SpeciesReferenceGlyph_t Class Reference

Detailed Description

layout A glyph for an SBML species reference.

The SpeciesReferenceGlyph element describes the graphical connection between a SpeciesGlyph_t and a ReactionGlyph_t (which would be an arrow or some curve in most cases). A SpeciesReferenceGlyph_t inherits from GraphicalObject_t, and adds a mandatory attribute 'speciesGlyph' and two optional attributes 'speciesReference' and 'role'. Optionally, the SpeciesReferenceGlyph_t also has a child element 'curve'.

If the curve is specified, it overrides the inherited bounding box.

Public Member Functions
SpeciesReferenceGlyph_t *	SpeciesReferenceGlyph_clone (const SpeciesReferenceGlyph_t *srg)
SpeciesReferenceGlyph_t *	SpeciesReferenceGlyph_create (void)
	Creates a new SpeciesReferenceGlyph_t structure and returns a pointer to it. More...
CubicBezier_t *	SpeciesReferenceGlyph_createCubicBezier (SpeciesReferenceGlyph_t *srg)
	Creates a new CubicBezier_t structure, adds it to the end of the list of curve segments of the curve and returns a reference to the newly created structure. More...
SpeciesReferenceGlyph_t *	SpeciesReferenceGlyph_createFrom (const SpeciesReferenceGlyph_t *temp)
	Creates a new SpeciesReferenceGlyph_t from a template. More...
LineSegment_t *	SpeciesReferenceGlyph_createLineSegment (SpeciesReferenceGlyph_t *srg)
	Creates a new LineSegment_t structure, adds it to the end of the list of curve segment of the curve and returns a reference to the newly created structure. More...
SpeciesReferenceGlyph_t *	SpeciesReferenceGlyph_createWith (const char *sid, const char *speciesGlyphId, const char *speciesReferenceId, SpeciesReferenceRole_t role)
	Creates a new SpeciesReferenceGlyph_t structure. More...
void	SpeciesReferenceGlyph_free (SpeciesReferenceGlyph_t *srg)
	Frees the memory for the SpeciesReferenceGlyph_t. More...
Curve_t *	SpeciesReferenceGlyph_getCurve (SpeciesReferenceGlyph_t *srg)
	Gets the Curve_t for the given species reference glyph. More...
const char *	SpeciesReferenceGlyph_getId (const SpeciesReferenceGlyph_t *srg)
	Returns the id. More...
SpeciesReferenceRole_t	SpeciesReferenceGlyph_getRole (const SpeciesReferenceGlyph_t *srg)
	Returns the role of the species reference. More...
const char *	SpeciesReferenceGlyph_getRoleString (const SpeciesReferenceGlyph_t *srg)
	Returns a string representation of the role of the species reference. More...
const char *	SpeciesReferenceGlyph_getSpeciesGlyphId (const SpeciesReferenceGlyph_t *srg)
	Gets the reference species id for the given species glyph. More...
const char *	SpeciesReferenceGlyph_getSpeciesReferenceId (const SpeciesReferenceGlyph_t *srg)
	Gets the reference species id for the given species glyph. More...
void	SpeciesReferenceGlyph_initDefaults (SpeciesReferenceGlyph_t *srg)
	Calls initDefaults on GraphicalObject_t and sets role to SPECIES_ROLE_INVALID. More...
int	SpeciesReferenceGlyph_isSetCurve (SpeciesReferenceGlyph_t *srg)
	Returns 1 (true) if the Curve_t has one or more LineSegment_t's. More...
int	SpeciesReferenceGlyph_isSetId (const SpeciesReferenceGlyph_t *srg)
	Returns 1 (true) if the id is set. More...
int	SpeciesReferenceGlyph_isSetRole (const SpeciesReferenceGlyph_t *srg)
	Returns 1 (true) if the role is not SPECIES_ROLE_INVALID. More...
int	SpeciesReferenceGlyph_isSetSpeciesGlyphId (const SpeciesReferenceGlyph_t *srg)
	Returns 0 (false) if the reference species reference has not been set for this glyph and 1 (true) otherwise. More...
int	SpeciesReferenceGlyph_isSetSpeciesReferenceId (const SpeciesReferenceGlyph_t *srg)
	Returns 0 (false) if the reference species reference has not been set for this glyph and 1 (true) otherwise. More...
void	SpeciesReferenceGlyph_setCurve (SpeciesReferenceGlyph_t *srg, Curve_t *c)
	Sets the curve for the species reference glyph. More...
int	SpeciesReferenceGlyph_setId (SpeciesReferenceGlyph_t *srg, const char *sid)
	Sets the id. More...
void	SpeciesReferenceGlyph_setRole (SpeciesReferenceGlyph_t *srg, const char *r)
	Sets the role of the species reference glyph based on the string. More...
void	SpeciesReferenceGlyph_setSpeciesGlyphId (SpeciesReferenceGlyph_t *srg, const char *id)
	Sets the species glyph reference for the species glyph. More...
void	SpeciesReferenceGlyph_setSpeciesReferenceId (SpeciesReferenceGlyph_t *srg, const char *id)
	Sets the reference species for the species glyph. More...
void	SpeciesReferenceGlyph_unsetId (SpeciesReferenceGlyph_t *srg)
	Unsets the id. More...

Member Function Documentation

SpeciesReferenceGlyph_t * SpeciesReferenceGlyph_clone

(

const SpeciesReferenceGlyph_t *

srg

)

Returns

a (deep) copy of this SpeciesReferenceGlyph_t.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

SpeciesReferenceGlyph_t * SpeciesReferenceGlyph_create

(

void

)

Creates a new SpeciesReferenceGlyph_t structure and returns a pointer to it.

CubicBezier_t * SpeciesReferenceGlyph_createCubicBezier

(

SpeciesReferenceGlyph_t *

srg

)

Creates a new CubicBezier_t structure, adds it to the end of the list of curve segments of the curve and returns a reference to the newly created structure.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

SpeciesReferenceGlyph_t * SpeciesReferenceGlyph_createFrom

(

const SpeciesReferenceGlyph_t *

temp

)

Creates a new SpeciesReferenceGlyph_t from a template.

Parameters

temp	the SpeciesReferenceGlyph_t structure to copy.

LineSegment_t * SpeciesReferenceGlyph_createLineSegment

(

SpeciesReferenceGlyph_t *

srg

)

Creates a new LineSegment_t structure, adds it to the end of the list of curve segment of the curve and returns a reference to the newly created structure.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

SpeciesReferenceGlyph_t * SpeciesReferenceGlyph_createWith	(	const char *	sid,
		const char *	speciesGlyphId,
		const char *	speciesReferenceId,
		SpeciesReferenceRole_t	role
	)

Creates a new SpeciesReferenceGlyph_t structure.

The id is given as the first argument, the id of the associated species glyph is given as the second argument. The third argument is the id of the associated species reference and the fourth argument is the role.

Parameters

sid	the string to use as the ID of the SpeciesReferenceGlyph_t.
speciesGlyphId	the string to use as the species glyph.
speciesReferenceId	the string to use as the species reference.
role	the role of the created SpeciesReferenceGlyph_t.

void SpeciesReferenceGlyph_free

(

SpeciesReferenceGlyph_t *

srg

)

Frees the memory for the SpeciesReferenceGlyph_t.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

Curve_t * SpeciesReferenceGlyph_getCurve

(

SpeciesReferenceGlyph_t *

srg

)

Gets the Curve_t for the given species reference glyph.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

const char * SpeciesReferenceGlyph_getId

(

const SpeciesReferenceGlyph_t *

srg

)

Returns the id.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

SpeciesReferenceRole_t SpeciesReferenceGlyph_getRole

(

const SpeciesReferenceGlyph_t *

srg

)

Returns the role of the species reference.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

const char * SpeciesReferenceGlyph_getRoleString

(

const SpeciesReferenceGlyph_t *

srg

)

