Inheritance diagram for libsbmlcs.QualModelPlugin:

Detailed Description

{qual}

qual Implementation of the 'qual' package extention to the Model construct. 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
int	addQualitativeSpecies (QualitativeSpecies qualitativeSpecies)
	Adds a copy of the given QualitativeSpecies object to the list of qual. More...

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

int	appendFrom (Model model)

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

void	connectToChild ()
	Sets the parent of this SBML object to child SBML objects (if any). More...

void	connectToParent (SBase sbase)
	Sets the parent SBML object of this plugin object to this object and child elements (if any). More...

SBase	createObject (XMLInputStream stream)
	Subclasses must override this method to create, store, and then return an SBML object corresponding to the next XMLToken in the XMLInputStream if they have their specific elements. 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...

override void	Dispose ()

void	divideAssignmentsToSIdByFunction (string id, ASTNode function)
	If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More...

void	enablePackageInternal (string pkgURI, string pkgPrefix, bool flag)
	Enables/Disables the given package with child elements in this plugin object (if any). More...

long	getColumn ()
	Returns the column number on which this object first appears in the XML representation of the SBML document. More...

SBase	getElementByMetaId (string metaid)
	Returns the first child element it can find with the given `metaid`, or `null` if no such object is found. More...

SBase	getElementBySId (string id)
	Returns the first child element found that has the given `id` in the model-wide SId namespace, or `null` if no such object is found. More...

string	getElementNamespace ()
	Returns the XML namespace (URI) of the package extension of this plugin object. More...

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

long	getLine ()
	Returns the line number on which this object first appears in the XML representation of the SBML document. More...

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

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

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

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

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

string	getPackageName ()
	Returns the package name of this plugin object. More...

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

SBase	getParentSBMLObject ()
	Returns the parent SBase object to which this plugin object connected. More...

string	getPrefix ()
	Returns the prefix of the package extension of this plugin object. More...

QualitativeSpecies	getQualitativeSpecies (long n)
	Returns the QualitativeSpecies object that belongs to the given index. More...

QualitativeSpecies	getQualitativeSpecies (string sid)
	Returns the qualitativeSpecies object based on its identifier. More...

SBMLDocument	getSBMLDocument ()
	Returns the parent SBMLDocument of this plugin object. More...

SBMLNamespaces	getSBMLNamespaces ()

Transition	getTransition (long n)
	Returns the Transition object that belongs to the given index. More...

Transition	getTransition (string sid)
	Returns the qualitativeSpecies object based on its identifier. More...

string	getURI ()
	Gets the URI to which this element belongs to. More...

long	getVersion ()
	Returns the SBML version of the package extension of this plugin object. More...

bool	hasIdentifierBeginningWith (string prefix)
	Check to see if the given prefix is used by any of the IDs defined by extension elements. More...

bool	hasRequiredElements ()
	Checks if this plugin object has all the required elements. More...

void	logUnknownElement (string element, long sbmlLevel, long sbmlVersion, long pkgVersion)
	Helper to log a common type of error for elements. More...

void	multiplyAssignmentsToSIdByFunction (string id, ASTNode function)
	If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More...

int	prependStringToAllIdentifiers (string prefix)
	Add the given string to all identifiers in the object. More...

	QualModelPlugin (string uri, string prefix, QualPkgNamespaces qualns)
	Constructor. More...

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

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

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

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

Transition	removeTransition (string sid)
	Removes the Transition object with the given id attribute from this plugin object and returns a pointer to it. More...

void	replaceSIDWithFunction (string id, ASTNode function)
	If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More...

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

bool	stripPackage (string pkgPrefix, bool flag)

int	transformIdentifiers (IdentifierTransformer sidTransformer)

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.QualModelPlugin.QualModelPlugin	(	string	uri,
		string	prefix,
		QualPkgNamespaces	qualns
	)

Constructor.

libsbmlcs.QualModelPlugin.QualModelPlugin ( QualModelPlugin orig )

Copy constructor.

Creates a copy of this SBase object.

Member Function Documentation

int libsbmlcs.QualModelPlugin.addQualitativeSpecies ( 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 operation. The possible return values are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.QualModelPlugin.addTransition ( 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 operation. The possible return values are:

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.QualModelPlugin.appendFrom ( Model model )

SBasePlugin libsbmlcs.QualModelPlugin.clone ( )

Creates and returns a deep copy of this QualModelPlugin object.

Returns: a (deep) copy of this SBase object

void libsbmlcs.QualModelPlugin.connectToChild ( )

Sets the *parent* of this SBML object to child SBML objects (if any).

(Creates a child-parent relationship by the parent)

See also: setSBMLDocument; enablePackageInternal

void libsbmlcs.QualModelPlugin.connectToParent ( SBase sbase )

Sets the parent SBML object of this plugin object to this object and child elements (if any).

(Creates a child-parent relationship by this plugin object)

This function is called when this object is created by the parent element. Subclasses must override this this function if they have one or more child elements.Also, SBasePlugin::connectToParent() must be called in the overridden function.

Parameters

sbase the SBase object to use

See also: setSBMLDocument; enablePackageInternal

SBase libsbmlcs.QualModelPlugin.createObject ( XMLInputStream stream )

Subclasses must override this method to create, store, and then return an SBML object corresponding to the next XMLToken in the XMLInputStream if they have their specific elements.

Returns: the SBML object corresponding to next XMLToken in the XMLInputStream or null if the token was not recognized.

QualitativeSpecies libsbmlcs.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

Transition libsbmlcs.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

override void libsbmlcs.QualModelPlugin.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBasePlugin.

void libsbmlcs.SBasePlugin.divideAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).

Note: This function does nothing itself–subclasses with ASTNode subelements must override this function.

void libsbmlcs.QualModelPlugin.enablePackageInternal	(	string	pkgURI,
		string	pkgPrefix,
		bool	flag
	)

Enables/Disables the given package with child elements in this plugin object (if any).

(This is an internal implementation invoked from SBase::enablePackageInternal() function)

Note: Subclasses in which one or more SBase derived elements are defined must override this function.

See also: setSBMLDocument; connectToParent

long libsbmlcs.SBasePlugin.getColumn ( )

inherited

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns: the column number of the underlying SBML object.

Note: The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also: getLine()

SBase libsbmlcs.SBasePlugin.getElementByMetaId ( string metaid )

inherited

Returns the first child element it can find with the given metaid, or null if no such object is found.

Parameters

metaid string representing the metaid of objects to find

Returns: pointer to the first element found with the given metaid.

SBase libsbmlcs.SBasePlugin.getElementBySId ( string id )

inherited

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

Parameters

id	string representing the id of objects to find

Returns: pointer to the first element found with the given id.

string libsbmlcs.SBasePlugin.getElementNamespace ( )

inherited

Returns the XML namespace (URI) of the package extension of this plugin object.

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

long libsbmlcs.SBasePlugin.getLevel ( )

inherited

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

Returns: the SBML level of the package extension of this plugin object.

long libsbmlcs.SBasePlugin.getLine ( )

inherited

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns: the line number of the underlying SBML object.

Note: The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also: getColumn()

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( )

inherited

ListOfQualitativeSpecies libsbmlcs.QualModelPlugin.getListOfQualitativeSpecies ( )

Returns the ListOfQualitativeSpecies in this plugin object.

Returns: ListOfQualitativeSpecies object in this plugin object.

ListOfTransitions libsbmlcs.QualModelPlugin.getListOfTransitions ( )

Returns the ListOfTransitions in this plugin object.

Returns: ListOfTransitions object in this plugin object.

long libsbmlcs.QualModelPlugin.getNumQualitativeSpecies ( )

Returns the number of QualitativeSpecies object in this plugin object.

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

long libsbmlcs.QualModelPlugin.getNumTransitions ( )

Returns the number of Transition object in this plugin object.

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

string libsbmlcs.SBasePlugin.getPackageName ( )

inherited

Returns the package name of this plugin object.

Returns: the package name of this plugin object.

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.

SBase libsbmlcs.SBasePlugin.getParentSBMLObject ( )

inherited

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

Returns: the parent SBase object to which this plugin object connected.

string libsbmlcs.SBasePlugin.getPrefix ( )

inherited

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

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

QualitativeSpecies libsbmlcs.QualModelPlugin.getQualitativeSpecies ( long 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.

QualitativeSpecies libsbmlcs.QualModelPlugin.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 null if no such QualitativeSpecies exists.

See also: getQualitativeSpecies(long n); getListOfQualitativeSpecies()

SBMLDocument libsbmlcs.SBasePlugin.getSBMLDocument ( )

inherited

Returns the parent SBMLDocument of this plugin object.

Returns: the parent SBMLDocument object of this plugin object.

SBMLNamespaces libsbmlcs.SBasePlugin.getSBMLNamespaces ( )

inherited

Transition libsbmlcs.QualModelPlugin.getTransition ( long 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.

Transition libsbmlcs.QualModelPlugin.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 null if no such Transition exists.

See also: getTransition(long n); getListOfTransitions()

string libsbmlcs.SBasePlugin.getURI ( )

inherited

Gets the URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace

Returns: the URI this elements

See also: getPackageName(); getElementNamespace(); SBMLDocument::getSBMLNamespaces(); getSBMLDocument()

long libsbmlcs.SBasePlugin.getVersion ( )

inherited

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

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

bool libsbmlcs.SBasePlugin.hasIdentifierBeginningWith ( string prefix )

inherited

Check to see if the given prefix is used by any of the IDs defined by extension elements.

A package that defines its own 'id' attribute for a core element would check that attribute here.

bool libsbmlcs.QualModelPlugin.hasRequiredElements ( )

Checks if this plugin object has all the required elements.

Subclasses should override this function if they have their specific elements.

Returns: true if this plugin object has all the required elements, otherwise false will be returned.

void libsbmlcs.SBasePlugin.logUnknownElement	(	string	element,
		long	sbmlLevel,
		long	sbmlVersion,
		long	pkgVersion
	)

inherited

Helper to log a common type of error for elements.

void libsbmlcs.SBasePlugin.multiplyAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).

int libsbmlcs.SBasePlugin.prependStringToAllIdentifiers ( string prefix )

inherited

Add the given string to all identifiers in the object.

If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.

QualitativeSpecies libsbmlcs.QualModelPlugin.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. null is returned if the given index is out of range.

QualitativeSpecies libsbmlcs.QualModelPlugin.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. null is returned if the given index is out of range.

Transition libsbmlcs.QualModelPlugin.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. null is returned if the given index is out of range.

Transition libsbmlcs.QualModelPlugin.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. null is returned if the given index is out of range.

void libsbmlcs.SBasePlugin.replaceSIDWithFunction	(	string	id,
		ASTNode	function
	)

inherited

If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.

Note: This function does nothing itself–subclasses with ASTNode subelements must override this function.

int libsbmlcs.SBasePlugin.setElementNamespace ( string uri )

inherited

Sets the XML namespace to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Returns

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

bool libsbmlcs.SBasePlugin.stripPackage	(	string	pkgPrefix,
		bool	flag
	)

inherited

int libsbmlcs.SBasePlugin.transformIdentifiers ( IdentifierTransformer sidTransformer )

inherited

Member Data Documentation

bool libsbmlcs.SBasePlugin.swigCMemOwn

protectedinherited

Detailed Description

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation