khmm.cpp File Reference

#include "khmm.h"
#include "kc.h"

Include dependency graph for khmm.cpp:

Macros
#define	BUFFER_SIZE   1024
#define	STATE_CHANGE   100000.0 /*this is the expected changes (D value) in the transition matrix*/
#define	VITHUGE   100000000000.0
#define	FLOAT_MINIMUM   1.175494351e-38; /*this is indeed machine dependent*/
#define	DELTA   1

Functions
std::vector< int >	testVit_CHMM (CHMM hmm, int T, double *O1, double *O2, double *pfb, int *snpdist, double *plogproba)
	Run the main HMM algorithm.
double	b1iot (int state, double *mean, double *sd, double uf, double o)
	O1 emission probability.
double	b2iot (int state, double *mean, double *sd, double uf, double pfb, double b)
	O2 emission probability.
std::vector< int >	ViterbiLogNP_CHMM (CHMM *phmm, int T, double *O1, double *O2, double *pfb, int *snpdist, double **delta, int **psi, double *pprob)
	Viterbi algorithm.
CHMM	ReadCHMM (const char *filename)
	Read an HMM from a file.
void	FreeCHMM (CHMM *phmm)
	Free the memory allocated for an HMM.

Macro Definition Documentation

BUFFER_SIZE

#define BUFFER_SIZE   1024

DELTA

#define DELTA   1

FLOAT_MINIMUM

#define FLOAT_MINIMUM   1.175494351e-38; /*this is indeed machine dependent*/

STATE_CHANGE

#define STATE_CHANGE   100000.0 /*this is the expected changes (D value) in the transition matrix*/

VITHUGE

#define VITHUGE   100000000000.0

Function Documentation

b1iot()

double b1iot	(	int	state,
		double *	mean,
		double *	sd,
		double	uf,
		double	o
	)

O1 emission probability.

Here is the call graph for this function:

Here is the caller graph for this function:

b2iot()

double b2iot	(	int	state,
		double *	mean,
		double *	sd,
		double	uf,
		double	pfb,
		double	b
	)

O2 emission probability.

Here is the call graph for this function:

Here is the caller graph for this function:

FreeCHMM()

void FreeCHMM

(

CHMM *

phmm

)

Free the memory allocated for an HMM.

Here is the call graph for this function:

ReadCHMM()

CHMM ReadCHMM

(

const char *

filename

)

Read an HMM from a file.

Here is the call graph for this function:

Here is the caller graph for this function:

testVit_CHMM()

std::vector< int > testVit_CHMM	(	CHMM	hmm,
		int	T,
		double *	O1,
		double *	O2,
		double *	pfb,
		int *	snpdist,
		double *	plogproba
	)

Run the main HMM algorithm.

Here is the call graph for this function:

Here is the caller graph for this function:

ViterbiLogNP_CHMM()

std::vector< int > ViterbiLogNP_CHMM	(	CHMM *	phmm,
		int	T,
		double *	O1,
		double *	O2,
		double *	pfb,
		int *	snpdist,
		double **	delta,
		int **	psi,
		double *	pprob
	)

Viterbi algorithm.

Here is the call graph for this function:

Here is the caller graph for this function: