ModifierSpeciesReference_t Class Reference

Detailed Description

A reference to an SBML modifier species.

Sometimes a species appears in the kinetic rate formula of a reaction but is itself neither created nor destroyed in that reaction (for example, because it acts as a catalyst or inhibitor). In SBML, all such species are simply called modifiers without regard to the detailed role of those species in the model. The Reaction_t structure provides a way to express which species act as modifiers in a given reaction. This is the purpose of the list of modifiers available in Reaction_t. The list contains instances of ModifierSpeciesReference_t structures.

The ModifierSpeciesReference_t structure inherits the mandatory attribute "species" and optional attributes "id" and "name" from the parent class SimpleSpeciesReference_t. See the description of SimpleSpeciesReference_t for more information about these.

The value of the "species" attribute must be the identifier of a species defined in the enclosing Model_t; this species is designated as a modifier for the current reaction. A reaction may have any number of modifiers. It is permissible for a modifier species to appear simultaneously in the list of reactants and products of the same reaction where it is designated as a modifier, as well as to appear in the list of reactants, products and modifiers of other reactions in the model.

Public Member Functions
ModifierSpeciesReference_t *	ModifierSpeciesReference_clone (ModifierSpeciesReference_t *msr)
	Creates a deep copy of the given ModifierSpeciesReference_t structure. More...
ModifierSpeciesReference_t *	ModifierSpeciesReference_create (unsigned int level, unsigned int version)
	Creates a new ModifierSpeciesReference_t structure using the given SBML level and version values. More...
ModifierSpeciesReference_t *	ModifierSpeciesReference_createWithNS (SBMLNamespaces_t *sbmlns)
	Creates a new ModifierSpeciesReference_t structure using the given SBMLNamespaces_t structure, sbmlns. More...
void	ModifierSpeciesReference_free (ModifierSpeciesReference_t *msr)
	Frees the given ModifierSpeciesReference_t structure. More...
const char *	ModifierSpeciesReference_getId (const ModifierSpeciesReference_t *msr)
	Returns the value of the "id" attribute of the given ModifierSpeciesReference_t structure. More...
const char *	ModifierSpeciesReference_getName (const ModifierSpeciesReference_t *msr)
	Returns the value of the "name" attribute of the given ModifierSpeciesReference_t structure. More...
const char *	ModifierSpeciesReference_getSpecies (const ModifierSpeciesReference_t *msr)
	Returns the value of the "species" attribute of the given ModifierSpeciesReference_t structure. More...
int	ModifierSpeciesReference_hasRequiredAttributes (const ModifierSpeciesReference_t *msr)
	Predicate returning 1 (true) or 0 (false) depending on whether all the required attributes of the given ModifierSpeciesReference_t structure have been set. More...
int	ModifierSpeciesReference_isSetId (const ModifierSpeciesReference_t *msr)
	Predicate returning 1 (true) if the given ModifierSpeciesReference_t structure's "id" is set. More...
int	ModifierSpeciesReference_isSetName (const ModifierSpeciesReference_t *msr)
	Predicate returning 1 (true) if the given ModifierSpeciesReference_t structure's "name" is set. More...
int	ModifierSpeciesReference_isSetSpecies (const ModifierSpeciesReference_t *msr)
	Predicate returning 1 (true) if the given ModifierSpeciesReference_t structure's "species" is set. More...
int	ModifierSpeciesReference_setId (ModifierSpeciesReference_t *msr, const char *id)
	Sets the "id" attribute of the given ModifierSpeciesReference_t structure. More...
int	ModifierSpeciesReference_setName (ModifierSpeciesReference_t *msr, const char *name)
	Sets the "name" attribute of the given ModifierSpeciesReference_t structure. More...
int	ModifierSpeciesReference_setSpecies (ModifierSpeciesReference_t *msr, const char *species)
	Sets the "species" attribute of the given ModifierSpeciesReference_t structure. More...
int	ModifierSpeciesReference_unsetId (ModifierSpeciesReference_t *msr)
	Unsets the value of the "id" attribute of the given ModifierSpeciesReference_t structure. More...
int	ModifierSpeciesReference_unsetName (ModifierSpeciesReference_t *msr)
	Unsets the value of the "name" attribute of the given ModifierSpeciesReference_t structure. More...
int	ModifierSpeciesReference_unsetSpecies (ModifierSpeciesReference_t *msr)
	Unsets the value of the "species" attribute of the given ModifierSpeciesReference_t structure. More...

Member Function Documentation

ModifierSpeciesReference_t * ModifierSpeciesReference_clone

(

ModifierSpeciesReference_t *

msr

)

Creates a deep copy of the given ModifierSpeciesReference_t structure.

Parameters

msr	the ModifierSpeciesReference_t structure to be copied.

Returns

a (deep) copy of the given ModifierSpeciesReference_t structure, or a null pointer if a failure occurred.

ModifierSpeciesReference_t * ModifierSpeciesReference_create	(	unsigned int	level,
		unsigned int	version
	)

Creates a new ModifierSpeciesReference_t structure using the given SBML level and version values.

Parameters

level	an unsigned int, the SBML level to assign to this ModifierSpeciesReference_t structure.
version	an unsigned int, the SBML version to assign to this ModifierSpeciesReference_t structure.

Returns

the newly-created ModifierSpeciesReference_t structure, or a null pointer if an error occurred during construction.

Note

Attempting to add an object to an SBMLDocument_t having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument_t), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute.

ModifierSpeciesReference_t * ModifierSpeciesReference_createWithNS

(

SBMLNamespaces_t *

sbmlns

)

Creates a new ModifierSpeciesReference_t structure using the given SBMLNamespaces_t structure, sbmlns.

