Inheritance diagram for FbcModelPlugin:

Detailed Description

fbc Extension of Model.

The FbcModelPlugin object is used to extend the standard SBML Model object with features used in the SBML Level 3 Flux Balance Constraints (“fbc”) package. In Version 1 of the “fbc” specification, the extended Model class has two optional subobjects: ListOfObjectives and ListOfFluxBounds. In Version 2 of the specification, the extended Model object is defined differently: it is extended with a new required attribute named "strict", and the two optional subobjects ListOfObjectives and ListOfGeneProducts. (ListOfFluxBounds is not used in Version 2.)

The "strict" attribute on the (extended) Model class

The mandatory attribute "strict", of type boolean, in Version 2 of this package, is used to apply an additional set of restrictions to the model. The "strict" attribute helps ensure that the Flux Balance Constraints package can be used to encode legacy flux-balance analysis models expressible as Linear Programs (LP's) for software that is unable to analyze arbitrary mathematical expressions that may appear in an SBML model. In addition, a "strict" model is fully described and mathematically consistent, for example, by ensuring that all fluxes have a valid upper or lower bound.

The following restrictions are in effect if an “fbc” model object has a value of "true" for the attribute "strict" on Model:

Each Reaction in a Model must define values for the attributes "lowerFluxBound" and "upperFluxBound", with each attribute pointing to a valid Parameter object defined in the current Model.

Each Parameter object referred to by the Reaction attributes "lowerFluxBound" and "upperFluxBound" must have its "constant" attribute set to the value "true" and its "value" attribute set to a value of type double. This value may not be "NaN".

SpeciesReference objects in Reaction objects must have their "stoichiometry" attribute set to a double value that is not "NaN", nor "-INF", nor "INF". In addition, the value of their "constant" attribute must be set to "true".

InitialAssignment objects may not target the Parameter objects referenced by the Reaction attributes "lowerFluxBound" and "upperFluxBound", nor any SpeciesReference objects.

All defined FluxObjective objects must have their coefficient attribute set to a double value that is not "NaN", nor "-INF", nor "INF".

A Reaction "lowerFluxBound" attribute may not point to a Parameter object that has a value of "INF".

A Reaction "upperFluxBound" attribute may not point to a Parameter object that has a value of "-INF".

For all Reaction objects, the value of a "lowerFluxBound" attribute must be less than or equal to the value of the "upperFluxBound" attribute.

While it is not compulsory for a "strict" Flux Balance Constraints model to define an Objective, doing so does does allow the model to be formulated as a Linear Program and optimized. However, this decision is left to the modeler. Note that all other properties of the objects referred to in the list above are to be set as specified in the relevant SBML Level 3 Version 1 Core and Flux Balance Constraints (“fbc”) specifications.

Alternatively, if the value of the strict attribute is "false", then none of these restrictions apply and the model creator can choose to define “fbc” models that are not necessarily encodable as an LP. For example, if strict is "false", the InitialAssignment construct may be used to set any valid numerical entity, including Parameter values and stoichiometric coefficients, with any value of type double. In addition, Parameter elements are no longer required to be flagged as constant, thus allowing for a Flux Balance Constraints model's use in alternative, hybrid modeling strategies.

Lists of subobjects on the (extended) Model class

The ListOfObjectives is used to define the objectives of a given “fbc” model. Objectives generally consist of linear combinations of model variables (fluxes) and a direction for the optimality constraint (either maximization or minimization). Each Objective has a ListOfFluxObjectives subobjects.

In Version 2 of “fbc”, the ListOfGeneProducts is used to define the gene products represented by the “fbc” model.

In Version 1 of “fbc”, there is no ListOfGeneProducts, and instead, Model can have an optional ListOfFluxBounds.

See also: Objective; FluxObjective; FluxBound

Examples:: fbc_example1.cpp.

Public Member Functions
int	addFluxBound (const FluxBound *bound)
	Adds a copy of the given FluxBound object to the list of FluxBounds. More...

int	addGeneAssociation (const GeneAssociation *association)
	Adds a copy of the given GeneAssociation annotation object to the list of GeneAssociations. More...

int	addGeneProduct (const GeneProduct *gp)
	Adds a copy the given GeneProduct to this FbcModelPlugin. More...

int	addObjective (const Objective *o)
	Adds a copy the given Objective to this FbcModelPlugin. More...

virtual FbcModelPlugin *	clone () const
	Creates and returns a deep copy of this FbcModelPlugin object. More...

