SpeciesFeature_t Class Reference

Detailed Description

multi Defines a feature of a multi Species_t.

Each SpeciesFeature_t object is a child of the MultiSpeciesPlugin_t, which extends the Species_t. Each defines one feature of the parent Species_t. It has three optional attributes, "id", "name" and "component", and two required attributes, "speciesFeatureType" and "occur", and a required child ListOfSpeciesFeatureValues_t. SpeciesFeature_t serves to define the state of a component in a species by selecting values from the ListOfPossibleSpeciesFeatureValues_t of the referenced SpeciesFeatureType_t. Its "speciesFeatureType" attribue references the particular SpeciesFeatureType_t of which this Species_t is an example. The "occur" attribute defines the number of instances of the referenced SpeciesFeatureType_t. The optional "component" attribute, of type SIdRef, can be used to indicate which component of a Species_t the SpeciesFeature_t belongs to, and is required when the component cannot be identified only based on the speciesFeatureType attribute. The ListOfSpeciesFeatureValues_t contain one or more SpeciesFeatureValue_t objects—if more than one, the relationship between them is "or", defining a list of mutually exclusive possibilities. Each SpeciesFeatureValue_t serves to specify a value for a SpeciesFeature_t to select from the ListOfPossibleSpeciesFeatureValues_t defined in the referenced SpeciesFeatureType_t.

Public Member Functions
int	SpeciesFeature_addSpeciesFeatureValue (SpeciesFeature_t *sf, const SpeciesFeatureValue_t *sfv)
	Adds a copy of the given SpeciesFeatureValue_t to this SpeciesFeature_t. More...
SpeciesFeature_t *	SpeciesFeature_clone (const SpeciesFeature_t *sf)
	Creates and returns a deep copy of this SpeciesFeature_t object. More...
SpeciesFeature_t *	SpeciesFeature_create (unsigned int level, unsigned int version, unsigned int pkgVersion)
	Creates a new SpeciesFeature_t using the given SBML Level, Version and “multi” package version. More...
SpeciesFeatureValue_t *	SpeciesFeature_createSpeciesFeatureValue (SpeciesFeature_t *sf)
	Creates a new SpeciesFeatureValue_t object, adds it to this SpeciesFeature_t object and returns the SpeciesFeatureValue_t object created. More...
void	SpeciesFeature_free (SpeciesFeature_t *sf)
	Frees this SpeciesFeature_t object. More...
char *	SpeciesFeature_getComponent (const SpeciesFeature_t *sf)
	Returns the value of the "component" attribute of this SpeciesFeature_t. More...
char *	SpeciesFeature_getId (const SpeciesFeature_t *sf)
	Returns the value of the "id" attribute of this SpeciesFeature_t. More...
ListOf_t *	SpeciesFeature_getListOfSpeciesFeatureValues (SpeciesFeature_t *sf)
	Returns a ListOf_t * containing SpeciesFeatureValue_t objects from this SpeciesFeature_t. More...
char *	SpeciesFeature_getName (const SpeciesFeature_t *sf)
	Returns the value of the "name" attribute of this SpeciesFeature_t. More...
unsigned int	SpeciesFeature_getNumSpeciesFeatureValues (SpeciesFeature_t *sf)
	Get the number of SpeciesFeatureValue_t objects in this SpeciesFeature_t. More...
unsigned int	SpeciesFeature_getOccur (const SpeciesFeature_t *sf)
	Returns the value of the "occur" attribute of this SpeciesFeature_t. More...
char *	SpeciesFeature_getSpeciesFeatureType (const SpeciesFeature_t *sf)
	Returns the value of the "speciesFeatureType" attribute of this SpeciesFeature_t. More...
SpeciesFeatureValue_t *	SpeciesFeature_getSpeciesFeatureValue (SpeciesFeature_t *sf, unsigned int n)
	Get a SpeciesFeatureValue_t from the SpeciesFeature_t. More...
int	SpeciesFeature_hasRequiredAttributes (const SpeciesFeature_t *sf)
	Predicate returning 1 (true) if all the required attributes for this SpeciesFeature_t object have been set. More...
int	SpeciesFeature_isSetComponent (const SpeciesFeature_t *sf)
	Predicate returning 1 (true) if this SpeciesFeature_t's "component" attribute is set. More...
int	SpeciesFeature_isSetId (const SpeciesFeature_t *sf)
	Predicate returning 1 (true) if this SpeciesFeature_t's "id" attribute is set. More...
int	SpeciesFeature_isSetName (const SpeciesFeature_t *sf)
	Predicate returning 1 (true) if this SpeciesFeature_t's "name" attribute is set. More...
int	SpeciesFeature_isSetOccur (const SpeciesFeature_t *sf)
	Predicate returning 1 (true) if this SpeciesFeature_t's "occur" attribute is set. More...
int	SpeciesFeature_isSetSpeciesFeatureType (const SpeciesFeature_t *sf)
	Predicate returning 1 (true) if this SpeciesFeature_t's "speciesFeatureType" attribute is set. More...
SpeciesFeatureValue_t *	SpeciesFeature_removeSpeciesFeatureValue (SpeciesFeature_t *sf, unsigned int n)
	Removes the nth SpeciesFeatureValue_t from this SpeciesFeature_t and returns a pointer to it. More...
int	SpeciesFeature_setComponent (SpeciesFeature_t *sf, const char *component)
	Sets the value of the "component" attribute of this SpeciesFeature_t. More...
int	SpeciesFeature_setId (SpeciesFeature_t *sf, const char *id)
	Sets the value of the "id" attribute of this SpeciesFeature_t. More...
int	SpeciesFeature_setName (SpeciesFeature_t *sf, const char *name)
	Sets the value of the "name" attribute of this SpeciesFeature_t. More...
int	SpeciesFeature_setOccur (SpeciesFeature_t *sf, unsigned int occur)
	Sets the value of the "occur" attribute of this SpeciesFeature_t. More...
int	SpeciesFeature_setSpeciesFeatureType (SpeciesFeature_t *sf, const char *speciesFeatureType)
	Sets the value of the "speciesFeatureType" attribute of this SpeciesFeature_t. More...
int	SpeciesFeature_unsetComponent (SpeciesFeature_t *sf)
	Unsets the value of the "component" attribute of this SpeciesFeature_t. More...
int	SpeciesFeature_unsetId (SpeciesFeature_t *sf)
	Unsets the value of the "id" attribute of this SpeciesFeature_t. More...
int	SpeciesFeature_unsetName (SpeciesFeature_t *sf)
	Unsets the value of the "name" attribute of this SpeciesFeature_t. More...
int	SpeciesFeature_unsetOccur (SpeciesFeature_t *sf)
	Unsets the value of the "occur" attribute of this SpeciesFeature_t. More...
int	SpeciesFeature_unsetSpeciesFeatureType (SpeciesFeature_t *sf)
	Unsets the value of the "speciesFeatureType" attribute of this SpeciesFeature_t. More...

Member Function Documentation

int SpeciesFeature_addSpeciesFeatureValue	(	SpeciesFeature_t *	sf,
		const SpeciesFeatureValue_t *	sfv
	)

Adds a copy of the given SpeciesFeatureValue_t to this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure to which the SpeciesFeatureValue_t should be added.
sfv	the SpeciesFeatureValue_t object 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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT
• LIBSBML_LEVEL_MISMATCH
• LIBSBML_VERSION_MISMATCH
• LIBSBML_PKG_VERSION_MISMATCH
• LIBSBML_DUPLICATE_OBJECT_ID

SpeciesFeature_t * SpeciesFeature_clone

(

const SpeciesFeature_t *

sf

)

Creates and returns a deep copy of this SpeciesFeature_t object.

Parameters

sf	the SpeciesFeature_t structure.

Returns

a (deep) copy of this SpeciesFeature_t object.

Warning

The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf_appendAndOwn() or ListOf_insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

SpeciesFeature_t * SpeciesFeature_create	(	unsigned int	level,
		unsigned int	version,
		unsigned int	pkgVersion
	)

Creates a new SpeciesFeature_t using the given SBML Level, Version and “multi” package version.

Parameters

level	an unsigned int, the SBML Level to assign to this SpeciesFeature_t.
version	an unsigned int, the SBML Version to assign to this SpeciesFeature_t.
pkgVersion	an unsigned int, the SBML Multi Version to assign to this SpeciesFeature_t.

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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.

Warning

The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf_appendAndOwn() or ListOf_insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

SpeciesFeatureValue_t * SpeciesFeature_createSpeciesFeatureValue

(

SpeciesFeature_t *

sf

)

Creates a new SpeciesFeatureValue_t object, adds it to this SpeciesFeature_t object and returns the SpeciesFeatureValue_t object created.

