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/** discrete encodings of probabilistic biological sequences */
#ifndef PBS_CODE
#define PBS_CODE
#include <simplex_grid.h>
#include <lists.h>
#include <stringsplus.h>
#define MAX_NBYTES 4
/* needs to be <= sizeof(int) */
typedef struct {
SimplexGrid *sg; /** Simplex grid */
Vector **rp; /** array of representative points, by code
index (array has code_size elements) */
List **codes_by_region; /** code indices by simplex region;
codes_by_region[i] is a list of
the code indices associated with
simplex region i (array has
sg->nregs elements) */
unsigned nbytes; /** bytes of storage per encoded
"letter"; between 1 and MAX_NBYTES */
unsigned max_size; /** maximum code size: 256^nbytes - 1 (because of
reserved code for gaps) */
unsigned code_size; /** actual code size; at most
max_size */
unsigned gap_code; /** reserved code for gap characters */
} PbsCode;
/* package of data used in code estimation */
typedef struct {
PbsCode *code; /** code being estimated */
List *prob_vectors; /** raw training data: probability vectors */
List *counts; /** raw training data: counts */
List **vectors_by_region; /** element i is list of vectors for
simplex region i */
List **counts_by_region; /** element i is list of counts for
simplex region i */
List **vectors_by_code; /** element i is list of vectors for
code index i */
List **counts_by_code; /** element i is list of counts for
code index i */
double *error_by_region; /** element i is contribution of
region i to total approximation
error */
double *error_by_code; /** element i is contribution of code
index i to total approximation
error */
} PbsCodeTrainingData;
typedef enum {FULL, NO_GREEDY, NO_TRAIN} training_mode;
PbsCode *pbs_new(int dim, int nrows, int nbytes);
PbsCode *pbs_new_shell(int dim, int nrows, int nbytes, int code_size);
void pbs_free(PbsCode *code);
PbsCode *pbs_new_from_file(FILE *F);
void pbs_write(PbsCode *c, FILE *F, char *comment);
void pbs_assign_points(PbsCode *c);
unsigned pbs_get_index(PbsCode *code, Vector *p, double *error);
double pbs_estimate_from_data(PbsCode *code, List *prob_vectors, List *counts,
FILE *logf, training_mode mode);
void pbs_write_binary(PbsCode *code, unsigned code_idx, FILE *F);
int pbs_read_binary(PbsCode *code, unsigned *code_idx, FILE *F);
#endif
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