layout.h

Go to the documentation of this file.

/* MIT License
 */

//== FILEDOC =========================================================================

//== BEGINNING OF CODE ===============================================================

#ifndef __SBNW_LAYOUT_H_
#define __SBNW_LAYOUT_H_

//== INCLUDES ========================================================================

#include "SagittariusCore.h"
#include "autolayoutSBML.h"
#include "error.h"

#include <stdint.h>

//-- C methods --

#ifdef __cplusplus
extern "C" {
#endif

typedef struct {
    void* n;
} gf_network;

typedef struct {
    void* n;
} gf_node;

typedef struct {
    void* r;
} gf_reaction;

typedef struct {
    void* c;
} gf_curve;

typedef struct {
    void* c;
} gf_compartment;

typedef struct {
    void* canv;
} gf_canvas;

typedef struct {
    void* net;
    void* canv;
    char* cont;

    // sbml opts
    int level;
    int version;
} gf_layoutInfo;

//DEPRECATED: rename to gf_point
typedef struct {
    Real x;
    Real y;
} CPoint;

typedef struct {
    Real x;
    Real y;
} gf_point;

typedef struct {
    void* tf;
} gf_transform;

typedef struct {
    gf_point s;
    gf_point c1;
    gf_point c2;
    gf_point e;
} gf_curveCP;

typedef enum {
    GF_ROLE_SUBSTRATE,
    GF_ROLE_PRODUCT,
    GF_ROLE_SIDESUBSTRATE,
    GF_ROLE_SIDEPRODUCT,
    GF_ROLE_MODIFIER,
    GF_ROLE_ACTIVATOR,
    GF_ROLE_INHIBITOR
} gf_specRole;

_GraphfabExport void gf_freeLayoutInfo(gf_layoutInfo* l);

_GraphfabExport void gf_freeLayoutInfoHierarch(gf_layoutInfo* l);

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

_GraphfabExport gf_SBMLModel gf_SBMLModel_new();

_GraphfabExport gf_SBMLModel* gf_SBMLModel_newp();

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

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

// -- Input --

_GraphfabExport gf_layoutInfo* gf_processLayout(gf_SBMLModel* lo);

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

// -- Configuration --

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

_GraphfabExport const char* gf_getDefaultCompartmentId();

_GraphfabExport void gf_setDefaultCompartmentId(const char* id);

// -- Object API --

// Network

_GraphfabExport gf_network gf_getNetwork(gf_layoutInfo* l);

_GraphfabExport gf_network* gf_getNetworkp(gf_layoutInfo* l);

_GraphfabExport void gf_clearNetwork(gf_network* n);

_GraphfabExport void gf_releaseNetwork(gf_network* n);

_GraphfabExport char* gf_nw_getId(gf_network* n);

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

_GraphfabExport uint64_t gf_nw_getNumNodes(const gf_network* n);

_GraphfabExport uint64_t gf_nw_getNumUniqueNodes(const gf_network* n);

_GraphfabExport uint64_t gf_nw_getNumRxns(const gf_network* n);

_GraphfabExport uint64_t gf_nw_getNumComps(const gf_network* n);

_GraphfabExport gf_node gf_nw_getNode(gf_network* n, uint64_t i);

_GraphfabExport gf_node gf_nw_getUniqueNode(gf_network* n, uint64_t i);

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

_GraphfabExport gf_node* gf_nw_getUniqueNodep(gf_network* n, uint64_t i);

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

_GraphfabExport gf_reaction gf_nw_getRxn(gf_network* n, uint64_t i);

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

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

_GraphfabExport gf_compartment gf_nw_getCompartment(gf_network* n, uint64_t i);

_GraphfabExport gf_compartment* gf_nw_getCompartmentp(gf_network* n, uint64_t i);

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

_GraphfabExport void gf_nw_rebuildCurves(gf_network* n);

_GraphfabExport void gf_nw_recenterJunctions(gf_network* n);

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

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

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

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

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

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

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

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

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

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

_GraphfabExport int gf_nw_isLayoutSpecified(gf_network* nw);

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

_GraphfabExport int gf_nw_getNumAliasInstances(gf_network* nw, gf_node* n);

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

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

_GraphfabExport gf_node* gf_nw_getAliasInstancep(gf_network* nw, gf_node* n, uint64_t i);

// Node

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

_GraphfabExport void gf_clearNode(gf_node* n);

_GraphfabExport void gf_releaseNode(const gf_node* n);

_GraphfabExport int gf_node_isLocked(gf_node* n);

_GraphfabExport void gf_node_lock(gf_node* n);

_GraphfabExport void gf_node_unlock(gf_node* n);

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

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

_GraphfabExport int gf_node_isAliased(gf_node* n);

_GraphfabExport void gf_node_setIsAlias(gf_node* n, int isAlias);

_GraphfabExport gf_point gf_node_getCentroid(gf_node* n);

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

_GraphfabExport void gf_node_setCentroid(gf_node* n, gf_point p);

_GraphfabExport double gf_node_getWidth(gf_node* n);