FluxBound *	createFluxBound ()
	Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it. More...

GeneAssociation *	createGeneAssociation ()
	Creates a new GeneAssociation annotation object and adds it to the list of GeneAssociation objects and returns it. More...

GeneProduct *	createGeneProduct ()
	Creates a new GeneProduct object, adds it to this FbcModelPlugin's ListOfGeneProducts and returns the GeneProduct object created. More...

Objective *	createObjective ()
	Creates a new Objective object, adds it to this FbcModelPlugin's ListOfObjectives and returns the Objective object created. More...

	FbcModelPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns)
	Creates a new FbcModelPlugin object using the given parameters. More...

	FbcModelPlugin (const FbcModelPlugin &orig)
	Copy constructor for FbcModelPlugin. More...

Objective *	getActiveObjective ()
	Returns the current active objective. More...

const Objective *	getActiveObjective () const
	Returns the current active objective. More...

std::string	getActiveObjectiveId () const
	Returns the id of the current active objective. More...

virtual List *	getAllElements (ElementFilter *filter=NULL)
	Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...

virtual SBase *	getElementByMetaId (const std::string &metaid)
	Return the first child object found with a given meta identifier. More...

virtual SBase *	getElementBySId (const std::string &id)
	Return the first child object found with a given identifier. More...

const std::string &	getElementNamespace () const
	Returns the namespace URI of the package to which this plugin object belongs. More...

const FluxBound *	getFluxBound (unsigned int n) const
	Returns the FluxBound object that belongs to the given index. More...

FluxBound *	getFluxBound (unsigned int n)
	Returns the FluxBound object that belongs to the given index. More...

FluxBound *	getFluxBound (const std::string &sid)
	Returns the FluxBound object based on its identifier. More...

const FluxBound *	getFluxBound (const std::string &sid) const
	Returns the FluxBound object based on its identifier. More...

ListOfFluxBounds *	getFluxBoundsForReaction (const std::string &reaction) const
	Creates a new ListOfFluxBounds object that contains only the FluxBound objects associated with the given Reaction. More...

const GeneAssociation *	getGeneAssociation (unsigned int n) const
	Returns the GeneAssociation annotation object that belongs to the given index. More...

GeneAssociation *	getGeneAssociation (unsigned int n)
	Returns the GeneAssociation annotation object that belongs to the given index. More...

GeneAssociation *	getGeneAssociation (const std::string &sid)
	Returns the GeneAssociation annotation object based on its identifier. More...

const GeneAssociation *	getGeneAssociation (const std::string &sid) const
	Returns the GeneAssociation annotation object based on its identifier. More...

GeneProduct *	getGeneProduct (unsigned int n)
	Get a GeneProduct from the ListOfGeneProducts. More...

const GeneProduct *	getGeneProduct (unsigned int n) const
	Get a GeneProduct from the ListOfGeneProducts. More...

GeneProduct *	getGeneProduct (const std::string &sid)
	Get a GeneProduct from the ListOfGeneProducts based on its identifier. More...

const GeneProduct *	getGeneProduct (const std::string &sid) const
	Get a GeneProduct from the ListOfGeneProducts based on its identifier. More...

GeneProduct *	getGeneProductByLabel (const std::string &label)
	Get a GeneProduct from the ListOfGeneProducts based on its label. More...

unsigned int	getLevel () const
	Returns the SBML Level of the package extension of this plugin object. More...

const ListOfFluxBounds *	getListOfFluxBounds () const
	Returns the ListOfFluxBounds in this plugin object. More...

ListOfFluxBounds *	getListOfFluxBounds ()
	Returns the ListOfFluxBounds in this plugin object. More...

const ListOfGeneAssociations *	getListOfGeneAssociations () const
	Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object. More...

ListOfGeneAssociations *	getListOfGeneAssociations ()
	Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object. More...

const ListOfGeneProducts *	getListOfGeneProducts () const
	Returns the ListOfGeneProducts in this FbcModelPlugin object. More...

ListOfGeneProducts *	getListOfGeneProducts ()
	Returns the ListOfGeneProducts in this FbcModelPlugin object. More...

const ListOfObjectives *	getListOfObjectives () const
	Returns the ListOfObjectives in this FbcModelPlugin object. More...

ListOfObjectives *	getListOfObjectives ()
	Returns the ListOfObjectives in this FbcModelPlugin object. More...

unsigned int	getNumFluxBounds () const
	Returns the number of FluxBound object in this plugin object. More...

int	getNumGeneAssociations () const
	Returns the number of GeneAssociation annotation object in this plugin object. More...

unsigned int	getNumGeneProducts () const
	Get the number of GeneProduct objects in this FbcModelPlugin. More...

unsigned int	getNumObjectives () const
	Get the number of Objective objects in this FbcModelPlugin. More...

Objective *	getObjective (unsigned int n)
	Get an Objective from the ListOfObjectives. More...

const Objective *	getObjective (unsigned int n) const
	Get an Objective from the ListOfObjectives. More...

Objective *	getObjective (const std::string &sid)
	Get an Objective from the ListOfObjectives based on its identifier. More...

const Objective *	getObjective (const std::string &sid) const
	Get an Objective from the ListOfObjectives based on its identifier. More...

const std::string &	getPackageName () const
	Returns the short-form name of the package to which this plugin object belongs. More...

unsigned int	getPackageVersion () const
	Returns the package version of the package extension of this plugin object. More...

SBase *	getParentSBMLObject ()
	Returns the parent object to which this plugin object is connected. More...

const SBase *	getParentSBMLObject () const
	Returns the parent object to which this plugin object is connected. More...

const std::string &	getPrefix () const
	Returns the XML namespace prefix of the package to which this plugin object belongs. More...

SBMLDocument *	getSBMLDocument ()
	Returns the SBMLDocument object containing this object instance. More...

const SBMLDocument *	getSBMLDocument () const
	Returns the SBMLDocument object containing this object instance. More...

virtual bool	getStrict () const
	Returns the value of the "strict" attribute of this FbcModelPlugin. More...

std::string	getURI () const
	Returns the XML namespace URI for the package to which this object belongs. More...

unsigned int	getVersion () const
	Returns the Version within the SBML Level of the package extension of this plugin object. More...

virtual bool	isSetStrict () const
	Predicate returning `true` if this FbcModelPlugin's "strict" attribute is set. More...

virtual bool	isValidTypeForList (SBase *item) const

FbcModelPlugin &	operator= (const FbcModelPlugin &rhs)
	Assignment operator for FbcModelPlugin. More...

FluxBound *	removeFluxBound (unsigned int n)
	Removes the nth FluxBound object from this plugin object and returns a pointer to it. More...

FluxBound *	removeFluxBound (const std::string &sid)
	Removes the FluxBound object with the given `sid` attribute from this plugin object and returns a pointer to it. More...

GeneAssociation *	removeGeneAssociation (unsigned int n)
	Removes the nth GeneAssociation annotation object from this plugin object and returns a pointer to it. More...

GeneAssociation *	removeGeneAssociation (const std::string &sid)
	Removes the GeneAssociation annotation object with the given `sid` attribute from this plugin object and returns a pointer to it. More...

GeneProduct *	removeGeneProduct (unsigned int n)
	Removes the nth GeneProduct from the ListOfGeneProducts within this FbcModelPlugin. More...

GeneProduct *	removeGeneProduct (const std::string &sid)
	Removes the GeneProduct with the given identifier from the ListOfGeneProducts within this FbcModelPlugin and returns a pointer to it. More...

Objective *	removeObjective (unsigned int n)
	Removes the nth Objective from the ListOfObjectives within this FbcModelPlugin. More...

Objective *	removeObjective (const std::string &sid)
	Removes the Objective with the given identifier from the ListOfObjectives within this FbcModelPlugin and returns a pointer to it. More...

virtual void	renameMetaIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

virtual void	renameSIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

virtual void	renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

int	setActiveObjectiveId (const std::string &objectiveId)
	Sets the id of the active objective. More...

int	setElementNamespace (const std::string &uri)
	Sets the XML namespace to which this object belongs. More...

virtual int	setStrict (bool strict)
	Sets the value of the "strict" attribute of this FbcModelPlugin. More...

int	unsetActiveObjectiveId ()
	Unsets the "activeObjective" attribute of the ListOfObjectives. More...

virtual int	unsetStrict ()
	Unsets the value of the "strict" attribute of this FbcModelPlugin. More...

virtual	~FbcModelPlugin ()
	Destructor for FbcModelPlugin. More...

