Detailed Description

qual A transition of a QualitativeSpecies_t.

A Transition_t element contains at most one ListOfInputs_t and one ListOfOutputs_t and exactly one ListOfFunctionTerms_t.

A Transition_t defines the changes in level associated with the QualitativeSpecies_t that occur when a Transition_t is enabled.

In logical models, a Transition_t is used to specify the logical rule associated with a QualitativeSpecies_t (that appears as an Output_t of this Transition_t). For example, the rule "if A > 1 : B = 2" would be encapsulated as a Transition_t with QualitativeSpecies_t "A" as an Input_t and "B" as an Output_t; the "if A > 1" rule being encode by the math element of a FunctionTerm_t with the resultLevel attribute having a value "2".

In Petri net models, a Transition_t is interpreted, using the common Petri net semantics, as events that might occur within the system causing tokens to be moved.

Public Member Functions
int	Transition_addFunctionTerm (Transition_t t, FunctionTerm_t ft)
	Appends a copy of the given FunctionTerm_t structure to the given Transition_t structure. More...

int	Transition_addInput (Transition_t t, Input_t i)
	Appends a copy of the given Input_t structure to the given Transition_t structure. More...

int	Transition_addOutput (Transition_t t, Output_t o)
	Appends a copy of the given Output_t structure to the given Transition_t structure. More...

Transition_t *	Transition_clone (Transition_t *t)
	Returns a copy of the given Transition_t structure. More...

Transition_t *	Transition_create (unsigned int level, unsigned int version, unsigned int pkgVersion)
	Creates a new Transition_t structure using the given SBML `level` and `version`, and the `pkgVersion` package version. More...

FunctionTerm_t *	Transition_createFunctionTerm (Transition_t *t)
	Creates a new, empty FunctionTerm_t structure, adds it to the given Transition_t, and returns the FunctionTerm_t. More...

Input_t *	Transition_createInput (Transition_t *t)
	Creates a new, empty Input_t structure, adds it to the given Transition_t, and returns the Input_t. More...

Output_t *	Transition_createOutput (Transition_t *t)
	Creates a new, empty Output_t structure, adds it to the given Transition_t, and returns the Output_t. More...

void	Transition_free (Transition_t *t)
	Frees the given Transition_t structure. More...

FunctionTerm_t *	Transition_getFunctionTerm (Transition_t *t, unsigned int n)
	Return a specific FunctionTerm_t structure of the given Transition_t. More...

FunctionTerm_t *	Transition_getFunctionTermById (Transition_t t, const char sid)
	Return the FunctionTerm_t indicated by the given `sid`. More...

char *	Transition_getId (Transition_t *t)
	Takes an Transition_t structure and returns its identifier. More...

Input_t *	Transition_getInput (Transition_t *t, unsigned int n)
	Return a specific Input_t structure of the given Transition_t. More...

Input_t *	Transition_getInputById (Transition_t t, const char sid)
	Return the Input_t indicated by the given `sid`. More...

ListOf_t *	Transition_getListOfFunctionTerms (Transition_t *t)
	Get the list of FunctionTerm_t structures from the given Transition_t structure. More...

ListOf_t *	Transition_getListOfInputs (Transition_t *t)
	Get the list of Input_t structures from the given Transition_t structure. More...

ListOf_t *	Transition_getListOfOutputs (Transition_t *t)
	Get the list of Output_t structures from the given Transition_t structure. More...

char *	Transition_getName (Transition_t *t)
	Takes a Transition_t structure and returns its name. More...

unsigned int	Transition_getNumFunctionTerms (Transition_t *t)
	Returns the number of EventAssignment_t structures attached to the given Transition_t. More...

unsigned int	Transition_getNumInputs (Transition_t *t)
	Returns the number of EventAssignment_t structures attached to the given Transition_t. More...

unsigned int	Transition_getNumOutputs (Transition_t *t)
	Returns the number of EventAssignment_t structures attached to the given Transition_t. More...

Output_t *	Transition_getOutput (Transition_t *t, unsigned int n)
	Return a specific Output_t structure of the given Transition_t. More...

Output_t *	Transition_getOutputById (Transition_t t, const char sid)
	Return the Output_t indicated by the given `sid`. More...

int	Transition_hasRequiredAttributes (Transition_t *t)
	Predicate returning `true` or `false` depending on whether all the required attributes for the given Transition_t structure have been set. More...

int	Transition_hasRequiredElements (Transition_t *t)
	Predicate returning `true` or `false` depending on whether all the required elements for the given Transition_t structure have been set. More...

int	Transition_isSetId (Transition_t *t)
	Predicate returning `1` (true) or `0` (false) depending on whether the given Transition_t structure's identifier is set. More...

int	Transition_isSetName (Transition_t *t)
	Predicate returning `1` (true) or `0` (false) depending on whether the given Transition_t structure's name is set. More...

FunctionTerm_t *	Transition_removeFunctionTerm (Transition_t *t, unsigned int n)
	Removes the nth FunctionTerm_t structure from the given Transition_t structure and returns a pointer to it. More...

FunctionTerm_t *	Transition_removeFunctionTermById (Transition_t t, const char sid)
	Removes the FunctionTerm_t structure with the given `sid` from the given Transition_t structure and returns a pointer to it. More...

Input_t *	Transition_removeInput (Transition_t *t, unsigned int n)
	Removes the nth Input_t structure from the given Transition_t structure and returns a pointer to it. More...

Input_t *	Transition_removeInputById (Transition_t t, const char sid)
	Removes the Input_t structure with the given `sid` from the given Transition_t structure and returns a pointer to it. More...

Output_t *	Transition_removeOutput (Transition_t *t, unsigned int n)
	Removes the nth Output_t structure from the given Transition_t structure and returns a pointer to it. More...

Output_t *	Transition_removeOutputById (Transition_t t, const char sid)
	Removes the Output_t structure with the given `sid` from the given Transition_t structure and returns a pointer to it. More...

int	Transition_setId (Transition_t t, const char sid)
	Assigns the identifier of an Transition_t structure. More...

int	Transition_setName (Transition_t t, const char name)
	Sets the name of the given Transition_t to a copy of `name`. More...

int	Transition_unsetId (Transition_t *t)
	Unsets the "id" attribute of the given Transition_t structure. More...

int	Transition_unsetName (Transition_t *t)
	Unsets the "name" attribute of the given Transition_t structure. More...

Member Function Documentation

int Transition_addFunctionTerm	(	Transition_t *	t,
		FunctionTerm_t *	ft
	)

Appends a copy of the given FunctionTerm_t structure to the given Transition_t structure.

Parameters

t	the Transition_t structure to which the FunctionTerm_t should be added.
ft	a FunctionTerm_t structure to add.

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:

int Transition_addInput	(	Transition_t *	t,
		Input_t *	i
	)

Appends a copy of the given Input_t structure to the given Transition_t structure.

Parameters

t	the Transition_t structure to which the Input_t should be added.
i	an Input_t structure to add.

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:

int Transition_addOutput	(	Transition_t *	t,
		Output_t *	o
	)

Appends a copy of the given Output_t structure to the given Transition_t structure.

Parameters

t	the Transition_t structure to which the Output_t should be added.
o	an Output_t structure to add.

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:

Transition_t * Transition_clone ( Transition_t * t )

Returns a copy of the given Transition_t structure.

Parameters

t	the Transition_t structure to copy.

Returns: a (deep) copy of the Transition_t.

Transition_t * Transition_create	(	unsigned int	level,
		unsigned int	version,
		unsigned int	pkgVersion
	)

Creates a new Transition_t structure using the given SBML level and version, and the pkgVersion package version.

Parameters

level	an unsigned int, the SBML Level to assign to this Transition_t.
version	an unsigned int, the SBML Version to assign to this Transition_t.
pkgVersion	an unsigned int, the SBML 'Qual' package Version to assign to this Transition_t.

Returns: a pointer to the newly created Transition_t structure.

FunctionTerm_t * Transition_createFunctionTerm ( Transition_t * t )

Creates a new, empty FunctionTerm_t structure, adds it to the given Transition_t, and returns the FunctionTerm_t.

Parameters

t	the Transition_t structure to which the FunctionTerm_t should be added.

Returns: the newly-created empty FunctionTerm_t.

Input_t * Transition_createInput ( Transition_t * t )

Creates a new, empty Input_t structure, adds it to the given Transition_t, and returns the Input_t.

Parameters

t	the Transition_t structure to which the Input_t should be added.

Returns: the newly-created empty Input_t.

Output_t * Transition_createOutput ( Transition_t * t )

Creates a new, empty Output_t structure, adds it to the given Transition_t, and returns the Output_t.