The SBMLNamespaces_t 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_t facilities is to create an SBMLNamespaces_t object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces_t as arguments.

Parameters

sbmlns

an SBMLNamespaces_t structure.

Returns

the newly-created ModifierSpeciesReference_t structure, or a null pointer if an error occurred during construction.

Note

Attempting to add an object to an SBMLDocument_t having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument_t), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute.

void ModifierSpeciesReference_free

(

ModifierSpeciesReference_t *

msr

)

Frees the given ModifierSpeciesReference_t structure.

Parameters

msr	the ModifierSpeciesReference_t structure to be freed.

const char * ModifierSpeciesReference_getId

(

const ModifierSpeciesReference_t *

msr

)

Returns the value of the "id" attribute of the given ModifierSpeciesReference_t structure.

Parameters

msr	the ModifierSpeciesReference_t structure.

Returns

the id of this structure.

const char * ModifierSpeciesReference_getName

(

const ModifierSpeciesReference_t *

msr

)

Returns the value of the "name" attribute of the given ModifierSpeciesReference_t structure.

Parameters

msr	the ModifierSpeciesReference_t structure.

Returns

the name of this structure.

const char * ModifierSpeciesReference_getSpecies

(

const ModifierSpeciesReference_t *

msr

)

Returns the value of the "species" attribute of the given ModifierSpeciesReference_t structure.

Parameters

msr	the ModifierSpeciesReference_t structure.

Returns

the species of this structure.

int ModifierSpeciesReference_hasRequiredAttributes

(

const ModifierSpeciesReference_t *

msr

)

Predicate returning 1 (true) or 0 (false) depending on whether all the required attributes of the given ModifierSpeciesReference_t structure have been set.

Parameters

msr	the ModifierSpeciesReference_t structure to check.

Returns

1 (true) if all the required attributes for this structure have been defined, 0 (false) otherwise.

int ModifierSpeciesReference_isSetId

(

const ModifierSpeciesReference_t *

msr

)

Predicate returning 1 (true) if the given ModifierSpeciesReference_t structure's "id" is set.

Parameters

msr	the ModifierSpeciesReference_t structure.

Returns

1 (true) if the "id" of this ModifierSpeciesReference_t structure is set, 0 (false) otherwise.

int ModifierSpeciesReference_isSetName

(

const ModifierSpeciesReference_t *

msr

)

Predicate returning 1 (true) if the given ModifierSpeciesReference_t structure's "name" is set.

Parameters

msr	the ModifierSpeciesReference_t structure.

Returns

1 (true) if the "name" of this ModifierSpeciesReference_t structure is set, 0 (false) otherwise.

int ModifierSpeciesReference_isSetSpecies

(

const ModifierSpeciesReference_t *

msr

)

Predicate returning 1 (true) if the given ModifierSpeciesReference_t structure's "species" is set.

Parameters

msr	the ModifierSpeciesReference_t structure.

Returns

1 (true) if the "species" of this ModifierSpeciesReference_t structure is set, 0 (false) otherwise.

int ModifierSpeciesReference_setId	(	ModifierSpeciesReference_t *	msr,
		const char *	id
	)

Sets the "id" attribute of the given ModifierSpeciesReference_t structure.

This function copies the string given in id. If the string is a null pointer, this function is equivalent to calling ModifierSpeciesReference_unsetId().

Parameters

msr	the ModifierSpeciesReference_t structure.
id	the string to which the structures "id" attribute should be set.

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
• LIBSBML_INVALID_OBJECT

Note

Using this function with a null pointer for id is equivalent to unsetting the value of the "id" attribute.

int ModifierSpeciesReference_setName	(	ModifierSpeciesReference_t *	msr,
		const char *	name
	)

Sets the "name" attribute of the given ModifierSpeciesReference_t structure.

This function copies the string given in name. If the string is a null pointer, this function is equivalent to calling ModifierSpeciesReference_unsetName().

Parameters

msr	the ModifierSpeciesReference_t structure.
name	the string to which the structures "name" attribute should be set.

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
• LIBSBML_INVALID_OBJECT

Note

Using this function with a null pointer for name is equivalent to unsetting the value of the "name" attribute.

int ModifierSpeciesReference_setSpecies	(	ModifierSpeciesReference_t *	msr,
		const char *	species
	)

Sets the "species" attribute of the given ModifierSpeciesReference_t structure.

This function copies the string given in species. If the string is a null pointer, this function is equivalent to calling ModifierSpeciesReference_unsetSpecies().

Parameters

msr	the ModifierSpeciesReference_t structure.
species	the string to which the structures "species" attribute should be set.

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
• LIBSBML_INVALID_OBJECT

Note

Using this function with a null pointer for species is equivalent to unsetting the value of the "species" attribute.

int ModifierSpeciesReference_unsetId

(

ModifierSpeciesReference_t *

msr

)

Unsets the value of the "id" attribute of the given ModifierSpeciesReference_t structure.

Parameters

msr	the ModifierSpeciesReference_t structure.

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
• LIBSBML_INVALID_OBJECT

int ModifierSpeciesReference_unsetName

(

ModifierSpeciesReference_t *

msr

)

Unsets the value of the "name" attribute of the given ModifierSpeciesReference_t structure.

Parameters

msr	the ModifierSpeciesReference_t structure.

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
• LIBSBML_INVALID_OBJECT

int ModifierSpeciesReference_unsetSpecies

(

ModifierSpeciesReference_t *

msr

)

Unsets the value of the "species" attribute of the given ModifierSpeciesReference_t structure.

Parameters

msr	the ModifierSpeciesReference_t structure.

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
• LIBSBML_INVALID_OBJECT