Inheritance diagram for MultiSpeciesPlugin:

Detailed Description

multi Extension of Species for the "multi" package.

The MultiSpeciesPlugin class extends the Species class to have a new attribute "speciesType", and two extra optional ListOfOutwardBindingSites and ListOfSpeciesFeatures children. A species may have a ListOfOutwardBindingSites child and/or a ListOfSpeciesFeatures child only when its speciesType attribute has been defined. The relationship among the elements of a ListOfOutwardBindingSites or a ListOfSpeciesFeatures is "and".

Public Member Functions
int	addOutwardBindingSite (const OutwardBindingSite *outwardBindingSite)
	Adds a copy of the given OutwardBindingSite to the ListOfOutwardBindingSites. More...

int	addSpeciesFeature (const SpeciesFeature *speciesFeature)
	Adds a copy of the given SpeciesFeature to the ListOfSpeciesFeatures of this "multi" Species. More...

int	addSubListOfSpeciesFeatures (SubListOfSpeciesFeatures *subListOfSpeciesFeatures)
	Adds a copy of the given SubListOfSpeciesFeatures to the ListOfSpeciesFeatures. More...

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

OutwardBindingSite *	createOutwardBindingSite ()
	Creates a new OutwardBindingSite object and adds it to the ListOfOutwardBindingSites. More...

SpeciesFeature *	createSpeciesFeature ()
	Creates a new SpeciesFeature object and adds it to the ListOfSpeciesFeatures of this "multi" Species. More...

SubListOfSpeciesFeatures *	createSubListOfSpeciesFeatures ()
	Creates a new SubListOfSpeciesFeatures object and adds it to the SubListOfSpeciesFeatures. 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)
	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...

ListOfOutwardBindingSites *	getListOfOutwardBindingSites ()
	Returns the ListOfOutwardBindingSites of this "multi" Species. More...

const ListOfOutwardBindingSites *	getListOfOutwardBindingSites () const
	Returns the ListOfOutwardBindingSites of this "multi" Species. More...

ListOfSpeciesFeatures *	getListOfSpeciesFeatures ()
	Returns the ListOfSpeciesFeatures of this "multi" Species. More...

const ListOfSpeciesFeatures *	getListOfSpeciesFeatures () const
	Returns the ListOfSpeciesFeatures of this "multi" Species. More...

unsigned int	getNumOutwardBindingSites () const
	Returns the number of OutwardBindingSite objects of this "multi" Species. More...

unsigned int	getNumSpeciesFeatures () const
	Returns the number of SpeciesFeature objects of this "multi" Species. More...

unsigned int	getNumSubListOfSpeciesFeatures () const
	Returns the number of SubListOfSpeciesFeatures objects of this "multi" Species. More...

OutwardBindingSite *	getOutwardBindingSite (const std::string &sid)
	Returns the OutwardBindingSite object with the given identifier `sid`. More...

const OutwardBindingSite *	getOutwardBindingSite (const std::string &sid) const
	Returns the OutwardBindingSite object with the given identifier `sid`. More...

OutwardBindingSite *	getOutwardBindingSite (unsigned int n)
	Returns the nth OutwardBindingSite object. More...

const OutwardBindingSite *	getOutwardBindingSite (unsigned int n) const
	Returns the nth OutwardBindingSite 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...

SpeciesFeature *	getSpeciesFeature (const std::string &sid)
	Returns the SpeciesFeature object with the given identifier `sid`. More...

const SpeciesFeature *	getSpeciesFeature (const std::string &sid) const
	Returns the SpeciesFeature object with the given identifier `sid`. More...

SpeciesFeature *	getSpeciesFeature (unsigned int n)
	Returns the nth SpeciesFeature object. More...

const SpeciesFeature *	getSpeciesFeature (unsigned int n) const
	Returns the nth SpeciesFeature object. More...

virtual const std::string &	getSpeciesType () const
	Returns the value of the "speciesType" attribute of this "multi" Species. More...

SubListOfSpeciesFeatures *	getSubListOfSpeciesFeatures (const std::string &sid)
	Returns the SubListOfSpeciesFeatures object with the given identifier `sid`. More...

const SubListOfSpeciesFeatures *	getSubListOfSpeciesFeatures (const std::string &sid) const
	Returns the SubListOfSpeciesFeatures object with the given identifier `sid`. More...

SubListOfSpeciesFeatures *	getSubListOfSpeciesFeatures (unsigned int n)
	Returns the nth SubListOfSpeciesFeatures object. More...

const SubListOfSpeciesFeatures *	getSubListOfSpeciesFeatures (unsigned int n) const
	Returns the nth SubListOfSpeciesFeatures object. 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	hasRequiredElements () const
	Returns `true` if this object has all the required elements. More...

virtual bool	isSetSpeciesType () const
	Returns `true` if the "speciesType" attribute of this "multi" Species has been set. More...

virtual bool	isValidTypeForList (SBase *item) const

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

	MultiSpeciesPlugin (const std::string &uri, const std::string &prefix, MultiPkgNamespaces *multins)
	Creates a new MultiSpeciesPlugin object. More...

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

OutwardBindingSite *	removeOutwardBindingSite (const std::string &sid)
	Removes the OutwardBindingSite object with the given id `sid` and returns a pointer to it. More...

OutwardBindingSite *	removeOutwardBindingSite (unsigned int n)
	Removes the nth OutwardBindingSite object and returns a pointer to it. More...

SpeciesFeature *	removeSpeciesFeature (const std::string &sid)
	Removes the SpeciesFeature object with the given identifier `sid`. More...

SpeciesFeature *	removeSpeciesFeature (unsigned int n)
	Removes the nth SpeciesFeature object 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)

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

virtual int	setSpeciesType (const std::string &speciesType)
	Sets the value of the "speciesType" attribute on this "multi" Species. More...

virtual int	unsetSpeciesType ()
	Unsets the value of the "speciesType" attribute on this "multi" Species. More...

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

Constructor & Destructor Documentation

◆ MultiSpeciesPlugin() [1/2]

MultiSpeciesPlugin::MultiSpeciesPlugin	(	const std::string &	uri,
		const std::string &	prefix,
		MultiPkgNamespaces *	multins
	)

Creates a new MultiSpeciesPlugin object.

: 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.
multins	the namespaces object for the package.

◆ MultiSpeciesPlugin() [2/2]

MultiSpeciesPlugin::MultiSpeciesPlugin ( const MultiSpeciesPlugin & orig )

Copy constructor for MultiSpeciesPlugin.

Parameters

orig	the MultiSpeciesPlugin instance to copy.

◆ ~MultiSpeciesPlugin()

MultiSpeciesPlugin::~MultiSpeciesPlugin ( )

virtual

Destructor for MultiSpeciesPlugin.

Member Function Documentation

◆ addOutwardBindingSite()

int MultiSpeciesPlugin::addOutwardBindingSite ( const OutwardBindingSite * outwardBindingSite )

Adds a copy of the given OutwardBindingSite to the ListOfOutwardBindingSites.

Parameters

outwardBindingSite the outwardBindingSite to be added.

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

◆ addSpeciesFeature()

int MultiSpeciesPlugin::addSpeciesFeature ( const SpeciesFeature * speciesFeature )

Adds a copy of the given SpeciesFeature to the ListOfSpeciesFeatures of this "multi" Species.

Parameters

speciesFeature the SpeciesFeature to be added.

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

◆ addSubListOfSpeciesFeatures()

int MultiSpeciesPlugin::addSubListOfSpeciesFeatures ( SubListOfSpeciesFeatures * subListOfSpeciesFeatures )

Adds a copy of the given SubListOfSpeciesFeatures to the ListOfSpeciesFeatures.

Parameters

subListOfSpeciesFeatures the SubListOfSpeciesFeatures to be added.

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

◆ clone()

MultiSpeciesPlugin * MultiSpeciesPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this MultiSpeciesPlugin object.

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

Reimplemented from SBasePlugin.

◆ createOutwardBindingSite()

OutwardBindingSite * MultiSpeciesPlugin::createOutwardBindingSite ( )

Creates a new OutwardBindingSite object and adds it to the ListOfOutwardBindingSites.

Returns: the newly created OutwardBindingSite object.

◆ createSpeciesFeature()

SpeciesFeature * MultiSpeciesPlugin::createSpeciesFeature ( )

Creates a new SpeciesFeature object and adds it to the ListOfSpeciesFeatures of this "multi" Species.

Returns: the newly created SpeciesFeature object.

◆ createSubListOfSpeciesFeatures()

SubListOfSpeciesFeatures * MultiSpeciesPlugin::createSubListOfSpeciesFeatures ( )

Creates a new SubListOfSpeciesFeatures object and adds it to the SubListOfSpeciesFeatures.

Returns: the newly created SubListOfSpeciesFeatures object.

◆ getAllElements()

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

virtual

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

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 child objects.

Reimplemented from SBasePlugin.

◆ getElementByMetaId()

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 SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, QualModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ getElementBySId()

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 SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, QualModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ 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.

◆ 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()

◆ getListOfOutwardBindingSites() [1/2]

ListOfOutwardBindingSites * MultiSpeciesPlugin::getListOfOutwardBindingSites ( )

Returns the ListOfOutwardBindingSites of this "multi" Species.

Returns: the ListOfOutwardBindingSites object.

◆ getListOfOutwardBindingSites() [2/2]

const ListOfOutwardBindingSites * MultiSpeciesPlugin::getListOfOutwardBindingSites ( ) const

Returns the ListOfOutwardBindingSites of this "multi" Species.

Returns: the ListOfOutwardBindingSites object.

◆ getListOfSpeciesFeatures() [1/2]

ListOfSpeciesFeatures * MultiSpeciesPlugin::getListOfSpeciesFeatures ( )

Returns the ListOfSpeciesFeatures of this "multi" Species.

Returns: ListOfSpeciesFeatures object in this plugin object.

◆ getListOfSpeciesFeatures() [2/2]

const ListOfSpeciesFeatures * MultiSpeciesPlugin::getListOfSpeciesFeatures ( ) const

Returns the ListOfSpeciesFeatures of this "multi" Species.

Returns: ListOfSpeciesFeatures object in this plugin object.

◆ getNumOutwardBindingSites()

unsigned int MultiSpeciesPlugin::getNumOutwardBindingSites ( ) const

Returns the number of OutwardBindingSite objects of this "multi" Species.

Returns: the number of OutwardBindingSite objects in this plugin object.

◆ getNumSpeciesFeatures()

unsigned int MultiSpeciesPlugin::getNumSpeciesFeatures ( ) const

Returns the number of SpeciesFeature objects of this "multi" Species.

Returns: the number of SpeciesFeature objects in this plugin object.

◆ getNumSubListOfSpeciesFeatures()

unsigned int MultiSpeciesPlugin::getNumSubListOfSpeciesFeatures ( ) const

Returns the number of SubListOfSpeciesFeatures objects of this "multi" Species.

Returns: the number of SubListOfSpeciesFeatures objects in this plugin object.

◆ getOutwardBindingSite() [1/4]

OutwardBindingSite * MultiSpeciesPlugin::getOutwardBindingSite ( const std::string & sid )

Returns the OutwardBindingSite object with the given identifier sid.

Parameters

sid	a string representing the id of the OutwardBindingSite to get.

Returns: OutwardBindingSite in the ListOfOutwardBindingSites with the given id or NULL if no such OutwardBindingSite exists.

◆ getOutwardBindingSite() [2/4]

const OutwardBindingSite * MultiSpeciesPlugin::getOutwardBindingSite ( const std::string & sid ) const

Returns the OutwardBindingSite object with the given identifier sid.

Parameters

sid	a string representing the id of the OutwardBindingSite to get.

Returns: OutwardBindingSite in the ListOfOutwardBindingSites with the given id or NULL if no such OutwardBindingSite exists.

◆ getOutwardBindingSite() [3/4]

OutwardBindingSite * MultiSpeciesPlugin::getOutwardBindingSite ( unsigned int n )

Returns the nth OutwardBindingSite object.

Parameters

n	the index number of the OutwardBindingSite to get

Returns: the nth OutwardBindingSite in the ListOfOutwardBindingSites. If the index is invalid, NULL is returned.

◆ getOutwardBindingSite() [4/4]

const OutwardBindingSite * MultiSpeciesPlugin::getOutwardBindingSite ( unsigned int n ) const

Returns the nth OutwardBindingSite object.

Parameters

n	the index number of the OutwardBindingSite to get

Returns: the nth OutwardBindingSite in the ListOfOutwardBindingSites. If the index is invalid, NULL is returned.

◆ 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()

◆ getSpeciesFeature() [1/4]

SpeciesFeature * MultiSpeciesPlugin::getSpeciesFeature ( const std::string & sid )

Returns the SpeciesFeature object with the given identifier sid.

Parameters

sid	a string representing the id of the SpeciesFeature to get

Returns: SpeciesFeature in the ListOfSpeciesFeatures with the given id sid, or NULL if no such SpeciesFeature exists.

◆ getSpeciesFeature() [2/4]

const SpeciesFeature * MultiSpeciesPlugin::getSpeciesFeature ( const std::string & sid ) const

Returns the SpeciesFeature object with the given identifier sid.

Parameters

sid	a string representing the id of the SpeciesFeature to get

Returns: SpeciesFeature in the ListOfSpeciesFeatures with the given id sid, or NULL if no such SpeciesFeature exists.

◆ getSpeciesFeature() [3/4]

SpeciesFeature * MultiSpeciesPlugin::getSpeciesFeature ( unsigned int n )

Returns the nth SpeciesFeature object.

Parameters

n	the index number of the SpeciesFeature to get.

Returns: the nth SpeciesFeature in the ListOfSpeciesFeatures. If the index is invalid, NULL is returned.

◆ getSpeciesFeature() [4/4]

const SpeciesFeature * MultiSpeciesPlugin::getSpeciesFeature ( unsigned int n ) const

Returns the nth SpeciesFeature object.

Parameters

n	the index number of the SpeciesFeature to get.

Returns: the nth SpeciesFeature in the ListOfSpeciesFeatures. If the index is invalid, NULL is returned.

◆ getSpeciesType()

const std::string & MultiSpeciesPlugin::getSpeciesType ( ) const

virtual

Returns the value of the "speciesType" attribute of this "multi" Species.

Returns: the value of the "speciesType" attribute.

◆ getSubListOfSpeciesFeatures() [1/4]

SubListOfSpeciesFeatures * MultiSpeciesPlugin::getSubListOfSpeciesFeatures ( const std::string & sid )

Returns the SubListOfSpeciesFeatures object with the given identifier sid.

Parameters

sid	the id of the SubListOfSpeciesFeatures to get.

Returns: SubListOfSpeciesFeatures in the ListOfSpeciesFeatures with the given id sid, or NULL if no such SubListOfSpeciesFeatures exists.

◆ getSubListOfSpeciesFeatures() [2/4]

const SubListOfSpeciesFeatures * MultiSpeciesPlugin::getSubListOfSpeciesFeatures ( const std::string & sid ) const

Returns the SubListOfSpeciesFeatures object with the given identifier sid.

Parameters

sid	the id of the SubListOfSpeciesFeatures to get.

Returns: SubListOfSpeciesFeatures in the ListOfSpeciesFeatures with the given id sid, or NULL if no such SubListOfSpeciesFeatures exists.

◆ getSubListOfSpeciesFeatures() [3/4]

SubListOfSpeciesFeatures * MultiSpeciesPlugin::getSubListOfSpeciesFeatures ( unsigned int n )

Returns the nth SubListOfSpeciesFeatures object.

Parameters

n	the index number of the SubListOfSpeciesFeatures to get

Returns: the nth SubListOfSpeciesFeatures in the ListOfSpeciesFeatures. If the index is invalid, NULL is returned.

◆ getSubListOfSpeciesFeatures() [4/4]

const SubListOfSpeciesFeatures * MultiSpeciesPlugin::getSubListOfSpeciesFeatures ( unsigned int n ) const

Returns the nth SubListOfSpeciesFeatures object.

Parameters

n	the index number of the SubListOfSpeciesFeatures to get

Returns: the nth SubListOfSpeciesFeatures in the ListOfSpeciesFeatures. If the index is invalid, NULL is returned.

◆ 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()

◆ hasRequiredElements()

bool MultiSpeciesPlugin::hasRequiredElements ( ) const

virtual

Returns true if this object has all the required elements.

Returns: true if this object has all the elements required by the package specification; otherwise, false will be returned.

◆ isSetSpeciesType()

bool MultiSpeciesPlugin::isSetSpeciesType ( ) const

virtual

Returns true if the "speciesType" attribute of this "multi" Species has been set.

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

◆ isValidTypeForList()

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

virtualinherited

◆ operator=()

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

Assignment operator for MultiSpeciesPlugin.

Parameters

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

◆ removeOutwardBindingSite() [1/2]

OutwardBindingSite * MultiSpeciesPlugin::removeOutwardBindingSite ( const std::string & sid )

Removes the OutwardBindingSite object with the given id sid and returns a pointer to it.

Parameters

sid	a string representing the id of the OutwardBindingSite to remove.

Returns: the OutwardBindingSite object removed or NULL index was out of range. Note that the caller owns the returned object and is responsible for deleting it.

◆ removeOutwardBindingSite() [2/2]

OutwardBindingSite * MultiSpeciesPlugin::removeOutwardBindingSite ( unsigned int n )

Removes the nth OutwardBindingSite object and returns a pointer to it.

Parameters

n	the index of the OutwardBindingSite to remove.

Returns: the OutwardBindingSite object removed or NULL index was out of range. Note that the caller owns the returned object and is responsible for deleting it.

◆ removeSpeciesFeature() [1/2]

SpeciesFeature * MultiSpeciesPlugin::removeSpeciesFeature ( const std::string & sid )

Removes the SpeciesFeature object with the given identifier sid.

Parameters

sid	a string representing the id of the SpeciesFeature to get.

Returns: the SpeciesFeature object removed or NULL index was out of range. Note that the caller owns the returned object and is responsible for deleting it.

◆ removeSpeciesFeature() [2/2]

SpeciesFeature * MultiSpeciesPlugin::removeSpeciesFeature ( unsigned int n )

Removes the nth SpeciesFeature object and returns a pointer to it.

Parameters

n	the index of the SpeciesFeature to remove.

Returns: the SpeciesFeature object removed or NULL index was out of range. Note that the caller owns the returned object and is responsible for deleting it.

◆ 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.

◆ 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.

◆ setSpeciesType()

int MultiSpeciesPlugin::setSpeciesType ( const std::string & speciesType )

virtual

Sets the value of the "speciesType" attribute on this "multi" Species.

Parameters

speciesType the new value for the attribute.

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:

◆ unsetSpeciesType()

int MultiSpeciesPlugin::unsetSpeciesType ( )

virtual

Unsets the value of the "speciesType" attribute on this "multi" Species.

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

◆ MultiSpeciesPlugin() [1/2]

◆ MultiSpeciesPlugin() [2/2]

◆ ~MultiSpeciesPlugin()

Member Function Documentation

◆ addOutwardBindingSite()

◆ addSpeciesFeature()

◆ addSubListOfSpeciesFeatures()

◆ clone()

◆ createOutwardBindingSite()

◆ createSpeciesFeature()

◆ createSubListOfSpeciesFeatures()

◆ getAllElements()

◆ getElementByMetaId()

◆ getElementBySId()

◆ getElementNamespace()

◆ getLevel()

◆ getListOfOutwardBindingSites() [1/2]

◆ getListOfOutwardBindingSites() [2/2]

◆ getListOfSpeciesFeatures() [1/2]

◆ getListOfSpeciesFeatures() [2/2]

◆ getNumOutwardBindingSites()

◆ getNumSpeciesFeatures()

◆ getNumSubListOfSpeciesFeatures()

◆ getOutwardBindingSite() [1/4]

◆ getOutwardBindingSite() [2/4]

◆ getOutwardBindingSite() [3/4]

◆ getOutwardBindingSite() [4/4]

◆ getPackageName()

◆ getPackageVersion()

◆ getParentSBMLObject() [1/2]

◆ getParentSBMLObject() [2/2]

◆ getPrefix()

◆ getSBMLDocument() [1/2]

◆ getSBMLDocument() [2/2]

◆ getSpeciesFeature() [1/4]

◆ getSpeciesFeature() [2/4]

◆ getSpeciesFeature() [3/4]

◆ getSpeciesFeature() [4/4]

◆ getSpeciesType()

◆ getSubListOfSpeciesFeatures() [1/4]

◆ getSubListOfSpeciesFeatures() [2/4]

◆ getSubListOfSpeciesFeatures() [3/4]

◆ getSubListOfSpeciesFeatures() [4/4]

◆ getURI()

◆ getVersion()

◆ hasRequiredElements()

◆ isSetSpeciesType()

◆ isValidTypeForList()

◆ operator=()

◆ removeOutwardBindingSite() [1/2]

◆ removeOutwardBindingSite() [2/2]

◆ removeSpeciesFeature() [1/2]

◆ removeSpeciesFeature() [2/2]

◆ renameMetaIdRefs()

◆ renameSIdRefs()

◆ renameUnitSIdRefs()

◆ setElementNamespace()

◆ setSpeciesType()

◆ unsetSpeciesType()