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

F_L - Static variable in class org.sbml.jsbml.util.ModelBuilder

Typical size scale of a cell, hence needed as default volume unit in CBM.

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

Refers to the X component of the force vector that drives movement

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

Refers to the Y component of the force vector that drives movement

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

Refers to the Z component of the force vector that drives movement

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

Computes the factorial!

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(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(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.

FailedMathMLReadOfDouble - org.sbml.jsbml.SBMLException.Code

Failed to read floating-point number

FailedMathMLReadOfExponential - org.sbml.jsbml.SBMLException.Code

Failed to read an exponential expression

FailedMathMLReadOfInteger - org.sbml.jsbml.SBMLException.Code

Failed to read an integer

FailedMathMLReadOfRational - org.sbml.jsbml.SBMLException.Code

Failed to read a rational expression

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

FARAD - org.sbml.jsbml.Unit.Kind

The farad unit.

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

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

FATAL - org.sbml.jsbml.SBMLError.SEVERITY

FATAL - org.sbml.jsbml.SBMLException.Type

FBC_10100 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2010100:

FBC_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2010101: To conform to Version 1 of the Flux Balance Constraints package specification for SBML Level 3, an SBML document must declare the use of the following XML Namespace: 'http://www.sbml.org/sbml/level3/version1/fbc/version1' Reference: L3V1 Fbc V1 Section 3.1

FBC_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2010102: Wherever they appear in an SBML document, elements and attributes from the Flux Balance Constraints package must be declared either implicitly or explicitly to be in the XML namespace 'http://www.sbml.org/sbml/level3/version1/fbc/version1' Reference: L3V1 Fbc V1 Section 3.1

FBC_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2010301: (Extends validation rule #10301 in the SBML Level 3 Version 1 Core specification.)

FBC_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2010302: The value of a fbc:id attribute must always conform to the syntax of the SBML data type SId.

FBC_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020101: In all SBML documents using the Flux Balance Constraints package, the SBML object must include a value for the attribute 'fbc:required'.

FBC_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020102: The value of attribute 'fbc:required' on the SBML object must be of the data type Boolean.

FBC_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020103: The value of attribute 'fbc:required' on the SBML object must be set to 'false'.

FBC_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020201: There may be at most one instance of each of the following kinds of objects within a <model> object using Flux Balance Constraints: <listOfFluxBounds> (V1 only), <listOfObjectives> and <listOfGeneProducts> (V2).

FBC_20202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020202: The various ListOf subobjects with a <model> object are optional, but if present, these container object must not be empty.

FBC_20203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020203: Apart from the general notes and annotation subobjects permitted on all SBML objects, a <listOfFluxBounds> container object may only contain <fluxBound> objects.

FBC_20204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020204: Apart from the general notes and annotation subobjects permitted on all SBML objects, a <listOfObjectives> container object may only contain <objective> objects.

FBC_20205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020205: A <listOfFluxBounds> object may have the optional attributes 'metaid' and 'sboTerm' defined by SBML Level 3 Core.

FBC_20206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020206: A <listOfFluxBounds> object may have the optional attributes 'metaid' and 'sboTerm' defined by SBML Level 3 Core.

FBC_20207 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020207: The value of attribute 'fbc:activeObjective' on the <listOfObjectives> object must be of the data type SIdRef.

FBC_20208 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020208: The value of attribute 'fbc:activeObjective' on the <listOfObjectives> object must be the identifier of an existing <objective>.

FBC_20209 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020209: A <model> object must have the required attributes 'strict'.

FBC_20210 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020210: The attribute 'fbc:strict' on the <model> object must have a value of datatype Boolean.

FBC_20211 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020211: Apart from the general notes and annotation subobjects permitted on all SBML objects, a <listOfGeneProducts> container object may only contain <geneProduct> objects.

FBC_20212 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020212: A <listOfGeneProducts> object may have the optional attributes 'metaid' and 'sboTerm' defined by SBML Level 3 Core.

FBC_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020301: A SBML <species> object may have the optional attributes 'fbc:charge' and 'fbc:chemicalFormula'.

FBC_20302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020302: The value of attribute 'fbc:charge' on SBML <species> object must be of the data type integer.

FBC_20303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020303: The value of attribute 'fbc:chemicalFormula' on the SBML <species> object must be set to a string consisting only of atomic names or user defined compounds and their occurrence.

FBC_20401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020401: A <fluxBound> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

FBC_20402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020402: A <fluxBound> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

FBC_20403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020403: A <fluxBound> object must have the required attributes 'fbc:reaction', 'fbc:operation' and 'fbc:value', and may have the optional attributes 'fbc:id' and 'fbc:name'.

FBC_20404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020404: The attribute 'fbc:reaction' of a <fluxBound> must be of the data type SIdRef.

FBC_20405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020405: The attribute 'fbc:name' of a <fluxBound> must be of the data type string.

FBC_20406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020406: The attribute 'fbc:operation' of a <fluxBound> must be of the data type FbcOperation and thus it's value must be one of 'lessEqual', 'greaterEqual' or 'equal'.

FBC_20407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020407: The attribute 'fbc:value' of a <fluxBound> must be of the data type double.

FBC_20408 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020408: The value of the attribute 'fbc:reaction' of a <fluxBound> object must be the identifier of an existing <reaction> object defined in the enclosing <model> object.

FBC_20409 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020409: The combined set of all <fluxBound>'s with identical values for 'fbc:reaction' must be consistent.

FBC_20501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020501: An <objective> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

FBC_20502 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020502: An <objective> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

FBC_20503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020503: An <objective> object must have the required attributes 'fbc:id' and 'fbc:type' and may have the optional attribute 'fbc:name'.

FBC_20504 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020504: The attribute 'fbc:name' on an <objective> must be of the data type 'string'.

FBC_20505 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020505: The attribute 'fbc:type' on an <objective> must be of the data type FbcType and thus its value must be one of 'minimize' or 'maximize.

FBC_20506 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020506: An <objective> object must have one and only one instance of the <listOfFluxObjectives> object.

FBC_20507 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020507: The <listOfFluxObjectives> subobject within an <objective> object must not be empty.

FBC_20508 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020508: Apart from the general notes and annotation subobjects permitted on all SBML objects, a <listOfFluxObjectives> container object may only contain <fluxObjective> objects.

FBC_20509 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020509: A <listOfFluxObjectives> object may have the optional 'metaid' and 'sboTerm' defined by SBML Level 3 Core.

FBC_20601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020601: A <fluxObjective> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

FBC_20602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020602: A <fluxObjective> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

FBC_20603 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020603: A <fluxObjective> object must have the required attributes 'fbc:reaction' and 'fbc:coefficient', and may have the optional attributes 'fbc:id' and 'fbc:name'.

FBC_20604 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020604: The attribute 'fbc:name' on a <fluxObjective> must be of the data type 'string'.

FBC_20605 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020605: The value of the attribute 'fbc:reaction' of a <fluxObjective> object must conform to the syntax of the SBML data type 'SIdRef'.

FBC_20606 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020606: The value of the attribute 'fbc:reaction' of a <fluxObjective> object must be the identifier of an existing <reaction> object defined in the enclosing <model> object.

FBC_20607 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020607: The value of the attribute 'fbc:coefficient' of a <fluxObjective> object must conform to the syntax of the SBML data type 'double'.

FBC_20608 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020608: When the value of the <model> 'fbc:strict' attribute is true, the value of the attribute 'fbc:coefficient' of a <fluxObjective> object must not be set to 'NaN', 'INF' or '-INF'.

FBC_20701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020701: There may be at most one instance of a <GeneProductAssociation> within a <Reaction> object using Flux BalanceConstraints.

FBC_20702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020702: An SBML <Reaction> object may have the optional attributes 'fbc:lowerFluxBound' and 'fbc:upperFluxBound'.

FBC_20703 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020703: The attribute 'fbc:lowerFluxBound' of a <Reaction> must be of the data type 'SIdRef'.

FBC_20704 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020704: The attribute 'fbc:upperFluxBound' of a <Reaction> must be of the data type 'SIdRef'.

FBC_20705 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020705: The attribute 'fbc:lowerFluxBound' of a <Reaction> must point to an existing <Parameter> in the model.

FBC_20706 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020706: The attribute 'fbc:upperFluxBound' of a <Reaction> must point to an existing <Parameter> in the model.

FBC_20707 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020707: When the value of the <Model>s 'fbc:strict' attribute is 'true', a <Reaction> must define the attributes 'fbc:lowerFluxBound' and 'fbc:upperFluxBound'.

FBC_20708 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020708: When the value of the <Model>s 'fbc:strict' attribute is 'true', the <Parameter> objects referred to by the attributes 'fbc:lowerFluxBound' and 'fbc:upperFluxBound' must have their 'constant' attribute set to 'true'.

FBC_20709 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020709: When the value of the <Model>s 'fbc:strict' attribute is 'true', the <Parameter> objects referred to by the attributes 'fbc:lowerFluxBound' and 'fbc:upperFluxBound' must have a defined value for their 'value' attribute, which may not be 'NaN'.

FBC_20710 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020710: When the value of the <Model>s 'fbc:strict' attribute is 'true', the <Parameter> objects referred to by the attributes 'fbc:lowerFluxBound' and 'fbc:upperFluxBound' may not be targeted by an <InitialAssignment>.

FBC_20711 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020711: When the value of the <Model>s 'fbc:strict' attribute is 'true', the <Parameter> objects referred to by the attribute 'fbc:lowerFluxBound' may not have the value 'INF'.

FBC_20712 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020712: When the value of the <Model>s 'fbc:strict' attribute is 'true', the <Parameter> object referred to by the attribute 'fbc:upperFluxBound' may not have the value '-INF'.

FBC_20713 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020713: When the value of the <Model>s 'fbc:strict' attribute is 'true', the <Parameter> object referred to by the attribute 'fbc:lowerFluxBound' must be less than or equal to the value of the <Parameter> object referred to by the attribute 'fbc:upperFluxBound' .

FBC_20714 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020714: When the value of the <Model>s 'fbc:strict' attribute is 'true', the 'constant' attribute of <SpeciesReference> elements of a <Reaction> must be set to 'true'.

FBC_20715 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020715: When the value of the <Model>s 'fbc:strict' attribute is 'true', the value of a <SpeciesReference>'s 'stoichiometry> attribute must not be set to 'NaN', '-INF' or 'INF'.

FBC_20716 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020716: When the value of the <Model>s 'fbc:strict' attribute is 'true', the <SpeciesReference> elements of a <Reaction> may not be targeted by an <InitialAssignment>.

FBC_20801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020801: A <GeneProductAssociation> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

FBC_20802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020802: A <GeneProductAssociation> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

FBC_20803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020803: A <GeneProductAssociation> object may have the optional attributes 'fbc:id' and 'fbc:name'.

FBC_20804 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020804: The attribute 'fbc:id' on a <GeneProductAssociation> must be of the data type 'SId'.

FBC_20805 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020805: A <GeneProductAssociation> object must have one and only one of the concrete <Association> objects: <GeneProductRef>, <And> or <Or>.

FBC_20806 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020806: The attribute 'fbc:name' on a <GeneProductAssociation> must be of the data type 'string'.

FBC_20901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020901: A <GeneProductRef> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

FBC_20902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020902: A <GeneProductRef> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

FBC_20903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020903: A <GeneProductRef> object must have the required attribute 'fbc:geneProduct' and may have the optional attribute 'fbc:id'.

FBC_20904 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020904: The attribute 'fbc:geneProduct' on a <GeneProductRef> must be of the data type 'SIdRef'.

FBC_20908 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2020908: The attribute 'fbc:geneProduct' on a <GeneProductRef> if set, must refer to 'id' of a <GeneProduct> in the <Model>.

FBC_21001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021001: An <And> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

FBC_21002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021002: An <And> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

FBC_21003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021003: An <And> object must have two or more concrete <Association> objects: <GeneProductRef>, <And>, or <Or>.

FBC_21101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021101: An <Or> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

FBC_21102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021102: An <Or> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

FBC_21103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021103: An <Or> object must have two or more concrete <Association> objects: <GeneProductRef>, <And>, or <Or>.

FBC_21201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021201: A <GeneProduct> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

FBC_21202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021202: A <GeneProduct> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

FBC_21203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021203: A <GeneProduct> object must have the required attributes 'fbc:id' and 'fbc:label' may have the optional attributes 'fbc:name' and 'fbc:associatedSpecies'.

FBC_21204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021204: The attribute 'fbc:label' on a <GeneProduct> must be of the data type 'string'.

FBC_21205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021205: The attribute 'fbc:label' on a <GeneProduct> must be unique among the set of all <GeneProduct> elements defined in the <Model>.

FBC_21206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021206: The attribute 'fbc:name' on a <GeneProduct> must be of the data type 'string'.

FBC_21207 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 2021207: The attribute 'fbc:associatedSpecies' on a <GeneProduct> must be the identifier of an existing <Species> defined in the enclosing <Model>.

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

Creates a new FBCModelPlugin instance.

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

Extends the SBML Level 3 Version 1 Core Reaction class with the addition of a new optional element GeneProductAssociation as well as two optional attributes lowerFluxBound and upperFluxBound.