Returns a string representation of the role of the species reference.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

const char * SpeciesReferenceGlyph_getSpeciesGlyphId

(

const SpeciesReferenceGlyph_t *

srg

)

Gets the reference species id for the given species glyph.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

const char * SpeciesReferenceGlyph_getSpeciesReferenceId

(

const SpeciesReferenceGlyph_t *

srg

)

Gets the reference species id for the given species glyph.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

void SpeciesReferenceGlyph_initDefaults

(

SpeciesReferenceGlyph_t *

srg

)

Calls initDefaults on GraphicalObject_t and sets role to SPECIES_ROLE_INVALID.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

int SpeciesReferenceGlyph_isSetCurve

(

SpeciesReferenceGlyph_t *

srg

)

Returns 1 (true) if the Curve_t has one or more LineSegment_t's.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

int SpeciesReferenceGlyph_isSetId

(

const SpeciesReferenceGlyph_t *

srg

)

Returns 1 (true) if the id is set.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

int SpeciesReferenceGlyph_isSetRole

(

const SpeciesReferenceGlyph_t *

srg

)

Returns 1 (true) if the role is not SPECIES_ROLE_INVALID.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

int SpeciesReferenceGlyph_isSetSpeciesGlyphId

(

const SpeciesReferenceGlyph_t *

srg

)

Returns 0 (false) if the reference species reference has not been set for this glyph and 1 (true) otherwise.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

int SpeciesReferenceGlyph_isSetSpeciesReferenceId

(

const SpeciesReferenceGlyph_t *

srg

)

Returns 0 (false) if the reference species reference has not been set for this glyph and 1 (true) otherwise.

Parameters

srg	the SpeciesReferenceGlyph_t structure.

void SpeciesReferenceGlyph_setCurve	(	SpeciesReferenceGlyph_t *	srg,
		Curve_t *	c
	)

Sets the curve for the species reference glyph.

Parameters

srg	the SpeciesReferenceGlyph_t structure.
c	the Curve_t to set for the SpeciesReferenceGlyph_t.

int SpeciesReferenceGlyph_setId	(	SpeciesReferenceGlyph_t *	srg,
		const char *	sid
	)

Sets the id.

Parameters

srg	the SpeciesReferenceGlyph_t structure.
sid	the string to use as the ID of the SpeciesReferenceGlyph_t.

void SpeciesReferenceGlyph_setRole	(	SpeciesReferenceGlyph_t *	srg,
		const char *	r
	)

Sets the role of the species reference glyph based on the string.

The string can be one of:

• "substrate" (SPECIES_ROLE_SUBSTRATE)
• "product" (SPECIES_ROLE_PRODUCT)
• "sidesubstrate" (SPECIES_ROLE_SIDESUBSTRATE)
• "sideproduct" (SPECIES_ROLE_SIDEPRODUCT)
• "modifier" (SPECIES_ROLE_MODIFIER)
• "activator" (SPECIES_ROLE_ACTIVATOR)
• "inhibitor" (SPECIES_ROLE_INHIBITOR)
• "undefined" (SPECIES_ROLE_UNDEFINED)

If it is none of those, the role is set to SPECIES_ROLE_INVALID.

Parameters

srg	the SpeciesReferenceGlyph_t structure.
r	the role to use for the SpeciesReferenceGlyph_t.

void SpeciesReferenceGlyph_setSpeciesGlyphId	(	SpeciesReferenceGlyph_t *	srg,
		const char *	id
	)

Sets the species glyph reference for the species glyph.

Parameters

srg	the SpeciesReferenceGlyph_t structure.
id	the string to use as the species glyph.

void SpeciesReferenceGlyph_setSpeciesReferenceId	(	SpeciesReferenceGlyph_t *	srg,
		const char *	id
	)

Sets the reference species for the species glyph.

Parameters

srg	the SpeciesReferenceGlyph_t structure.
id	the string to use as the species reference.

void SpeciesReferenceGlyph_unsetId

(

SpeciesReferenceGlyph_t *

srg

)

Unsets the id.

Parameters

srg	the SpeciesReferenceGlyph_t structure.