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libSBNW
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libSBNW
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Functions | |
| _GraphfabExport char * | gf_getLastError () |
| Gets the last error. 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_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_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_layoutInfo * | gf_processLayout (gf_SBMLModel *lo) |
| Process the layout info from a document. The layout info holds the network (nodes, reactions, etc.), canvas, and SBML content. More... | |
| _GraphfabExport gf_layoutInfo * | gf_loadSBMLIntoLayoutEngine (const char *buf, gf_SBMLModel *r) |
| Load SBML document from memory buffer and process. More... | |
| _GraphfabExport void | gf_setModelNamespace (gf_layoutInfo *l, unsigned long level, unsigned long version) |
| Set the level and version of the SBML. More... | |
| _GraphfabExport gf_network | gf_getNetwork (gf_layoutInfo *l) |
| Get the network associated with the model. 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, user frees memory. More... | |
| _GraphfabExport size_t | gf_nw_getNumNodes (const gf_network *n) |
| Get the number of nodes. More... | |
| _GraphfabExport size_t | gf_nw_getNumRxns (const gf_network *n) |
| Get the number of reactions. More... | |
| _GraphfabExport size_t | gf_nw_getNumComps (const gf_network *n) |
| Get the number of compartments. More... | |
| _GraphfabExport gf_node | gf_nw_getNode (gf_network *n, size_t i) |
| Get the node at index i. More... | |
| _GraphfabExport gf_node * | gf_nw_getNodep (gf_network *n, size_t i) |
| Get the node at index i. More... | |
| _GraphfabExport gf_reaction | gf_nw_getRxn (gf_network *n, size_t i) |
| Get the node at index i. More... | |
| _GraphfabExport gf_reaction * | gf_nw_getRxnp (gf_network *n, size_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_getCompartment (gf_network *n, size_t i) |
| Get the compartment at index i. More... | |
| _GraphfabExport gf_compartment * | gf_nw_getCompartmentp (gf_network *n, size_t i) |
| Get the node at index i. More... | |
| _GraphfabExport void | gf_nw_rebuildCurves (gf_network *n) |
| Rebuild the curves. More... | |
| _GraphfabExport void | gf_nw_recenterJunctions (gf_network *n) |
| Recenter reaction junctions. 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_newNodep (gf_network *nw, const char *id, const char *name, gf_compartment *compartment) |
| Add a new node to the network. More... | |
| _GraphfabExport int | gf_nw_removeNode (gf_network *nw, gf_node *node) |
| Remove a node from the network. More... | |
| _GraphfabExport int | gf_nw_isLayoutSpecified (gf_network *nw) |
| Did the SBML model include layout? More... | |
| _GraphfabExport void | gf_node_setCompartment (gf_node *n, gf_compartment *c) |
| Add a node to a compartment. More... | |
| _GraphfabExport void | gf_clearNode (gf_node *n) |
| Clear the node - does not deallocate. 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_alias (gf_node *n, gf_network *m) |
| Alias the 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 const char * | gf_node_getName (gf_node *n) |
| Get the name. 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 void | gf_releaseRxn (const gf_reaction *r) |
| Release the reaction. 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 size_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, size_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 size_t | gf_reaction_specGeti (const gf_reaction *r, size_t i) |
| Get the index of the species in the network. More... | |
| _GraphfabExport size_t | gf_reaction_getNumCurves (const gf_reaction *r) |
| Get the number of curves in the reaction. More... | |
| _GraphfabExport gf_curve | gf_reaction_getCurve (const gf_reaction *r, size_t i) |
| Get the curve i. More... | |
| _GraphfabExport gf_curve * | gf_reaction_getCurvep (const gf_reaction *r, size_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 the comp. 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 size_t | gf_compartment_getNumElt (gf_compartment *c) |
| Get the number of species in the compartment. 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 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 of the transform. More... | |
| _GraphfabExport void | gf_dump_transform (gf_transform *tf) |
| Dump transform. More... | |
| _GraphfabExport void | gf_release_transform (gf_transform *tf) |
| Release transform. More... | |
| _GraphfabExport gf_canvas | gf_getCanvas (gf_layoutInfo *l) |
| Get the canvas associated with the model. 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_getNodeCentroid (gf_layoutInfo *l, const char *id, CPoint *p) |
| Get the centroid of a node. 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 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_strfree (char *str) |
| Free a C string (char*) More... | |
| _GraphfabExport void gf_aliasNodebyDegree | ( | gf_layoutInfo * | l, |
| const int | minDegree | ||
| ) |
Create node aliases by node degree.
| [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.
| [in] | role | Role type |
| _GraphfabExport unsigned long gf_arrowheadNumStyles | ( | ) |
Get the number of arrowhead styles.
| _GraphfabExport void gf_arrowheadSetStyle | ( | gf_specRole | role, |
| int | style | ||
| ) |
Set the arrowhead style for a specific role type.
| [in] | role | Role type |
| [in] | style | Arrowhead style number |
| _GraphfabExport int gf_arrowheadStyleGetNumVerts | ( | int | style | ) |
Get the number of vertices in the arrowhead polygon.
| [in] | style | Arrowhead style number |
| _GraphfabExport gf_point gf_arrowheadStyleGetVert | ( | int | style, |
| int | n | ||
| ) |
Get the nth vertex of the arrow polygon.
| [in] | style | Arrowhead style number |
| [in] | n | The vertex index |
| _GraphfabExport int gf_arrowheadStyleIsFilled | ( | int | style | ) |
Is the given style filled?
| [in] | style | Arrowhead style number |
| _GraphfabExport unsigned int gf_canvGetHeight | ( | gf_canvas * | c | ) |
Get the height of the canvas.
| [in] | c | The canvas |
| _GraphfabExport unsigned int gf_canvGetWidth | ( | gf_canvas * | c | ) |
Get the width of the canvas.
| [in] | c | The canvas |
| _GraphfabExport void gf_canvSetHeight | ( | gf_canvas * | c, |
| unsigned long | height | ||
| ) |
Set the height of the canvas.
| [in] | c | The canvas |
| [in] | height | The height |
| _GraphfabExport void gf_canvSetWidth | ( | gf_canvas * | c, |
| unsigned long | width | ||
| ) |
Set the width of the canvas.
| [in] | c | The canvas |
| [out] | width | The width |
| _GraphfabExport void gf_clearCanvas | ( | gf_canvas * | c | ) |
Get the canvas associated with the model.
| [in] | l | The layout info |
| _GraphfabExport void gf_clearNetwork | ( | gf_network * | n | ) |
Clear the network - does not deallocate.
| [in] | n | Network |
| _GraphfabExport void gf_clearNode | ( | gf_node * | n | ) |
Clear the node - does not deallocate.
| [in] | n | Node |
| _GraphfabExport double gf_compartment_getHeight | ( | gf_compartment * | c | ) |
Get the height of the compartment.
| [in] | c | Compartment |
| _GraphfabExport char* gf_compartment_getID | ( | gf_compartment * | c | ) |
Get the id, user frees memory.
| [in] | c | Compartment |
| _GraphfabExport gf_point gf_compartment_getMaxCorner | ( | gf_compartment * | c | ) |
Get the "lower right" corner.
| [in] | c | Compartment |
| _GraphfabExport gf_point gf_compartment_getMinCorner | ( | gf_compartment * | c | ) |
Get the "upper left" corner.
| [in] | c | Compartment |
| _GraphfabExport size_t gf_compartment_getNumElt | ( | gf_compartment * | c | ) |
Get the number of species in the compartment.
| [in] | c | Compartment |
| _GraphfabExport double gf_compartment_getWidth | ( | gf_compartment * | c | ) |
Get the width of the compartment.
| [in] | c | Compartment |
| _GraphfabExport void gf_compartment_setMaxCorner | ( | gf_compartment * | c, |
| gf_point | p | ||
| ) |
Set the "lower right" corner.
| [in] | c | Compartment |
| [in] | p | Corner |
| _GraphfabExport void gf_compartment_setMinCorner | ( | gf_compartment * | c, |
| gf_point | p | ||
| ) |
Set the "upper left" corner.
| [in] | c | Compartment |
| [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.
| [in] | c | Cubic Bezier control points |
| [in] | line_start | The start of the line |
| [in] | line_end | The end of the line |
| _GraphfabExport gf_point gf_computeCubicBezierPoint | ( | gf_curveCP * | c, |
| Real | t | ||
| ) |
Compute a point on the parametric curve.
| [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.
| [in] | c | 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.
| [in] | c | Curve Get the role of the species with the given curve |
| [in] | c | Curve |
| _GraphfabExport int gf_curve_hasArrowhead | ( | const gf_curve * | c | ) |
Returns true if the given curve should be drawn with an arrowhead.
| [in] | c | Curve |
| _GraphfabExport void gf_doLayoutAlgorithm | ( | fr_options | opt, |
| gf_layoutInfo * | l | ||
| ) |
Run the autolayout (Fruchterman-Reingold) algorithm on a given layout structure.
| [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
| [in] | opt | The options controlling the layout algorithm |
| in/out] | n The network | |
| [in] | c | The canvas (may be NULL) |
| _GraphfabExport void gf_dump_transform | ( | gf_transform * | tf | ) |
Dump transform.
| [in] | tf | Transform |
| _GraphfabExport void gf_fit_to_window | ( | gf_layoutInfo * | l, |
| double | left, | ||
| double | top, | ||
| double | right, | ||
| double | bottom | ||
| ) |
Fit to the specified window.
| [in] | l | Layout |
| [in] | left | Left edge of screen (other args similar) |
| _GraphfabExport void gf_free | ( | void * | x | ) |
Frees the memory block at x.
| _GraphfabExport void gf_freeLayoutInfo | ( | gf_layoutInfo * | l | ) |
Call to clean up an instance of gf_layoutInfo when it is no longer needed.
| [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.
| [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.
| [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.
| [in] | lo | The SBML model; all memory used by the model is freed |
| _GraphfabExport gf_canvas gf_getCanvas | ( | gf_layoutInfo * | l | ) |
Get the canvas associated with the model.
| [in] | l | The layout info |
| _GraphfabExport gf_canvas* gf_getCanvasp | ( | gf_layoutInfo * | l | ) |
Get the canvas associated with the model.
| [in] | l | The layout info |
| _GraphfabExport const char* gf_getCurrentLibraryVersion | ( | void | ) |
Returns the current version of the library.
| _GraphfabExport gf_curveCP gf_getCurveCPs | ( | const gf_curve * | c | ) |
Get the CPs for the curve.
| [in] | c | Curve |
| _GraphfabExport char* gf_getLastError | ( | ) |
Gets the last error.
| _GraphfabExport void gf_getLayoutOptDefaults | ( | fr_options * | opt | ) |
Generate default values for the layout options.
| [out] | l | The layout info in which to store the options |
| _GraphfabExport gf_network gf_getNetwork | ( | gf_layoutInfo * | l | ) |
Get the network associated with the model.
| [in] | l | The layout info; contains the network |
| _GraphfabExport gf_network* gf_getNetworkp | ( | gf_layoutInfo * | l | ) |
Get the network associated with the model.
| [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.
| [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 const char* gf_getSBMLwithLayoutStr | ( | gf_SBMLModel * | m, |
| gf_layoutInfo * | l | ||
| ) |
String version of writeSBMLwithLayout.
| [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 |
| _GraphfabExport void gf_layout_setStiffness | ( | fr_options * | opt, |
| double | k | ||
| ) |
Set the stiffness for the FR algorithm.
| [out] | opt | The layout info in which to store the stiffness |
| [in] | k | The stiffness |
| _GraphfabExport gf_SBMLModel* gf_loadSBMLbuf | ( | const char * | buf | ) |
Load SBML from memory buffer. Struct contains a pointer to the document.
| [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.
| [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_layoutInfo* gf_loadSBMLIntoLayoutEngine | ( | const char * | buf, |
| gf_SBMLModel * | r | ||
| ) |
Load SBML document from memory buffer and process.
| [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 |
| _GraphfabExport int gf_node_alias | ( | gf_node * | n, |
| gf_network * | m | ||
| ) |
Alias the node.
| [in] | n | The node to alias |
| _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.
| [in] | n | Node |
| [out] | num | The number of curves |
| [out] | rxns | The curve array (callee must free with gf_free) |
Get the centroid of the node.
| [in] | n | Node |
| _GraphfabExport void gf_node_getCentroidXY | ( | gf_node * | n, |
| double * | x, | ||
| double * | y | ||
| ) |
Get the centroid of the node.
| [in] | n | Node |
| [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.
| [in] | n | Node |
| [out] | num | The number of reactions |
| [out] | rxns | The reaction array (callee must free with gf_free) |
| _GraphfabExport double gf_node_getHeight | ( | gf_node * | n | ) |
Get the height of the node.
| [in] | n | Node |
| _GraphfabExport char* gf_node_getID | ( | gf_node * | n | ) |
Get the id, user frees memory.
| [in] | n | Node |
| _GraphfabExport const char* gf_node_getName | ( | gf_node * | n | ) |
Get the name.
| [in] | n | Node |
| _GraphfabExport double gf_node_getWidth | ( | gf_node * | n | ) |
Get the width of the node.
| [in] | n | Node |
| _GraphfabExport int gf_node_isAliased | ( | gf_node * | n | ) |
Is the node aliased?
| [in] | n | Node |
| _GraphfabExport int gf_node_isLocked | ( | gf_node * | n | ) |
Is the node locked?
| [in] | n | Node |
| _GraphfabExport void gf_node_lock | ( | gf_node * | n | ) |
Lock the node.
| [in] | n | Node |
Set the centroid of the node.
| [in] | n | Node |
| _GraphfabExport void gf_node_setCompartment | ( | gf_node * | n, |
| gf_compartment * | c | ||
| ) |
Add a node to a compartment.
| [in] | c | Compartment |
| [in] | n | Node |
| _GraphfabExport void gf_node_setHeight | ( | gf_node * | n, |
| double | height | ||
| ) |
Set the height of the node.
| [in] | n | Node |
| _GraphfabExport void gf_node_setWidth | ( | gf_node * | n, |
| double | width | ||
| ) |
Set the width of the node.
| [in] | n | Node |
| _GraphfabExport void gf_node_unlock | ( | gf_node * | n | ) |
Unlock the node.
| [in] | n | Node |
| _GraphfabExport gf_compartment gf_nw_getCompartment | ( | gf_network * | n, |
| size_t | i | ||
| ) |
Get the compartment at index i.
| [in] | n | Network |
| [in] | i | Node index |
| _GraphfabExport gf_compartment* gf_nw_getCompartmentp | ( | gf_network * | n, |
| size_t | i | ||
| ) |
Get the node at index i.
| [in] | n | Network |
| [in] | i | Node index |
| _GraphfabExport char* gf_nw_getID | ( | gf_network * | n | ) |
Get the id, user frees memory.
| [in] | n | Network |
| _GraphfabExport gf_node gf_nw_getNode | ( | gf_network * | n, |
| size_t | i | ||
| ) |
Get the node at index i.
| [in] | n | Network |
| [in] | i | Node index |
| _GraphfabExport gf_node* gf_nw_getNodep | ( | gf_network * | n, |
| size_t | i | ||
| ) |
Get the node at index i.
| [in] | n | Network |
| [in] | i | Node index |
| _GraphfabExport size_t gf_nw_getNumComps | ( | const gf_network * | n | ) |
Get the number of compartments.
| [in] | n | Network |
| _GraphfabExport size_t gf_nw_getNumNodes | ( | const gf_network * | n | ) |
Get the number of nodes.
| [in] | n | Network |
| _GraphfabExport size_t gf_nw_getNumRxns | ( | const gf_network * | n | ) |
Get the number of reactions.
| [in] | n | Network |
| _GraphfabExport gf_reaction gf_nw_getRxn | ( | gf_network * | n, |
| size_t | i | ||
| ) |
Get the node at index i.
| [in] | n | Network |
| [in] | i | Node index |
| _GraphfabExport gf_reaction* gf_nw_getRxnp | ( | gf_network * | n, |
| size_t | i | ||
| ) |
Get the node at index i.
| [in] | n | Network |
| [in] | i | Node index |
| _GraphfabExport int gf_nw_isLayoutSpecified | ( | gf_network * | nw | ) |
Did the SBML model include layout?
| [in] | n | Network |
| _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.
| [in] | nw | Network |
| [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_node* gf_nw_newNodep | ( | gf_network * | nw, |
| const char * | id, | ||
| const char * | name, | ||
| gf_compartment * | compartment | ||
| ) |
Add a new node to the network.
| [in] | nw | Network |
| [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 void gf_nw_rebuildCurves | ( | gf_network * | n | ) |
Rebuild the curves.
| [in] | n | Network |
| _GraphfabExport void gf_nw_recenterJunctions | ( | gf_network * | n | ) |
Recenter reaction junctions.
| [in] | n | Network |
| _GraphfabExport int gf_nw_removeNode | ( | gf_network * | nw, |
| gf_node * | node | ||
| ) |
Remove a node from the network.
| [in] | n | Network |
| _GraphfabExport void gf_nw_removeRxn | ( | gf_network * | n, |
| gf_reaction * | r | ||
| ) |
Remove the given reaction.
| [in] | n | Network |
| [in] | i | Node index |
| _GraphfabExport gf_layoutInfo* gf_processLayout | ( | gf_SBMLModel * | lo | ) |
Process the layout info from a document. The layout info holds the network (nodes, reactions, etc.), canvas, and SBML content.
| [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 |
| _GraphfabExport void gf_randomizeLayout | ( | gf_layoutInfo * | m | ) |
Randomize node positions.
| [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.
| [in] | n | Network |
| [in] | c | Canvas |
| _GraphfabExport gf_point gf_reaction_getCentroid | ( | gf_reaction * | r | ) |
Get the centroid of the reaction.
| [in] | r | Reaction |
| _GraphfabExport gf_curve gf_reaction_getCurve | ( | const gf_reaction * | r, |
| size_t | i | ||
| ) |
Get the curve i.
| [in] | r | Reaction |
| _GraphfabExport gf_curve* gf_reaction_getCurvep | ( | const gf_reaction * | r, |
| size_t | i | ||
| ) |
Get the curve i.
| [in] | r | Reaction |
| _GraphfabExport char* gf_reaction_getID | ( | gf_reaction * | r | ) |
Get the id, user frees memory.
| [in] | r | Reaction |
| _GraphfabExport size_t gf_reaction_getNumCurves | ( | const gf_reaction * | r | ) |
Get the number of curves in the reaction.
| [in] | r | Reaction |
| _GraphfabExport size_t gf_reaction_getNumSpec | ( | const gf_reaction * | r | ) |
Get the number of species in the reaction.
| [in] | r | Reaction |
| _GraphfabExport gf_specRole gf_reaction_getSpecRole | ( | const gf_reaction * | r, |
| size_t | i | ||
| ) |
Get the role for spec i.
| [in] | r | Reaction |
| _GraphfabExport int gf_reaction_hasSpec | ( | const gf_reaction * | r, |
| const gf_node * | n | ||
| ) |
Return true if the reaction has the given species.
| [in] | r | Reaction |
| _GraphfabExport void gf_reaction_recalcCurveCPs | ( | gf_reaction * | r | ) |
Recalculate the curve CPs, don't recenter.
| [in] | n | Reaction |
| _GraphfabExport void gf_reaction_recenter | ( | gf_reaction * | r | ) |
Recenter reaction centroid.
| [in] | n | Reaction |
| _GraphfabExport void gf_reaction_setCentroid | ( | gf_reaction * | r, |
| gf_point | p | ||
| ) |
Set the centroid of the reaction.
| [in] | r | Reaction |
| _GraphfabExport size_t gf_reaction_specGeti | ( | const gf_reaction * | r, |
| size_t | i | ||
| ) |
Get the index of the species in the network.
| [in] | r | Reaction |
| _GraphfabExport void gf_release_transform | ( | gf_transform * | tf | ) |
Release transform.
| [in] | tf | Transform |
| _GraphfabExport void gf_releaseCanvas | ( | gf_canvas * | c | ) |
Release the canvas.
| [in] | c | The canvas |
| _GraphfabExport void gf_releaseCompartment | ( | const gf_compartment * | c | ) |
Release the comp.
| [in] | c | Comp |
| _GraphfabExport void gf_releaseCurve | ( | const gf_curve * | c | ) |
Release the curve.
| [in] | c | Curve |
| _GraphfabExport void gf_releaseNetwork | ( | gf_network * | n | ) |
Release the network.
| [in] | n | Network |
| _GraphfabExport void gf_releaseNode | ( | const gf_node * | n | ) |
Release the node.
| [in] | n | Node |
| _GraphfabExport void gf_releaseRxn | ( | const gf_reaction * | r | ) |
Release the reaction.
| [in] | r | Reaction |
| _GraphfabExport const char* gf_renderTikZ | ( | gf_layoutInfo * | l | ) |
Render the model as a TikZ image.
| [in] | l | The model/layout infor |
| _GraphfabExport int gf_renderTikZFile | ( | gf_layoutInfo * | l, |
| const char * | filename | ||
| ) |
Render the model as a TikZ image.
| [in] | l | The model/layout infor |
| _GraphfabExport const char* gf_roleToStr | ( | gf_specRole | role | ) |
Convert role to string.
| [in] | role | Role |
| _GraphfabExport void gf_setModelNamespace | ( | gf_layoutInfo * | l, |
| unsigned long | level, | ||
| unsigned long | version | ||
| ) |
Set the level and version of the SBML.
| [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*)
| [in] | str | The string to free |
| _GraphfabExport gf_specRole gf_strToRole | ( | const char * | str | ) |
| _GraphfabExport CPoint gf_tf_apply_to_point | ( | gf_transform * | tf, |
| CPoint | p | ||
| ) |
Apply transform to point.
| [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)
| [in] | l | Layout |
| [in] | left | Left edge of screen (other args similar) |
| _GraphfabExport gf_point gf_tf_getDisplacement | ( | gf_transform * | tf | ) |
Get the displacement of the transform.
| [in] | tf | Transform |
| _GraphfabExport gf_point gf_tf_getPostDisplacement | ( | gf_transform * | tf | ) |
Get the displacement of the transform.
| [in] | tf | Transform |
| _GraphfabExport gf_point gf_tf_getScale | ( | gf_transform * | tf | ) |
Get the scale of the transform.
| [in] | tf | Transform |
| _GraphfabExport int gf_writeSBML | ( | const char * | filename, |
| gf_SBMLModel * | m | ||
| ) |
Write an SBML file (does not include layout.
| [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.
| [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 |
1.8.7
