QualitativeSpecies_t Class Reference

Detailed Description

qual Extension of Species_t.

Similarly to the Species_t in SBML, the components of qualitative models refer to pools of entities that are considered indistinguishable and are each located in a specific Compartment_t. However, here components are characterised by their qualitative influences rather than by taking part in reactions. Therefore, we define the QualitativeSpecies_t element to represent such pools of entities.

In a Petri net, qualitative species refer to the places of the model, while in a logical model, they refer to the variables of this model (i.e. nodes of the influence graph).

A QualitativeSpecies_t describes a pool of indistinguishable entities in a Compartment_t. It is associated with a level (an integer representing e.g. an activity state, or a functional level of concentration, etc.)

Public Member Functions
QualitativeSpecies_t *	QualitativeSpecies_clone (QualitativeSpecies_t *qs)
	Returns a copy of the given QualitativeSpecies_t structure. More...
QualitativeSpecies_t *	QualitativeSpecies_create (unsigned int level, unsigned int version, unsigned int pkgVersion)
	Creates a new QualitativeSpecies_t structure using the given SBML level and version, and the pkgVersion package version. More...
void	QualitativeSpecies_free (QualitativeSpecies_t *qs)
	Frees the given QualitativeSpecies_t structure. More...
char *	QualitativeSpecies_getCompartment (QualitativeSpecies_t *qs)
	Takes a QualitativeSpecies_t structure and returns its compartment. More...
int	QualitativeSpecies_getConstant (QualitativeSpecies_t *qs)
	Takes a QualitativeSpecies_t structure and returns its constant. More...
char *	QualitativeSpecies_getId (QualitativeSpecies_t *qs)
	Takes a QualitativeSpecies_t structure and returns its identifier. More...
int	QualitativeSpecies_getInitialLevel (QualitativeSpecies_t *qs)
	Takes a QualitativeSpecies_t structure and returns its initialLevel. More...
int	QualitativeSpecies_getMaxLevel (QualitativeSpecies_t *qs)
	Takes a QualitativeSpecies_t structure and returns its maxLevel. More...
char *	QualitativeSpecies_getName (QualitativeSpecies_t *qs)
	Takes a QualitativeSpecies_t structure and returns its name. More...
int	QualitativeSpecies_hasRequiredAttributes (QualitativeSpecies_t *qs)
	Predicate returning true or false depending on whether all the required attributes for the given QualitativeSpecies_t structure have been set. More...
int	QualitativeSpecies_isSetCompartment (QualitativeSpecies_t *qs)
	Predicate returning 1 (true) or 0 (false) depending on whether the given QualitativeSpecies_t structure's compartment is set. More...
int	QualitativeSpecies_isSetConstant (QualitativeSpecies_t *qs)
	Predicate returning 1 (true) or 0 (false) depending on whether the given QualitativeSpecies_t structure's constant is set. More...
int	QualitativeSpecies_isSetId (QualitativeSpecies_t *qs)
	Predicate returning 1 (true) or 0 (false) depending on whether the given QualitativeSpecies_t structure's identifier is set. More...
int	QualitativeSpecies_isSetInitialLevel (QualitativeSpecies_t *qs)
	Predicate returning 1 (true) or 0 (false) depending on whether the given QualitativeSpecies_t structure's initialLevel is set. More...
int	QualitativeSpecies_isSetMaxLevel (QualitativeSpecies_t *qs)
	Predicate returning 1 (true) or 0 (false) depending on whether the given QualitativeSpecies_t structure's maxLevel is set. More...
int	QualitativeSpecies_isSetName (QualitativeSpecies_t *qs)
	Predicate returning 1 (true) or 0 (false) depending on whether the given QualitativeSpecies_t structure's name is set. More...
int	QualitativeSpecies_setCompartment (QualitativeSpecies_t *qs, const char *compartment)
	Sets the compartment of the given QualitativeSpecies_t to a copy of compartment. More...
int	QualitativeSpecies_setConstant (QualitativeSpecies_t *qs, int constant)
	Sets the "constant" attribute of this QualitativeSpecies_t to constant. More...
int	QualitativeSpecies_setId (QualitativeSpecies_t *qs, const char *sid)
	Assigns the identifier of a QualitativeSpecies_t structure. More...
int	QualitativeSpecies_setInitialLevel (QualitativeSpecies_t *qs, int initialLevel)
	Sets the "initialLevel" attribute of the given QualitativeSpecies_t structure. More...
int	QualitativeSpecies_setMaxLevel (QualitativeSpecies_t *qs, int maxLevel)
	Sets the "maxLevel" attribute of the given QualitativeSpecies_t structure. More...
int	QualitativeSpecies_setName (QualitativeSpecies_t *qs, const char *name)
	Sets the name of the given QualitativeSpecies_t to a copy of name. More...
int	QualitativeSpecies_unsetCompartment (QualitativeSpecies_t *qs)
	Unsets the "compartment" attribute of the given QualitativeSpecies_t structure. More...
int	QualitativeSpecies_unsetConstant (QualitativeSpecies_t *qs)
	Unsets the "constant" attribute of the given QualitativeSpecies_t structure. More...
int	QualitativeSpecies_unsetId (QualitativeSpecies_t *qs)
	Unsets the "id" attribute of the given QualitativeSpecies_t structure. More...
int	QualitativeSpecies_unsetInitialLevel (QualitativeSpecies_t *qs)
	Unsets the "initialLevel" attribute of the given QualitativeSpecies_t structure. More...
int	QualitativeSpecies_unsetMaxLevel (QualitativeSpecies_t *qs)
	Unsets the "maxLevel" attribute of the given QualitativeSpecies_t structure. More...
int	QualitativeSpecies_unsetName (QualitativeSpecies_t *qs)
	Unsets the "name" attribute of the given QualitativeSpecies_t structure. More...

Member Function Documentation

QualitativeSpecies_t * QualitativeSpecies_clone

(

QualitativeSpecies_t *

qs

)

Returns a copy of the given QualitativeSpecies_t structure.

Parameters

qs	the QualitativeSpecies_t structure to copy.

Returns

a (deep) copy of the QualitativeSpecies_t.

QualitativeSpecies_t * QualitativeSpecies_create	(	unsigned int	level,
		unsigned int	version,
		unsigned int	pkgVersion
	)

Creates a new QualitativeSpecies_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 QualitativeSpecies_t.
version	an unsigned int, the SBML Version to assign to this QualitativeSpecies_t.
pkgVersion	an unsigned int, the SBML 'Qual' package Version to assign to this QualitativeSpecies_t.

Returns

a pointer to the newly created QualitativeSpecies_t structure.

void QualitativeSpecies_free

(

QualitativeSpecies_t *

qs

)

Frees the given QualitativeSpecies_t structure.

Parameters

qs	the QualitativeSpecies_t structure to free.

char * QualitativeSpecies_getCompartment

(

QualitativeSpecies_t *

qs

)

Takes a QualitativeSpecies_t structure and returns its compartment.

Parameters

qs	the QualitativeSpecies_t whose compartment is sought.

Returns

the compartment of the given QualitativeSpecies_t, as a pointer to a string.

int QualitativeSpecies_getConstant

(

QualitativeSpecies_t *

qs

)

Takes a QualitativeSpecies_t structure and returns its constant.

Parameters

qs	the QualitativeSpecies_t whose constant is sought.

Returns

1 (true) if the given QualitativeSpecies_t structure's "constant" attribute value is nonzero, 0 (false) otherwise.

char * QualitativeSpecies_getId

(

QualitativeSpecies_t *

qs

)

Takes a QualitativeSpecies_t structure and returns its identifier.

Parameters

qs	the QualitativeSpecies_t structure whose identifier is sought.

Returns

the identifier of this QualitativeSpecies_t, as a pointer to a string.

int QualitativeSpecies_getInitialLevel

(

QualitativeSpecies_t *

qs

)

Takes a QualitativeSpecies_t structure and returns its initialLevel.

Parameters

qs	the QualitativeSpecies_t whose initialLevel is sought.

Returns

the initialLevel attribute of the given QualitativeSpecies_t, as an int.

int QualitativeSpecies_getMaxLevel

(

QualitativeSpecies_t *

qs

)

Takes a QualitativeSpecies_t structure and returns its maxLevel.

Parameters

qs	the QualitativeSpecies_t whose maxLevel is sought.

Returns

the maxLevel attribute of the given QualitativeSpecies_t, as an int.

char * QualitativeSpecies_getName

(

QualitativeSpecies_t *

qs

)

Takes a QualitativeSpecies_t structure and returns its name.

Parameters

qs	the QualitativeSpecies_t whose name is sought.

Returns

the name of this QualitativeSpecies_t, as a pointer to a string.

int QualitativeSpecies_hasRequiredAttributes

(

QualitativeSpecies_t *

qs

)

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

Note

The required attributes for a QualitativeSpecies_t structure are:

• id
• compartment
• constant

int QualitativeSpecies_isSetCompartment

(

QualitativeSpecies_t *

qs

)

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

Parameters

qs	the QualitativeSpecies_t structure to query.