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

Creates a new FBCReactionPlugin instance.

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

Creates a new FBCReactionPlugin instance.

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

Creates a new FBCReactionPlugin instance.

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

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

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

Extends the SBML core 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

FbcV1ToCobraConverter - Class in org.sbml.jsbml.ext.fbc.converters

Converts SBML FBC Version 1 files to old COBRA SBML files.

FbcV1ToCobraConverter() - Constructor for class org.sbml.jsbml.ext.fbc.converters.FbcV1ToCobraConverter

FbcV1ToFbcV2Converter - Class in org.sbml.jsbml.ext.fbc.converters

Converts SBML FBC Version 1 files to SBML FBC Version 2.

FbcV1ToFbcV2Converter() - Constructor for class org.sbml.jsbml.ext.fbc.converters.FbcV1ToFbcV2Converter

FbcV2ToCobraConverter - Class in org.sbml.jsbml.ext.fbc.converters

Converts SBML FBC Version 2 files to old COBRA SBML files.

FbcV2ToCobraConverter() - Constructor for class org.sbml.jsbml.ext.fbc.converters.FbcV2ToCobraConverter

FbcV2ToFbcV1Converter - Class in org.sbml.jsbml.ext.fbc.converters

Converts SBML FBC Version 2 files to SBML FBC Version 1.

FbcV2ToFbcV1Converter() - Constructor for class org.sbml.jsbml.ext.fbc.converters.FbcV2ToFbcV1Converter

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

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

fill(int, char, String) - 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) - Method in class org.sbml.jsbml.math.ASTUnknown

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 class org.sbml.jsbml.AbstractTreeNode

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

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 class org.sbml.jsbml.AbstractTreeNode

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

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.

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_IS_FUNCTION - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

FILTER_IS_NAME - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

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

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

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

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.

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

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, 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 class org.sbml.jsbml.AbstractSBase

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.

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

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

filterResources(Pattern...) - 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.

findLayout(GraphicalObject) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Find the Layout to which the given GraphicalObject belongs.

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 for SBML level 1) 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 for SBML level 1) 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.

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

Returns a SBase element that has the given unique '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 - Class in org.sbml.jsbml.util.compilers

Finds if an ASTNode is using any units attribute.

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

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.AbstractASTNodePlugin

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.AbstractASTNodePlugin

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.AbstractASTNodePlugin

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.

flatten(SBMLDocument) - Method in class org.sbml.jsbml.ext.comp.util.CompFlatteningConverter

Public method to call on a CompflatteningConverter object.

FLOAT - org.sbml.jsbml.ext.spatial.DataKind

To indicate single-precision (32-bit) floating point values

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(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

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

FLUX_VALUE - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants

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(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(FluxBound) - 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 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

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

The FontFamily enumeration gives a hint as to which font is to be used when rendering Text elements.

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(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.

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

Format date to W3CDTF.

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

FORMULA - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants

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

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

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.math.compiler.FormulaCompiler

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

FormulaInLevel1KL - org.sbml.jsbml.SBMLException.Code

Only predefined functions are permitted in SBML Level 1 formulas

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

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

Constructor with InputStream.

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

Constructor with InputStream and supplied encoding

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.math.parser.FormulaParser

Constructor.

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

Constructor.

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

Constructor with generated Token Manager.

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 - 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.math.parser.FormulaParserASTNode2

Constructor with InputStream.

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

Constructor with InputStream.

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

Constructor with InputStream and supplied encoding

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.math.parser.FormulaParserASTNode2

Constructor.

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

Constructor.

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

Constructor with generated Token Manager.

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

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

Constructor with InputStream.

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

Constructor with InputStream and supplied encoding

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.math.parser.FormulaParserLL3

Constructor.

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

Constructor.

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

Constructor with generated Token Manager.

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

Constructor with generated Token Manager.

FormulaParserLL3.LOG_BEHAVIOR - Enum in org.sbml.jsbml.text.parser

Defines the different behaviors the parser can have regarding the 'log' operator.

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

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

Constructor with InputStream.

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

Constructor with InputStream and supplied encoding

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.math.parser.FormulaParserLL3ASTNode2

Constructor.

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

Constructor.

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

Constructor with generated Token Manager.

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 - Class in org.sbml.jsbml.text.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(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 - Class in org.sbml.jsbml.text.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(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 - Class in org.sbml.jsbml.text.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(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) - Static method in class org.sbml.jsbml.JSBML

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

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

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

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

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

A fraction of two int values.

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

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

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

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

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

A fraction of two int values.

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

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

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

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

Deprecated.

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

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

Creates a new ASTDivideNode with the given numerator and denominator.

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

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

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

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

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

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

Fraction of two ASTNodes

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

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

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

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

Deprecated.

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

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

Creates a new ASTDivideNode with the given nodes as children.

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

Fraction of two ASTNode2s

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

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

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

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

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

Creates a new ASTNode that divides two CallableSBase objects.

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

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

Returns the Type corresponding to the given String.

FuncDefNotValidComponent - org.sbml.jsbml.SBMLException.Code

Function definitions are not supported in this Level+Version of SBML

function(String, 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.StaticallyComputableCompiler

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

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

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

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

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

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

Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

FUNCTION - org.sbml.jsbml.ASTNode.Type

The type of an ASTNode containing a reference to a user-defined FunctionDefinition.

FUNCTION_ABS - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCCOS - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCCOSH - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCCOT - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCCOTH - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCCSC - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCCSCH - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCSEC - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCSECH - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCSIN - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCSINH - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCTAN - org.sbml.jsbml.ASTNode.Type

FUNCTION_ARCTANH - org.sbml.jsbml.ASTNode.Type

FUNCTION_CEILING - org.sbml.jsbml.ASTNode.Type

FUNCTION_COS - org.sbml.jsbml.ASTNode.Type

FUNCTION_COSH - org.sbml.jsbml.ASTNode.Type

FUNCTION_COT - org.sbml.jsbml.ASTNode.Type

FUNCTION_COTH - org.sbml.jsbml.ASTNode.Type

FUNCTION_CSC - org.sbml.jsbml.ASTNode.Type

FUNCTION_CSCH - org.sbml.jsbml.ASTNode.Type

FUNCTION_CSYMBOL - org.sbml.jsbml.ASTNode.Type

Generic csymbol to facilitate the addition of csymbol by other libraries or packages.

FUNCTION_DELAY - org.sbml.jsbml.ASTNode.Type

FUNCTION_EXP - org.sbml.jsbml.ASTNode.Type

FUNCTION_FACTORIAL - org.sbml.jsbml.ASTNode.Type

FUNCTION_FLOOR - org.sbml.jsbml.ASTNode.Type

FUNCTION_LN - org.sbml.jsbml.ASTNode.Type

FUNCTION_LOG - org.sbml.jsbml.ASTNode.Type

FUNCTION_MAX - org.sbml.jsbml.ASTNode.Type

FUNCTION_MIN - org.sbml.jsbml.ASTNode.Type

FUNCTION_PIECEWISE - org.sbml.jsbml.ASTNode.Type

FUNCTION_POWER - org.sbml.jsbml.ASTNode.Type

An ASTNode of this ASTNode.Type represents a function call of the 'pow' function.

FUNCTION_QUOTIENT - org.sbml.jsbml.ASTNode.Type

The quotient element is the operator used for division modulo a particular base.

FUNCTION_RATE_OF - org.sbml.jsbml.ASTNode.Type

FUNCTION_REM - org.sbml.jsbml.ASTNode.Type

The rem element is the operator that returns the "remainder" of a division modulo a particular base.

FUNCTION_ROOT - org.sbml.jsbml.ASTNode.Type

FUNCTION_SEC - org.sbml.jsbml.ASTNode.Type

FUNCTION_SECH - org.sbml.jsbml.ASTNode.Type

FUNCTION_SELECTOR - org.sbml.jsbml.ASTNode.Type

FUNCTION_SIN - org.sbml.jsbml.ASTNode.Type

FUNCTION_SINH - org.sbml.jsbml.ASTNode.Type

FUNCTION_TAN - org.sbml.jsbml.ASTNode.Type

FUNCTION_TANH - org.sbml.jsbml.ASTNode.Type

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

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

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

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

Process an ASTNode that contain an extended csymbol function.

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

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

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

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

Deprecated.

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

Creates a FunctionDefinition instance from a level and version.

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

Creates a FunctionDefinition instance from an id, 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(FunctionDefinition) - Constructor for class org.sbml.jsbml.FunctionDefinition

Creates a FunctionDefinition instance from a given FunctionDefinition.

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

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

FunctionDefMathNotLambda - org.sbml.jsbml.SBMLException.Code

Invalid expression in function definition

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

Creates a new FunctionTerm instance.

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

Creates a new FunctionTerm instance.

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

Creates a new FunctionTerm instance.

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

Creates a FunctionTerm instance from a given FunctionTerm.

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

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

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

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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