Index (jsbml-fbc 1.6.1 API)

A C D E F G H I J L M N O P R S T U V W

A

AbstractFBCSBasePlugin - Class in org.sbml.jsbml.ext.fbc: Represents the basic properties of all SBasePlugin in the FBC package.
AbstractFBCSBasePlugin() - Constructor for class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin
AbstractFBCSBasePlugin(AbstractFBCSBasePlugin) - Constructor for class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin
AbstractFBCSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin
activeObjective - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
addAllAssociations(List<Association>) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Sets the given ListOf<Association>.
addAssociation(Association) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Adds a new Association to the LogicalOperator.listOfAssociations.
addChild(Association) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Identical to calling LogicalOperator.addAssociation(Association).
addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AndConstraints
addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FBCReactionPluginConstraints
addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints
addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ObjectiveConstraints
addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrConstraints
addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AndConstraints
addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FBCReactionPluginConstraints
addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints
addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ObjectiveConstraints
addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrConstraints
addFluxBound(FluxBound) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
addFluxObjective(FluxObjective) - Method in class org.sbml.jsbml.ext.fbc.Objective: Adds a new FluxObjective to the listOfFluxObjectives.
addGeneProduct(GeneProduct) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Adds a new GeneProduct to the FBCModelPlugin.listOfGeneProducts.
addObjective(Objective) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Adds a new Objective to the listOfObjectives.
and - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2.
And - Class in org.sbml.jsbml.ext.fbc: This class represents a set of two or more associations that are related in an order independent ‘and’ relationship.
And() - Constructor for class org.sbml.jsbml.ext.fbc.And: Creates a new And instance.
And(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.And: Creates a new And instance.
And(And) - Constructor for class org.sbml.jsbml.ext.fbc.And: Creates a new And instance.
AndConstraints - Class in org.sbml.jsbml.validator.offline.constraints
AndConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AndConstraints
associatedSpecies - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2.
association - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2.
Association - Interface in org.sbml.jsbml.ext.fbc: Represents either a single gene, or a collection of genes in a logical expression and is only ever instantiated as one of its subclasses: GeneProductRef, And and Or.

C

charge - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
CHARGE - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
checkFbcLabelGeneProductUnique(FBCModelPlugin, Set<String>) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints
chemicalFormula - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
clone() - Method in class org.sbml.jsbml.ext.fbc.And
clone() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
clone() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
clone() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
clone() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
clone() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: clones this class
clone() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct
clone() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation
clone() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef
clone() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives
clone() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator
clone() - Method in class org.sbml.jsbml.ext.fbc.Objective
clone() - Method in class org.sbml.jsbml.ext.fbc.Or
CobraConstants - Class in org.sbml.jsbml.ext.fbc
CobraConstants() - Constructor for class org.sbml.jsbml.ext.fbc.CobraConstants
CobraToFbcV1Converter - Class in org.sbml.jsbml.ext.fbc.converters: converts old COBRA SBML files to SBML FBCV1
CobraToFbcV1Converter() - Constructor for class org.sbml.jsbml.ext.fbc.converters.CobraToFbcV1Converter
CobraToFbcV2Converter - Class in org.sbml.jsbml.ext.fbc.converters: Converts old COBRA SBML files to SBML level 3 FBC version 2.
CobraToFbcV2Converter() - Constructor for class org.sbml.jsbml.ext.fbc.converters.CobraToFbcV2Converter
coefficient - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
convert(SBMLDocument) - Method in class org.sbml.jsbml.ext.fbc.converters.CobraToFbcV1Converter
convert(SBMLDocument) - Method in class org.sbml.jsbml.ext.fbc.converters.CobraToFbcV2Converter
convert(SBMLDocument) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV1ToCobraConverter
convert(SBMLDocument) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV1ToFbcV2Converter
convert(SBMLDocument) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV2ToCobraConverter
convert(SBMLDocument) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV2ToFbcV1Converter
createAnd() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new Association element and adds it to the LogicalOperator.listOfAssociations list.
createFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
createFluxBound(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
createFluxObjective() - Method in class org.sbml.jsbml.ext.fbc.Objective: Creates a new FluxObjective element and adds it to the ListOfFluxObjectives list
createFluxObjective(String) - Method in class org.sbml.jsbml.ext.fbc.Objective: Creates a new FluxObjective element and adds it to the ListOfFluxObjectives list
createFluxObjective(String, String) - Method in class org.sbml.jsbml.ext.fbc.Objective
createFluxObjective(String, String, double, String) - Method in class org.sbml.jsbml.ext.fbc.Objective
createFluxObjective(String, String, double, Reaction) - Method in class org.sbml.jsbml.ext.fbc.Objective
createGeneProduct() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Creates a new GeneProduct element and adds it to the ListOfGeneProducts list.
createGeneProduct(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Creates a new GeneProduct element and adds it to the FBCModelPlugin.listOfGeneProducts list.
createGeneProductAssociation() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
createGeneProductAssociation(String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
createGeneProductRef() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new Association element and adds it to the LogicalOperator.listOfAssociations list.
createGeneProductRef(String) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new Association element and adds it to the LogicalOperator.listOfAssociations list.
createObjective() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Creates a new Objective element and adds it to the FBCModelPlugin.listOfObjectives.
createObjective(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Creates a new Objective element and adds it to the FBCModelPlugin.listOfObjectives.
createObjective(String, String, Objective.Type) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Creates a new Objective element and adds it to the FBCModelPlugin.listOfObjectives.
createObjective(String, Objective.Type) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Creates a new Objective element and adds it to the FBCModelPlugin.listOfObjectives.
createOr() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new Association element and adds it to the LogicalOperator.listOfAssociations list.
createPluginFor(ASTNode) - Method in class org.sbml.jsbml.xml.parsers.FBCParser
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.FBCParser

