trnsprob.h File Reference

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Macros
#define	MAXEDGE   1.2
#define	ATOLPARAM   0.0001
#define	RTOLPARAM   0.001

Enumerations
enum	{   T, C, A, G,   N, N1, N2 }
enum	{ REV, TN93, HKY85 }

Functions
char	encodeBase (char c)
char	decodeBase (char c)
void	normalizeBaseFreqs (double *F, double fT, double fC, double fA, double fG)
void	normalizeRateParams (double *X, double a, double b, double c, double d, double e, double f)
void	initTrnsprob (double ****PP)
void	uninitTrnsprob (double ****PP)
void	getTrnsprob (double **P, double ***PP, double d)
void	updateTrnsprob (double ***PP, double *F, double *X, short M)

Macro Definition Documentation

#define MAXEDGE   1.2

Definition at line 15 of file trnsprob.h.

#define ATOLPARAM   0.0001

Definition at line 17 of file trnsprob.h.

Referenced by normalizeBaseFreqs(), and normalizeRateParams().

#define RTOLPARAM   0.001

Definition at line 18 of file trnsprob.h.

Enumeration Type Documentation

anonymous enum

Enumerator
T
C
A
G
N
N1
N2

Definition at line 20 of file trnsprob.h.

anonymous enum

Enumerator
REV
TN93
HKY85

Definition at line 21 of file trnsprob.h.

Function Documentation

char encodeBase

(

char

c

)

Definition at line 80 of file trnsprob.cxx.

References A, C, G, N, and T.

Referenced by Align().

char decodeBase

(

char

c

)

Definition at line 95 of file trnsprob.cxx.

References A, C, G, N, and T.

Referenced by Align(), drawLowerPath(), and drawPath().

void normalizeBaseFreqs	(	double *	F,
		double	fT,
		double	fC,
		double	fA,
		double	fG
	)

Definition at line 110 of file trnsprob.cxx.

References A, ATOLPARAM, C, G, REAL_MIN, s, and T.

Referenced by Align().

void normalizeRateParams	(	double *	X,
		double	a,
		double	b,
		double	c,
		double	d,
		double	e,
		double	f
	)

Definition at line 132 of file trnsprob.cxx.

References ATOLPARAM, REAL_MIN, and s.

Referenced by Align().

void initTrnsprob

(

double ****

PP

)

Definition at line 155 of file trnsprob.cxx.

References N, newMatrix(), newVector, and P.

Referenced by updateScore().

void uninitTrnsprob

(

double ****

PP

)

Definition at line 167 of file trnsprob.cxx.

References freeBlock, freeMatrix, and P.

Referenced by updateScore().

void getTrnsprob	(	double **	P,
		double ***	PP,
		double	d
	)

Definition at line 179 of file trnsprob.cxx.

References A, C, copy(), dot(), EPS, G, I, ipol(), J, long, N, T, and Z.

Referenced by updateScore().

void updateTrnsprob	(	double ***	PP,
		double *	F,
		double *	X,
		short	M
	)

Definition at line 226 of file trnsprob.cxx.

References A, addmul(), C, dot(), EPS, G, HKY85, identity(), ih_assert, N, REV, s, T, and TN93.

Referenced by updateScore().