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/* General hidden Markov models (discrete; of alphabetic strings)
* SRE, Fri Jul 18 08:54:41 2008 [Janelia]
#ifndef eslHMM_INCLUDED
#define eslHMM_INCLUDED
#include "esl_config.h"
#include "esl_alphabet.h"
#include "esl_random.h"
typedef struct {
int M; /* number of states in the model */
int K; /* size of alphabet (redundant w/ abc->K) */
float *pi; /* initial (begin) distribution (0..M) */
float **t; /* Mx(M+1) state transition probabilities */
float **e; /* MxK emission probabilities */
float **eo; /* K'xM emission odds ratios */
const ESL_ALPHABET *abc; /* ptr to alphabet */
typedef struct {
float **dp; /* [0..L][0..M-1] DP matrix */
float *sc; /* [0..L+1] scale factors (log probs) */
int M; /* actual model dimension (0..M-1) */
int L; /* actual sequence dimension (1..L) */
float *dp_mem; /* memory allocated for the resizable DP matrix */
int allocR; /* current allocated # of rows: L+1 <= validR <= allocR */
int validR; /* # of dp rows actually pointing at DP memory */
int allocM; /* current set row width; M <= allocM */
uint64_t ncells; /* total allocation of dp_mem; ncells >= (validR)(allocM)*/
extern ESL_HMM *esl_hmm_Create(const ESL_ALPHABET *abc, int M);
extern ESL_HMM *esl_hmm_Clone(const ESL_HMM *hmm);
extern int esl_hmm_Configure(ESL_HMM *hmm, float *fq);
extern int esl_hmm_SetDegeneracies(ESL_HMM *hmm);
extern void esl_hmm_Destroy(ESL_HMM *hmm);
extern ESL_HMX *esl_hmx_Create(int allocL, int allocM);
extern int esl_hmx_GrowTo (ESL_HMX *mx, int L, int M);
extern void esl_hmx_Destroy(ESL_HMX *mx);
extern int esl_hmm_Emit(ESL_RANDOMNESS *r, const ESL_HMM *hmm, ESL_DSQ **opt_dsq, int **opt_path, int *opt_L);
extern int esl_hmm_Forward(const ESL_DSQ *dsq, int L, const ESL_HMM *hmm, ESL_HMX *fwd, float *opt_sc);
extern int esl_hmm_Backward(const ESL_DSQ *dsq, int L, const ESL_HMM *hmm, ESL_HMX *bck, float *opt_sc);
#endif /*eslHMM_INCLUDED*/
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