D

DEFAULT_GENE_ASSOCIATION_SPELLING - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
DEFAULT_LOWER_BOUND_NAME - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
DEFAULT_UPPER_BOUND_NAME - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants

E

EQUAL - org.sbml.jsbml.ext.fbc.FluxBound.Operation: Deprecated.

equal
equals(Object) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
equals(Object) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
equals(Object) - Method in class org.sbml.jsbml.ext.fbc.FluxObjective
equals(Object) - Method in class org.sbml.jsbml.ext.fbc.GeneProduct
equals(Object) - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef
equals(Object) - Method in class org.sbml.jsbml.ext.fbc.Objective

F

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

G

geneProduct - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
GeneProduct - Class in org.sbml.jsbml.ext.fbc: Defines a single gene product.
GeneProduct() - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct: Creates a new GeneProduct instance.
GeneProduct(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct: Creates a new GeneProduct instance.
GeneProduct(String) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct: Creates a new GeneProduct instance.
GeneProduct(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct: Creates a new GeneProduct instance.
GeneProduct(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct: Creates a new GeneProduct instance.
GeneProduct(GeneProduct) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct: Creates a new GeneProduct instance.
geneProductAssociation - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
GeneProductAssociation - Class in org.sbml.jsbml.ext.fbc: Contains a single Association.
GeneProductAssociation() - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Creates a new GeneProductAssociation instance.
GeneProductAssociation(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Creates a new GeneProductAssociation instance.
GeneProductAssociation(String) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Creates a new GeneProductAssociation instance.
GeneProductAssociation(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Creates a new GeneProductAssociation instance.
GeneProductAssociation(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Creates a new GeneProductAssociation instance.
GeneProductAssociation(GeneProductAssociation) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Creates a new GeneProductAssociation instance.
GeneProductConstraints - Class in org.sbml.jsbml.validator.offline.constraints
GeneProductConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints
geneProductIdentifier - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
GeneProductRef - Class in org.sbml.jsbml.ext.fbc: References a GeneProduct.
GeneProductRef() - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef: Creates a new GeneProductRef instance.
GeneProductRef(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef: Creates a new GeneProductRef instance.
GeneProductRef(String) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef: Creates a new GeneProductRef instance.
GeneProductRef(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef: Creates a new GeneProductRef instance.
GeneProductRef(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef: Creates a new GeneProductRef instance.
GeneProductRef(GeneProductRef) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef: Creates a new GeneProductRef instance.
geneProductReference - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
geneProteinAssociation - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Deprecated.
getActiveObjective() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Gets the activeObjective.
getActiveObjective() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives: Returns the value of activeObjective
getActiveObjectiveInstance() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
getActiveObjectiveInstance() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives: Returns the active Objective.
getAllowsChildren() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
getAllowsChildren() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
getAllowsChildren() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
getAllowsChildren() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation
getAllowsChildren() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator
getAssociatedSpecies() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Returns the value of GeneProduct.associatedSpecies.
getAssociation() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Returns the value of GeneProductAssociation.association.
getAssociation(int) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Gets an element from the LogicalOperator.listOfAssociations at the given index.
getAssociationCount() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Returns the number of Associations in this LogicalOperator.
getCharge() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Returns the value of FBCSpeciesPlugin.charge.
getChemicalFormula() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Returns the value of FBCSpeciesPlugin.chemicalFormula.
getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation
getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator
getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.Objective
getChildCount() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
getChildCount() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
getChildCount() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
getChildCount() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation
getChildCount() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator
getChildCount() - Method in class org.sbml.jsbml.ext.fbc.Objective
getCoefficient() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Returns the value of coefficient
getElementName() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives
getFluxBound(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
getFluxBoundCount() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
getFluxObjectiveCount() - Method in class org.sbml.jsbml.ext.fbc.Objective
getGeneProduct() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Returns the value of GeneProductRef.geneProduct.
getGeneProduct(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Gets an element from the FBCModelPlugin.listOfGeneProducts at the given index.
getGeneProduct(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Gets an element from the listOfGeneProducts, with the given id.
getGeneProductAssociation() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Returns the value of FBCReactionPlugin.geneProductAssociation.
getGeneProductCount() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns the number of GeneProducts in this FBCModelPlugin.
getGeneProductInstance() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Returns the GeneProduct referenced by this GeneProductRef.
getLabel() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Returns the value of GeneProduct.label
getListOfAssociations() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Returns the LogicalOperator.listOfAssociations.
getListOfFluxBounds() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
getListOfFluxObjectives() - Method in class org.sbml.jsbml.ext.fbc.Objective: Returns the listOfFluxObjectives
getListOfGeneProducts() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns the FBCModelPlugin.listOfGeneProducts.
getListOfObjectives() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns the FBCModelPlugin.listOfObjectives.
getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.FBCParser
getLowerFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Returns the value of FBCReactionPlugin.lowerFluxBound.
getLowerFluxBoundInstance() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.FBCParser
getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.FBCParser
getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.FBCParser
getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.fbc.FBCConstants: Returns a namespace URI corresponding to the given SBML level and version.
getNamespaceURI(int, int, int) - Static method in class org.sbml.jsbml.ext.fbc.FBCConstants: Returns a namespace URI corresponding to the given SBML level and version and package version.
getNumAssociations() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Returns the number of Associations in this LogicalOperator.
getNumFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
getNumFluxObjectives() - Method in class org.sbml.jsbml.ext.fbc.Objective: Deprecated.
use Objective.getFluxObjectiveCount()
getNumGeneProducts() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns the number of GeneProducts in this FBCModelPlugin.
getNumObjective() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Return the number of Objectives in this FBCModelPlugin.
getObjective(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Gets an element from the listOfObjectives at the given index.
getObjectiveCount() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Return the number of Objective in this FBCModelPlugin.
getOperation() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
getPackageName() - Method in class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin
getPackageName() - Method in class org.sbml.jsbml.xml.parsers.FBCParser
getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.FBCParser
getParent() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
getParent() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
getParentSBMLObject() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
getParentSBMLObject() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
getPrefix() - Method in class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin
getReaction() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
getReaction() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Returns the value of reaction
getReactionInstance() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
getReactionInstance() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Returns the Reaction associated with this FluxObjective.
getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.FBCParser
getStrict() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns the value of FBCModelPlugin.strict.
getType() - Method in class org.sbml.jsbml.ext.fbc.Objective: Returns the type.
getUpperFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Returns the value of FBCReactionPlugin.upperFluxBound.
getUpperFluxBoundInstance() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
getURI() - Method in class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin
getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AndConstraints
getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FBCReactionPluginConstraints
getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints
getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ObjectiveConstraints
getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrConstraints
getValue() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
GPRParser - Class in org.sbml.jsbml.ext.fbc.converters: Provides a method to converts gene association string as used in COBRA in SBML level 2 into GeneProductAssociation used in SBML level 3.
GPRParser() - Constructor for class org.sbml.jsbml.ext.fbc.converters.GPRParser
GREATER - org.sbml.jsbml.ext.fbc.FluxBound.Operation: Deprecated.

greater
GREATER_EQUAL - org.sbml.jsbml.ext.fbc.FluxBound.Operation: Deprecated.

greaterEqual

H

hashCode() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
hashCode() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
hashCode() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective
hashCode() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct
hashCode() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef
hashCode() - Method in class org.sbml.jsbml.ext.fbc.Objective

I

initDefaults() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Initializes the default values.
initDefaults() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
initDefaults() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Initializes the default values using the namespace.
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef
isIdMandatory() - Method in class org.sbml.jsbml.ext.fbc.Objective
isRequired() - Method in class org.sbml.jsbml.xml.parsers.FBCParser
isSetActiveObjective() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
isSetActiveObjective() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives: Returns whether activeObjective is set
isSetAssociatedSpecies() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Returns whether GeneProduct.associatedSpecies is set.
isSetAssociation() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Returns whether GeneProductAssociation.association is set.
isSetCharge() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Returns whether FBCSpeciesPlugin.charge is set.
isSetChemicalFormula() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Returns whether FBCSpeciesPlugin.chemicalFormula is set.
isSetCoefficient() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Returns whether coefficient is set
isSetGeneProduct() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Returns whether GeneProductRef.geneProduct is set.
isSetGeneProductAssociation() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Returns whether FBCReactionPlugin.geneProductAssociation is set.
isSetGeneProductInstance() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Returns whether the gene product id is set and this id is a valid GeneProduct id in this model.
isSetLabel() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Returns whether GeneProduct.label is set
isSetListOfAssociations() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Returns true if LogicalOperator.listOfAssociations contains at least one element.
isSetListOfFluxBounds() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
isSetListOfFluxObjectives() - Method in class org.sbml.jsbml.ext.fbc.Objective
isSetListOfGeneProducts() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns true if FBCModelPlugin.listOfGeneProducts contains at least one element.
isSetListOfObjectives() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns true if listOfObjectives is not null.
isSetLowerFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Returns whether FBCReactionPlugin.lowerFluxBound is set.
isSetLowerFluxBoundInstance() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
isSetOperation() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
isSetReaction() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
isSetReaction() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Returns whether reaction is set
isSetReactionInstance() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
isSetReactionInstance() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Returns whether reaction is set and is a valid Reaction in the model.
isSetStrict() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns whether FBCModelPlugin.strict is set.
isSetType() - Method in class org.sbml.jsbml.ext.fbc.Objective: Returns whether type is set
isSetUpperFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Returns whether FBCReactionPlugin.upperFluxBound is set.
isSetUpperFluxBoundInstance() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
isSetValue() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
isStrict() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns the value of FBCModelPlugin.strict.

J

JSBML_DUPLICATED_GENE_PRODUCT_SET - Static variable in class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints

L

label - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
leftChild - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2: The left child of a logical association rule.
LESS - org.sbml.jsbml.ext.fbc.FluxBound.Operation: Deprecated.

less
LESS_EQUAL - org.sbml.jsbml.ext.fbc.FluxBound.Operation: Deprecated.

lessEqual
listOfFluxBounds - org.sbml.jsbml.ext.fbc.FBCList
listOfFluxBounds - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
listOfFluxes - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: old name of the listOfFluxObjectives.
listOfFluxObjectives - org.sbml.jsbml.ext.fbc.FBCList
listOfFluxObjectives - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
listOfGeneProducts - org.sbml.jsbml.ext.fbc.FBCList: Introduced in FBC version 2.
listOfGeneProducts - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
listOfObjectives - org.sbml.jsbml.ext.fbc.FBCList
listOfObjectives - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
ListOfObjectives - Class in org.sbml.jsbml.ext.fbc: ListOfObjectives adds an additional required attribute: 'activeObjective'.
ListOfObjectives() - Constructor for class org.sbml.jsbml.ext.fbc.ListOfObjectives: Creates a new ListOfObjectives instance.
ListOfObjectives(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.ListOfObjectives: Creates a new ListOfObjectives instance.
ListOfObjectives(ListOfObjectives) - Constructor for class org.sbml.jsbml.ext.fbc.ListOfObjectives: Creates a new ListOfObjectives instance.
ListOfObjectives(ListOf<Objective>) - Constructor for class org.sbml.jsbml.ext.fbc.ListOfObjectives: Creates a new ListOfObjectives instance.
LogicalOperator - Class in org.sbml.jsbml.ext.fbc: Represents a collection of genes in a logical expression.
LogicalOperator() - Constructor for class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new LogicalOperator instance.
LogicalOperator(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new LogicalOperator instance.
LogicalOperator(LogicalOperator) - Constructor for class org.sbml.jsbml.ext.fbc.LogicalOperator: Creates a new LogicalOperator instance.
LOWER_BOUND - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
lowerFluxBound - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2.

M

main(String[]) - Static method in class org.sbml.jsbml.xml.parsers.FBCParser: Tests this class
MAXIMIZE - org.sbml.jsbml.ext.fbc.Objective.Type
MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
MINIMIZE - org.sbml.jsbml.ext.fbc.Objective.Type
mmol_per_gDW_per_hr - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants

N

namespaces - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
namespaceURI - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: The latest namespace URI of this parser, this value can change between releases.
namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: The namespace URI of this parser for SBML level 3, version 1 and package version 1.
namespaceURI_L3V1V2 - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: The namespace URI of this parser for SBML level 3, version 1 and package version 2.
none - org.sbml.jsbml.ext.fbc.FBCList
NotesToAnnotation - Class in org.sbml.jsbml.ext.fbc.converters: NotesToAnnotation transfers information from the Cobra style notes to the annotations.
NotesToAnnotation() - Constructor for class org.sbml.jsbml.ext.fbc.converters.NotesToAnnotation

O

objective - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
Objective - Class in org.sbml.jsbml.ext.fbc: An integral component in a complete description of a steady-state model is the so-called 'objective function' which generally consists of a linear combination of model variables (fluxes) and a sense (direction).
Objective() - Constructor for class org.sbml.jsbml.ext.fbc.Objective: Creates an Objective instance
Objective(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.Objective: Creates a Objective instance with a level and version.
Objective(String) - Constructor for class org.sbml.jsbml.ext.fbc.Objective: Creates a Objective instance with an id.
Objective(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.Objective: Creates a Objective instance with an id, level, and version.
Objective(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.Objective: Creates a Objective instance with an id, name, level, and version.
Objective(Objective) - Constructor for class org.sbml.jsbml.ext.fbc.Objective: Clone constructor
OBJECTIVE_COEFFICIENT - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
Objective.Type - Enum in org.sbml.jsbml.ext.fbc
ObjectiveConstraints - Class in org.sbml.jsbml.validator.offline.constraints
ObjectiveConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ObjectiveConstraints
operation - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
or - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2.
Or - Class in org.sbml.jsbml.ext.fbc: This class represents a set of two or more associations that are related in an order independent ‘and’ relationship.
Or() - Constructor for class org.sbml.jsbml.ext.fbc.Or: Creates a new Or instance.
Or(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.Or: Creates a new Or instance.
Or(Or) - Constructor for class org.sbml.jsbml.ext.fbc.Or: Creates a new Or instance.
OrConstraints - Class in org.sbml.jsbml.validator.offline.constraints
OrConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.OrConstraints
org.sbml.jsbml.ext.fbc - package org.sbml.jsbml.ext.fbc: Provides classes for the Flux Balance Constraints package (FBC).
org.sbml.jsbml.ext.fbc.converters - package org.sbml.jsbml.ext.fbc.converters
org.sbml.jsbml.validator.offline.constraints - package org.sbml.jsbml.validator.offline.constraints
org.sbml.jsbml.xml.parsers - package org.sbml.jsbml.xml.parsers

P

packageName - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
parseGPR(Reaction, String, boolean) - Static method in class org.sbml.jsbml.ext.fbc.converters.GPRParser: Parses a gene association string as used in COBRA in SBML level 2 into a GeneProductAssociation used in SBML level 3.
parseGPR(Reaction, String, boolean, boolean) - Static method in class org.sbml.jsbml.ext.fbc.converters.GPRParser: Parses a gene association string as used in COBRA in SBML level 2 into a GeneProductAssociation used in SBML level 3.
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.FBCParser
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.FBCParser
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.FBCParser

R

reaction - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.fbc.FluxObjective
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.fbc.GeneProduct
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.fbc.Objective
removeAllAssociations() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Returns true if LogicalOperator.listOfAssociations contains at least one element, otherwise false.
removeAssociation(int) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Removes an element from the listOfAssociations at the given index.
removeAssociation(Association) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator: Removes an element from the LogicalOperator.listOfAssociations.
removeFluxBound(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
removeFluxBound(FluxBound) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
removeFluxObjective(int) - Method in class org.sbml.jsbml.ext.fbc.Objective: Removes an element from the listOfFluxObjectives at the given index.
removeFluxObjective(String) - Method in class org.sbml.jsbml.ext.fbc.Objective: Removes an element from the listOfFluxObjectives with the given id.
removeFluxObjective(FluxObjective) - Method in class org.sbml.jsbml.ext.fbc.Objective: Removes an element from the listOfFluxObjectives.
removeGeneProduct(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Removes an element from the listOfGeneProducts at the given index.
removeGeneProduct(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Removes an element from the FBCModelPlugin.listOfGeneProducts.
removeGeneProduct(GeneProduct) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Removes an element from the FBCModelPlugin.listOfGeneProducts.
removeObjective(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Removes an element from the listOfObjectives at the given index.
removeObjective(Objective) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Removes an element from the listOfObjectives.
rightChild - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2: The right child of a logical association rule.

S

setActiveObjective(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: The activeObjective refers to the id of an existing objective.
setActiveObjective(String) - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives: Sets the active objective.
setActiveObjective(Objective) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
setActiveObjective(Objective) - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives: Sets the value of ListOfObjectives.activeObjective to the id of the given Objective.
setAssociatedSpecies(String) - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Sets the value of associatedSpecies
setAssociation(Association) - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Sets the value of association
setCharge(int) - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Sets the value of charge.
setChemicalFormula(String) - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Sets the value of chemicalFormula.
setCoefficient(double) - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: The coefficient attribute takes the value of the coefficient that the FluxObjective takes in the context of the enclosing Objective class.
setGeneProduct(String) - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Sets the value of geneProduct
setGeneProductAssociation(GeneProductAssociation) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Sets the value of FBCReactionPlugin.geneProductAssociation
setLabel(String) - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Sets the value of GeneProduct.label
setListOfFluxBounds(ListOf<FluxBound>) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
setListOfFluxObjectives(ListOf<FluxObjective>) - Method in class org.sbml.jsbml.ext.fbc.Objective: This list houses the actual fluxes to partake in this objective function, which are encoded by FluxObjective Sets the given ListOf<FluxObjective>.
setListOfGeneProducts(ListOf<GeneProduct>) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Sets the given ListOf<GeneProduct>.
setListOfObjectives(ListOfObjectives) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Sets the given ListOfObjectives.
setListOfObjectives(ListOf<Objective>) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Sets the given ListOf<Objective>.
setLowerFluxBound(String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Sets the value of lowerFluxBound
setLowerFluxBound(Parameter) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
setNotesKeyToUserObject(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
setOperation(FluxBound.Operation) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.CobraToFbcV1Converter
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.CobraToFbcV2Converter
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV1ToCobraConverter
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV1ToFbcV2Converter
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV2ToCobraConverter
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV2ToFbcV1Converter
setReaction(String) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
setReaction(String) - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Sets the reaction that this FluxObjective is associated with in the context of the enclosing Objective class.
setReaction(Reaction) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
setReaction(Reaction) - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Sets the Reaction that this FluxObjective is associated with in the context of the enclosing Objective class.
setStrict(boolean) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Sets the value of strict
setType(String) - Method in class org.sbml.jsbml.ext.fbc.Objective: The required type attribute contains a Objective.Type which represents the sense of the optimality constraint and can take one of two values, minimize or maximize.
setType(Objective.Type) - Method in class org.sbml.jsbml.ext.fbc.Objective: Sets the value of type
setUpperFluxBound(String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Sets the value of upperFluxBound
setUpperFluxBound(Parameter) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
setValue(double) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
shortLabel - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
strict - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in Version 2 Release 4.

T

toString() - Method in enum org.sbml.jsbml.ext.fbc.FluxBound.Operation: Deprecated.
toString() - Method in enum org.sbml.jsbml.ext.fbc.Objective.Type
transfer(SBMLDocument, String[]) - Method in class org.sbml.jsbml.ext.fbc.converters.NotesToAnnotation: Transfers information from the Cobra style notes of species and reactions to the annotations (see example below).
type - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

U

unsetActiveObjective() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives: Unsets the variable activeObjective
unsetAssociatedSpecies() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Unsets the variable associatedSpecies.
unsetAssociation() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Unsets the variable association.
unsetCharge() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Unsets the variable charge
unsetChemicalFormula() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Unsets the variable chemicalFormula
unsetCoefficient() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Unsets the variable coefficient
unsetGeneProduct() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Unsets the variable geneProduct
unsetGeneProductAssociation() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Unsets the variable FBCReactionPlugin.geneProductAssociation.
unsetLabel() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Unsets the variable GeneProduct.label
unsetListOfFluxBounds() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
unsetListOfFluxObjectives() - Method in class org.sbml.jsbml.ext.fbc.Objective: Unsets the listOfFluxObjectives.
unsetListOfGeneProducts() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns true if FBCModelPlugin.listOfGeneProducts contains at least one element, otherwise false.
unsetListOfObjectives() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Returns true if listOfObjectives contain at least one element, otherwise false
unsetLowerFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Unsets the variable lowerFluxBound.
unsetOperation() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
unsetReaction() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
unsetReaction() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Unsets the variable reaction
unsetStrict() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Unsets the variable strict.
unsetType() - Method in class org.sbml.jsbml.ext.fbc.Objective: Unsets the variable type
unsetUpperFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Unsets the variable upperFluxBound.
unsetValue() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
UPPER_BOUND - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
upperFluxBound - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2.

V

value - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
valueOf(String) - Static method in enum org.sbml.jsbml.ext.fbc.FBCList: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.ext.fbc.FluxBound.Operation: Deprecated.

Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.ext.fbc.Objective.Type: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.sbml.jsbml.ext.fbc.FBCList: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.ext.fbc.FluxBound.Operation: Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.ext.fbc.Objective.Type: Returns an array containing the constants of this enum type, in the order they are declared.

W

writeElement(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.FBCParser
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.fbc.Objective

A C D E F G H I J L M N O P R S T U V W