Parameters

sf	the SpeciesFeature_t structure to which the SpeciesFeatureValue_t should be added.

Returns

a new SpeciesFeatureValue_t object instance.

Note

The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

void SpeciesFeature_free

(

SpeciesFeature_t *

sf

)

Frees this SpeciesFeature_t object.

Parameters

sf	the SpeciesFeature_t structure.

char * SpeciesFeature_getComponent

(

const SpeciesFeature_t *

sf

)

Returns the value of the "component" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure whose component is sought.

Returns

the value of the "component" attribute of this SpeciesFeature_t as a pointer to a string.

Warning

The string returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the string will not be reflected in any resulting SBML document unless the string is added to an SBML Document. Even in this case, the string should be deleted, as adding a string to an SBML Document adds a copy of the string, and does not transfer ownership of that string.

char * SpeciesFeature_getId

(

const SpeciesFeature_t *

sf

)

Returns the value of the "id" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure whose id is sought.

Returns

the value of the "id" attribute of this SpeciesFeature_t as a pointer to a string.

Warning

The string returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the string will not be reflected in any resulting SBML document unless the string is added to an SBML Document. Even in this case, the string should be deleted, as adding a string to an SBML Document adds a copy of the string, and does not transfer ownership of that string.

ListOf_t * SpeciesFeature_getListOfSpeciesFeatureValues

(

SpeciesFeature_t *

sf

)

Returns a ListOf_t * containing SpeciesFeatureValue_t objects from this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure whose ListOfSpeciesFeatureValues_t is sought.

Returns

the ListOfSpeciesFeatureValues_t from this SpeciesFeature_t as a ListOf_t *.

Note

The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also

SpeciesFeature_addSpeciesFeatureValue()

SpeciesFeature_createSpeciesFeatureValue()

SpeciesFeature_getSpeciesFeatureValue()

SpeciesFeature_getNumSpeciesFeatureValues()

SpeciesFeature_removeSpeciesFeatureValue()

char * SpeciesFeature_getName

(

const SpeciesFeature_t *

sf

)

Returns the value of the "name" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure whose name is sought.

Returns

the value of the "name" attribute of this SpeciesFeature_t as a pointer to a string.

Warning

The string returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the string will not be reflected in any resulting SBML document unless the string is added to an SBML Document. Even in this case, the string should be deleted, as adding a string to an SBML Document adds a copy of the string, and does not transfer ownership of that string.

unsigned int SpeciesFeature_getNumSpeciesFeatureValues

(

SpeciesFeature_t *

sf

)

Get the number of SpeciesFeatureValue_t objects in this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure to query.

Returns

the number of SpeciesFeatureValue_t objects in this SpeciesFeature_t.

unsigned int SpeciesFeature_getOccur

(

const SpeciesFeature_t *

sf

)

Returns the value of the "occur" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure whose occur is sought.

Returns

the value of the "occur" attribute of this SpeciesFeature_t as a unsigned integer.

char * SpeciesFeature_getSpeciesFeatureType

(

const SpeciesFeature_t *

sf

)

Returns the value of the "speciesFeatureType" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure whose speciesFeatureType is sought.

Returns

the value of the "speciesFeatureType" attribute of this SpeciesFeature_t as a pointer to a string.

Warning

The string returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the string will not be reflected in any resulting SBML document unless the string is added to an SBML Document. Even in this case, the string should be deleted, as adding a string to an SBML Document adds a copy of the string, and does not transfer ownership of that string.

SpeciesFeatureValue_t * SpeciesFeature_getSpeciesFeatureValue	(	SpeciesFeature_t *	sf,
		unsigned int	n
	)

Get a SpeciesFeatureValue_t from the SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure to search.
n	an unsigned int representing the index of the SpeciesFeatureValue_t to retrieve.

Returns

the nth SpeciesFeatureValue_t in the ListOfSpeciesFeatureValues_t within this SpeciesFeature_t. If the index n is invalid, NULL is returned.

Note

The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

int SpeciesFeature_hasRequiredAttributes

(

const SpeciesFeature_t *

sf

)

Predicate returning 1 (true) if all the required attributes for this SpeciesFeature_t object have been set.

Parameters

sf	the SpeciesFeature_t structure.

Returns

1 (true) to indicate that all the required attributes of this SpeciesFeature_t have been set, otherwise 0 (false) is returned.

