Inheritance diagram for FbcSpeciesPlugin:

Detailed Description

fbc Extension of Species.

The FbcSpeciesPlugin class codifies an extension of the core SBML Species class defined in the SBML Level 3 Flux Balance Constraints (“fbc”) package. The “fbc” package adds two attributes named "charge" and "chemicalFormula" to Species.

The optional attribute "charge" can contain a signed integer that refers to the Species object's electrical charge (in terms of electrons, not the SI unit of coulombs). Note that this attribute is therefore defined as it is in the SBML Level 2 Version 1 specification. (The charge attribute was removed in higher Versions and Levels of SBML, and is not an attribute of SBML Species in core SBML Level 3. However, it is useful for flux balance constraints models, and thus, the Level 3 “fbc” package adds it.)

The optional attribute "chemicalFormula" can contain a text string that represents the elemental composition of the substance represented by the Species object. The purpose of the "chemicalFormula" attribute is to allow balancing and validating reactions. This is particularly important in constraint-based models. The format of "chemicalFormula" must consist only of atomic names (as given in the Periodic Table of elements) or user-defined compounds, either of which take the form of a single capital letter followed by zero or more lowercase letters. Where there is more than a single atom present, this is indicated with an integer. With regards to order (and to enhance interoperability of models), users are advised to employ the Hill system order. Using this notation, the number of carbon atoms in a molecule is indicated first, followed by the number of hydrogen atoms, and then the number of all other chemical elements in alphabetical order. When the formula contains no carbon, all elements including hydrogen are listed alphabetically.

Here is an example of the XML form of an extended Species definition with these attributes:

<species metaid="meta_M_atp_c" id="M_atp_c" name="ATP" compartment="Cytosol"
boundaryCondition="false" initialConcentration="0" hasOnlySubstanceUnits="false"
fbc:charge="-4" fbc:chemicalFormula="C10H12N5O13P3"/>

Public Member Functions
virtual FbcSpeciesPlugin *	clone () const
	Creates and returns a deep copy of this FbcSpeciesPlugin object. More...

	FbcSpeciesPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns)
	Creates a new FbcSpeciesPlugin. More...

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

virtual List *	getAllElements (ElementFilter *filter=NULL)
	Returns all child objects of this object. More...

virtual int	getCharge () const
	doxygenLibsbmlInternal More...

virtual const std::string &	getChemicalFormula () const
	Returns the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. 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...

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

virtual bool	isSetCharge () const
	Predicate returning `true` or `false` depending on whether this FbcSpeciesPlugin's "charge" attribute has been set. More...

virtual bool	isSetChemicalFormula () const
	Predicate returning `true` or `false` depending on whether this FbcSpeciesPlugin's "chemicalFormula" attribute has been set. More...

virtual bool	isValidTypeForList (SBase *item) const

FbcSpeciesPlugin &	operator= (const FbcSpeciesPlugin &rhs)
	Assignment operator for FbcSpeciesPlugin. 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...

virtual int	setCharge (int charge)
	Sets the value of the "charge" attribute of this FbcSpeciesPlugin. More...

virtual int	setChemicalFormula (const std::string &chemicalFormula)
	Sets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. More...

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

virtual int	unsetCharge ()
	Unsets the value of the "charge" attribute of this FbcSpeciesPlugin. More...

virtual int	unsetChemicalFormula ()
	Unsets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. More...

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

Constructor & Destructor Documentation

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

Creates a new FbcSpeciesPlugin.

FbcSpeciesPlugin::FbcSpeciesPlugin ( const FbcSpeciesPlugin & orig )

Copy constructor for FbcSpeciesPlugin.

Parameters

orig; the FbcSpeciesPlugin instance to copy.

FbcSpeciesPlugin::~FbcSpeciesPlugin ( )

virtual

Destructor for FbcSpeciesPlugin.

Member Function Documentation

FbcSpeciesPlugin * FbcSpeciesPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this FbcSpeciesPlugin object.

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

Reimplemented from SBasePlugin.

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

virtualinherited

Returns all child objects of this object.

This returns a List object containing all child SBase objects of this one, at any nesting depth. Optionally, callers can supply a filter that will establish the search criteria for matching objects.

Parameters

filter a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.

Returns: a List of pointers to all children objects.

Reimplemented in GroupsModelPlugin, FbcModelPlugin, MultiCompartmentPlugin, LayoutModelPlugin, RenderListOfLayoutsPlugin, MultiSpeciesPlugin, FbcReactionPlugin, MultiSimpleSpeciesReferencePlugin, CompModelPlugin, CompSBasePlugin, CompSBMLDocumentPlugin, RenderLayoutPlugin, MultiSpeciesReferencePlugin, MultiModelPlugin, and QualModelPlugin.

int FbcSpeciesPlugin::getCharge ( ) const

virtual

doxygenLibsbmlInternal

doxygenLibsbmlInternal doxygenLibsbmlInternal doxygenLibsbmlInternal doxygenLibsbmlInternal Returns the value of the "charge" attribute of this FbcSpeciesPlugin.

Returns: the value of the "charge" attribute of this FbcSpeciesPlugin as a integer.

const std::string & FbcSpeciesPlugin::getChemicalFormula ( ) const

virtual

Returns the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.

Returns: the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin as a string.

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.

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 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(); 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 FbcSpeciesPlugin::isSetCharge ( ) const

virtual

Predicate returning true or false depending on whether this FbcSpeciesPlugin's "charge" attribute has been set.

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

bool FbcSpeciesPlugin::isSetChemicalFormula ( ) const

virtual

Predicate returning true or false depending on whether this FbcSpeciesPlugin's "chemicalFormula" attribute has been set.

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

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

virtualinherited

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

Assignment operator for FbcSpeciesPlugin.

Parameters

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

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 FbcSpeciesPlugin::setCharge ( int charge )

virtual

Sets the value of the "charge" attribute of this FbcSpeciesPlugin.

Parameters

charge; int value of the "charge" 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:

int FbcSpeciesPlugin::setChemicalFormula ( const std::string & chemicalFormula )

virtual

Sets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.

Parameters

chemicalFormula; const std::string& value of the "chemicalFormula" 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:

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 FbcSpeciesPlugin::unsetCharge ( )

virtual

Unsets the value of the "charge" attribute of this FbcSpeciesPlugin.

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 FbcSpeciesPlugin::unsetChemicalFormula ( )

virtual

Unsets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.

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:

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation