Classes
struct	gf_network
	A reaction network. More...

struct	gf_node
	A species in a model. More...

struct	gf_reaction
	A reaction in a model. More...

struct	gf_curve
	A 2D cubic Bezier curve. More...

struct	gf_compartment
	A compartment in a model. More...

struct	gf_canvas
	Drawing canvas. More...

struct	gf_layoutInfo
	Type which holds layout info. More...

struct	gf_point
	A point in 2D space. More...

struct	gf_transform
	A 2D affine transform. More...

struct	gf_curveCP
	A curve control points. More...

struct	__fr_options
	Options passed to the Fruchterman-Reingold algorithm. More...

Typedefs
typedef struct __fr_options	fr_options
	Options passed to the Fruchterman-Reingold algorithm. More...

Enumerations
enum	gf_specRole { GF_ROLE_SUBSTRATE, GF_ROLE_PRODUCT, GF_ROLE_SIDESUBSTRATE, GF_ROLE_SIDEPRODUCT, GF_ROLE_MODIFIER, GF_ROLE_ACTIVATOR, GF_ROLE_INHIBITOR }
	Species role in a reaction. More...

Functions
_GraphfabExport char *	gf_getLastError ()
	Gets the last error. More...

_GraphfabExport int	gf_haveError ()
	Gets whether an error occurred. More...

_GraphfabExport void	gf_clearError ()
	Clears the last error.

_GraphfabExport const char *	gf_renderTikZ (gf_layoutInfo *l)
	Render the model as a TikZ image. More...

_GraphfabExport int	gf_renderTikZFile (gf_layoutInfo l, const char filename)
	Render the model as a TikZ image. More...

_GraphfabExport void	gf_freeLayoutInfo (gf_layoutInfo *l)
	Call to clean up an instance of gf_layoutInfo when it is no longer needed. More...

_GraphfabExport void	gf_freeLayoutInfoHierarch (gf_layoutInfo *l)
	Call to clean up an instance of gf_layoutInfo and all contained data structures. More...

_GraphfabExport void	gf_freeModelAndLayout (gf_SBMLModel mod, gf_layoutInfo l)
	Call to clean up an instance of gf_layoutInfo and gf_SBMLModel when they are no longer needed. More...

_GraphfabExport gf_SBMLModel *	gf_SBMLModel_newp ()
	Create a new SBML model. More...

_GraphfabExport gf_layoutInfo *	gf_layoutInfo_newp (uint64_t level, uint64_t version, uint64_t width, uint64_t height)
	Create a new layout info object. More...

_GraphfabExport gf_layoutInfo *	gf_processLayout (gf_SBMLModel *lo)
	Process the layout info from a document. More...

_GraphfabExport void	gf_setModelNamespace (gf_layoutInfo *l, unsigned long level, unsigned long version)
	Set the level and version of the SBML. More...

_GraphfabExport const char *	gf_getDefaultCompartmentId ()
	Get the id of the default SBML compartment. More...

_GraphfabExport void	gf_setDefaultCompartmentId (const char *id)
	Set the id of the default SBML compartment. More...

_GraphfabExport gf_network *	gf_getNetworkp (gf_layoutInfo *l)
	Get the network associated with the model. More...

_GraphfabExport void	gf_clearNetwork (gf_network *n)
	Clear the network - does not deallocate. More...

_GraphfabExport void	gf_releaseNetwork (gf_network *n)
	Release the network. More...

_GraphfabExport char *	gf_nw_getId (gf_network *n)
	Get the id of the network (i.e. the SBML model) More...

_GraphfabExport void	gf_nw_setId (gf_network n, const char id)
	Set the id of the network (via the SBML model) More...

_GraphfabExport uint64_t	gf_nw_getNumNodes (const gf_network *n)
	Get the number of nodes. More...

_GraphfabExport uint64_t	gf_nw_getNumUniqueNodes (const gf_network *n)
	Get the number of unique nodes. More...

_GraphfabExport uint64_t	gf_nw_getNumRxns (const gf_network *n)
	Get the number of reactions. More...

_GraphfabExport uint64_t	gf_nw_getNumComps (const gf_network *n)
	Get the number of compartments. More...

_GraphfabExport gf_node *	gf_nw_getNodep (gf_network *n, uint64_t i)
	Get the node at index i. More...

_GraphfabExport gf_node *	gf_nw_getUniqueNodep (gf_network *n, uint64_t i)
	Get the node at index i. More...

_GraphfabExport gf_node *	gf_nw_getNodepFromId (gf_network nw, const char id)
	Get the node with the given id. More...

_GraphfabExport gf_reaction *	gf_nw_getRxnp (gf_network *n, uint64_t i)
	Get the node at index i. More...

_GraphfabExport void	gf_nw_removeRxn (gf_network n, gf_reaction r)
	Remove the given reaction. More...

_GraphfabExport gf_compartment *	gf_nw_getCompartmentp (gf_network *n, uint64_t i)
	Get the compartment at index i. More...

_GraphfabExport gf_compartment *	gf_nw_findCompartmentById (gf_network n, const char id)
	Find a compartment by id. More...

_GraphfabExport void	gf_nw_rebuildCurves (gf_network *n)
	Rebuild all curves in the network. More...

_GraphfabExport void	gf_nw_recenterJunctions (gf_network *n)
	Recenter reaction junctions. More...

_GraphfabExport gf_compartment *	gf_nw_newCompartmentp (gf_network nw, const char id, const char *name)
	Add a new compartment to the network. More...

_GraphfabExport gf_node *	gf_nw_newNodep (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_newAliasNodep (gf_network nw, gf_node source)
	Create and add an alias node from a given source node. More...

_GraphfabExport int	gf_nw_removeNode (gf_network nw, gf_node node)
	Remove a node from the network. More...

_GraphfabExport int	gf_nw_connectNode (gf_network nw, gf_node node, gf_reaction *reaction, gf_specRole role)
	Connect a node to a reaction. More...

_GraphfabExport int	gf_nw_connectNodeRoleStr (gf_network nw, gf_node n, gf_reaction r, const char role_str)
	Connect a node to a reaction. More...

_GraphfabExport int	gf_nw_isNodeConnected (gf_network nw, gf_node node, gf_reaction *reaction)
	Return whether the given node is connected to the given reaction. More...

_GraphfabExport int	gf_nw_isLayoutSpecified (gf_network *nw)
	Did the SBML model include layout? More...

_GraphfabExport int	gf_nw_getNumAliasInstances (gf_network nw, gf_node n)
	Get the number of instances of the node. More...

_GraphfabExport gf_node *	gf_nw_getAliasInstancep (gf_network nw, gf_node n, uint64_t i)
	Get the ith instance of an aliased node. More...

_GraphfabExport void	gf_node_setCompartment (gf_node n, gf_compartment c)
	Add a node to a compartment. More...

_GraphfabExport void	gf_releaseNode (const gf_node *n)
	Release the node. More...

_GraphfabExport int	gf_node_isLocked (gf_node *n)
	Is the node locked? More...

_GraphfabExport void	gf_node_lock (gf_node *n)
	Lock the node. More...

_GraphfabExport void	gf_node_unlock (gf_node *n)
	Unlock the node. More...

_GraphfabExport int	gf_node_make_alias (gf_node n, gf_network m)
	Create aliases of a given node. More...

_GraphfabExport int	gf_node_isAliased (gf_node *n)
	Is the node aliased? More...

_GraphfabExport gf_point	gf_node_getCentroid (gf_node *n)
	Get the centroid of the node. More...

_GraphfabExport void	gf_node_getCentroidXY (gf_node n, double x, double *y)
	Get the centroid of the node. More...

_GraphfabExport void	gf_node_setCentroid (gf_node *n, gf_point p)
	Set the centroid of the node. More...

_GraphfabExport double	gf_node_getWidth (gf_node *n)
	Get the width of the node. More...

_GraphfabExport void	gf_node_setWidth (gf_node *n, double width)
	Set the width of the node. More...

_GraphfabExport double	gf_node_getHeight (gf_node *n)
	Get the height of the node. More...

_GraphfabExport void	gf_node_setHeight (gf_node *n, double height)
	Set the height of the node. More...

_GraphfabExport char *	gf_node_getID (gf_node *n)
	Get the id, user frees memory. More...

_GraphfabExport void	gf_node_setID (gf_node n, const char id)
	Get the id, user frees memory. More...

_GraphfabExport const char *	gf_node_getName (gf_node *n)
	Get the name, client must free memory. More...

_GraphfabExport void	gf_node_setName (gf_node n, const char name)
	Set the name of a node. More...

_GraphfabExport int	gf_node_getConnectedReactions (gf_node n, gf_network m, unsigned int num, gf_reaction *rxns)
	Get a list of all reactions connected to the node. More...

_GraphfabExport int	gf_node_getAttachedCurves (gf_node n, gf_network m, unsigned int num, gf_curve *curves)
	Get a list of all curves connected to the node. More...

_GraphfabExport int	gf_nw_nodeHasCompartment (gf_network nw, gf_node x)
	Return true if the node has a compartment assigned. More...

_GraphfabExport gf_compartment *	gf_nw_nodeGetCompartment (gf_network nw, gf_node x)
	Get the compartment which contains node x. More...

_GraphfabExport void	gf_releaseRxn (const gf_reaction *r)
	Release the reaction. More...

_GraphfabExport gf_reaction *	gf_nw_newReactionp (gf_network nw, const char id, const char *name)
	Add a new reaction to the network. More...

_GraphfabExport char *	gf_reaction_getID (gf_reaction *r)
	Get the id, user frees memory. More...

_GraphfabExport gf_point	gf_reaction_getCentroid (gf_reaction *r)
	Get the centroid of the reaction. More...

_GraphfabExport void	gf_reaction_setCentroid (gf_reaction *r, gf_point p)
	Set the centroid of the reaction. More...

_GraphfabExport uint64_t	gf_reaction_getNumSpec (const gf_reaction *r)
	Get the number of species in the reaction. More...

_GraphfabExport int	gf_reaction_hasSpec (const gf_reaction r, const gf_node n)
	Return true if the reaction has the given species. More...

_GraphfabExport gf_specRole	gf_reaction_getSpecRole (const gf_reaction *r, uint64_t i)
	Get the role for spec i. More...

_GraphfabExport const char *	gf_roleToStr (gf_specRole role)
	Convert role to string. More...

_GraphfabExport gf_specRole	gf_strToRole (const char *str)
	Convert string to role. More...

_GraphfabExport uint64_t	gf_reaction_specGeti (const gf_reaction *r, uint64_t i)
	Get the global index of a reactant/product/participant given its local index in a reaction. More...

_GraphfabExport uint64_t	gf_reaction_getNumCurves (const gf_reaction *r)
	Get the number of curves in the reaction. More...

_GraphfabExport gf_curve *	gf_reaction_getCurvep (const gf_reaction *r, uint64_t i)
	Get the curve i. More...

_GraphfabExport void	gf_reaction_recenter (gf_reaction *r)
	Recenter reaction centroid. More...

_GraphfabExport void	gf_reaction_recalcCurveCPs (gf_reaction *r)
	Recalculate the curve CPs, don't recenter. More...

_GraphfabExport void	gf_releaseCurve (const gf_curve *c)
	Release the curve. More...

_GraphfabExport gf_specRole	gf_curve_getRole (gf_curve *c)
	Get the id, user frees memory. More...

_GraphfabExport gf_curveCP	gf_getCurveCPs (const gf_curve *c)
	Get the CPs for the curve. More...

_GraphfabExport int	gf_curve_hasArrowhead (const gf_curve *c)
	Returns true if the given curve should be drawn with an arrowhead. More...

_GraphfabExport int	gf_curve_getArrowheadVerts (const gf_curve c, unsigned int n, gf_point **v)
	Get the vertices for the curve's arrowhead. More...

_GraphfabExport void	gf_releaseCompartment (const gf_compartment *c)
	Release a compartment object. More...

_GraphfabExport char *	gf_compartment_getID (gf_compartment *c)
	Get the id, user frees memory. More...

_GraphfabExport gf_point	gf_compartment_getMinCorner (gf_compartment *c)
	Get the "upper left" corner. More...

