Internal C API (do not use)

Classes
struct	CPoint
	A point in 2D space. More...

Functions
_GraphfabExport gf_SBMLModel	gf_SBMLModel_new ()
	Create a new SBML model. More...
_GraphfabExport gf_layoutInfo	gf_layoutInfo_new (uint64_t level, uint64_t version, uint64_t width, uint64_t height)
	Create a new layout info object. More...
_GraphfabExport gf_layoutInfo *	gf_loadSBMLIntoLayoutEngine (const char *buf, gf_SBMLModel *r)
	[DEPRECATED] Load SBML document from memory buffer and process More...
_GraphfabExport gf_network	gf_getNetwork (gf_layoutInfo *l)
	Get the network associated with the model. More...
_GraphfabExport gf_node	gf_nw_getNode (gf_network *n, uint64_t i)
	Get the node at index i. More...
_GraphfabExport gf_node	gf_nw_getUniqueNode (gf_network *n, uint64_t i)
	Get the unique node at index i. More...
_GraphfabExport gf_reaction	gf_nw_getRxn (gf_network *n, uint64_t i)
	Get the node at index i. More...
_GraphfabExport gf_compartment	gf_nw_getCompartment (gf_network *n, uint64_t i)
	Get the compartment at index i. More...
_GraphfabExport gf_compartment	gf_nw_newCompartment (gf_network *nw, const char *id, const char *name)
	Add a new compartment to the network. More...
_GraphfabExport gf_node	gf_nw_newNode (gf_network *nw, const char *id, const char *name, gf_compartment *compartment)
	Add a new node to the network. More...
_GraphfabExport gf_node	gf_nw_aliasOf (gf_network *nw, gf_node *n)
	Creates a new node that is the alias of a given node. More...
_GraphfabExport int	gf_nw_getNumInstances (gf_network *nw, gf_node *n)
	Get the number of instances of the node. More...
_GraphfabExport gf_node	gf_nw_getInstance (gf_network *nw, gf_node *n, uint64_t i)
	Get the ith instance of an aliased node. More...
_GraphfabExport gf_node *	gf_nw_getInstancep (gf_network *nw, gf_node *n, uint64_t i)
	Get the ith instance of an aliased node. More...
_GraphfabExport void	gf_clearNode (gf_node *n)
	Clear the node - does not deallocate. More...
_GraphfabExport int	gf_node_alias (gf_node *n, gf_network *m)
	Alias the node. More...
_GraphfabExport void	gf_node_setIsAlias (gf_node *n, int isAlias)
	Set whether the node is an alias node or not. More...
_GraphfabExport int	gf_node_isIdentical (gf_node *u, gf_node *v)
	Tests whether two nodes are identical. More...
_GraphfabExport gf_reaction	gf_nw_newReaction (gf_network *nw, const char *id, const char *name)
	Add a new reaction to the network. More...
_GraphfabExport gf_curve	gf_reaction_getCurve (const gf_reaction *r, uint64_t i)
	Get the curve i. More...
_GraphfabExport void	gf_dump_transform (gf_transform *tf)
	Dump transform. More...
_GraphfabExport gf_canvas	gf_getCanvas (gf_layoutInfo *l)
	Get the canvas associated with the model. More...
_GraphfabExport void	gf_getNodeCentroid (gf_layoutInfo *l, const char *id, CPoint *p)
	Get the centroid of a node. More...

Detailed Description

Function Documentation

_GraphfabExport void gf_clearNode

(

gf_node *

n

)

Clear the node - does not deallocate.

Parameters

[in]

n

The node object

_GraphfabExport void gf_dump_transform

(

gf_transform *

tf

)

Dump transform.

Parameters

[in]

tf

Transform

_GraphfabExport gf_canvas gf_getCanvas

(

gf_layoutInfo *

l

)

Get the canvas associated with the model.

Parameters

[in]

l

The layout info

_GraphfabExport gf_network gf_getNetwork

(

gf_layoutInfo *

l

)

Get the network associated with the model.

Parameters

[in]

l

The layout info; contains the network

_GraphfabExport void gf_getNodeCentroid	(	gf_layoutInfo *	l,
		const char *	id,
		CPoint *	p
	)

Get the centroid of a node.

Parameters

[in]	l	The layout info; contains the network that holds the list of nodes and their centroids
[in]	id	The node id; used to find the correct node in the layout
[in]	p	The point; used to store the coordinates of the node centroid

_GraphfabExport gf_layoutInfo gf_layoutInfo_new	(	uint64_t	level,
		uint64_t	version,
		uint64_t	width,
		uint64_t	height
	)

Create a new layout info object.

Returns

The new layout info

_GraphfabExport gf_layoutInfo* gf_loadSBMLIntoLayoutEngine	(	const char *	buf,
		gf_SBMLModel *	r
	)

[DEPRECATED] Load SBML document from memory buffer and process

Deprecated:

DEPRECATED

Parameters

[in]	buf	The buffer containing the SBML file; used to create the SBML model
[in]	r	A pointer to an empty SBML model; the model will be created from the buffer and used to build the layout
[out]	l	The layout info; pointer to the layout info generated from SBML is returned

Warning

DO NOT USE!!!!!!!!

_GraphfabExport int gf_node_alias	(	gf_node *	n,
		gf_network *	m
	)

Alias the node.

Parameters

[in]

n

The node to alias

_GraphfabExport int gf_node_isIdentical	(	gf_node *	u,
		gf_node *	v
	)

Tests whether two nodes are identical.

Parameters

[in]	u	A node object
[in]	v	A node object

_GraphfabExport void gf_node_setIsAlias	(	gf_node *	n,
		int	isAlias
	)

Set whether the node is an alias node or not.

Parameters

[in]

n

The node object

_GraphfabExport gf_node gf_nw_aliasOf	(	gf_network *	nw,
		gf_node *	n
	)

Creates a new node that is the alias of a given node.

Parameters

[in]	nw	The network object
[in]	n	The source node

_GraphfabExport gf_compartment gf_nw_getCompartment	(	gf_network *	n,
		uint64_t	i
	)

Get the compartment at index i.

Parameters

[in]	n	The network object
[in]	i	Node index

_GraphfabExport gf_node gf_nw_getInstance	(	gf_network *	nw,
		gf_node *	n,
		uint64_t	i
	)

Get the ith instance of an aliased node.

Parameters

[in]	nw	The network object
[in]	n	The node object
[in]	i	The instance index

_GraphfabExport gf_node* gf_nw_getInstancep	(	gf_network *	nw,
		gf_node *	n,
		uint64_t	i
	)

Get the ith instance of an aliased node.

Parameters

[in]	n	The node object
[in]	i	The instance index

Note

Caller must free returned pointer using gf_free

_GraphfabExport gf_node gf_nw_getNode	(	gf_network *	n,
		uint64_t	i
	)

Get the node at index i.

Parameters

[in]	n	The network object
[in]	i	Node index

_GraphfabExport int gf_nw_getNumInstances	(	gf_network *	nw,
		gf_node *	n
	)

Get the number of instances of the node.

Parameters

[in]	nw	The network object
[in]	n	The node object

_GraphfabExport gf_reaction gf_nw_getRxn	(	gf_network *	n,
		uint64_t	i
	)

Get the node at index i.

Parameters

[in]	n	The network object
[in]	i	Node index

Note

Caller must free returned pointer using gf_free

_GraphfabExport gf_node gf_nw_getUniqueNode	(	gf_network *	n,
		uint64_t	i
	)

Get the unique node at index i.

Parameters

[in]	n	The network object
[in]	i	Node index

_GraphfabExport gf_compartment gf_nw_newCompartment	(	gf_network *	nw,
		const char *	id,
		const char *	name
	)

Add a new compartment to the network.

Parameters

[in]	nw	The network object
[in]	id	The compartment's requested ID (or null to determine it automatically)
[in]	name	The compartment's name

_GraphfabExport gf_node gf_nw_newNode	(	gf_network *	nw,
		const char *	id,
		const char *	name,
		gf_compartment *	compartment
	)

Add a new node to the network.

Parameters

[in]	nw	The network object
[in]	id	The node's requested ID (or null to determine it automatically)
[in]	name	The node's name
[in]	compartment	The compartment to place the node in (may be NULL for no compartment)

_GraphfabExport gf_reaction gf_nw_newReaction	(	gf_network *	nw,
		const char *	id,
		const char *	name
	)

Add a new reaction to the network.

Parameters

[in]	nw	The network object
[in]	id	The reaction's requested ID (or null to determine it automatically)
[in]	name	The reaction's name

_GraphfabExport gf_curve gf_reaction_getCurve	(	const gf_reaction *	r,
		uint64_t	i
	)

Get the curve i.

Parameters

[in]

r

The reaction object

_GraphfabExport gf_SBMLModel gf_SBMLModel_new

(

)

Create a new SBML model.

Returns

The new SBML model