layout.h

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/*== SAGITTARIUS =====================================================================
 * Copyright (c) 2012, Jesse K Medley
 * All rights reserved.

 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
    * Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.
    * Redistributions in binary form must reproduce the above copyright
      notice, this list of conditions and the following disclaimer in the
      documentation and/or other materials provided with the distribution.
    * Neither the name of The University of Washington nor the
      names of its contributors may be used to endorse or promote products
      derived from this software without specific prior written permission.

 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE
 * BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
 * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

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

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

#ifndef __SBNW_LAYOUT_H_
#define __SBNW_LAYOUT_H_

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

#include "graphfab/core/SagittariusCore.h"
#include "graphfab/sbml/autolayoutSBML.h"
#include "graphfab/diag/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);

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

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

_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);

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

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



#endif

#endif