Constructor & Destructor Documentation

FbcModelPlugin::FbcModelPlugin	(	const std::string &	uri,
		const std::string &	prefix,
		FbcPkgNamespaces *	fbcns
	)

Creates a new FbcModelPlugin object using the given parameters.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

: The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

uri	the URI of the SBML Level 3 package implemented by this libSBML package extension.
prefix	the XML namespace prefix being used for the package.
fbcns	the namespaces object for the package.

FbcModelPlugin::FbcModelPlugin ( const FbcModelPlugin & orig )

Copy constructor for FbcModelPlugin.

Parameters

orig	the FbcModelPlugin instance to copy.

FbcModelPlugin::~FbcModelPlugin ( )

virtual

Destructor for FbcModelPlugin.

Member Function Documentation

int FbcModelPlugin::addFluxBound ( const FluxBound * bound )

Adds a copy of the given FluxBound object to the list of FluxBounds.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Parameters

bound the FluxBound object to be added to the list of FluxBounds.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int FbcModelPlugin::addGeneAssociation ( const GeneAssociation * association )

Adds a copy of the given GeneAssociation annotation object to the list of GeneAssociations.

Parameters

association the GeneAssociation annotation object to be added to the list of GeneAssociations.

Note: GeneAssociation objects are not defined in any version of the "Flux Balance Constraints" specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int FbcModelPlugin::addGeneProduct ( const GeneProduct * gp )

Adds a copy the given GeneProduct to this FbcModelPlugin.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Parameters

gp	the GeneProduct object to add.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int FbcModelPlugin::addObjective ( const Objective * o )

Adds a copy the given Objective to this FbcModelPlugin.

Parameters

o	the Objective object to add.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

FbcModelPlugin * FbcModelPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this FbcModelPlugin object.

Returns: a (deep) copy of this FbcModelPlugin object.

Reimplemented from SBasePlugin.

FluxBound * FbcModelPlugin::createFluxBound ( )

Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Returns: a newly created FluxBound object.

Examples:: fbc_example1.cpp.

GeneAssociation * FbcModelPlugin::createGeneAssociation ( )

Creates a new GeneAssociation annotation object and adds it to the list of GeneAssociation objects and returns it.

Returns: a newly created GeneAssociation annotation object.

GeneProduct * FbcModelPlugin::createGeneProduct ( )

Creates a new GeneProduct object, adds it to this FbcModelPlugin's ListOfGeneProducts and returns the GeneProduct object created.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Returns: a new GeneProduct object instance.

See also: addGeneProduct(const GeneProduct* gp)

Objective * FbcModelPlugin::createObjective ( )

Creates a new Objective object, adds it to this FbcModelPlugin's ListOfObjectives and returns the Objective object created.

Returns: a new Objective object instance.

See also: addObjective(const Objective* o)

Examples:: fbc_example1.cpp.

Objective * FbcModelPlugin::getActiveObjective ( )

Returns the current active objective.

Returns: the Objective pointed to by the 'activeObjective' attribute, or NULL if no such Objective can be found.

const Objective * FbcModelPlugin::getActiveObjective ( ) const

Returns the current active objective.

Returns: the Objective pointed to by the 'activeObjective' attribute, or NULL if no such Objective can be found.

std::string FbcModelPlugin::getActiveObjectiveId ( ) const

Returns the id of the current active objective.

Returns: the value of the "activeObjective" attribute of the ListOfObjectives.

List * FbcModelPlugin::getAllElements ( ElementFilter * filter = NULL )

virtual

Returns a List of all child SBase objects, including those nested to an arbitrary depth.

Parameters

filter an ElementFilter that may impose restrictions on the objects to be retrieved.

Returns: a List of pointers to all child objects.

Reimplemented from SBasePlugin.

SBase * SBasePlugin::getElementByMetaId ( const std::string & metaid )

virtualinherited

Return the first child object found with a given meta identifier.

This method searches all the subobjects under this one, compares their meta identifiers to metaid, and returns the first one that machines.

Parameters

metaid string, the metaid of the object to find.

Returns: pointer to the first object found with the given metaid.

Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

SBase * SBasePlugin::getElementBySId ( const std::string & id )

virtualinherited

Return the first child object found with a given identifier.

This method searches all the subobjects under this one, compares their identifiers to id, and returns the first one that machines. It uses SBasePlugin::getAllElements(ElementFilter* filter) to get the list of identifiers, so the order in which identifiers are searched is the order in which they appear in the results returned by that method.