Parameters

t	the Transition_t structure to which the Output_t should be added.

Returns: the newly-created empty Output_t.

void Transition_free ( Transition_t * t )

Frees the given Transition_t structure.

Parameters

t	the Transition_t structure to free.

FunctionTerm_t * Transition_getFunctionTerm	(	Transition_t *	t,
		unsigned int	n
	)

Return a specific FunctionTerm_t structure of the given Transition_t.

Parameters

t	the Transition_t structure to use.
n	an integer, the index of the FunctionTerm_t structure to return.

Returns: the nth FunctionTerm_t of the given Transition_t, or NULL if no such FunctionTerm_t exists.

FunctionTerm_t * Transition_getFunctionTermById	(	Transition_t *	t,
		const char *	sid
	)

Return the FunctionTerm_t indicated by the given sid.

Parameters

t	the Transition_t structure to use.
sid	a string, the identifier of the FunctionTerm_t being sought.

Returns: the FunctionTerm_t for the given variable, or NULL if no such FunctionTerm_t exists.

char * Transition_getId ( Transition_t * t )

Takes an Transition_t structure and returns its identifier.

Parameters

t	the Transition_t structure whose identifier is sought.

Returns: the identifier of this Transition_t, as a pointer to a string.

Input_t * Transition_getInput	(	Transition_t *	t,
		unsigned int	n
	)

Return a specific Input_t structure of the given Transition_t.

Parameters

t	the Transition_t structure to use.
n	an integer, the index of the Input_t structure to return.

Returns: the nth Input_t of the given Transition_t, or NULL if no such Input_t exists.

Input_t * Transition_getInputById	(	Transition_t *	t,
		const char *	sid
	)

Return the Input_t indicated by the given sid.

Parameters

t	the Transition_t structure to use.
sid	a string, the identifier of the Input_t being sought.

Returns: the Input_t for the given variable, or NULL if no such Input_t exists.

ListOf_t * Transition_getListOfFunctionTerms ( Transition_t * t )

Get the list of FunctionTerm_t structures from the given Transition_t structure.

Parameters

t	the Transition_t structure to use.

Returns: the list of FunctionTerm_t's for the given Transition_t.

ListOf_t * Transition_getListOfInputs ( Transition_t * t )

Get the list of Input_t structures from the given Transition_t structure.

Parameters

t	the Transition_t structure to use.

Returns: the list of Input_t's for the given Transition_t.

ListOf_t * Transition_getListOfOutputs ( Transition_t * t )

Get the list of Output_t structures from the given Transition_t structure.

Parameters

t	the Transition_t structure to use.

Returns: the list of Output_t's for the given Transition_t.

char * Transition_getName ( Transition_t * t )

Takes a Transition_t structure and returns its name.

Parameters

t	the Transition_t whose name is sought.

Returns: the name of this Transition_t, as a pointer to a string.

unsigned int Transition_getNumFunctionTerms ( Transition_t * t )

Returns the number of EventAssignment_t structures attached to the given Transition_t.

Parameters

t	the Transition_t structure to use.

Returns: the number of EventAssignment_t structures in the given Transition_t.

unsigned int Transition_getNumInputs ( Transition_t * t )

Returns the number of EventAssignment_t structures attached to the given Transition_t.

Parameters

t	the Transition_t structure to use.

Returns: the number of EventAssignment_t structures in the given Transition_t.

unsigned int Transition_getNumOutputs ( Transition_t * t )

Returns the number of EventAssignment_t structures attached to the given Transition_t.

Parameters

t	the Transition_t structure to use.

Returns: the number of EventAssignment_t structures in the given Transition_t.

Output_t * Transition_getOutput	(	Transition_t *	t,
		unsigned int	n
	)

Return a specific Output_t structure of the given Transition_t.

Parameters

t	the Transition_t structure to use.
n	an integer, the index of the Output_t structure to return.

Returns: the nth Output_t of the given Transition_t, or NULL if no such Output_t exists.

Output_t * Transition_getOutputById	(	Transition_t *	t,
		const char *	sid
	)

Return the Output_t indicated by the given sid.

Parameters

t	the Transition_t structure to use.
sid	a string, the identifier of the Output_t being sought.

Returns: the Output_t for the given variable, or NULL if no such Output_t exists.

int Transition_hasRequiredAttributes ( Transition_t * t )

Predicate returning true or false depending on whether all the required attributes for the given Transition_t structure have been set.

int Transition_hasRequiredElements ( Transition_t * t )

Predicate returning true or false depending on whether all the required elements for the given Transition_t structure have been set.

Note

The required elements for an Transition_t structure are:

a "defaultTerm" child of the child ListOfFunctionTerms_t.

int Transition_isSetId ( Transition_t * t )

Predicate returning 1 (true) or 0 (false) depending on whether the given Transition_t structure's identifier is set.

Parameters

t	the Transition_t structure to query.

Returns: 1 (true) if the "id" attribute of the given Transition_t structure is set, 0 (false) otherwise.

int Transition_isSetName ( Transition_t * t )

Predicate returning 1 (true) or 0 (false) depending on whether the given Transition_t structure's name is set.

Parameters

t	the Transition_t structure to query.

Returns: 1 (true) if the "name" attribute of the given Transition_t structure is set, 0 (false) otherwise.

FunctionTerm_t * Transition_removeFunctionTerm	(	Transition_t *	t,
		unsigned int	n
	)

Removes the nth FunctionTerm_t structure from the given Transition_t structure and returns a pointer to it.

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

Parameters

t	the Transition_t structure.
n	the integer index of the FunctionTerm_t sought.

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

FunctionTerm_t * Transition_removeFunctionTermById	(	Transition_t *	t,
		const char *	sid
	)

Removes the FunctionTerm_t structure with the given sid from the given Transition_t structure and returns a pointer to it.

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

Parameters

t	the Transition_t structure.
sid	the string of the "id" attribute of the FunctionTerm_t sought.

Returns: the FunctionTerm_t structure removed. As mentioned above, the caller owns the returned structure. NULL is returned if no FunctionTerm_t structure with the "id" attribute exists in the given Transition_t structure.

Input_t * Transition_removeInput	(	Transition_t *	t,
		unsigned int	n
	)

Removes the nth Input_t structure from the given Transition_t structure and returns a pointer to it.

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

Parameters

t	the Transition_t structure.
n	the integer index of the Input_t sought.

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

Input_t * Transition_removeInputById	(	Transition_t *	t,
		const char *	sid
	)

Removes the Input_t structure with the given sid from the given Transition_t structure and returns a pointer to it.

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

Parameters

t	the Transition_t structure.
sid	the string of the "id" attribute of the Input_t sought.

Returns: the Input_t structure removed. As mentioned above, the caller owns the returned structure. NULL is returned if no Input_t structure with the "id" attribute exists in the given Transition_t structure.

Output_t * Transition_removeOutput	(	Transition_t *	t,
		unsigned int	n
	)

Removes the nth Output_t structure from the given Transition_t structure and returns a pointer to it.

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

Parameters

t	the Transition_t structure.
n	the integer index of the Output_t sought.

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

Output_t * Transition_removeOutputById	(	Transition_t *	t,
		const char *	sid
	)

Removes the Output_t structure with the given sid from the given Transition_t structure and returns a pointer to it.

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

Parameters

t	the Transition_t structure.
sid	the string of the "id" attribute of the Output_t sought.

Returns: the Output_t structure removed. As mentioned above, the caller owns the returned structure. NULL is returned if no Output_t structure with the "id" attribute exists in the given Transition_t structure.

int Transition_setId	(	Transition_t *	t,
		const char *	sid
	)

Assigns the identifier of an Transition_t structure.

This makes a copy of the string passed in the parameter sid.

Parameters

t	the Transition_t structure to set.
sid	the string to use as the identifier.

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:

Note: Using this function with an sid of NULL is equivalent to unsetting the "id" attribute.

int Transition_setName	(	Transition_t *	t,
		const char *	name
	)

Sets the name of the given Transition_t to a copy of name.

Parameters

t	the Transition_t structure to set.
name	the name to assign to the given Transition_t's "name" 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:

Note: Using this function with the name set to NULL is equivalent to unsetting the "name" attribute.

int Transition_unsetId ( Transition_t * t )

Unsets the "id" attribute of the given Transition_t structure.

Parameters

t	the Transition_t structure to unset.

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:

int Transition_unsetName ( Transition_t * t )

Unsets the "name" attribute of the given Transition_t structure.

Parameters

t	the Transition_t structure to unset.

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

Member Function Documentation