GraphAlignment/src/GraphAlignment.h

Go to the documentation of this file.

#ifndef GA_GRAPH_ALIGNMENT
#define GA_GRAPH_ALIGNMENT
/* ----------------------------------------------------------------------------
 * R package for graph alignment
 * ----------------------------------------------------------------------------
 *
 * Author: Joern P. Meier <mail@ionflux.org>
 * 
 * The package can be used freely for non-commercial purposes. If you use this 
 * package, the appropriate paper to cite is J. Berg and M. Lässig, 
 * "Cross-species analysis of biological networks by Bayesian alignment", 
 * PNAS 103 (29), 10967-10972 (2006)
 * 
 * This software is made available in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY 
 * or FITNESS FOR A PARTICULAR PURPOSE.
 * 
 * This software contains code for solving linear assignment problems which was 
 * written by Roy Jonker, MagicLogic Optimization Inc.. Please note that this 
 * code is copyrighted, &copy; 2003 MagicLogic Systems Inc., Canada and may be 
 * used for non-commercial purposes only. See 
 * https://www.magiclogic.com/assignment.html for the latest version of the LAP 
 * code and details on licensing.
 *
 * ----------------------------------------------------------------------------
 * Package API functions.
 * ----------------------------------------------------------------------------
 */

#include "R.h"
#include "Rinternals.h"
#include "Rdefines.h"
#include "R_ext/Rdynload.h"
#include "GA_message.h"
#include "GA_vector.h"
#include "GA_matrix.h"

#ifdef __cplusplus
extern "C"
{
#endif

void R_init_GraphAlignment(DllInfo* info);

void R_unload_GraphAlignment(DllInfo* info);

void GA_msg_R(const char* text, GAMessageLevel level);

GAVectorInt* GA_linear_assignment_solve(GAMatrixInt* costMatrix);

GAMatrixReal* GA_encode_directed_graph(GAMatrixReal* matrix, GAVectorInt* p);

SEXP GA_encode_directed_graph_R(SEXP matrix, SEXP p);

SEXP GA_linear_assignment_solve_R(SEXP costMatrix);

enum GADirectedMode_Impl
{
        GA_DIRECTED_ENABLED = 1,
        GA_DIRECTED_DISABLED = 0,
};

typedef enum GADirectedMode_Impl GADirectedMode;

GADirectedMode GA_directed_mode_from_R(SEXP robj);

GAMatrixReal* GA_compute_M(GAMatrixReal* na, GAMatrixReal* nb, 
        GAMatrixReal* r, GAVectorInt* p, GAMatrixReal* linkScore, 
        GAMatrixReal* selfLinkScore, GAVectorReal* nodeScore1, 
        GAVectorReal* nodeScore2, GAVectorReal* lookupLink, 
        GAVectorReal* lookupNode, GAClampMode clamp);

SEXP GA_compute_M_R(SEXP a, SEXP b, SEXP r, SEXP p, SEXP linkScore, 
        SEXP selfLinkScore, SEXP nodeScore1, SEXP nodeScore2, SEXP lookupLink, 
        SEXP lookupNode, SEXP clamp);

#ifdef __cplusplus
}
#endif
#endif

---