Inheritance diagram for QualModelPlugin:

Detailed Description

qual Extension of Model.

The extension of SBML Level 3 Core's Model class is relatively straightforward: the Qualitative Models Package adds two lists, one for holding qualitativeSpecies (ListOfQualitativeSpecies), and the other for holding transitions (ListOfTransitions). The Model element may contain at most one ListOfQualitativeSpecies, which must contain at least one QualitativeSpecies. It may also contain at most one ListOfTransitions which must contain at least one Transition.

Examples:: qual_example1.cpp.

Public Member Functions
int	addQualitativeSpecies (const QualitativeSpecies *qualitativeSpecies)
	Adds a copy of the given QualitativeSpecies object to the list of qual. More...

int	addTransition (const Transition *transition)
	Adds a copy of the given Transition object to the list of qual. More...

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

QualitativeSpecies *	createQualitativeSpecies ()
	Creates a new qual object and adds it to the list of qual objects and returns it. More...

Transition *	createTransition ()
	Creates a new qual object and adds it to the list of qual objects and returns it. More...

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

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

const ListOfQualitativeSpecies *	getListOfQualitativeSpecies () const
	Returns the ListOfQualitativeSpecies in this plugin object. More...

ListOfQualitativeSpecies *	getListOfQualitativeSpecies ()
	Returns the ListOfQualitativeSpecies in this plugin object. More...

const ListOfTransitions *	getListOfTransitions () const
	Returns the ListOfTransitions in this plugin object. More...

ListOfTransitions *	getListOfTransitions ()
	Returns the ListOfTransitions in this plugin object. More...

unsigned int	getNumQualitativeSpecies () const
	Returns the number of QualitativeSpecies object in this plugin object. More...

unsigned int	getNumTransitions () const
	Returns the number of Transition object in 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...

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

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

QualitativeSpecies *	getQualitativeSpecies (const std::string &sid)
	Returns the qualitativeSpecies object based on its identifier. More...

const QualitativeSpecies *	getQualitativeSpecies (const std::string &sid) const
	Returns the qualitativeSpecies object based on its identifier. 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...

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

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

Transition *	getTransition (const std::string &sid)
	Returns the qualitativeSpecies object based on its identifier. More...

const Transition *	getTransition (const std::string &sid) const
	Returns the qualitativeSpecies object based on its identifier. 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	isValidTypeForList (SBase *item) const

QualModelPlugin &	operator= (const QualModelPlugin &orig)
	Assignment operator for QualModelPlugin. More...

	QualModelPlugin (const std::string &uri, const std::string &prefix, QualPkgNamespaces *qualns)
	Creates a new QualModelPlugin object using the given parameters. More...

	QualModelPlugin (const QualModelPlugin &orig)
	Copy constructor. More...

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

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

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

Transition *	removeTransition (const std::string &sid)
	Removes the Transition object with the given id attribute from this plugin object 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	setElementNamespace (const std::string &uri)
	Sets the XML namespace to which this object belongs. More...

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

Constructor & Destructor Documentation

QualModelPlugin::QualModelPlugin	(	const std::string &	uri,
		const std::string &	prefix,
		QualPkgNamespaces *	qualns
	)

Creates a new QualModelPlugin 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.
qualns	the namespaces object for the package.

QualModelPlugin::QualModelPlugin ( const QualModelPlugin & orig )

Copy constructor.

Creates a copy of this object.

Parameters

orig	the instance to copy.

QualModelPlugin::~QualModelPlugin ( )

virtual

Destroy this object.

Member Function Documentation

int QualModelPlugin::addQualitativeSpecies ( const QualitativeSpecies * qualitativeSpecies )

Adds a copy of the given QualitativeSpecies object to the list of qual.

Parameters

qualitativeSpecies the QualitativeSpecies object to be added to the list of qual.

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

int QualModelPlugin::addTransition ( const Transition * transition )

Adds a copy of the given Transition object to the list of qual.

Parameters

transition the Transition object to be added to the list of qual.

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

QualModelPlugin * QualModelPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this QualModelPlugin object.

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

Reimplemented from SBasePlugin.

QualitativeSpecies* QualModelPlugin::createQualitativeSpecies ( )

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

Returns: a newly created QualitativeSpecies object.

Examples:: qual_example1.cpp.

Transition* QualModelPlugin::createTransition ( )

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

Returns: a newly created Transition object.

Examples:: qual_example1.cpp.

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

virtual

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

Returns: a List of pointers to all child objects.

Reimplemented from SBasePlugin.

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

virtual

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.

Reimplemented from SBasePlugin.

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

virtual

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.

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.

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 ListOfQualitativeSpecies* QualModelPlugin::getListOfQualitativeSpecies ( ) const

Returns the ListOfQualitativeSpecies in this plugin object.

Returns: ListOfQualitativeSpecies object in this plugin object.

ListOfQualitativeSpecies* QualModelPlugin::getListOfQualitativeSpecies ( )

Returns the ListOfQualitativeSpecies in this plugin object.

Returns: ListOfQualitativeSpecies object in this plugin object.

const ListOfTransitions* QualModelPlugin::getListOfTransitions ( ) const

Returns the ListOfTransitions in this plugin object.

Returns: ListOfTransitions object in this plugin object.

ListOfTransitions* QualModelPlugin::getListOfTransitions ( )

Returns the ListOfTransitions in this plugin object.

Returns: ListOfTransitions object in this plugin object.

unsigned int QualModelPlugin::getNumQualitativeSpecies ( ) const

Returns the number of QualitativeSpecies object in this plugin object.

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

unsigned int QualModelPlugin::getNumTransitions ( ) const

Returns the number of Transition object in this plugin object.

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

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.

const QualitativeSpecies* QualModelPlugin::getQualitativeSpecies ( unsigned int n ) const

Returns the QualitativeSpecies object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters

n	the index number of the QualitativeSpecies to get.

Returns: the nth QualitativeSpecies in the ListOfQualitativeSpecies. If the index n is invalid, NULL is returned.

QualitativeSpecies* QualModelPlugin::getQualitativeSpecies ( unsigned int n )

Returns the QualitativeSpecies object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters

n	the index number of the QualitativeSpecies to get.

Returns: the nth QualitativeSpecies in the ListOfQualitativeSpecies. If the index n is invalid, NULL is returned.

QualitativeSpecies* QualModelPlugin::getQualitativeSpecies ( const std::string & sid )

Returns the qualitativeSpecies object based on its identifier.

Parameters

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

Returns: QualitativeSpecies in the ListOfQualitativeSpecies with the given id or NULL if no such QualitativeSpecies exists.

See also: getQualitativeSpecies(unsigned int n); getListOfQualitativeSpecies()

const QualitativeSpecies* QualModelPlugin::getQualitativeSpecies ( const std::string & sid ) const

Returns the qualitativeSpecies object based on its identifier.

Parameters

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

Returns: QualitativeSpecies in the ListOfQualitativeSpecies with the given id or NULL if no such QualitativeSpecies exists.

See also: getQualitativeSpecies(unsigned int n); getListOfQualitativeSpecies()

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()

const Transition* QualModelPlugin::getTransition ( unsigned int n ) const

Returns the Transition object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters

n	the index number of the Transition to get.

Returns: the nth Transition in the ListOfTransitions. If the index n is invalid, NULL is returned.

Transition* QualModelPlugin::getTransition ( unsigned int n )

Returns the Transition object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters

n	the index number of the Transition to get.

Returns: the nth Transition in the ListOfTransitions. If the index n is invalid, NULL is returned.

Transition* QualModelPlugin::getTransition ( const std::string & sid )

Returns the qualitativeSpecies object based on its identifier.

Parameters

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

Returns: Transition in the ListOfTransitions with the given id or NULL if no such Transition exists.

See also: getTransition(unsigned int n); getListOfTransitions()

const Transition* QualModelPlugin::getTransition ( const std::string & sid ) const

Returns the qualitativeSpecies object based on its identifier.

Parameters

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

Returns: Transition in the ListOfTransitions with the given id or NULL if no such Transition exists.

See also: getTransition(unsigned int n); getListOfTransitions()

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()

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

virtualinherited

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

Assignment operator for QualModelPlugin.

QualitativeSpecies* QualModelPlugin::removeQualitativeSpecies ( unsigned int n )

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

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

Parameters

n	the index of the QualitativeSpecies object to remove.

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

QualitativeSpecies* QualModelPlugin::removeQualitativeSpecies ( const std::string & sid )

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

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

Parameters

sid	the id attribute of the QualitativeSpecies object to remove.

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

Transition* QualModelPlugin::removeTransition ( unsigned int n )

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

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

Parameters

n	the index of the Transition object to remove.

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

Transition* QualModelPlugin::removeTransition ( const std::string & sid )

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

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

Parameters

sid	the id attribute of the Transition object to remove.

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

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 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.

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation