Inheritance diagram for FbcModelPlugin:

Detailed Description

fbc Extension of Model.

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 object to the list of GeneAssociations. More...

int	addObjective (const Objective *bound)
	Adds a copy of the given Objective object to the list of Objectives. 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 object and adds it to the list of GeneAssociation objects and returns it. More...

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

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

	FbcModelPlugin (const FbcModelPlugin &orig)
	Copy constructor. 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)
	Returns the first child element it can find with the given `metaid`, or itself if it has the given `metaid`, or `NULL` if no such object is found. More...

virtual SBase *	getElementBySId (const std::string &id)
	Returns the first child element found that has the given `id` in the model-wide SId namespace, or `NULL` if no such object is found. 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

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

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

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

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

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

const ListOfFluxBounds *	getListOfFluxBounds () const
	------------------------------------------------------------------ More...

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

const ListOfGeneAssociations *	getListOfGeneAssociations () const
	Returns the ListOfObjectives in this plugin object. More...

ListOfGeneAssociations *	getListOfGeneAssociations ()
	Returns the ListOfGeneAssociations in this plugin object. More...

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

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

unsigned int	getNumObjectives () const
	Returns the number of Objective object in this plugin object. More...

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

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

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

const Objective *	getObjective (const std::string &sid) const
	Returns the Objective object 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...

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...

FbcModelPlugin &	operator= (const FbcModelPlugin &orig)
	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 object from this plugin object and returns a pointer to it. More...

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

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

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

void	unsetActiveObjectiveId ()
	Unsets the active objective. More...

virtual	~FbcModelPlugin ()
	Destroy this object. More...

Constructor & Destructor Documentation

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

Constructor.

FbcModelPlugin::FbcModelPlugin ( const FbcModelPlugin & orig )

Copy constructor.

Creates a copy of this FbcModelPlugin object.

FbcModelPlugin::~FbcModelPlugin ( )

virtual

Destroy this object.

Member Function Documentation

int FbcModelPlugin::addFluxBound ( const FluxBound * bound )

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

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:

LIBSBML_OPERATION_SUCCESS

int FbcModelPlugin::addGeneAssociation ( const GeneAssociation * association )

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

Parameters

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

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::addObjective ( const Objective * bound )

Adds a copy of the given Objective object to the list of Objectives.

Parameters

bound the Objective object to be added to the list of Objectives.

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

FbcModelPlugin * FbcModelPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this FbcModelPlugin object.

Returns: a (deep) copy of this FbcModelPlugin object

Implements SBasePlugin.

FluxBound * FbcModelPlugin::createFluxBound ( )

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

Returns: a newly created FluxBound object

Examples:: fbc_example1.cpp.

GeneAssociation * FbcModelPlugin::createGeneAssociation ( )

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

Returns: a newly created GeneAssociation object

Objective * FbcModelPlugin::createObjective ( )

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

Returns: a newly created Objective object

Examples:: fbc_example1.cpp.

Objective * FbcModelPlugin::getActiveObjective ( )

Returns the current active objective.

const Objective * FbcModelPlugin::getActiveObjective ( ) const

Returns the current active objective.

std::string FbcModelPlugin::getActiveObjectiveId ( ) const

returns the id of the current active objective.

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

virtual

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

Returns: a List* of pointers to all children objects.

Reimplemented from SBasePlugin.

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

virtual

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or NULL if no such object is found.

Parameters

metaid string representing the metaid of objects to find

Returns: a pointer to the SBase element with the given metaid.

Reimplemented from SBasePlugin.

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

virtual

Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.

Parameters

id	string representing the id of objects to find

Returns: a pointer to the SBase element with the given id.

Reimplemented from SBasePlugin.

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.

Parameters

n	the index number of the FluxBound to get.

Returns: the nth FluxBound in the ListOfFluxBounds.

FluxBound * FbcModelPlugin::getFluxBound ( unsigned int n )

Returns the FluxBound object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters

n	the index number of the FluxBound to get.

Returns: the nth FluxBound in the ListOfFluxBounds.

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

Returns the FluxBound object based on its identifier.

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.

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

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

Returns the GeneAssociation object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters

n	the index number of the GeneAssociation to get.

Returns: the nth GeneAssociation in the ListOfGeneAssociations.

GeneAssociation * FbcModelPlugin::getGeneAssociation ( unsigned int n )

Returns the GeneAssociation object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters

n	the index number of the GeneAssociation to get.

Returns: the nth GeneAssociation in the ListOfGeneAssociations.

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

Returns the GeneAssociation object based on its identifier.

Parameters

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

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

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

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

Returns the GeneAssociation object based on its identifier.

Parameters

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

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

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

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

------------------------------------------------------------------

Additional public functions

------------------------------------------------------------------ Returns the ListOfFluxBounds in this plugin object.

Returns: ListOfFluxBounds object in this plugin object.

ListOfFluxBounds * FbcModelPlugin::getListOfFluxBounds ( )

Returns the ListOfFluxBounds in this plugin object.

Returns: ListOfFluxBounds object in this plugin object.

const ListOfGeneAssociations * FbcModelPlugin::getListOfGeneAssociations ( ) const

Returns the ListOfObjectives in this plugin object.

Returns: ListOfObjectives object in this plugin object.

ListOfGeneAssociations * FbcModelPlugin::getListOfGeneAssociations ( )

Returns the ListOfGeneAssociations in this plugin object.

Returns: ListOfGeneAssociations object in this plugin object.

const ListOfObjectives * FbcModelPlugin::getListOfObjectives ( ) const

Returns the ListOfObjectives in this plugin object.

Returns: ListOfObjectives object in this plugin object.

ListOfObjectives * FbcModelPlugin::getListOfObjectives ( )

Returns the ListOfObjectives in this plugin object.

Returns: ListOfObjectives object in this plugin object.

unsigned int FbcModelPlugin::getNumFluxBounds ( ) const

Returns the number of FluxBound object in this plugin object.

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

int FbcModelPlugin::getNumGeneAssociations ( ) const

Returns the number of GeneAssociation object in this plugin object.

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

unsigned int FbcModelPlugin::getNumObjectives ( ) const

Returns the number of Objective object in this plugin object.

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

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

Returns the Objective object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters

n	the index number of the Objective to get.

Returns: the nth Objective in the ListOfObjectives.

Objective * FbcModelPlugin::getObjective ( unsigned int n )

Returns the Objective object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters

n	the index number of the Objective to get.

Returns: the nth Objective in the ListOfObjectives.

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

Returns the Objective object based on its identifier.

Parameters

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

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

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

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

Returns the Objective object based on its identifier.

Parameters

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

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

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

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()

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(); SBMLDocument::getSBMLNamespaces(); 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()

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

Assignment operator for FbcModelPlugin .

FluxBound * FbcModelPlugin::removeFluxBound ( unsigned int n )

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