_GraphfabExport void	gf_compartment_setMinCorner (gf_compartment *c, gf_point p)
	Set the "upper left" corner. More...

_GraphfabExport gf_point	gf_compartment_getMaxCorner (gf_compartment *c)
	Get the "lower right" corner. More...

_GraphfabExport void	gf_compartment_setMaxCorner (gf_compartment *c, gf_point p)
	Set the "lower right" corner. More...

_GraphfabExport double	gf_compartment_getWidth (gf_compartment *c)
	Get the width of the compartment. More...

_GraphfabExport double	gf_compartment_getHeight (gf_compartment *c)
	Get the height of the compartment. More...

_GraphfabExport uint64_t	gf_compartment_getNumElt (gf_compartment *c)
	Get the number of species in the compartment. More...

_GraphfabExport int	gf_compartment_addNode (gf_compartment c, gf_node n)
	Add a node to the compartment. More...

_GraphfabExport int	gf_compartment_removeNode (gf_compartment c, gf_node n)
	Remove a node from the compartment. More...

_GraphfabExport int	gf_compartment_containsNode (gf_compartment c, gf_node n)
	Return whether the compartment contains this node. More...

_GraphfabExport int	gf_compartment_containsReaction (gf_compartment c, gf_reaction r)
	Return whether the compartment contains this node. More...

_GraphfabExport void	gf_fit_to_window (gf_layoutInfo *l, double left, double top, double right, double bottom)
	Fit to the specified window. More...

_GraphfabExport gf_transform *	gf_tf_fitToWindow (gf_layoutInfo *l, double left, double top, double right, double bottom)
	Fit to the specified window (do not apply transform) More...

_GraphfabExport void	gf_moveNetworkToFirstQuad (gf_layoutInfo *l, double x_disp, double y_disp)
	Move the entire network to the first quadrant. More...

_GraphfabExport CPoint	gf_tf_apply_to_point (gf_transform *tf, CPoint p)
	Apply transform to point. More...

_GraphfabExport gf_point	gf_tf_getScale (gf_transform *tf)
	Get the scale of the transform. More...

_GraphfabExport gf_point	gf_tf_getDisplacement (gf_transform *tf)
	Get the displacement of the transform. More...

_GraphfabExport gf_point	gf_tf_getPostDisplacement (gf_transform *tf)
	Get the displacement component of the transform. More...

_GraphfabExport void	gf_release_transform (gf_transform *tf)
	Release transform. More...

_GraphfabExport gf_canvas *	gf_getCanvasp (gf_layoutInfo *l)
	Get the canvas associated with the model. More...

_GraphfabExport void	gf_clearCanvas (gf_canvas *c)
	Get the canvas associated with the model. More...

_GraphfabExport void	gf_releaseCanvas (gf_canvas *c)
	Release the canvas. More...

_GraphfabExport unsigned int	gf_canvGetWidth (gf_canvas *c)
	Get the width of the canvas. More...

_GraphfabExport unsigned int	gf_canvGetHeight (gf_canvas *c)
	Get the height of the canvas. More...

_GraphfabExport void	gf_canvSetWidth (gf_canvas *c, unsigned long width)
	Set the width of the canvas. More...

_GraphfabExport void	gf_canvSetHeight (gf_canvas *c, unsigned long height)
	Set the height of the canvas. More...

_GraphfabExport void	gf_aliasNodebyDegree (gf_layoutInfo *l, const int minDegree)
	Create node aliases by node degree. More...

_GraphfabExport void	gf_randomizeLayout (gf_layoutInfo *m)
	Randomize node positions. More...

_GraphfabExport void	gf_randomizeLayout2 (gf_network n, gf_canvas c)
	Randomize node positions for a given network & canvas. More...

_GraphfabExport void	gf_randomizeLayout_fromExtents (gf_network *n, double left, double top, double right, double bottom)
	Randomize node positions for a given network & extents. More...

_GraphfabExport int	gf_writeSBMLwithLayout (const char filename, gf_SBMLModel m, gf_layoutInfo *l)
	Write an SBML file, including layout. More...

_GraphfabExport int	gf_writeSBML (const char filename, gf_SBMLModel m)
	Write an SBML file (does not include layout. More...

_GraphfabExport const char *	gf_getSBMLwithLayoutStr (gf_SBMLModel m, gf_layoutInfo l)
	String version of writeSBMLwithLayout. More...

_GraphfabExport const char *	gf_getCurrentLibraryVersion (void)
	Returns the current version of the library. More...

_GraphfabExport void	gf_free (void *x)
	Frees the memory block at x. More...

_GraphfabExport gf_point	gf_computeCubicBezierPoint (gf_curveCP *c, Real t)
	Compute a point on the parametric curve. More...

_GraphfabExport gf_point *	gf_computeCubicBezierLineIntersec (gf_curveCP c, gf_point line_start, gf_point *line_end)
	Compute the intersection between a cubic Bezier and a line. More...

_GraphfabExport int	gf_arrowheadStyleGetNumVerts (int style)
	Get the number of vertices in the arrowhead polygon. More...

_GraphfabExport gf_point	gf_arrowheadStyleGetVert (int style, int n)
	Get the nth vertex of the arrow polygon. More...

_GraphfabExport int	gf_arrowheadStyleIsFilled (int style)
	Is the given style filled? More...

_GraphfabExport unsigned long	gf_arrowheadNumStyles ()
	Get the number of arrowhead styles. More...

_GraphfabExport void	gf_arrowheadSetStyle (gf_specRole role, int style)
	Set the arrowhead style for a specific role type. More...

_GraphfabExport int	gf_arrowheadGetStyle (gf_specRole role)
	Get the style for the role type. More...

_GraphfabExport void	gf_doLayoutAlgorithm (fr_options opt, gf_layoutInfo *l)
	Run the autolayout (Fruchterman-Reingold) algorithm on a given layout structure. More...

_GraphfabExport void	gf_doLayoutAlgorithm2 (fr_options opt, gf_network n, gf_canvas c)
	Run the autolayout (Fruchterman-Reingold) algorithm on a a network and optional canvas. More...

_GraphfabExport void	gf_getLayoutOptDefaults (fr_options *opt)
	Generate default values for the layout options. More...

_GraphfabExport void	gf_layout_setStiffness (fr_options *opt, double k)
	Set the stiffness for the FR algorithm. More...

_GraphfabExport void	gf_freeSBMLModel (gf_SBMLModel *lo)
	Destructor for gf_SBMLModel. More...

_GraphfabExport gf_SBMLModel *	gf_loadSBMLbuf (const char *buf)
	Load SBML from memory buffer. Struct contains a pointer to the document. More...

_GraphfabExport gf_SBMLModel *	gf_loadSBMLfile (const char *file)
	Load SBML from memory buffer. Struct contains a pointer to the document. More...

_GraphfabExport void	gf_strfree (char *str)
	Free a C string (char*) More...

Detailed Description

Typedef Documentation

typedef struct __fr_options fr_options

Options passed to the Fruchterman-Reingold algorithm.

Author: JKM

This structure holds the settings used by the Fruchterman-Reingold algorithm.

Enumeration Type Documentation

enum gf_specRole

Species role in a reaction.

Author: JKM

Represents the SBML species role in a reaction. Species can be reactants, products, modifiers, etc.

Function Documentation

_GraphfabExport void gf_aliasNodebyDegree	(	gf_layoutInfo *	l,
		const int	minDegree
	)

Create node aliases by node degree.

Parameters

[in]	l	The layout info; contains the network that holds the list of nodes and reactions necessary for aliasing
[in]	minDegree	The minimum node degree; Nodes that are of the minimum degree or higher will be aliased

_GraphfabExport int gf_arrowheadGetStyle ( gf_specRole role )

Get the style for the role type.

Parameters

[in] role Role type

_GraphfabExport unsigned long gf_arrowheadNumStyles ( )

Get the number of arrowhead styles.

Returns: The number of arrowhead styles

_GraphfabExport void gf_arrowheadSetStyle	(	gf_specRole	role,
		int	style
	)

Set the arrowhead style for a specific role type.

Parameters

[in]	role	Role type
[in]	style	Arrowhead style number

_GraphfabExport int gf_arrowheadStyleGetNumVerts ( int style )

Get the number of vertices in the arrowhead polygon.

Parameters

[in] style Arrowhead style number

Returns: The arrowhead polygon vertex count

_GraphfabExport gf_point gf_arrowheadStyleGetVert	(	int	style,
		int	n
	)

Get the nth vertex of the arrow polygon.

Parameters

[in]	style	Arrowhead style number
[in]	n	The vertex index

Returns: The nth vertex of the polygon

_GraphfabExport int gf_arrowheadStyleIsFilled ( int style )

Is the given style filled?

Parameters

[in] style Arrowhead style number

Returns: Nonzero if the arrow polygon should be filled

_GraphfabExport unsigned int gf_canvGetHeight ( gf_canvas * c )

Get the height of the canvas.

Parameters

[in] c The canvas

_GraphfabExport unsigned int gf_canvGetWidth ( gf_canvas * c )

Get the width of the canvas.

Parameters

[in] c The canvas

_GraphfabExport void gf_canvSetHeight	(	gf_canvas *	c,
		unsigned long	height
	)

Set the height of the canvas.

Parameters

[in]	c	The canvas
[in]	height	The height

_GraphfabExport void gf_canvSetWidth	(	gf_canvas *	c,
		unsigned long	width
	)

Set the width of the canvas.

Parameters

[in]	c	The canvas
[out]	width	The width

_GraphfabExport void gf_clearCanvas ( gf_canvas * c )

Get the canvas associated with the model.

Parameters

[in] l The layout info

_GraphfabExport void gf_clearNetwork ( gf_network * n )

Clear the network - does not deallocate.

Parameters

[in] n The network object

_GraphfabExport int gf_compartment_addNode	(	gf_compartment *	c,
		gf_node *	n
	)

Add a node to the compartment.

The node must already exist in the network

Parameters

[in]	c	The compartment object
[in]	n	The node to add

Returns: Zero for success

_GraphfabExport int gf_compartment_containsNode	(	gf_compartment *	c,
		gf_node *	n
	)

Return whether the compartment contains this node.

Parameters

[in]	c	The compartment object
[in]	n	The node

Returns: Nonzero if true

_GraphfabExport int gf_compartment_containsReaction	(	gf_compartment *	c,
		gf_reaction *	r
	)

Return whether the compartment contains this node.

Parameters

[in]	c	The compartment object
[in]	r	The reaction

Returns: Nonzero if true

_GraphfabExport double gf_compartment_getHeight ( gf_compartment * c )

Get the height of the compartment.

Parameters

[in] c The compartment object

_GraphfabExport char* gf_compartment_getID ( gf_compartment * c )

Get the id, user frees memory.

Parameters

[in] c The compartment object

_GraphfabExport gf_point gf_compartment_getMaxCorner ( gf_compartment * c )

Get the "lower right" corner.

Parameters

[in] c The compartment object

_GraphfabExport gf_point gf_compartment_getMinCorner ( gf_compartment * c )

Get the "upper left" corner.

Parameters

[in] c Compartment

_GraphfabExport uint64_t gf_compartment_getNumElt ( gf_compartment * c )

Get the number of species in the compartment.

Parameters

[in] c The compartment object

_GraphfabExport double gf_compartment_getWidth ( gf_compartment * c )

Get the width of the compartment.

Parameters

[in] c The compartment object

_GraphfabExport int gf_compartment_removeNode	(	gf_compartment *	c,
		gf_node *	n
	)

Remove a node from the compartment.

Parameters

[in]	c	The compartment object
[in]	n	The node to remove

Returns: Zero for success

_GraphfabExport void gf_compartment_setMaxCorner	(	gf_compartment *	c,
		gf_point	p
	)

Set the "lower right" corner.

Parameters

[in]	c	The compartment object
[in]	p	Corner

_GraphfabExport void gf_compartment_setMinCorner	(	gf_compartment *	c,
		gf_point	p
	)

Set the "upper left" corner.

Parameters

[in]	c	The compartment object
[in]	p	Corner

_GraphfabExport gf_point* gf_computeCubicBezierLineIntersec	(	gf_curveCP *	c,
		gf_point *	line_start,
		gf_point *	line_end
	)

Compute the intersection between a cubic Bezier and a line.

Parameters

[in]	c	Cubic Bezier control points
[in]	line_start	The start of the line
[in]	line_end	The end of the line

Returns: An array of intersection points with a 0, 0 sentinel

_GraphfabExport gf_point gf_computeCubicBezierPoint	(	gf_curveCP *	c,
		Real	t
	)

Compute a point on the parametric curve.

Parameters

[in]	c	Cubic Bezier control points
[in]	t	Cubic Bezier parameter

_GraphfabExport int gf_curve_getArrowheadVerts	(	const gf_curve *	c,
		unsigned int *	n,
		gf_point **	v
	)

Get the vertices for the curve's arrowhead.

Parameters

[in]	c	The curve
[out]	n	Number of arrowhead verts
[out]	v	The vertices (new arrow, callee owns)

_GraphfabExport gf_specRole gf_curve_getRole ( gf_curve * c )

Get the id, user frees memory.

Parameters

[in]	c	The curve Get the role of the species with the given curve
[in]	c	The curve

Returns: The index of the matching species in the reaction

_GraphfabExport int gf_curve_hasArrowhead ( const gf_curve * c )

Returns true if the given curve should be drawn with an arrowhead.

Parameters

[in] c The curve

_GraphfabExport void gf_doLayoutAlgorithm	(	fr_options	opt,
		gf_layoutInfo *	l
	)

Run the autolayout (Fruchterman-Reingold) algorithm on a given layout structure.

Author: JKM

Note: l should be a layout info object obtained from a call to gf_processLayout.

Parameters

[in]	opt	The options controlling the layout algorithm
	in/out]	l The layout info

_GraphfabExport void gf_doLayoutAlgorithm2	(	fr_options	opt,
		gf_network *	n,
		gf_canvas *	c
	)

Run the autolayout (Fruchterman-Reingold) algorithm on a a network and optional canvas.

Can be used when full layout struct is not available

Parameters

[in]	opt	The options controlling the layout algorithm
	in/out]	n The network
[in]	c	The canvas (may be NULL)

_GraphfabExport void gf_fit_to_window	(	gf_layoutInfo *	l,
		double	left,
		double	top,
		double	right,
		double	bottom
	)

Fit to the specified window.

Given a network layout and a window, constructs a 2D affine transform to fit the network within the window. The 2D affine transform is applied directly to the network.

Parameters

[in]	l	The layout info object
[in]	left	Left edge of screen (other args similar)

_GraphfabExport void gf_free ( void * x )

Frees the memory block at x.

Note: For strings (char*), use gf_strfree

_GraphfabExport void gf_freeLayoutInfo ( gf_layoutInfo * l )

Call to clean up an instance of gf_layoutInfo when it is no longer needed.

Parameters

[in] l The layout info; Entire layout is freed

_GraphfabExport void gf_freeLayoutInfoHierarch ( gf_layoutInfo * l )

Call to clean up an instance of gf_layoutInfo and all contained data structures.

Parameters

[in] l The layout info; Entire layout is freed

_GraphfabExport void gf_freeModelAndLayout	(	gf_SBMLModel *	mod,
		gf_layoutInfo *	l
	)

Call to clean up an instance of gf_layoutInfo and gf_SBMLModel when they are no longer needed.

The network object (which can be obtained via gf_getNetworkp is freed as well.

Parameters

[in]	mod	The SBML model
[in]	l	The layout info; Entire layout is freed

_GraphfabExport void gf_freeSBMLModel ( gf_SBMLModel * lo )

Destructor for gf_SBMLModel.

Parameters

[in] lo The SBML model; all memory used by the model is freed

_GraphfabExport gf_canvas* gf_getCanvasp ( gf_layoutInfo * l )

Get the canvas associated with the model.

Parameters

[in] l The layout info

_GraphfabExport const char* gf_getCurrentLibraryVersion ( void )

Returns the current version of the library.

Returns: Static string

_GraphfabExport gf_curveCP gf_getCurveCPs ( const gf_curve * c )

Get the CPs for the curve.

Parameters

[in] c The curve

_GraphfabExport const char* gf_getDefaultCompartmentId ( )

Get the id of the default SBML compartment.

Note: The default compartment is not rendered

Returns: The id (memory owned by the library)

_GraphfabExport char* gf_getLastError ( )

Gets the last error.

Returns: The error message (owned by callee)

_GraphfabExport void gf_getLayoutOptDefaults ( fr_options * opt )

Generate default values for the layout options.

Parameters

[out] l The layout info in which to store the options

_GraphfabExport gf_network* gf_getNetworkp ( gf_layoutInfo * l )

Get the network associated with the model.

Parameters

[in] l The layout info; contains the network

Returns: A pointer to the network

Note: Caller must free returned pointer using gf_free

_GraphfabExport const char* gf_getSBMLwithLayoutStr	(	gf_SBMLModel *	m,
		gf_layoutInfo *	l
	)

String version of writeSBMLwithLayout.

Parameters

[in]	m	The SBML model; required since this tool only handles layout
[in]	l	The layout info; the SBML in string form is written to the layout

Returns: Raw SBML as UTF-8 string (owned by callee)

_GraphfabExport int gf_haveError ( )

Gets whether an error occurred.

Returns: True if an error has been set

_GraphfabExport void gf_layout_setStiffness	(	fr_options *	opt,
		double	k
	)

Set the stiffness for the FR algorithm.

Parameters

[out]	opt	The layout info in which to store the stiffness
[in]	k	The stiffness

_GraphfabExport gf_layoutInfo* gf_layoutInfo_newp	(	uint64_t	level,
		uint64_t	version,
		uint64_t	width,
		uint64_t	height
	)

Create a new layout info object.

Returns: The new layout info

Note: Caller must free returned pointer using gf_free

_GraphfabExport gf_SBMLModel* gf_loadSBMLbuf ( const char * buf )

Load SBML from memory buffer. Struct contains a pointer to the document.

Parameters

[in]	buf	The buffer containing the SBML file
[out]	r	The SBML model; the model that contains the SBML info from the buffer

_GraphfabExport gf_SBMLModel* gf_loadSBMLfile ( const char * file )

Load SBML from memory buffer. Struct contains a pointer to the document.

Parameters

[in]	buf	The buffer containing the SBML file
[out]	r	The SBML model; the model that contains the SBML info from the buffer

_GraphfabExport void gf_moveNetworkToFirstQuad	(	gf_layoutInfo *	l,
		double	x_disp,
		double	y_disp
	)

Move the entire network to the first quadrant.

Uses the network's bounding box to move all coordinates to the first quadrant. x_disp and y_disp are an additional offset to apply to the bounding box's minimum corner. If they are zero, the corner will be at the origin.

Parameters

[in]	l	The layout info object
[in]	x_disp	X displacement to post-apply to the bounding box
[in]	y_disp	Y displacement to post-apply to the bounding box

_GraphfabExport int gf_node_getAttachedCurves	(	gf_node *	n,
		gf_network *	m,
		unsigned int *	num,
		gf_curve **	curves
	)

Get a list of all curves connected to the node.

Parameters

[in]	n	The node object
[out]	num	The number of curves
[out]	rxns	The curve array (callee must free with gf_free)

Returns: Reserved

_GraphfabExport gf_point gf_node_getCentroid ( gf_node * n )

Get the centroid of the node.

Parameters

[in] n The node object

_GraphfabExport void gf_node_getCentroidXY	(	gf_node *	n,
		double *	x,
		double *	y
	)

Get the centroid of the node.

Parameters

[in]	n	The node object
[out]	x	X coord of centroid
[out]	y	Y coord of centroid

_GraphfabExport int gf_node_getConnectedReactions	(	gf_node *	n,
		gf_network *	m,
		unsigned int *	num,
		gf_reaction **	rxns
	)

Get a list of all reactions connected to the node.

Parameters

[in]	n	The node object
[out]	num	The number of reactions
[out]	rxns	The reaction array (callee must free with gf_free)

Returns: Reserved

_GraphfabExport double gf_node_getHeight ( gf_node * n )

Get the height of the node.

Parameters

[in] n The node object

_GraphfabExport char* gf_node_getID ( gf_node * n )

Get the id, user frees memory.

Parameters

[in] n The node object

_GraphfabExport const char* gf_node_getName ( gf_node * n )

Get the name, client must free memory.

Parameters

[in] n The node object

_GraphfabExport double gf_node_getWidth ( gf_node * n )

Get the width of the node.

Parameters

[in] n The node object

_GraphfabExport int gf_node_isAliased ( gf_node * n )

Is the node aliased?

Parameters

[in] n The node object

_GraphfabExport int gf_node_isLocked ( gf_node * n )

Is the node locked?

Parameters

[in] n The node object

_GraphfabExport void gf_node_lock ( gf_node * n )

Lock the node.

Parameters

[in] n The node object

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

Create aliases of a given node.

Creates alais nodes of a given node. One alias will be created for each reaction the node participates in. The aliases will appear as separate nodes in the network. The function gf_node_isAliased may be called to determine whether a given node is an alias or not.

Parameters

[in,out]	n	The node to alias. Do not continue to use this pointer after the call - it will be invalid
[in,out]	m	The network containing n. The nodes and reactions in this network may be modified by the call. The pointer m will remain valid.

_GraphfabExport void gf_node_setCentroid	(	gf_node *	n,
		gf_point	p
	)

Set the centroid of the node.

Parameters

[in] n The node object

_GraphfabExport void gf_node_setCompartment	(	gf_node *	n,
		gf_compartment *	c
	)

Add a node to a compartment.

Parameters

[in]	c	Compartment
[in]	n	The node object

_GraphfabExport void gf_node_setHeight	(	gf_node *	n,
		double	height
	)

Set the height of the node.

Parameters

[in] n The node object

_GraphfabExport void gf_node_setID	(	gf_node *	n,
		const char *	id
	)

Get the id, user frees memory.

Parameters

[in] n The node object

_GraphfabExport void gf_node_setName	(	gf_node *	n,
		const char *	name
	)

Set the name of a node.

Parameters

[in] n The node object

_GraphfabExport void gf_node_setWidth	(	gf_node *	n,
		double	width
	)

Set the width of the node.

Parameters

[in] n The node object

_GraphfabExport void gf_node_unlock ( gf_node * n )

Unlock the node.

Parameters

[in] n The node object

_GraphfabExport int gf_nw_connectNode	(	gf_network *	nw,
		gf_node *	node,
		gf_reaction *	reaction,
		gf_specRole	role
	)

Connect a node to a reaction.

Parameters

[in]	nw	The network object
[in]	node	The node to connect
[in]	reaction	The reaction to connect to
[in]	role	The species role to use

_GraphfabExport int gf_nw_connectNodeRoleStr	(	gf_network *	nw,
		gf_node *	n,
		gf_reaction *	r,
		const char *	role_str
	)

Connect a node to a reaction.

Parameters

[in]	nw	The network object
[in]	node	The node to connect
[in]	reaction	The reaction to connect to
[in]	role	The species role to use (must be one of SUBSTRATE,PRODUCT,MODIFIER,ACTIVATOR,INHIBITOR)

_GraphfabExport gf_compartment* gf_nw_findCompartmentById	(	gf_network *	n,
		const char *	id
	)

Find a compartment by id.

Returns NULL if no such compartment exists

Parameters

[in]	n	The network object
[in]	id	The compartment ID

Note: Caller must free returned pointer using gf_free

_GraphfabExport gf_node* gf_nw_getAliasInstancep	(	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_compartment* gf_nw_getCompartmentp	(	gf_network *	n,
		uint64_t	i
	)

Get the compartment at index i.

Parameters

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

Note: Caller must free returned pointer using gf_free

_GraphfabExport char* gf_nw_getId ( gf_network * n )

Get the id of the network (i.e. the SBML model)

The id of the network is determined by the SBML model object

Note: Memory must be freed by caller

Parameters

[in] n The network object

_GraphfabExport gf_node* gf_nw_getNodep	(	gf_network *	n,
		uint64_t	i
	)

Get the node at index i.

Parameters

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

Returns: A pointer to the node

Note: Caller must free returned pointer using gf_free

_GraphfabExport gf_node* gf_nw_getNodepFromId	(	gf_network *	nw,
		const char *	id
	)

Get the node with the given id.

Parameters

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

Returns: A pointer to the node with the given id; returns NULL if no such node exists

_GraphfabExport int gf_nw_getNumAliasInstances	(	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 uint64_t gf_nw_getNumComps ( const gf_network * n )

Get the number of compartments.

Parameters

[in] n The network object

_GraphfabExport uint64_t gf_nw_getNumNodes ( const gf_network * n )

Get the number of nodes.

Parameters

[in] n The network object

_GraphfabExport uint64_t gf_nw_getNumRxns ( const gf_network * n )

Get the number of reactions.

Parameters

[in] n The network object

_GraphfabExport uint64_t gf_nw_getNumUniqueNodes ( const gf_network * n )

Get the number of unique nodes.

This method only counts the unique nodes in a network, i.e. if a node is aliased, all instances count as a single node.

Parameters

[in] n The network object

_GraphfabExport gf_reaction* gf_nw_getRxnp	(	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_getUniqueNodep	(	gf_network *	n,
		uint64_t	i
	)

Get the node at index i.

Parameters

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

Returns: A pointer to the node

Note: Caller must free returned pointer using gf_free

_GraphfabExport int gf_nw_isLayoutSpecified ( gf_network * nw )

Did the SBML model include layout?

Returns: 1 for yes, 0 for no

Parameters

[in] n The network object

_GraphfabExport int gf_nw_isNodeConnected	(	gf_network *	nw,
		gf_node *	node,
		gf_reaction *	reaction
	)

Return whether the given node is connected to the given reaction.

Parameters

[in]	nw	The network object
[in]	node	The node to connect
[in]	reaction	The reaction to connect to

Returns: True if this not is connected

_GraphfabExport gf_node* gf_nw_newAliasNodep	(	gf_network *	nw,
		gf_node *	source
	)

Create and add an alias node from a given source node.

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]	source	The original source node

Note: Caller must free returned pointer using gf_free

_GraphfabExport gf_compartment* gf_nw_newCompartmentp	(	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

Note: Caller must free returned pointer using gf_free

_GraphfabExport gf_node* gf_nw_newNodep	(	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 or NULL for the "default" compartment in SBML parlance)

Note: Caller must free returned pointer using gf_free

_GraphfabExport gf_reaction* gf_nw_newReactionp	(	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

Note: Caller must free returned pointer using gf_free

_GraphfabExport gf_compartment* gf_nw_nodeGetCompartment	(	gf_network *	nw,
		gf_node *	x
	)

Get the compartment which contains node x.

Parameters

[in]	nw	The network object
[in]	x	A node object

Note: Caller must free returned pointer using gf_free

_GraphfabExport int gf_nw_nodeHasCompartment	(	gf_network *	nw,
		gf_node *	x
	)

Return true if the node has a compartment assigned.

Parameters

[in]	nw	The network object
[in]	x	A node object

_GraphfabExport void gf_nw_rebuildCurves ( gf_network * n )

Rebuild all curves in the network.

Rebuild all curves in each reaction, connecting substrates, products, modifiers, etc. Automatically calculate control points.

Parameters

in/out] n The network object

_GraphfabExport void gf_nw_recenterJunctions ( gf_network * n )

Recenter reaction junctions.

Parameters

[in] n The network object

_GraphfabExport int gf_nw_removeNode	(	gf_network *	nw,
		gf_node *	node
	)

Remove a node from the network.

Parameters

[in] n The network object

_GraphfabExport void gf_nw_removeRxn	(	gf_network *	n,
		gf_reaction *	r
	)

Remove the given reaction.

Parameters

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

_GraphfabExport void gf_nw_setId	(	gf_network *	n,
		const char *	id
	)

Set the id of the network (via the SBML model)

This will be used as the ID of the model object in the serialized SBML

Note: Memory must be freed by caller

Parameters

[in,out]	n	The network object
[in]	id	The id to use

_GraphfabExport gf_layoutInfo* gf_processLayout ( gf_SBMLModel * lo )

Process the layout info from a document.

Author: JKM

The layout info holds the network (nodes, reactions, etc.), canvas, and SBML content. gf_processLayout should be called after loading a network (via e.g. gf_loadSBMLfile). If the SBML model has layout information, the returned gf_layoutInfo will preserve this information. Otherwise, it will generate it automatically using the Fruchterman-Reingold algorithm.

gf_processLayout should be called only once for a loaded model (subsequent calls will have no effect). To manually re-run the Fruchterman-Reingold algorithm, call gf_doLayoutAlgorithm.

Parameters

[in]	lo	The SBML model; the layout info is generated from the SBML model
[out]	l	The layout info; pointer to the layout info generated from SBML model is returned

Warning: Call gf_freeLayoutInfo to free the returned pointer. Do not call gf_free.

_GraphfabExport void gf_randomizeLayout ( gf_layoutInfo * m )

Randomize node positions.

Parameters

[in] m The layout info; contains the network of nodes and reactions, the coordinates of which will be randomized

_GraphfabExport void gf_randomizeLayout2	(	gf_network *	n,
		gf_canvas *	c
	)

Randomize node positions for a given network & canvas.

Parameters

[in]	n	Network
[in]	c	Canvas

_GraphfabExport void gf_randomizeLayout_fromExtents	(	gf_network *	n,
		double	left,
		double	top,
		double	right,
		double	bottom
	)

Randomize node positions for a given network & extents.

Parameters

[in]	n	Network
[in]	left	The minimum X coord of the bounding box
[in]	top	The minimum Y coord of the bounding box
[in]	right	The maximum X coord of the bounding box
[in]	bottom	The maximum Y coord of the bounding box

_GraphfabExport gf_point gf_reaction_getCentroid ( gf_reaction * r )

Get the centroid of the reaction.

Parameters

[in] r The reaction object

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

Get the curve i.

Parameters

[in] r The reaction object

Note: Caller must free returned pointer using gf_free

_GraphfabExport char* gf_reaction_getID ( gf_reaction * r )

Get the id, user frees memory.

Parameters

[in] r The reaction object

_GraphfabExport uint64_t gf_reaction_getNumCurves ( const gf_reaction * r )

Get the number of curves in the reaction.

Parameters

[in] r The reaction object

_GraphfabExport uint64_t gf_reaction_getNumSpec ( const gf_reaction * r )

Get the number of species in the reaction.

Parameters

[in] r The reaction object

_GraphfabExport gf_specRole gf_reaction_getSpecRole	(	const gf_reaction *	r,
		uint64_t	i
	)

Get the role for spec i.

Parameters

[in] r The reaction object

_GraphfabExport int gf_reaction_hasSpec	(	const gf_reaction *	r,
		const gf_node *	n
	)

Return true if the reaction has the given species.

Parameters

[in] r The reaction object

_GraphfabExport void gf_reaction_recalcCurveCPs ( gf_reaction * r )

Recalculate the curve CPs, don't recenter.

Parameters

[in] n The reaction object

_GraphfabExport void gf_reaction_recenter ( gf_reaction * r )

Recenter reaction centroid.

Parameters

[in] n The reaction object

_GraphfabExport void gf_reaction_setCentroid	(	gf_reaction *	r,
		gf_point	p
	)

Set the centroid of the reaction.

Parameters

[in] r The reaction object

_GraphfabExport uint64_t gf_reaction_specGeti	(	const gf_reaction *	r,
		uint64_t	i
	)

Get the global index of a reactant/product/participant given its local index in a reaction.

Parameters

[in] r The reaction object

_GraphfabExport void gf_release_transform ( gf_transform * tf )

Release transform.

Parameters

[in] tf Transform

_GraphfabExport void gf_releaseCanvas ( gf_canvas * c )

Release the canvas.

Parameters

[in] c The canvas

_GraphfabExport void gf_releaseCompartment ( const gf_compartment * c )

Release a compartment object.

Parameters

[in] c The compartment object

_GraphfabExport void gf_releaseCurve ( const gf_curve * c )

Release the curve.

Parameters

[in] c The curve

_GraphfabExport void gf_releaseNetwork ( gf_network * n )

Release the network.

Parameters

[in] n The network object

_GraphfabExport void gf_releaseNode ( const gf_node * n )

Release the node.

Parameters

[in] n The node object

_GraphfabExport void gf_releaseRxn ( const gf_reaction * r )

Release the reaction.

Parameters

[in] r The reaction object

_GraphfabExport const char* gf_renderTikZ ( gf_layoutInfo * l )

Render the model as a TikZ image.

Parameters

[in] l The model/layout infor

_GraphfabExport int gf_renderTikZFile	(	gf_layoutInfo *	l,
		const char *	filename
	)

Render the model as a TikZ image.

Parameters

[in] l The model/layout infor

_GraphfabExport const char* gf_roleToStr ( gf_specRole role )

Convert role to string.

Parameters

[in] role Role

Returns: Static string indicating the role

_GraphfabExport gf_SBMLModel* gf_SBMLModel_newp ( )

Create a new SBML model.

Returns: The new SBML model

Note: Caller must free returned pointer using gf_free

_GraphfabExport void gf_setDefaultCompartmentId ( const char * id )

Set the id of the default SBML compartment.

Note: The default compartment is not rendered

Parameters

[in] id The id of the default compartment

_GraphfabExport void gf_setModelNamespace	(	gf_layoutInfo *	l,
		unsigned long	level,
		unsigned long	version
	)

Set the level and version of the SBML.

Parameters

[out]	l	The SBML model with layout info
[in]	level	The SBML level
[in]	version	The SBML version

_GraphfabExport void gf_strfree ( char * str )

Free a C string (char*)

Parameters

[in] str The string to free

_GraphfabExport gf_specRole gf_strToRole ( const char * str )

Convert string to role.

Parameters

[in] str String returned from gf_roleToStr

Returns: Role

_GraphfabExport CPoint gf_tf_apply_to_point	(	gf_transform *	tf,
		CPoint	p
	)

Apply transform to point.

Parameters

[in]	tf	Transform
[in]	p	Point

_GraphfabExport gf_transform* gf_tf_fitToWindow	(	gf_layoutInfo *	l,
		double	left,
		double	top,
		double	right,
		double	bottom
	)

Fit to the specified window (do not apply transform)

Given a network layout and a window, constructs a 2D affine transform to fit the network within the window. The 2D affine transform is returned from this function (to be used by e.g. client-side rendering code) and the layout coordinates of the network are unaffected.

Parameters

[in]	l	The layout info object
[in]	left	Left edge of screen (other args similar)

Returns: The new transform (not applied)

_GraphfabExport gf_point gf_tf_getDisplacement ( gf_transform * tf )

Get the displacement of the transform.

Gets just the displacement component of a 2D affine transform, ignoring the rotation and scaling.

Parameters

[in] tf Transform

_GraphfabExport gf_point gf_tf_getPostDisplacement ( gf_transform * tf )

Get the displacement component of the transform.

Like gf_tf_getDisplacement, but applies the inverse of the linear portion of the original transform to the output.

Parameters

[in] tf Transform

Returns: The displacement with the transform applied

_GraphfabExport gf_point gf_tf_getScale ( gf_transform * tf )

Get the scale of the transform.

Parameters

[in] tf Transform

_GraphfabExport int gf_writeSBML	(	const char *	filename,
		gf_SBMLModel *	m
	)

Write an SBML file (does not include layout.

Returns: 0 for success

Parameters

[in]	filename	The output file
[in]	m	The SBML model; required since this tool only handles layout

_GraphfabExport int gf_writeSBMLwithLayout	(	const char *	filename,
		gf_SBMLModel *	m,
		gf_layoutInfo *	l
	)

Write an SBML file, including layout.

Returns: 0 for success

Parameters

[in]	filename	The output file
[in]	m	The SBML model; required since this tool only handles layout
[in]	l	The layout info; replaces any currently existing SBML layout in the model in the generated file

Classes

Typedefs

Enumerations

Functions

Detailed Description

Typedef Documentation

Enumeration Type Documentation

Function Documentation