Inheritance diagram for libsbml.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.

Public Member Functions
def	__init__ (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

def	addQualitativeSpecies (self, qualitativeSpecies)
	Adds a copy of the given QualitativeSpecies object to the list of qual. More...

def	addTransition (self, transition)
	Adds a copy of the given Transition object to the list of qual. More...

def	clone (self)
	Creates and returns a deep copy of this QualModelPlugin object. More...

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

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

def	getElementByMetaId (self, metaid)
	Returns the first child element that has the given `metaid`, or `None` if no such object is found. More...

def	getElementBySId (self, id)
	Returns the first child element that has the given `id` in the model-wide SId namespace, or `None` if no such object is found. More...

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

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

def	getListOfAllElements (self, filter=None)
	Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...

def	getListOfQualitativeSpecies (self, args)
	Returns the ListOfQualitativeSpecies in this plugin object. More...

def	getListOfTransitions (self, args)
	Returns the ListOfTransitions in this plugin object. More...

def	getNumQualitativeSpecies (self)
	Returns the number of QualitativeSpecies object in this plugin object. More...

def	getNumTransitions (self)
	Returns the number of Transition object in this plugin object. More...

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

def	getPackageVersion (self)
	Returns the package version of the package extension of this plugin object. More...

def	getParentSBMLObject (self, args)
	Returns the parent object to which this plugin object is connected. More...

def	getPrefix (self)
	Returns the XML namespace prefix of the package to which this plugin object belongs. More...

def	getQualitativeSpecies (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

def	getSBMLDocument (self, args)
	Returns the SBMLDocument object containing this object instance. More...

def	getTransition (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

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

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

def	isValidTypeForList (self, item)

def	removeQualitativeSpecies (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

def	removeTransition (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

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

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

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

def	setElementNamespace (self, uri)
	Sets the XML namespace to which this object belongs. More...

Constructor & Destructor Documentation

def libsbml.QualModelPlugin.__init__	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

__init__(string uri, string prefix, QualPkgNamespaces qualns)   QualModelPlugin
__init__(QualModelPlugin orig)   QualModelPlugin

Each variant is described separately below.

Method variant with the following signature:

QualModelPlugin(QualModelPlugin orig)

Copy constructor. Creates a copy of this object.

Parameters

orig	the instance to copy.

Method variant with the following signature:

QualModelPlugin(string uri, 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.

Member Function Documentation

def libsbml.QualModelPlugin.addQualitativeSpecies	(	self,
		qualitativeSpecies
	)

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

addQualitativeSpecies(QualitativeSpecies qualitativeSpecies)   int

Parameters

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

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

def libsbml.QualModelPlugin.addTransition	(	self,
		transition
	)

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

addTransition(Transition transition)   int

Parameters

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

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

def libsbml.QualModelPlugin.clone ( self )

Creates and returns a deep copy of this QualModelPlugin object.

clone()   QualModelPlugin

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

def libsbml.QualModelPlugin.createQualitativeSpecies ( self )

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

createQualitativeSpecies()   QualitativeSpecies

Returns: a newly created QualitativeSpecies object.

def libsbml.QualModelPlugin.createTransition ( self )

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

createTransition()   Transition

Returns: a newly created Transition object.

def libsbml.QualModelPlugin.getElementByMetaId	(	self,
		metaid
	)

Returns the first child element that has the given metaid, or None if no such object is found.

getElementByMetaId(string metaid)   SBase

Parameters

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

Returns: a pointer to the SBase element with the given metaid.

def libsbml.QualModelPlugin.getElementBySId	(	self,
		id
	)

Returns the first child element that has the given id in the model-wide SId namespace, or None if no such object is found.

getElementBySId(string id)   SBase

Parameters

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

Returns: a pointer to the SBase element with the given id.

def libsbml.SBasePlugin.getElementNamespace ( self )

inherited

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

getElementNamespace()   string

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

def libsbml.SBasePlugin.getLevel ( self )

inherited

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

getLevel()   long

Returns: the SBML Level.

See also: getVersion()

def libsbml.SBasePlugin.getListOfAllElements	(	self,
		filter = `None`
	)

inherited

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

getListOfAllElements(ElementFilter filter)   SBaseList
getListOfAllElements()   SBaseList

Returns: a list of all objects that are children of this object.

def libsbml.QualModelPlugin.getListOfQualitativeSpecies	(	self,
		args
	)

Returns the ListOfQualitativeSpecies in this plugin object.

getListOfQualitativeSpecies()   ListOfQualitativeSpecies

Returns: ListOfQualitativeSpecies object in this plugin object.

def libsbml.QualModelPlugin.getListOfTransitions	(	self,
		args
	)

Returns the ListOfTransitions in this plugin object.

getListOfTransitions()   ListOfTransitions

Returns: ListOfTransitions object in this plugin object.

def libsbml.QualModelPlugin.getNumQualitativeSpecies ( self )

Returns the number of QualitativeSpecies object in this plugin object.

getNumQualitativeSpecies()   long

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

def libsbml.QualModelPlugin.getNumTransitions ( self )

Returns the number of Transition object in this plugin object.

getNumTransitions()   long

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

def libsbml.SBasePlugin.getPackageName ( self )

inherited

Returns the short-form name of the package to which this plugin object belongs.

getPackageName()   string

Returns: the short-form package name (or nickname) of the SBML package implemented by this package extension.

def libsbml.SBasePlugin.getPackageVersion ( self )

inherited

Returns the package version of the package extension of this plugin object.

getPackageVersion()   long

Returns: the package version of the package extension of this plugin object.

See also: getLevel(); getVersion()

def libsbml.SBasePlugin.getParentSBMLObject	(	self,
		args
	)

inherited

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

getParentSBMLObject()   SBase

Returns: the parent object of this object.

def libsbml.SBasePlugin.getPrefix ( self )

inherited

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

getPrefix()   string

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

def libsbml.QualModelPlugin.getQualitativeSpecies	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

getQualitativeSpecies(long  n)   QualitativeSpecies
getQualitativeSpecies(string sid)   QualitativeSpecies

Each variant is described separately below.

Method variant with the following signature:

getQualitativeSpecies(long n)

Returns the QualitativeSpecies object that belongs to the given index. If the index is invalid, None 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, None is returned.

Method variant with the following signature:

getQualitativeSpecies(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 None if no such QualitativeSpecies exists.

See also: getQualitativeSpecies(); getListOfQualitativeSpecies()

def libsbml.SBasePlugin.getSBMLDocument	(	self,
		args
	)

inherited

Returns the SBMLDocument object containing this object instance.

getSBMLDocument()   SBMLDocument

: 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()

def libsbml.QualModelPlugin.getTransition	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

getTransition(long  n)   Transition
getTransition(string sid)   Transition

Each variant is described separately below.

Method variant with the following signature:

getTransition(long n)

Returns the Transition object that belongs to the given index. If the index is invalid, None 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, None is returned.

Method variant with the following signature:

getTransition(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 None if no such Transition exists.

See also: getTransition(); getListOfTransitions()

def libsbml.SBasePlugin.getURI ( self )

inherited

Returns the XML namespace URI for the package to which this object belongs.

getURI()   string

: 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()

def libsbml.SBasePlugin.getVersion ( self )

inherited

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

getVersion()   long

Returns: the SBML Version.

See also: getLevel()

def libsbml.SBasePlugin.isValidTypeForList	(	self,
		item
	)

inherited

isValidTypeForList(SBase item)   bool

def libsbml.QualModelPlugin.removeQualitativeSpecies	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

removeQualitativeSpecies(long  n)   QualitativeSpecies
removeQualitativeSpecies(string sid)   QualitativeSpecies

Each variant is described separately below.

Method variant with the following signature:

removeQualitativeSpecies(long 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. None is returned if the given index is out of range.

Method variant with the following signature:

removeQualitativeSpecies(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. None is returned if the given index is out of range.

def libsbml.QualModelPlugin.removeTransition	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

removeTransition(long  n)   Transition
removeTransition(string sid)   Transition

Each variant is described separately below.

Method variant with the following signature:

removeTransition(long 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. None is returned if the given index is out of range.

Method variant with the following signature:

removeTransition(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. None is returned if the given index is out of range.

def libsbml.SBasePlugin.renameMetaIdRefs	(	self,
		oldid,
		newid
	)

inherited

Replaces all uses of a given meta identifier attribute value with another value.

renameMetaIdRefs(string oldid, string newid)

: 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.

def libsbml.SBasePlugin.renameSIdRefs	(	self,
		oldid,
		newid
	)

inherited

Replaces all uses of a given SIdRef type attribute value with another value.

renameSIdRefs(string oldid, string newid)

: 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.

def libsbml.SBasePlugin.renameUnitSIdRefs	(	self,
		oldid,
		newid
	)

inherited

Replaces all uses of a given UnitSIdRef type attribute value with another value.

renameUnitSIdRefs(string oldid, string newid)

: 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.

def libsbml.SBasePlugin.setElementNamespace	(	self,
		uri
	)

inherited

Sets the XML namespace to which this object belongs.

setElementNamespace(string uri)   int

: 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()

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation