jsbml.ext.render

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

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

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

fontStyleItalicToString(boolean) - Static method in class org.sbml.jsbml.ext.render.XMLTools

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

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

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

fontWeightBoldToString(boolean) - Static method in class org.sbml.jsbml.ext.render.XMLTools

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

format(double) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

This method returns a StringBuffer representing a properly LaTeX formatted number.

format(double) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

This method returns a StringBuffer representing a properly LaTeX formatted number.

formatToW3CDTF(Date) - Method in class org.sbml.jsbml.xml.stax.DateProcessor

Format date to W3CDTF.

formatToW3CDTF(String) - Method in class org.sbml.jsbml.xml.stax.DateProcessor

Format datetime string to W3CDTF.

formatToW3CDTF(Timestamp) - Method in class org.sbml.jsbml.xml.stax.DateProcessor

Format datetime to W3CDTF.

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

FORMULA_ARGUMENT_SEPARATOR - Static variable in class org.sbml.jsbml.util.compilers.FormulaCompiler

FormulaCompiler - Class in org.sbml.jsbml.math.compiler

This class creates C-like infix formula Strings that represent the content of ASTNode2s.

FormulaCompiler() - Constructor for class org.sbml.jsbml.math.compiler.FormulaCompiler

FormulaCompiler - Class in org.sbml.jsbml.util.compilers

This class creates C-like infix formula Strings that represent the content of ASTNodes.

FormulaCompiler() - Constructor for class org.sbml.jsbml.util.compilers.FormulaCompiler

FormulaCompilerLibSBML - Class in org.sbml.jsbml.util.compilers

This class creates C-like infix formula Strings that represent the content of ASTNodes and try to reproduce the output generated by the LibSBML L3 parser.

FormulaCompilerLibSBML() - Constructor for class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML

FormulaCompilerNoPiecewise - Class in org.sbml.jsbml.util.compilers

Produces an infix formula like FormulaCompiler but removes all the piecewise functions.

FormulaCompilerNoPiecewise() - Constructor for class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise

FormulaParser - Class in org.sbml.jsbml.math.parser

Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).

FormulaParser(InputStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParser

Constructor with InputStream.

FormulaParser(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.FormulaParser

Constructor with InputStream and supplied encoding

FormulaParser(Reader) - Constructor for class org.sbml.jsbml.math.parser.FormulaParser

Constructor.

FormulaParser(FormulaParserTokenManager) - Constructor for class org.sbml.jsbml.math.parser.FormulaParser

Constructor with generated Token Manager.

FormulaParser - Class in org.sbml.jsbml.text.parser

Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).

FormulaParser(InputStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser

Constructor with InputStream.

FormulaParser(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser

Constructor with InputStream and supplied encoding

FormulaParser(Reader) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser

Constructor.

FormulaParser(FormulaParserTokenManager) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser

Constructor with generated Token Manager.

FormulaParserASTNode2 - Class in org.sbml.jsbml.math.parser

Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).

FormulaParserASTNode2(InputStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2

Constructor with InputStream.

FormulaParserASTNode2(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2

Constructor with InputStream and supplied encoding

FormulaParserASTNode2(Reader) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2

Constructor.

FormulaParserASTNode2(FormulaParserASTNode2TokenManager) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2

Constructor with generated Token Manager.

FormulaParserASTNode2 - Class in org.sbml.jsbml.text.parser

Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).

FormulaParserASTNode2(InputStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2

Constructor with InputStream.

FormulaParserASTNode2(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2

Constructor with InputStream and supplied encoding

FormulaParserASTNode2(Reader) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2

Constructor.

FormulaParserASTNode2(FormulaParserASTNode2TokenManager) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2

Constructor with generated Token Manager.

FormulaParserASTNode2Constants - Interface in org.sbml.jsbml.math.parser

Token literal values and constants.

FormulaParserASTNode2Constants - Interface in org.sbml.jsbml.text.parser

Token literal values and constants.

FormulaParserASTNode2TokenManager - Class in org.sbml.jsbml.math.parser

Token Manager.

FormulaParserASTNode2TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager

Constructor.

FormulaParserASTNode2TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager

Constructor.

FormulaParserASTNode2TokenManager - Class in org.sbml.jsbml.text.parser

Token Manager.

FormulaParserASTNode2TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager

Constructor.

FormulaParserASTNode2TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager

Constructor.

FormulaParserConstants - Interface in org.sbml.jsbml.math.parser

Token literal values and constants.

FormulaParserConstants - Interface in org.sbml.jsbml.text.parser

Token literal values and constants.

FormulaParserLL3 - Class in org.sbml.jsbml.math.parser

Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).

FormulaParserLL3(InputStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3

Constructor with InputStream.

FormulaParserLL3(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3

Constructor with InputStream and supplied encoding

FormulaParserLL3(Reader) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3

Constructor.

FormulaParserLL3(FormulaParserLL3TokenManager) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3

Constructor with generated Token Manager.

FormulaParserLL3 - Class in org.sbml.jsbml.text.parser

Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).

FormulaParserLL3(InputStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3

Constructor with InputStream.

FormulaParserLL3(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3

Constructor with InputStream and supplied encoding

FormulaParserLL3(Reader) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3

Constructor.

FormulaParserLL3(FormulaParserLL3TokenManager) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3

Constructor with generated Token Manager.

FormulaParserLL3ASTNode2 - Class in org.sbml.jsbml.math.parser

Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).

FormulaParserLL3ASTNode2(InputStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2

Constructor with InputStream.

FormulaParserLL3ASTNode2(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2

Constructor with InputStream and supplied encoding

FormulaParserLL3ASTNode2(Reader) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2

Constructor.

FormulaParserLL3ASTNode2(FormulaParserLL3ASTNode2TokenManager) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2

Constructor with generated Token Manager.

FormulaParserLL3ASTNode2 - Class in org.sbml.jsbml.text.parser

Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).

FormulaParserLL3ASTNode2(InputStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2

Constructor with InputStream.

FormulaParserLL3ASTNode2(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2

Constructor with InputStream and supplied encoding

FormulaParserLL3ASTNode2(Reader) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2

Constructor.

FormulaParserLL3ASTNode2(FormulaParserLL3ASTNode2TokenManager) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2

Constructor with generated Token Manager.

FormulaParserLL3ASTNode2Constants - Interface in org.sbml.jsbml.math.parser

Token literal values and constants.

FormulaParserLL3ASTNode2Constants - Interface in org.sbml.jsbml.text.parser

Token literal values and constants.

FormulaParserLL3ASTNode2TokenManager - Class in org.sbml.jsbml.math.parser

Token Manager.

FormulaParserLL3ASTNode2TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager

Constructor.

FormulaParserLL3ASTNode2TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager

Constructor.

FormulaParserLL3ASTNode2TokenManager - Class in org.sbml.jsbml.text.parser

Token Manager.

FormulaParserLL3ASTNode2TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager

Constructor.

FormulaParserLL3ASTNode2TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager

Constructor.

FormulaParserLL3Constants - Interface in org.sbml.jsbml.math.parser

Token literal values and constants.

FormulaParserLL3Constants - Interface in org.sbml.jsbml.text.parser

Token literal values and constants.

FormulaParserLL3TokenManager - Class in org.sbml.jsbml.math.parser

Token Manager.

FormulaParserLL3TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager

Constructor.

FormulaParserLL3TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager

Constructor.

FormulaParserLL3TokenManager - Class in org.sbml.jsbml.text.parser

Token Manager.

FormulaParserLL3TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager

Constructor.

FormulaParserLL3TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager

Constructor.

FormulaParserTokenManager - Class in org.sbml.jsbml.math.parser

Token Manager.

FormulaParserTokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserTokenManager

Constructor.

FormulaParserTokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserTokenManager

Constructor.

FormulaParserTokenManager - Class in org.sbml.jsbml.text.parser

Token Manager.

FormulaParserTokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserTokenManager

Constructor.

FormulaParserTokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserTokenManager

Constructor.

formulaToString(ASTNode) - Static method in class org.sbml.jsbml.ASTNode

Returns the formula from the given ASTNode as an SBML Level 1 text-string mathematical formula.

formulaToString(ASTNode, FormulaCompiler) - Static method in class org.sbml.jsbml.ASTNode

Returns the formula from the given ASTNode as an infix mathematical formula produce by the given FormulaCompiler.

formulaToString(ASTNode) - Static method in class org.sbml.jsbml.JSBML

Converts an ASTNode formula to a text string using a specific syntax for mathematical formulas.

formulaToString(ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Returns the formula from the given ASTNode2 as an SBML Level 1 text-string mathematical formula.

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

frac(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode

Creates a new ASTNode of type DIVIDE with the given nodes as children.

frac(int, ASTNode) - Static method in class org.sbml.jsbml.ASTNode

Creates a new ASTNode that of type DIVIDE with the given numerator and denominator.

frac(MathContainer, CallableSBase, CallableSBase) - Static method in class org.sbml.jsbml.ASTNode

Creates a new ASTNode that divides two CallableSBase objects.

frac(MathContainer, String, String) - Static method in class org.sbml.jsbml.ASTNode

Returns a new ASTNode that of type DIVIDE with the two entities as numerator and denominator.

frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

frac(int, int) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

frac(int, int) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

frac(int, int) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

frac(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Creates a new ASTDivideNode with the given nodes as children.

frac(int, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Creates a new ASTDivideNode with the given numerator and denominator.

frac(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

Fraction of two ASTNode2s

frac(int, int) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

A fraction of two int values.

frac(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

frac(int, int) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

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

Returns a fraction with the given elements as numerator and denominator.

frac(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

frac(int, int) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

frac(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

frac(int, int) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

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

frac(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

frac(int, int) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

frac(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

Fraction of two ASTNodes

frac(int, int) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

A fraction of two int values.

frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

frac(int, int) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

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

Returns a fraction with the given elements as numerator and denominator.

frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

frac(int, int) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

frac(int, int) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

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

frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

frac(int, int) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

frac(int, int) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

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

Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Deprecated.

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

Deprecated.

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

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

FunctionDefinition - Class in org.sbml.jsbml

Represents the functionDefinition XML element of a SBML file.

FunctionDefinition() - Constructor for class org.sbml.jsbml.FunctionDefinition

Creates a FunctionDefinition instance.

FunctionDefinition(FunctionDefinition) - Constructor for class org.sbml.jsbml.FunctionDefinition

Creates a FunctionDefinition instance from a given FunctionDefinition.

FunctionDefinition(int, int) - Constructor for class org.sbml.jsbml.FunctionDefinition

Creates a FunctionDefinition instance from a level and version.

FunctionDefinition(String, ASTNode, int, int) - Constructor for class org.sbml.jsbml.FunctionDefinition

Creates a FunctionDefinition instance from an id, ASTNode, level and version.

FunctionDefinition(String, int, int) - Constructor for class org.sbml.jsbml.FunctionDefinition

Creates a FunctionDefinition instance from an id, level and version.

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

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

FunctionTerm - Class in org.sbml.jsbml.ext.qual

Each FunctionTerm is also associated with a result and in addition to a Boolean function inside a Math element that can be used to set the conditions under which this term is selected.

FunctionTerm() - Constructor for class org.sbml.jsbml.ext.qual.FunctionTerm

Default constructor

FunctionTerm(int, int) - Constructor for class org.sbml.jsbml.ext.qual.FunctionTerm

FunctionTerm(ASTNode, int, int) - Constructor for class org.sbml.jsbml.ext.qual.FunctionTerm

FunctionTerm(FunctionTerm) - Constructor for class org.sbml.jsbml.ext.qual.FunctionTerm

Creates a FunctionTerm instance from a given FunctionTerm.

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

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

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

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

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