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
int	addKeyValuePair (const KeyValuePair *kvp)
	Adds a copy of the given KeyValuePair to this FbcSBasePlugin. More...

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

KeyValuePair *	createKeyValuePair ()
	Creates a new KeyValuePair object, adds it to this FbcSBasePlugin object and returns the KeyValuePair object created. More...

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

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

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

virtual int	getCharge () const
	doxygenLibsbmlInternal More...

virtual double	getChargeAsDouble () const
	Returns the value of the "charge" attribute of this FbcSpeciesPlugin. 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)
	Returns the first child element that 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 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...

KeyValuePair *	getKeyValuePair (const std::string &sid)
	Get a KeyValuePair from the FbcSBasePlugin based on its identifier. More...

const KeyValuePair *	getKeyValuePair (const std::string &sid) const
	Get a KeyValuePair from the FbcSBasePlugin based on its identifier. More...

KeyValuePair *	getKeyValuePair (unsigned int n)
	Get a KeyValuePair from the FbcSBasePlugin. More...

const KeyValuePair *	getKeyValuePair (unsigned int n) const
	Get a KeyValuePair from the FbcSBasePlugin. More...

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

ListOfKeyValuePairs *	getListOfKeyValuePairs ()
	Returns the ListOfKeyValuePairs from this FbcSBasePlugin. More...

const ListOfKeyValuePairs *	getListOfKeyValuePairs () const
	Returns the ListOfKeyValuePairs from this FbcSBasePlugin. More...

unsigned int	getNumKeyValuePairs () const
	Get the number of KeyValuePair objects in this FbcSBasePlugin. 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...

KeyValuePair *	removeKeyValuePair (const std::string &sid)
	Removes the KeyValuePair from this FbcSBasePlugin based on its identifier and returns a pointer to it. More...

KeyValuePair *	removeKeyValuePair (unsigned int n)
	Removes the nth KeyValuePair from this FbcSBasePlugin and returns a pointer to it. More...

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

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

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

virtual int	setCharge (double charge)
	Sets the value of the "charge" attribute of this FbcSpeciesPlugin. 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() [1/2]

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

Creates a new FbcSpeciesPlugin.

◆ FbcSpeciesPlugin() [2/2]

FbcSpeciesPlugin::FbcSpeciesPlugin ( const FbcSpeciesPlugin & orig )

Copy constructor for FbcSpeciesPlugin.

Parameters

orig; the FbcSpeciesPlugin instance to copy.

◆ ~FbcSpeciesPlugin()

FbcSpeciesPlugin::~FbcSpeciesPlugin ( )

virtual

Destructor for FbcSpeciesPlugin.

Member Function Documentation

◆ addKeyValuePair()

int FbcSBasePlugin::addKeyValuePair ( const KeyValuePair * kvp )

inherited

Adds a copy of the given KeyValuePair to this FbcSBasePlugin.

Parameters

kvp	the KeyValuePair 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:

Note: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ clone()

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 FbcSBasePlugin.

◆ createKeyValuePair()

KeyValuePair * FbcSBasePlugin::createKeyValuePair ( )

inherited

Creates a new KeyValuePair object, adds it to this FbcSBasePlugin object and returns the KeyValuePair object created.

Returns: a new KeyValuePair object instance.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getAllElements()

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

virtualinherited

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 pointer of pointers to all SBase child objects with any restriction imposed.

Reimplemented from SBasePlugin.

Reimplemented in FbcReactionPlugin, and FbcModelPlugin.

◆ getCharge()

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.

◆ getChargeAsDouble()

double FbcSpeciesPlugin::getChargeAsDouble ( ) const

virtual

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

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

◆ getChemicalFormula()

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.

◆ getElementByMetaId()

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

virtualinherited

Returns the first child element that has the given metaid, or NULL if no such object is found.

Parameters

metaid a string representing the metaid attribute of the object to retrieve.

Returns: a pointer to the SBase element with the given metaid. If no such object is found this method returns NULL.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin.

◆ getElementBySId()

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

virtualinherited

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

Parameters

id	a string representing the id attribute of the object to retrieve.

Returns: a pointer to the SBase element with the given id. If no such object is found, this method returns NULL.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin.

◆ getElementNamespace()

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.

◆ getKeyValuePair() [1/4]

KeyValuePair * FbcSBasePlugin::getKeyValuePair ( const std::string & sid )

inherited

Get a KeyValuePair from the FbcSBasePlugin based on its identifier.

Parameters

sid	a string representing the identifier of the KeyValuePair to retrieve.

Returns: the KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin with the given sid or NULL if no such KeyValuePair exists.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [2/4]

const KeyValuePair * FbcSBasePlugin::getKeyValuePair ( const std::string & sid ) const

inherited

Get a KeyValuePair from the FbcSBasePlugin based on its identifier.

Parameters

sid	a string representing the identifier of the KeyValuePair to retrieve.

Returns: the KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin with the given sid or NULL if no such KeyValuePair exists.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [3/4]

KeyValuePair * FbcSBasePlugin::getKeyValuePair ( unsigned int n )

inherited

Get a KeyValuePair from the FbcSBasePlugin.

Parameters

n	an unsigned int representing the index of the KeyValuePair to retrieve.

Returns: the nth KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin or NULL if no such object exists.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [4/4]

const KeyValuePair * FbcSBasePlugin::getKeyValuePair ( unsigned int n ) const

inherited

Get a KeyValuePair from the FbcSBasePlugin.

Parameters

n	an unsigned int representing the index of the KeyValuePair to retrieve.

Returns: the nth KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin or NULL if no such object exists.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getLevel()

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()

◆ getListOfKeyValuePairs() [1/2]

ListOfKeyValuePairs * FbcSBasePlugin::getListOfKeyValuePairs ( )

inherited

Returns the ListOfKeyValuePairs from this FbcSBasePlugin.

Returns: the ListOfKeyValuePairs from this FbcSBasePlugin.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getListOfKeyValuePairs() [2/2]

const ListOfKeyValuePairs * FbcSBasePlugin::getListOfKeyValuePairs ( ) const

inherited

Returns the ListOfKeyValuePairs from this FbcSBasePlugin.

Returns: the ListOfKeyValuePairs from this FbcSBasePlugin.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getNumKeyValuePairs()

unsigned int FbcSBasePlugin::getNumKeyValuePairs ( ) const

inherited

Get the number of KeyValuePair objects in this FbcSBasePlugin.

Returns: the number of KeyValuePair objects in this FbcSBasePlugin.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getPackageName()

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.

◆ getPackageVersion()

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()

◆ getParentSBMLObject() [1/2]

SBase * SBasePlugin::getParentSBMLObject ( )

inherited

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

Returns: the parent object of this object.

◆ getParentSBMLObject() [2/2]

const SBase * SBasePlugin::getParentSBMLObject ( ) const

inherited

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

Returns: the parent object of this object.

◆ getPrefix()

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.

◆ getSBMLDocument() [1/2]

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()

◆ getSBMLDocument() [2/2]

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()

◆ getURI()

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()

◆ getVersion()

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()

◆ isSetCharge()

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.

◆ isSetChemicalFormula()

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.

◆ isValidTypeForList()

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

virtualinherited

◆ operator=()

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

Assignment operator for FbcSpeciesPlugin.

Parameters

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

◆ removeKeyValuePair() [1/2]

KeyValuePair * FbcSBasePlugin::removeKeyValuePair ( const std::string & sid )

inherited

Removes the KeyValuePair from this FbcSBasePlugin based on its identifier and returns a pointer to it.

Parameters

sid	a string representing the identifier of the KeyValuePair to remove.

Returns: the KeyValuePair in this FbcSBasePlugin based on the identifier or NULL if no such KeyValuePair exists.

Warning: The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf::appendAndOwn() or ListOf::insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(unsigned int n)

◆ removeKeyValuePair() [2/2]

KeyValuePair * FbcSBasePlugin::removeKeyValuePair ( unsigned int n )

inherited

Removes the nth KeyValuePair from this FbcSBasePlugin and returns a pointer to it.

Parameters

n	an unsigned int representing the index of the KeyValuePair to remove.

Returns: a pointer to the nth KeyValuePair in this FbcSBasePlugin.

Warning: The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf::appendAndOwn() or ListOf::insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid)

◆ renameMetaIdRefs()

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.

◆ renameSIdRefs()

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.

◆ renameUnitSIdRefs()

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.

◆ setCharge() [1/2]

int FbcSpeciesPlugin::setCharge ( double charge )

virtual

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

Parameters

charge; double 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:

◆ setCharge() [2/2]

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:

◆ setChemicalFormula()

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:

◆ setElementNamespace()

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.

◆ unsetCharge()

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:

◆ unsetChemicalFormula()

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

◆ FbcSpeciesPlugin() [1/2]

◆ FbcSpeciesPlugin() [2/2]

◆ ~FbcSpeciesPlugin()

Member Function Documentation

◆ addKeyValuePair()

◆ clone()

◆ createKeyValuePair()

◆ getAllElements()

◆ getCharge()

◆ getChargeAsDouble()

◆ getChemicalFormula()

◆ getElementByMetaId()

◆ getElementBySId()

◆ getElementNamespace()

◆ getKeyValuePair() [1/4]

◆ getKeyValuePair() [2/4]

◆ getKeyValuePair() [3/4]

◆ getKeyValuePair() [4/4]

◆ getLevel()

◆ getListOfKeyValuePairs() [1/2]

◆ getListOfKeyValuePairs() [2/2]

◆ getNumKeyValuePairs()

◆ getPackageName()

◆ getPackageVersion()

◆ getParentSBMLObject() [1/2]

◆ getParentSBMLObject() [2/2]

◆ getPrefix()

◆ getSBMLDocument() [1/2]

◆ getSBMLDocument() [2/2]

◆ getURI()

◆ getVersion()

◆ isSetCharge()

◆ isSetChemicalFormula()

◆ isValidTypeForList()

◆ operator=()

◆ removeKeyValuePair() [1/2]

◆ removeKeyValuePair() [2/2]

◆ renameMetaIdRefs()

◆ renameSIdRefs()

◆ renameUnitSIdRefs()

◆ setCharge() [1/2]

◆ setCharge() [2/2]

◆ setChemicalFormula()

◆ setElementNamespace()

◆ unsetCharge()

◆ unsetChemicalFormula()