Note

The required attributes for the SpeciesFeature_t object are:

• "speciesFeatureType"
• "occur"

int SpeciesFeature_isSetComponent

(

const SpeciesFeature_t *

sf

)

Predicate returning 1 (true) if this SpeciesFeature_t's "component" attribute is set.

Parameters

sf	the SpeciesFeature_t structure.

Returns

1 (true) if this SpeciesFeature_t's "component" attribute has been set, otherwise 0 (false) is returned.

int SpeciesFeature_isSetId

(

const SpeciesFeature_t *

sf

)

Predicate returning 1 (true) if this SpeciesFeature_t's "id" attribute is set.

Parameters

sf	the SpeciesFeature_t structure.

Returns

1 (true) if this SpeciesFeature_t's "id" attribute has been set, otherwise 0 (false) is returned.

int SpeciesFeature_isSetName

(

const SpeciesFeature_t *

sf

)

Predicate returning 1 (true) if this SpeciesFeature_t's "name" attribute is set.

Parameters

sf	the SpeciesFeature_t structure.

Returns

1 (true) if this SpeciesFeature_t's "name" attribute has been set, otherwise 0 (false) is returned.

int SpeciesFeature_isSetOccur

(

const SpeciesFeature_t *

sf

)

Predicate returning 1 (true) if this SpeciesFeature_t's "occur" attribute is set.

Parameters

sf	the SpeciesFeature_t structure.

Returns

1 (true) if this SpeciesFeature_t's "occur" attribute has been set, otherwise 0 (false) is returned.

int SpeciesFeature_isSetSpeciesFeatureType

(

const SpeciesFeature_t *

sf

)

Predicate returning 1 (true) if this SpeciesFeature_t's "speciesFeatureType" attribute is set.

Parameters

sf	the SpeciesFeature_t structure.

Returns

1 (true) if this SpeciesFeature_t's "speciesFeatureType" attribute has been set, otherwise 0 (false) is returned.

SpeciesFeatureValue_t * SpeciesFeature_removeSpeciesFeatureValue	(	SpeciesFeature_t *	sf,
		unsigned int	n
	)

Removes the nth SpeciesFeatureValue_t from this SpeciesFeature_t and returns a pointer to it.

Parameters

sf	the SpeciesFeature_t structure to search.
n	an unsigned int representing the index of the SpeciesFeatureValue_t to remove.

Returns

a pointer to the nth SpeciesFeatureValue_t in this SpeciesFeature_t.

Warning

The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf_appendAndOwn() or ListOf_insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

int SpeciesFeature_setComponent	(	SpeciesFeature_t *	sf,
		const char *	component
	)

Sets the value of the "component" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure.
component	const char * value of the "component" attribute to 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

int SpeciesFeature_setId	(	SpeciesFeature_t *	sf,
		const char *	id
	)

Sets the value of the "id" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure.
id	const char * value of the "id" attribute to 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

Calling this function with id = NULL or an empty string is equivalent to calling SpeciesFeature_unsetId().

int SpeciesFeature_setName	(	SpeciesFeature_t *	sf,
		const char *	name
	)

Sets the value of the "name" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure.
name	const char * value of the "name" attribute to 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_OBJECT

Calling this function with name = NULL or an empty string is equivalent to calling SpeciesFeature_unsetName().

int SpeciesFeature_setOccur	(	SpeciesFeature_t *	sf,
		unsigned int	occur
	)

Sets the value of the "occur" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure.
occur	unsigned int value of the "occur" attribute to 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

int SpeciesFeature_setSpeciesFeatureType	(	SpeciesFeature_t *	sf,
		const char *	speciesFeatureType
	)

Sets the value of the "speciesFeatureType" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_t structure.
speciesFeatureType	const char * value of the "speciesFeatureType" attribute to 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

int SpeciesFeature_unsetComponent

(

SpeciesFeature_t *

sf

)

Unsets the value of the "component" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_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 SpeciesFeature_unsetId

(

SpeciesFeature_t *

sf

)

Unsets the value of the "id" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_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 SpeciesFeature_unsetName

(

SpeciesFeature_t *

sf

)

Unsets the value of the "name" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_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 SpeciesFeature_unsetOccur

(

SpeciesFeature_t *

sf

)

Unsets the value of the "occur" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_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 SpeciesFeature_unsetSpeciesFeatureType

(

SpeciesFeature_t *

sf

)

Unsets the value of the "speciesFeatureType" attribute of this SpeciesFeature_t.

Parameters

sf	the SpeciesFeature_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