Normally, SId type identifier values are unique across a model in SBML. However, in some circumstances they may not be, such as if a model is invalid because of multiple objects having the same identifier.

Parameters

id	string representing the identifier of the object to find.

Returns: pointer to the first object with the given id.

Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

const std::string & SBasePlugin::getElementNamespace ( ) const

inherited

Returns the namespace URI of the package to which this plugin object belongs.

Returns: the XML namespace URI of the SBML Level 3 package implemented by this libSBML package extension.

const FluxBound * FbcModelPlugin::getFluxBound ( unsigned int n ) const

Returns the FluxBound object that belongs to the given index.

If the index is invalid, NULL is returned.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Parameters

n	the index number of the FluxBound to get.

Returns: the nth FluxBound in the ListOfFluxBounds. If the index n is invalid, NULL is returned.

FluxBound * FbcModelPlugin::getFluxBound ( unsigned int n )

Returns the FluxBound object that belongs to the given index.

If the index is invalid, NULL is returned.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Parameters

n	the index number of the FluxBound to get.

Returns: the nth FluxBound in the ListOfFluxBounds. If the index n is invalid, NULL is returned.

FluxBound * FbcModelPlugin::getFluxBound ( const std::string & sid )

Returns the FluxBound object based on its identifier.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Parameters

sid	a string representing the identifier of the FluxBound to get.

Returns: FluxBound in the ListOfFluxBounds with the given sid or NULL if no such FluxBound exists.

See also: getFluxBound(unsigned int n); getListOfFluxBounds()

const FluxBound * FbcModelPlugin::getFluxBound ( const std::string & sid ) const

Returns the FluxBound object based on its identifier.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Parameters

sid	a string representing the identifier of the FluxBound to get.

Returns: FluxBound in the ListOfFluxBounds with the given sid or NULL if no such FluxBound exists.

See also: getFluxBound(unsigned int n); getListOfFluxBounds()

ListOfFluxBounds * FbcModelPlugin::getFluxBoundsForReaction ( const std::string & reaction ) const

Creates a new ListOfFluxBounds object that contains only the FluxBound objects associated with the given Reaction.

If no such Reaction can be found, or if there are no FluxBound objects associated with it, returns NULL. The caller owns the created object and is responsible for its deletion.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Parameters

reaction the id of an reaction to find FluxBound objects for.

Returns: a ListOfFluxBounds for the given reaction id.

const GeneAssociation * FbcModelPlugin::getGeneAssociation ( unsigned int n ) const

Returns the GeneAssociation annotation object that belongs to the given index.

If the index is invalid, NULL is returned.

Note: GeneAssociation objects are not defined in any version of the "Flux Balance Constraints" specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Parameters

n	the index number of the GeneAssociation annotation to get.

Returns: the nth GeneAssociation annotation in the ListOfGeneAssociations. If the index n is invalid, NULL is returned.

GeneAssociation * FbcModelPlugin::getGeneAssociation ( unsigned int n )

Returns the GeneAssociation annotation object that belongs to the given index.

If the index is invalid, NULL is returned.

Note: GeneAssociation objects are not defined in any version of the "Flux Balance Constraints" specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Parameters

n	the index number of the GeneAssociation annotation to get.

Returns: the nth GeneAssociation annotation in the ListOfGeneAssociations. If the index n is invalid, NULL is returned.

GeneAssociation * FbcModelPlugin::getGeneAssociation ( const std::string & sid )

Returns the GeneAssociation annotation object based on its identifier.

Note: GeneAssociation objects are not defined in any version of the "Flux Balance Constraints" specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Parameters

sid	a string representing the identifier of the GeneAssociation annotation to get.

Returns: GeneAssociation annotation in the ListOfGeneAssociations with the given sid or NULL if no such GeneAssociation annotation exists.

See also: getGeneAssociation(unsigned int n); getListOfGeneAssociations()

const GeneAssociation * FbcModelPlugin::getGeneAssociation ( const std::string & sid ) const

Returns the GeneAssociation annotation object based on its identifier.

Note: GeneAssociation objects are not defined in any version of the "Flux Balance Constraints" specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Parameters

sid	a string representing the identifier of the GeneAssociation annotation to get.

Returns: GeneAssociation annotation in the ListOfGeneAssociations with the given sid or NULL if no such GeneAssociation annotation exists.

See also: getGeneAssociation(unsigned int n); getListOfGeneAssociations()

GeneProduct * FbcModelPlugin::getGeneProduct ( unsigned int n )

Get a GeneProduct from the ListOfGeneProducts.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Parameters

n	the index number of the GeneProduct to get.

Returns: the nth GeneProduct in the ListOfGeneProducts within this FbcModelPlugin. If the index n is invalid, NULL is returned.

See also: getNumGeneProducts()

const GeneProduct * FbcModelPlugin::getGeneProduct ( unsigned int n ) const

Get a GeneProduct from the ListOfGeneProducts.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Parameters

n	the index number of the GeneProduct to get.

Returns: the nth GeneProduct in the ListOfGeneProducts within this FbcModelPlugin. If the index n is invalid, NULL is returned.

See also: getNumGeneProducts()

GeneProduct * FbcModelPlugin::getGeneProduct ( const std::string & sid )

Get a GeneProduct from the ListOfGeneProducts based on its identifier.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Parameters

sid	a string representing the identifier of the GeneProduct to get.

Returns: the GeneProduct in the ListOfGeneProducts with the given id or NULL if no such GeneProduct exists.

See also: getGeneProduct(unsigned int n); getNumGeneProducts()

const GeneProduct * FbcModelPlugin::getGeneProduct ( const std::string & sid ) const

Get a GeneProduct from the ListOfGeneProducts based on its identifier.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Parameters

sid	a string representing the identifier of the GeneProduct to get.

Returns: the GeneProduct in the ListOfGeneProducts with the given id or NULL if no such GeneProduct exists.

See also: getGeneProduct(unsigned int n); getNumGeneProducts()

GeneProduct * FbcModelPlugin::getGeneProductByLabel ( const std::string & label )

Get a GeneProduct from the ListOfGeneProducts based on its label.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Parameters

label a string representing the label of the GeneProduct to get.

Returns: the GeneProduct in the ListOfGeneProducts with the given label or NULL if no such GeneProduct exists.

See also: getGeneProduct(unsigned int n); getNumGeneProducts()

unsigned int SBasePlugin::getLevel ( ) const

inherited

Returns the SBML Level of the package extension of this plugin object.

Returns: the SBML Level.

See also: getVersion()

const ListOfFluxBounds * FbcModelPlugin::getListOfFluxBounds ( ) const

Returns the ListOfFluxBounds in this plugin object.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Returns: ListOfFluxBounds object in this plugin object.

ListOfFluxBounds * FbcModelPlugin::getListOfFluxBounds ( )

Returns the ListOfFluxBounds in this plugin object.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Returns: ListOfFluxBounds object in this plugin object.

const ListOfGeneAssociations * FbcModelPlugin::getListOfGeneAssociations ( ) const

Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object.

Note: GeneAssociation objects are not defined in any version of the "Flux Balance Constraints" specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Returns: ListOfGeneAssociations annotation object for level 1 in this plugin object.

ListOfGeneAssociations * FbcModelPlugin::getListOfGeneAssociations ( )

Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object.

Note: GeneAssociation objects are not defined in any version of the "Flux Balance Constraints" specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Returns: ListOfGeneAssociations annotation object for level 1 in this plugin object.

const ListOfGeneProducts * FbcModelPlugin::getListOfGeneProducts ( ) const

Returns the ListOfGeneProducts in this FbcModelPlugin object.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Returns: the ListOfGeneProducts child of this FbcModelPlugin.

ListOfGeneProducts * FbcModelPlugin::getListOfGeneProducts ( )

Returns the ListOfGeneProducts in this FbcModelPlugin object.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Returns: the ListOfGeneProducts child of this FbcModelPlugin.

const ListOfObjectives * FbcModelPlugin::getListOfObjectives ( ) const

Returns the ListOfObjectives in this FbcModelPlugin object.

Returns: the ListOfObjectives child of this FbcModelPlugin.

ListOfObjectives * FbcModelPlugin::getListOfObjectives ( )

Returns the ListOfObjectives in this FbcModelPlugin object.

Returns: the ListOfObjectives child of this FbcModelPlugin.

unsigned int FbcModelPlugin::getNumFluxBounds ( ) const

Returns the number of FluxBound object in this plugin object.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Returns: the number of FluxBound object in this plugin object.

int FbcModelPlugin::getNumGeneAssociations ( ) const

Returns the number of GeneAssociation annotation object in this plugin object.

Note: GeneAssociation objects are not defined in any version of the "Flux Balance Constraints" specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Returns: the number of GeneAssociation annotation object in this plugin object.

unsigned int FbcModelPlugin::getNumGeneProducts ( ) const

Get the number of GeneProduct objects in this FbcModelPlugin.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Returns: the number of GeneProduct objects in this FbcModelPlugin.

unsigned int FbcModelPlugin::getNumObjectives ( ) const

Get the number of Objective objects in this FbcModelPlugin.

Returns: the number of Objective objects in this FbcModelPlugin.

Objective * FbcModelPlugin::getObjective ( unsigned int n )

Get an Objective from the ListOfObjectives.

Parameters

n	the index number of the Objective to get.

Returns: the nth Objective in the ListOfObjectives within this FbcModelPlugin. If the index n is invalid, NULL is returned.

See also: getNumObjectives()

const Objective * FbcModelPlugin::getObjective ( unsigned int n ) const

Get an Objective from the ListOfObjectives.

Parameters

n	the index number of the Objective to get.

Returns: the nth Objective in the ListOfObjectives within this FbcModelPlugin. If the index n is invalid, NULL is returned.

See also: getNumObjectives()

Objective * FbcModelPlugin::getObjective ( const std::string & sid )

Get an Objective from the ListOfObjectives based on its identifier.

Parameters

sid	a string representing the identifier of the Objective to get.

Returns: the Objective in the ListOfObjectives with the given id or NULL if no such Objective exists.

See also: getObjective(unsigned int n); getNumObjectives()

const Objective * FbcModelPlugin::getObjective ( const std::string & sid ) const

Get an Objective from the ListOfObjectives based on its identifier.

Parameters

sid	a string representing the identifier of the Objective to get.

Returns: the Objective in the ListOfObjectives with the given id or NULL if no such Objective exists.

See also: getObjective(unsigned int n); getNumObjectives()

const std::string & SBasePlugin::getPackageName ( ) const

inherited

Returns the short-form name of the package to which this plugin object belongs.

Returns: the short-form package name (or nickname) of the SBML package implemented by this package extension.

unsigned int SBasePlugin::getPackageVersion ( ) const

inherited

Returns the package version of the package extension of this plugin object.

Returns: the package version of the package extension of this plugin object.

See also: getLevel(); getVersion()

SBase * SBasePlugin::getParentSBMLObject ( )

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

const SBase * SBasePlugin::getParentSBMLObject ( ) const

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

const std::string & SBasePlugin::getPrefix ( ) const

inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

Returns: the XML namespace prefix of the SBML Level 3 package implemented by this libSBML package extension.

SBMLDocument * SBasePlugin::getSBMLDocument ( )

inherited

Returns the SBMLDocument object containing this object instance.

: LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

const SBMLDocument * SBasePlugin::getSBMLDocument ( ) const

inherited

Returns the SBMLDocument object containing this object instance.

: LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

bool FbcModelPlugin::getStrict ( ) const

virtual

Returns the value of the "strict" attribute of this FbcModelPlugin.

Note: The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the "Flux Balance Constraints" specification, and has no equivalent in version 1 of the specification.

Returns: the value of the "strict" attribute of this FbcModelPlugin as a boolean.

std::string SBasePlugin::getURI ( ) const

inherited

Returns the XML namespace URI for the package to which this object belongs.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

This method first looks into the SBMLNamespaces object possessed by the parent SBMLDocument object of the current object. If this cannot be found, this method returns the result of getElementNamespace().

Returns: a string, the URI of the XML namespace to which this object belongs.

See also: getPackageName(); getElementNamespace(); getSBMLDocument()

unsigned int SBasePlugin::getVersion ( ) const

inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns: the SBML Version.

See also: getLevel()

bool FbcModelPlugin::isSetStrict ( ) const

virtual

Predicate returning true if this FbcModelPlugin's "strict" attribute is set.

Note: The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the "Flux Balance Constraints" specification, and has no equivalent in version 1 of the specification.

Returns: true if this FbcModelPlugin's "strict" attribute has been set, otherwise false is returned.

virtual bool SBasePlugin::isValidTypeForList ( SBase * item ) const

virtualinherited

FbcModelPlugin & FbcModelPlugin::operator= ( const FbcModelPlugin & rhs )

Assignment operator for FbcModelPlugin.

Parameters

rhs	the object whose values are used as the basis of the assignment.

FluxBound * FbcModelPlugin::removeFluxBound ( unsigned int n )

Removes the nth FluxBound object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Parameters

n	the index of the FluxBound object to remove.

Returns: the FluxBound object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

FluxBound * FbcModelPlugin::removeFluxBound ( const std::string & sid )

Removes the FluxBound object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Note: FluxBound objects are only defined for version 1 of the "Flux Balance Constraints" specification, and are replaced in version 2 by the "upperFluxBound" and "lowerFluxBound" attributes of the FbcReactionPlugin.

Parameters

sid	the id attribute of the FluxBound object to remove.

Returns: the FluxBound object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

GeneAssociation * FbcModelPlugin::removeGeneAssociation ( unsigned int n )

Removes the nth GeneAssociation annotation object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Note: GeneAssociation objects are not defined in any version of the "Flux Balance Constraints" specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Parameters

n	the index of the GeneAssociation annotation object to remove.

Returns: the GeneAssociation annotation object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

GeneAssociation * FbcModelPlugin::removeGeneAssociation ( const std::string & sid )

Removes the GeneAssociation annotation object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Note: GeneAssociation objects are not defined in any version of the "Flux Balance Constraints" specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Parameters

sid	the id attribute of the GeneAssociation annotation object to remove.

Returns: the GeneAssociation annotation object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

GeneProduct * FbcModelPlugin::removeGeneProduct ( unsigned int n )

Removes the nth GeneProduct from the ListOfGeneProducts within this FbcModelPlugin.

and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Parameters

n	the index of the GeneProduct to remove.

See also: getNumGeneProducts()

GeneProduct * FbcModelPlugin::removeGeneProduct ( const std::string & sid )

Removes the GeneProduct with the given identifier from the ListOfGeneProducts within this FbcModelPlugin and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then NULL is returned.

Note: GeneProduct objects are only defined for version 2 of the "Flux Balance Constraints" specification, and have no equivalent in version 1 of the specification.

Parameters

sid	the identifier of the GeneProduct to remove.

Returns: the GeneProduct removed. As mentioned above, the caller owns the returned item.

Objective * FbcModelPlugin::removeObjective ( unsigned int n )

Removes the nth Objective from the ListOfObjectives within this FbcModelPlugin.

and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it.

Parameters

n	the index of the Objective to remove.

See also: getNumObjectives()

Objective * FbcModelPlugin::removeObjective ( const std::string & sid )

Removes the Objective with the given identifier from the ListOfObjectives within this FbcModelPlugin and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then NULL is returned.

Parameters

sid	the identifier of the Objective to remove.

Returns: the Objective removed. As mentioned above, the caller owns the returned item.

virtual void SBasePlugin::renameMetaIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

Replaces all uses of a given meta identifier attribute value with another value.

: In SBML, object "meta" identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as "metaid refs", in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

virtual void SBasePlugin::renameSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

Replaces all uses of a given SIdRef type attribute value with another value.

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to an identifier", but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

Reimplemented in FbcReactionPlugin.

virtual void SBasePlugin::renameUnitSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

Replaces all uses of a given UnitSIdRef type attribute value with another value.

: In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to a unit identifier", but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

int FbcModelPlugin::setActiveObjectiveId ( const std::string & objectiveId )

Sets the id of the active objective.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Examples:: fbc_example1.cpp.

int SBasePlugin::setElementNamespace ( const std::string & uri )

inherited

Sets the XML namespace to which this object belongs.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

Parameters

uri	the URI to assign to this object.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getElementNamespace()

Examples:: convertLayout.cpp.

int FbcModelPlugin::setStrict ( bool strict )

virtual

Sets the value of the "strict" attribute of this FbcModelPlugin.

Note: The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the "Flux Balance Constraints" specification, and has no equivalent in version 1 of the specification.

Parameters

strict bool value of the "strict" attribute to be set.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int FbcModelPlugin::unsetActiveObjectiveId ( )

Unsets the "activeObjective" attribute of the ListOfObjectives.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

success status

int FbcModelPlugin::unsetStrict ( )

virtual

Unsets the value of the "strict" attribute of this FbcModelPlugin.

Note: The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the "Flux Balance Constraints" specification, and has no equivalent in version 1 of the specification.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

Detailed Description

The "strict" attribute on the (extended) Model class

Lists of subobjects on the (extended) Model class

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation