Inheritance diagram for libsbmlcs.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 (OutwardBindingSite outwardBindingSite)
	Adds a copy of the given OutwardBindingSite to the ListOfOutwardBindingSites. More...

int	addSpeciesFeature (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...

new SBasePlugin	clone ()
	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...

override void	Dispose ()

long	getColumn ()

new SBase	getElementByMetaId (string metaid)
	Return the first child object found with a given meta identifier. More...

new SBase	getElementBySId (string id)
	Return the first child object found with a given identifier. More...

string	getElementNamespace ()
	Returns the namespace URI of the package to which this plugin object belongs. More...

long	getLevel ()
	Returns the SBML Level of the package extension of this plugin object. More...

long	getLine ()

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

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

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

long	getNumOutwardBindingSites ()
	Returns the number of OutwardBindingSite objects of this 'multi' Species. More...

long	getNumSpeciesFeatures ()
	Returns the number of SpeciesFeature objects of this 'multi' Species. More...

long	getNumSubListOfSpeciesFeatures ()
	Returns the number of SubListOfSpeciesFeatures objects of this 'multi' Species. More...

OutwardBindingSite	getOutwardBindingSite (long n)
	Returns the nth OutwardBindingSite object. More...

OutwardBindingSite	getOutwardBindingSite (string sid)
	Returns the OutwardBindingSite object with the given identifier `sid`. More...

string	getPackageName ()
	Returns the short-form name of the package to which this plugin object belongs. More...

long	getPackageVersion ()
	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...

string	getPrefix ()
	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...

SBMLExtension	getSBMLExtension ()

SpeciesFeature	getSpeciesFeature (long n)
	Returns the nth SpeciesFeature object. More...

SpeciesFeature	getSpeciesFeature (string sid)
	Returns the SpeciesFeature object with the given identifier `sid`. More...

new string	getSpeciesType ()
	Returns the value of the 'speciesType' attribute of this 'multi' Species. More...

SubListOfSpeciesFeatures	getSubListOfSpeciesFeatures (long n)
	Returns the nth SubListOfSpeciesFeatures object. More...

SubListOfSpeciesFeatures	getSubListOfSpeciesFeatures (string sid)
	Returns the SubListOfSpeciesFeatures object with the given identifier `sid`. More...

string	getURI ()
	Returns the XML namespace URI for the package to which this object belongs. More...

long	getVersion ()
	Returns the Version within the SBML Level of the package extension of this plugin object. More...

new bool	hasRequiredElements ()
	Returns `true` if this object has all the required elements. More...

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

new bool	isValidTypeForList (SBase item)

	MultiSpeciesPlugin (string uri, string prefix, MultiPkgNamespaces multins)
	Creates a new MultiSpeciesPlugin object. More...

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

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

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

SpeciesFeature	removeSpeciesFeature (long n)
	Removes the nth SpeciesFeature object and returns a pointer to it. More...

SpeciesFeature	removeSpeciesFeature (string sid)
	Removes the SpeciesFeature object with the given identifier `sid`. More...

new void	renameMetaIdRefs (string oldid, string newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

new void	renameSIdRefs (string oldid, string newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

new void	renameUnitSIdRefs (string oldid, string newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

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

new int	setSpeciesType (string speciesType)
	Sets the value of the 'speciesType' attribute on this 'multi' Species. More...

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

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.MultiSpeciesPlugin.MultiSpeciesPlugin	(	string	uri,
		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.

libsbmlcs.MultiSpeciesPlugin.MultiSpeciesPlugin ( MultiSpeciesPlugin orig )

Copy constructor for MultiSpeciesPlugin.

Parameters

orig	the MultiSpeciesPlugin instance to copy.

Member Function Documentation

int libsbmlcs.MultiSpeciesPlugin.addOutwardBindingSite ( 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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.MultiSpeciesPlugin.addSpeciesFeature ( 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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

new SBasePlugin libsbmlcs.MultiSpeciesPlugin.clone ( )

Creates and returns a deep copy of this MultiSpeciesPlugin object.

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

OutwardBindingSite libsbmlcs.MultiSpeciesPlugin.createOutwardBindingSite ( )

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

Returns: the newly created OutwardBindingSite object.

SpeciesFeature libsbmlcs.MultiSpeciesPlugin.createSpeciesFeature ( )

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

Returns: the newly created SpeciesFeature object.

SubListOfSpeciesFeatures libsbmlcs.MultiSpeciesPlugin.createSubListOfSpeciesFeatures ( )

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

Returns: the newly created SubListOfSpeciesFeatures object.

override void libsbmlcs.MultiSpeciesPlugin.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBasePlugin.

long libsbmlcs.SBasePlugin.getColumn ( )

inherited

new SBase libsbmlcs.SBasePlugin.getElementByMetaId ( string metaid )

inherited

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.

new SBase libsbmlcs.SBasePlugin.getElementBySId ( string id )

inherited

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.

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.

string libsbmlcs.SBasePlugin.getElementNamespace ( )

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.

long libsbmlcs.SBasePlugin.getLevel ( )

inherited

Returns the SBML Level of the package extension of this plugin object.

Returns: the SBML Level.

See also: getVersion()

long libsbmlcs.SBasePlugin.getLine ( )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( )

inherited

ListOfOutwardBindingSites libsbmlcs.MultiSpeciesPlugin.getListOfOutwardBindingSites ( )

Returns the ListOfOutwardBindingSites of this 'multi' Species.

Returns: the ListOfOutwardBindingSites object.

ListOfSpeciesFeatures libsbmlcs.MultiSpeciesPlugin.getListOfSpeciesFeatures ( )

Returns the ListOfSpeciesFeatures of this 'multi' Species.

Returns: ListOfSpeciesFeatures object in this plugin object.

long libsbmlcs.MultiSpeciesPlugin.getNumOutwardBindingSites ( )

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

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

long libsbmlcs.MultiSpeciesPlugin.getNumSpeciesFeatures ( )

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

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

long libsbmlcs.MultiSpeciesPlugin.getNumSubListOfSpeciesFeatures ( )

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

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

OutwardBindingSite libsbmlcs.MultiSpeciesPlugin.getOutwardBindingSite ( long 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.

OutwardBindingSite libsbmlcs.MultiSpeciesPlugin.getOutwardBindingSite ( 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.

string libsbmlcs.SBasePlugin.getPackageName ( )

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.

long libsbmlcs.SBasePlugin.getPackageVersion ( )

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 libsbmlcs.SBasePlugin.getParentSBMLObject ( )

inherited

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

Returns: the parent object of this object.

string libsbmlcs.SBasePlugin.getPrefix ( )

inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

Returns: the XML namespace prefix of the SBML Level 3 package implemented by this libSBML package extension.

SBMLDocument libsbmlcs.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()

SBMLExtension libsbmlcs.SBasePlugin.getSBMLExtension ( )

inherited

SpeciesFeature libsbmlcs.MultiSpeciesPlugin.getSpeciesFeature ( long 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.

SpeciesFeature libsbmlcs.MultiSpeciesPlugin.getSpeciesFeature ( 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.

new string libsbmlcs.MultiSpeciesPlugin.getSpeciesType ( )

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

Returns: the value of the 'speciesType' attribute.

SubListOfSpeciesFeatures libsbmlcs.MultiSpeciesPlugin.getSubListOfSpeciesFeatures ( long 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.

SubListOfSpeciesFeatures libsbmlcs.MultiSpeciesPlugin.getSubListOfSpeciesFeatures ( 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.

string libsbmlcs.SBasePlugin.getURI ( )

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()

long libsbmlcs.SBasePlugin.getVersion ( )

inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns: the SBML Version.

See also: getLevel()

new bool libsbmlcs.MultiSpeciesPlugin.hasRequiredElements ( )

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.

new bool libsbmlcs.MultiSpeciesPlugin.isSetSpeciesType ( )

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.

new bool libsbmlcs.SBasePlugin.isValidTypeForList ( SBase item )

inherited

OutwardBindingSite libsbmlcs.MultiSpeciesPlugin.removeOutwardBindingSite ( long 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.

OutwardBindingSite libsbmlcs.MultiSpeciesPlugin.removeOutwardBindingSite ( 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.

SpeciesFeature libsbmlcs.MultiSpeciesPlugin.removeSpeciesFeature ( long 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.

SpeciesFeature libsbmlcs.MultiSpeciesPlugin.removeSpeciesFeature ( 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.

new void libsbmlcs.SBasePlugin.renameMetaIdRefs	(	string	oldid,
		string	newid
	)

inherited

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.

new void libsbmlcs.SBasePlugin.renameSIdRefs	(	string	oldid,
		string	newid
	)

inherited

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.

new void libsbmlcs.SBasePlugin.renameUnitSIdRefs	(	string	oldid,
		string	newid
	)

inherited

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 libsbmlcs.SBasePlugin.setElementNamespace ( 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. 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()

new int libsbmlcs.MultiSpeciesPlugin.setSpeciesType ( string speciesType )

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 possible values returned by this function are:

new int libsbmlcs.MultiSpeciesPlugin.unsetSpeciesType ( )

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

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

Member Data Documentation

bool libsbmlcs.SBasePlugin.swigCMemOwn

protectedinherited

Detailed Description

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation