Package org.sbml.jsbml.ext.fbc

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

The current JSBML implementation of this package follow the FBC version 1 release 1 specifications.

Since:

1.0

Author:

Nicolas Rodriguez

Interface Summary

Interface	Description
Association	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.

Class Summary

Class	Description
AbstractFBCSBasePlugin	Represents the basic properties of all SBasePlugin in the FBC package.
And	This class represents a set of two or more associations that are related in an order independent ‘and’ relationship.
CobraConstants
FBCConstants	Contains constants related to the FBC package.
FBCModelPlugin	FBCModelPlugin is the extended Model class for the FBC package.
FBCReactionPlugin	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.
FBCSpeciesPlugin	Extends the SBML core Species class with the additional attributes charge and chemicalFormula.
FluxBound	Deprecated. Only defined in FBC Version 1.
FluxObjective	The FluxObjective class is a relatively simple container for a model variable weighted by a signed linear coefficient.
GeneProduct	Defines a single gene product.
GeneProductAssociation	Contains a single Association.
GeneProductRef	References a GeneProduct.
ListOfObjectives	ListOfObjectives adds an additional required attribute: 'activeObjective'.
LogicalOperator	Represents a collection of genes in a logical expression.
Objective	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).
Or	This class represents a set of two or more associations that are related in an order independent ‘and’ relationship.

Enum Summary

Enum	Description
FBCList	Lists used in the FBC package.
FluxBound.Operation	Deprecated. Only defined in FBC version 1.
Objective.Type