_GraphfabExport void gf_node_setWidth(gf_node* n, double width);

_GraphfabExport double gf_node_getHeight(gf_node* n);

_GraphfabExport void gf_node_setHeight(gf_node* n, double height);

_GraphfabExport char* gf_node_getID(gf_node* n);

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

_GraphfabExport const char* gf_node_getName(gf_node* n);

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

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

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

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

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

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

// Reaction

_GraphfabExport void gf_releaseRxn(const gf_reaction* r);

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

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

_GraphfabExport char* gf_reaction_getID(gf_reaction* r);

_GraphfabExport gf_point gf_reaction_getCentroid(gf_reaction* r);

_GraphfabExport void gf_reaction_setCentroid(gf_reaction* r, gf_point p);

_GraphfabExport uint64_t gf_reaction_getNumSpec(const gf_reaction* r);

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

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

_GraphfabExport const char* gf_roleToStr(gf_specRole role);

_GraphfabExport gf_specRole gf_strToRole(const char* str);

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

_GraphfabExport uint64_t gf_reaction_getNumCurves(const gf_reaction* r);

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

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

_GraphfabExport void gf_reaction_recenter(gf_reaction* r);

_GraphfabExport void gf_reaction_recalcCurveCPs(gf_reaction* r);

// Curve

_GraphfabExport void gf_releaseCurve(const gf_curve* c);

// _GraphfabExport char* gf_curve_getID(gf_curve* c);

_GraphfabExport gf_specRole gf_curve_getRole(gf_curve* c);

_GraphfabExport gf_curveCP gf_getCurveCPs(const gf_curve* c);

_GraphfabExport int gf_curve_hasArrowhead(const gf_curve* c);


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

// Comparment

_GraphfabExport void gf_releaseCompartment(const gf_compartment* c);

_GraphfabExport char* gf_compartment_getID(gf_compartment* c);

_GraphfabExport gf_point gf_compartment_getMinCorner(gf_compartment* c);

_GraphfabExport void gf_compartment_setMinCorner(gf_compartment* c, gf_point p);

_GraphfabExport gf_point gf_compartment_getMaxCorner(gf_compartment* c);

_GraphfabExport void gf_compartment_setMaxCorner(gf_compartment* c, gf_point p);

_GraphfabExport double gf_compartment_getWidth(gf_compartment* c);

_GraphfabExport double gf_compartment_getHeight(gf_compartment* c);

_GraphfabExport uint64_t gf_compartment_getNumElt(gf_compartment* c);

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

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

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

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

// Transform

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

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

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

_GraphfabExport CPoint gf_tf_apply_to_point(gf_transform* tf, CPoint p);

_GraphfabExport gf_point gf_tf_getScale(gf_transform* tf);

_GraphfabExport gf_point gf_tf_getDisplacement(gf_transform* tf);

_GraphfabExport gf_point gf_tf_getPostDisplacement(gf_transform* tf);

_GraphfabExport void gf_dump_transform(gf_transform* tf);

_GraphfabExport void gf_release_transform(gf_transform* tf);

// Canvas

_GraphfabExport gf_canvas gf_getCanvas(gf_layoutInfo* l);

_GraphfabExport gf_canvas* gf_getCanvasp(gf_layoutInfo* l);

_GraphfabExport void gf_clearCanvas(gf_canvas* c);

_GraphfabExport void gf_releaseCanvas(gf_canvas* c);

_GraphfabExport unsigned int gf_canvGetWidth(gf_canvas* c);

_GraphfabExport unsigned int gf_canvGetHeight(gf_canvas* c);

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

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

// -- Queries --

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

// -- Configuration

_GraphfabExport int gf_lockNodeId(gf_layoutInfo* l, const char* id);

_GraphfabExport int gf_unlockNodeId(gf_layoutInfo* l, const char* id);

_GraphfabExport int gf_aliasNodeId(gf_layoutInfo* l, const char* id);

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

// -- Processing --

_GraphfabExport void gf_randomizeLayout(gf_layoutInfo* m);

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

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

// -- Output --

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

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

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

_GraphfabExport const char* gf_getCurrentLibraryVersion(void);

_GraphfabExport void gf_free(void* x);

_GraphfabExport gf_point gf_computeCubicBezierPoint(gf_curveCP* c, Real t);

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

_GraphfabExport int gf_arrowheadStyleGetNumVerts(int style);

_GraphfabExport gf_point gf_arrowheadStyleGetVert(int style, int n);

_GraphfabExport int gf_arrowheadStyleIsFilled(int style);

_GraphfabExport unsigned long gf_arrowheadNumStyles();

_GraphfabExport void gf_arrowheadSetStyle(gf_specRole role, int style);

_GraphfabExport int gf_arrowheadGetStyle(gf_specRole role);

_GraphfabExport void gf_layout_alignToOrigin(gf_layoutInfo* l, double pad_x, double pad_y);

#ifdef __cplusplus
}//extern "C"
#endif

//-- C++ methods --
#ifdef __cplusplus



#endif

#endif