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/* Double-precision two-dimensional matrices, and some linear algebra
*
* SRE, Tue Jul 13 14:41:07 2004 [St. Louis]
*/
#ifndef eslDMATRIX_INCLUDED
#define eslDMATRIX_INCLUDED
#include "esl_config.h"
#include <stdio.h>
typedef struct {
/*mx, mx[0] are allocated. */
/*::cexcerpt::dmatrix_obj::begin::*/
double **mx; /* mx[i][j] is i'th row, j'th col */
int n; /* rows */
int m; /* columns */
enum { eslGENERAL, eslUPPER } type;
/*::cexcerpt::dmatrix_obj::end::*/
int ncells; /* number of valid cells (nxm in standard matrix) */
} ESL_DMATRIX;
typedef struct {
int *pi;
int n;
} ESL_PERMUTATION;
/* 1. The ESL_DMATRIX object. */
extern ESL_DMATRIX *esl_dmatrix_Create(int n, int m);
extern ESL_DMATRIX *esl_dmatrix_CreateUpper(int n);
extern int esl_dmatrix_Destroy(ESL_DMATRIX *A);
extern int esl_dmatrix_Copy (const ESL_DMATRIX *src, ESL_DMATRIX *dest);
extern ESL_DMATRIX *esl_dmatrix_Clone (const ESL_DMATRIX *old);
extern int esl_dmatrix_Compare (const ESL_DMATRIX *A, const ESL_DMATRIX *B, double tol);
extern int esl_dmatrix_CompareAbs (const ESL_DMATRIX *A, const ESL_DMATRIX *B, double tol);
extern int esl_dmatrix_Set (ESL_DMATRIX *A, double x);
extern int esl_dmatrix_SetZero (ESL_DMATRIX *A);
extern int esl_dmatrix_SetIdentity(ESL_DMATRIX *A);
/* 2. Debugging/validation for ESL_DMATRIX. */
extern int esl_dmatrix_Dump(FILE *ofp, const ESL_DMATRIX *A,
const char *rowlabel, const char *collabel);
/* 3. Visualization tools. */
extern int esl_dmatrix_PlotHeatMap(FILE *fp, ESL_DMATRIX *D, double min, double max);
/* 4. The ESL_PERMUTATION object. */
extern ESL_PERMUTATION *esl_permutation_Create(int n);
extern int esl_permutation_Destroy(ESL_PERMUTATION *P);
extern int esl_permutation_Reuse(ESL_PERMUTATION *P);
/* 5. Debugging/validation for ESL_PERMUTATION. */
extern int esl_permutation_Dump(FILE *ofp, const ESL_PERMUTATION *P,
const char *rowlabel, const char *collabel);
/* 6. The rest of the dmatrix API. */
extern double esl_dmx_Max (const ESL_DMATRIX *A);
extern double esl_dmx_Min (const ESL_DMATRIX *A);
extern double esl_dmx_Sum (const ESL_DMATRIX *A);
extern int esl_dmx_MinMax(const ESL_DMATRIX *A, double *ret_min, double *ret_max);
extern int esl_dmx_FrobeniusNorm(const ESL_DMATRIX *A, double *ret_fnorm);
extern int esl_dmx_Multiply(const ESL_DMATRIX *A, const ESL_DMATRIX *B, ESL_DMATRIX *C);
extern int esl_dmx_Exp(const ESL_DMATRIX *Q, double t, ESL_DMATRIX *P);
extern int esl_dmx_Transpose(ESL_DMATRIX *A);
extern int esl_dmx_Add(ESL_DMATRIX *A, const ESL_DMATRIX *B);
extern int esl_dmx_Scale(ESL_DMATRIX *A, double k);
extern int esl_dmx_AddScale(ESL_DMATRIX *A, double k, const ESL_DMATRIX *B);
extern int esl_dmx_Permute_PA(const ESL_PERMUTATION *P, const ESL_DMATRIX *A, ESL_DMATRIX *B);
extern int esl_dmx_LUP_decompose(ESL_DMATRIX *A, ESL_PERMUTATION *P);
extern int esl_dmx_LU_separate(const ESL_DMATRIX *LU, ESL_DMATRIX *L, ESL_DMATRIX *U);
extern int esl_dmx_Invert(const ESL_DMATRIX *A, ESL_DMATRIX *Ai);
/* 7. Optional: interoperability with GSL */
#ifdef HAVE_LIBGSL
#include <gsl/gsl_matrix.h>
extern int esl_dmx_MorphGSL(const ESL_DMATRIX *E, gsl_matrix **ret_G);
extern int esl_dmx_UnmorphGSL(const gsl_matrix *G, ESL_DMATRIX **ret_E);
#endif
/* 8. Optional: interfaces to LAPACK */
#ifdef HAVE_LIBLAPACK
extern int esl_dmx_Diagonalize(const ESL_DMATRIX *A, double **ret_Er, double **ret_Ei, ESL_DMATRIX **ret_UL, ESL_DMATRIX **ret_UR);
#endif
#endif /*eslDMATRIX_INCLUDED*/
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