khmm.h File Reference

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Classes
struct	CHMM

Functions
CHMM	ReadCHMM (const char *filename)
	Read an HMM from a file.
void	FreeCHMM (CHMM *phmm)
	Free the memory allocated for an HMM.
std::vector< int >	testVit_CHMM (CHMM hmm, int T, double *O1, double *O2, double *pfb, int *snpdist, double *plogproba)
	Run the main HMM algorithm.
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.
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.

Function Documentation

b1iot()

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

O1 emission probability.

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b2iot()

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

O2 emission probability.

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FreeCHMM()

void FreeCHMM

(

CHMM *

phmm

)

Free the memory allocated for an HMM.

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ReadCHMM()

CHMM ReadCHMM

(

const char *

filename

)

Read an HMM from a file.

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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.

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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.

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