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

A

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

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).

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

Introduced to FBC in version 2.

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

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

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

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

Introduced to FBC in version 2.

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

Introduced to FBC in version 2.

Association - Interface in org.sbml.jsbml.ext.fbc

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

Introduced to FBC in version 2.

C

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

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

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

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, Reaction) - Method in class org.sbml.jsbml.ext.fbc.Objective

createFluxObjective(String, String, double, String) - 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, 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, 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(SBase) - Method in class org.sbml.jsbml.xml.parsers.FBCParser

createPluginFor(ASTNode) - Method in class org.sbml.jsbml.xml.parsers.FBCParser

E

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

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

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

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

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

Introduced to FBC in version 2.

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

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

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

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

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

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

Clone constructor

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

Creates an FBCSpeciesPlugin instance

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

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

Deprecated.

Only defined in FBC Version 1.

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

Deprecated.

Only defined in FBC version 1.

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

Deprecated.

Only defined in FBC version 1.

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

Deprecated.

Only defined in FBC version 1.

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

Deprecated.

Only defined in FBC version 1.

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

Deprecated.

Only defined in FBC version 1.

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

Deprecated.

Only defined in FBC version 1.

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

Deprecated.

Only defined in FBC version 1.

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

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

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

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

Creates an FluxObjective instance

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

Creates a FluxObjective instance with a level and version.

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

Creates a FluxObjective instance with an id.

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

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

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

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

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

Clone constructor

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

Introduced to FBC in version 2.

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

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

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

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

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

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

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

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

Introduced to FBC in version 2.

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

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

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

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

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

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

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

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

Introduced to FBC in version 2.

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

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

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

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

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

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

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

Iterates through this list until it finds

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(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.

getGeneProduct() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef

Returns the value of GeneProductRef.geneProduct.

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

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(int, int) - Static method in class org.sbml.jsbml.ext.fbc.FBCConstants

getNamespaceURI(int, int, int) - Static method in class org.sbml.jsbml.ext.fbc.FBCConstants

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.FBCParser

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

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

getValue() - Method in class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

Only defined in FBC version 1.

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

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

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.

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.

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

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

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

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

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

Unlike other SBML ListOf classes, ListOfObjectives adds an additional required attribute activeObjective.

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

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

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

ListOfObjectives(ListOf<Objective>) - Constructor for class org.sbml.jsbml.ext.fbc.ListOfObjectives

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

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

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

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

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

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

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.

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

Clone constructor

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

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

Introduced to FBC in version 2.

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

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

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

org.sbml.jsbml.ext.fbc - package org.sbml.jsbml.ext.fbc

Provides classes for the Flux Balance Constraints package (FBC).

org.sbml.jsbml.xml.parsers - package org.sbml.jsbml.xml.parsers

P

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

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(Association) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

Removes an element from the LogicalOperator.listOfAssociations.

removeAssociation(int) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

Removes an element from the listOfAssociations at the given index.

removeFluxBound(FluxBound) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Deprecated.

Only defined in FBC version 1.

removeFluxBound(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Deprecated.

Only defined in FBC version 1.

removeFluxObjective(FluxObjective) - Method in class org.sbml.jsbml.ext.fbc.Objective

Removes an element from the listOfFluxObjectives.

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.

removeGeneProduct(GeneProduct) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Removes an element from the FBCModelPlugin.listOfGeneProducts.

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.

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(Objective) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

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

This attribute refers to an id of an existing Objective.

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(ListOf<Objective>) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Sets the given ListOf<Objective>.

setListOfObjectives(ListOfObjectives) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Sets the given ListOfObjectives.

setLowerFluxBound(Parameter) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

setLowerFluxBound(String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

Sets the value of lowerFluxBound

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.

setReaction(Reaction) - 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.FluxBound

Deprecated.

Only defined in FBC version 1.

setReaction(Reaction) - Method in class org.sbml.jsbml.ext.fbc.FluxObjective

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.

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(Parameter) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

setUpperFluxBound(String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

Sets the value of upperFluxBound

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

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.

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

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