Returns

1 (true) if the "compartment" attribute of the given QualitativeSpecies_t structure is set, 0 (false) otherwise.

int QualitativeSpecies_isSetConstant

(

QualitativeSpecies_t *

qs

)

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

Parameters

qs	the QualitativeSpecies_t structure to query.

Returns

1 (true) if the "constant" attribute of the given QualitativeSpecies_t structure is set, 0 (false) otherwise.

int QualitativeSpecies_isSetId

(

QualitativeSpecies_t *

qs

)

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

Parameters

qs	the QualitativeSpecies_t structure to query.

Returns

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

int QualitativeSpecies_isSetInitialLevel

(

QualitativeSpecies_t *

qs

)

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

Parameters

qs	the QualitativeSpecies_t structure to query.

Returns

1 (true) if the "initialLevel" attribute of the given QualitativeSpecies_t structure is set, 0 (false) otherwise.

int QualitativeSpecies_isSetMaxLevel

(

QualitativeSpecies_t *

qs

)

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

Parameters

qs	the QualitativeSpecies_t structure to query.

Returns

1 (true) if the "maxLevel" attribute of the given QualitativeSpecies_t structure is set, 0 (false) otherwise.

int QualitativeSpecies_isSetName

(

QualitativeSpecies_t *

qs

)

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

Parameters

qs	the QualitativeSpecies_t structure to query.

Returns

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

int QualitativeSpecies_setCompartment	(	QualitativeSpecies_t *	qs,
		const char *	compartment
	)

Sets the compartment of the given QualitativeSpecies_t to a copy of compartment.

Parameters

qs	the QualitativeSpecies_t structure to set.
compartment	the compartment to assign to the given QualitativeSpecies_t's "compartment" 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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

Note

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

int QualitativeSpecies_setConstant	(	QualitativeSpecies_t *	qs,
		int	constant
	)

Sets the "constant" attribute of this QualitativeSpecies_t to constant.

Parameters

qs	the QualitativeSpecies_t structure to set.
constant	the value of the "constant" attribute, converted to a boolean: all nonzero values set the "constant" attribute to 'true', and a value of 0 (zero) will set the "constant" attribute to 'false'.

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
• LIBSBML_UNEXPECTED_ATTRIBUTE

int QualitativeSpecies_setId	(	QualitativeSpecies_t *	qs,
		const char *	sid
	)

Assigns the identifier of a QualitativeSpecies_t structure.

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

Parameters

qs	the QualitativeSpecies_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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

Note

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

int QualitativeSpecies_setInitialLevel	(	QualitativeSpecies_t *	qs,
		int	initialLevel
	)

Sets the "initialLevel" attribute of the given QualitativeSpecies_t structure.

Parameters

qs	the QualitativeSpecies_t structure.
initialLevel	the value of initialLevel to assign to the "initialLevel" 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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_UNEXPECTED_ATTRIBUTE

int QualitativeSpecies_setMaxLevel	(	QualitativeSpecies_t *	qs,
		int	maxLevel
	)

Sets the "maxLevel" attribute of the given QualitativeSpecies_t structure.

Parameters

qs	the QualitativeSpecies_t structure.
maxLevel	the value of maxLevel to assign to the "maxLevel" 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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_UNEXPECTED_ATTRIBUTE

int QualitativeSpecies_setName	(	QualitativeSpecies_t *	qs,
		const char *	name
	)

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

Parameters

qs	the QualitativeSpecies_t structure to set.
name	the name to assign to the given QualitativeSpecies_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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

Note

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

int QualitativeSpecies_unsetCompartment

(

QualitativeSpecies_t *

qs

)

Unsets the "compartment" attribute of the given QualitativeSpecies_t structure.

Parameters

qs	the QualitativeSpecies_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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

int QualitativeSpecies_unsetConstant

(

QualitativeSpecies_t *

qs

)

Unsets the "constant" attribute of the given QualitativeSpecies_t structure.

Parameters

qs	the QualitativeSpecies_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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

int QualitativeSpecies_unsetId

(

QualitativeSpecies_t *

qs

)

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

Parameters

qs	the QualitativeSpecies_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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

int QualitativeSpecies_unsetInitialLevel

(

QualitativeSpecies_t *

qs

)

Unsets the "initialLevel" attribute of the given QualitativeSpecies_t structure.

Parameters

qs	the QualitativeSpecies_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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

int QualitativeSpecies_unsetMaxLevel

(

QualitativeSpecies_t *

qs

)

Unsets the "maxLevel" attribute of the given QualitativeSpecies_t structure.

Parameters

qs	the QualitativeSpecies_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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

int QualitativeSpecies_unsetName

(

QualitativeSpecies_t *

qs

)

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

Parameters

qs	the QualitativeSpecies_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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED