ARB: ST_base_vector Struct Reference

ARB

#include <st_ml.hxx>

Collaboration diagram for ST_base_vector:

Collaboration graph

Public Member Functions
void	setTo (ST_FLOAT freq)

void	multiplyWith (ST_FLOAT factor)

void	increaseBy (ST_FLOAT inc)

void	makeInverseOf (const ST_base_vector &other, ST_FLOAT other_min_freq)

void	setBase (const ST_base_vector &frequencies, char base)

void	check_overflow ()

void	print ()

ST_FLOAT	summarize () const

ST_FLOAT	min_frequency ()

ST_FLOAT	max_frequency ()

ST_base_vector &	operator*= (const ST_base_vector &other)

Public Attributes
ST_FLOAT	b [ST_MAX_BASE]

int	ld_lik

ST_FLOAT	lik

Detailed Description

Definition at line 59 of file st_ml.hxx.

Member Function Documentation

void ST_base_vector::setTo ( ST_FLOAT freq )

inline

Definition at line 64 of file st_ml.hxx.

References ST_A, and ST_MAX_BASE.

Referenced by check_overflow().

void ST_base_vector::multiplyWith ( ST_FLOAT factor )

inline

Definition at line 69 of file st_ml.hxx.

References ST_A, and ST_MAX_BASE.

Referenced by check_overflow().

void ST_base_vector::increaseBy ( ST_FLOAT inc )

inline

Definition at line 74 of file st_ml.hxx.

References ST_A, and ST_MAX_BASE.

void ST_base_vector::makeInverseOf	(	const ST_base_vector &	other,
		ST_FLOAT	other_min_freq
	)

inline

Definition at line 79 of file st_ml.hxx.

References b, ST_A, and ST_MAX_BASE.

void ST_base_vector::setBase	(	const ST_base_vector &	frequencies,
		char	base
	)

Definition at line 55 of file ST_ml.cxx.

References b, DNA_Table::char_to_enum(), ld_lik, lik, ST_A, ST_C, ST_G, ST_GAP, ST_MAX_BASE, ST_T, and ST_UNKNOWN.

void ST_base_vector::check_overflow ( )

inline

Definition at line 79 of file ST_ml.cxx.

References ld_lik, multiplyWith(), setTo(), and summarize().

Referenced by MostLikelySeq::calculate_ancestor().

void ST_base_vector::print ( )

Definition at line 110 of file ST_ml.cxx.

References b, and ST_MAX_BASE.

ST_FLOAT ST_base_vector::summarize ( ) const

inline

Definition at line 90 of file st_ml.hxx.

References ST_A, ST_C, ST_G, ST_GAP, and ST_T.

Referenced by check_overflow(), ST_rate_matrix::transform(), and ST_ML::update_ml_likelihood().

ST_FLOAT ST_base_vector::min_frequency ( )

inline

Definition at line 91 of file st_ml.hxx.

References min, ST_A, ST_C, ST_G, ST_GAP, and ST_T.

ST_FLOAT ST_base_vector::max_frequency ( )

inline

Definition at line 92 of file st_ml.hxx.

References max, ST_A, ST_C, ST_G, ST_GAP, and ST_T.

Referenced by ST_ML::get_color_string(), and st_ml_add_sequence_part_to_stat().

ST_base_vector & ST_base_vector::operator*= ( const ST_base_vector & other )

inline

Definition at line 97 of file ST_ml.cxx.

References b, ld_lik, lik, ST_A, ST_C, ST_G, ST_GAP, and ST_T.

Member Data Documentation

ST_FLOAT ST_base_vector::b[ST_MAX_BASE]

Definition at line 60 of file st_ml.hxx.

Referenced by MostLikelySeq::calc_out(), ST_ML::get_color_string(), makeInverseOf(), operator*=(), print(), setBase(), st_ml_add_sequence_part_to_stat(), ST_rate_matrix::transform(), and ST_ML::update_ml_likelihood().

int ST_base_vector::ld_lik

Definition at line 61 of file st_ml.hxx.

Referenced by check_overflow(), operator*=(), setBase(), and ST_rate_matrix::transform().

ST_FLOAT ST_base_vector::lik

Definition at line 62 of file st_ml.hxx.

Referenced by MostLikelySeq::calculate_ancestor(), operator*=(), setBase(), and ST_rate_matrix::transform().

The documentation for this struct was generated from the following files:

STAT/st_ml.hxx
STAT/ST_ml.cxx