khmm.h

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#ifndef _KHMM_H
#define _KHMM_H
 
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string>
#include <vector>
#include <map>
 
typedef struct {
    int N;          /* number of states;  Q={1,2,...,N} */
    int M;          /* number of observation symbols; V={1,2,...,M}*/
    double **A;     /* A[1..N][1..N]. a[i][j] is the transition prob
                of going from state i at time t to state j
                at time t+1 */
    double **B;     /* B[1..N][1..M]. b[j][k] is the probability of
                of observing symbol k in state j */
    double *pi;     /* pi[1..N] pi[i] is the initial state distribution. */
    double *B1_mean;    /* B1_mean[1..N] mean of a continuous Gaussian distribution for state 1 through N*/
    double *B1_sd;      /*B1_sd standard deviation of B1 values, which is the same for all states*/
    double B1_uf;       /*B1_uniform_fraction: the contribution of uniform distribution to the finite mixture model */
    double *B2_mean;    /* B2_mean[1..4] is the average of B_allele_freq*/
    double *B2_sd;      /* B2_sd[1..4] is the standard deviation of four B_allele_freq, B2_sd[5] is specially for state1, where B is modelled as a wide normal distribution */
    double B2_uf;       /* B2_uniform_fraction: the fraction of uniform distribution in the finite mixture model */
    
    int NP_flag;        /*flag of 1 and 0 to indicate whether Non-Polymorhpic marker information is contained with HMM file*/
    double *B3_mean;    /* B3_mean[1..N] mean of non-polymorphic probe for state 1 through N*/
    double *B3_sd;      /* B3_sd[1..4] is the standard deviation of B3 values*/
    double B3_uf;       /* B3_uniform_fraction: */
    int dist;       /* new parameter to facilitate CNV calling from resequencing data (2009 April) */
} CHMM;
typedef struct  {…};
 
 
/************************************
*subroutines for processing continuous HMM models
************************************/
 
CHMM ReadCHMM (const char *filename);
 
void FreeCHMM(CHMM *phmm);
 
std::vector<int> testVit_CHMM (CHMM hmm, int T, double *O1, double *O2, double *pfb, int *snpdist, double *plogproba);
 
std::vector<int> ViterbiLogNP_CHMM(CHMM *phmm, int T, double *O1, double *O2, double *pfb, int *snpdist, double **delta, int **psi, double *pprob);
 
double b1iot (int state, double *mean, double *sd, double uf, double o);
 
double b2iot (int state, double *mean, double *sd, double uf, double pfb, double b);
 
#endif // _HMM_H_