trnsprob.cxx File Reference

#include "trnsprob.h"
#include "defs.h"
#include "mem.h"
#include <arb_simple_assert.h>
#include <stdio.h>

Include dependency graph for trnsprob.cxx:

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Macros
#define	ih_assert(bed)   arb_assert(bed)
#define	EPS   0.00001

Functions
static void	identity (double **i)
static void	copy (double **i, double **j)
static void	ipol (double **i, double **j, double **k, double f)
static void	addmul (double **i, double **j, double f)
static void	dot (double **i, double **j, double **k)
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 ih_assert

(

bed

)

arb_assert(bed)

Definition at line 18 of file trnsprob.cxx.

Referenced by updateTrnsprob().

#define EPS   0.00001

Definition at line 19 of file trnsprob.cxx.

Referenced by getTrnsprob(), and updateTrnsprob().

Function Documentation

static void identity ( double **  i )

static

Definition at line 23 of file trnsprob.cxx.

References A, C, G, and T.

Referenced by updateTrnsprob().

static void copy ( double **  i, double **  j  )

static

Definition at line 32 of file trnsprob.cxx.

References A, C, G, and T.

Referenced by ExportFieldTracker::add_tracked_to(), aw_insert_message_in_tmp_message_delayed(), PartRegistry::build_sorted_list(), TrackedFile::callAll(), copy_content(), gb_load_dictionary_data(), gbl_split(), genbank_verify_accession(), XString::get_x_string(), getTrnsprob(), part_of(), ClustersData::restore_all(), ClustersData::store_all(), update_rulesAwar(), write_entry(), and write_IE().

static void ipol ( double **  i, double **  j, double **  k, double  f  )

static

Definition at line 41 of file trnsprob.cxx.

References A, C, G, and T.

Referenced by getTrnsprob().

static void addmul ( double **  i, double **  j, double  f  )

static

Definition at line 50 of file trnsprob.cxx.

References A, C, G, and T.

Referenced by updateTrnsprob().

static void dot ( double **  i, double **  j, double **  k  )

static

Definition at line 59 of file trnsprob.cxx.

References A, C, G, and T.

Referenced by ARB_main(), detect_bitmap_size(), get_suffix(), getTrnsprob(), DI_MATRIX::save(), TokenMatcher::TokenMatcher(), updateTrnsprob(), and NodeTextBuilder::work().

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().