MostLikelySeq Class Reference

#include <MostLikelySeq.hxx>

Inheritance diagram for MostLikelySeq:

Collaboration diagram for MostLikelySeq:

Public Member Functions
	MostLikelySeq (const AliView *aliview, ST_ML *st_ml_)
	~MostLikelySeq () OVERRIDE
bool	is_up_to_date () const
AP_sequence *	dup () const OVERRIDE
GB_ERROR	bind_to_species (GBDATA *gb_species)
void	unbind_from_species (bool remove_callbacks)
GBDATA *	get_bound_species_data () const
void	sequence_change ()
void	set_sequence ()
void	calculate_ancestor (const MostLikelySeq *lefts, double leftl, const MostLikelySeq *rights, double rightl)
void	forget_sequence ()
void	calc_out (const MostLikelySeq *sequence_of_brother, double dist)
void	print ()
Public Member Functions inherited from AP_sequence
	AP_sequence (const AliView *aliview)
virtual	~AP_sequence ()
GB_ERROR	bind_to_species (GBDATA *gb_species)
void	unbind_from_species ()
bool	is_bound_to_species () const
GBDATA *	get_bound_species_data () const
void	lazy_load_sequence () const
void	ensure_sequence_loaded () const
bool	hasSequence () const
void	forget_sequence ()
size_t	get_sequence_length () const
const AP_filter *	get_filter () const
const AP_weights *	get_weights () const
const AliView *	get_aliview () const

Public Attributes
ST_ML_Color *	color_out
int *	color_out_valid_till

Static Public Attributes
static ST_base_vector *	tmp_out = NULp

Additional Inherited Members
Protected Member Functions inherited from AP_sequence
void	mark_sequence_set (bool is_set)
void	do_lazy_load () const
Protected Attributes inherited from AP_sequence
AP_FLOAT	cached_wbc

Detailed Description

Definition at line 39 of file MostLikelySeq.hxx.

Constructor & Destructor Documentation

MostLikelySeq::MostLikelySeq	(	const AliView *	aliview,
		ST_ML *	st_ml_
	)

Definition at line 160 of file ST_ml.cxx.

Referenced by dup().

MostLikelySeq::~MostLikelySeq

(

)

Definition at line 169 of file ST_ml.cxx.

References color_out, color_out_valid_till, and AP_sequence::unbind_from_species().

Member Function Documentation

bool MostLikelySeq::is_up_to_date ( ) const

inline

Definition at line 64 of file MostLikelySeq.hxx.

AP_sequence * MostLikelySeq::dup ( ) const

virtual

Implements AP_sequence.

Definition at line 213 of file ST_ml.cxx.

References AP_sequence::get_aliview(), and MostLikelySeq().

GB_ERROR MostLikelySeq::bind_to_species

(

GBDATA *

gb_species

)

Definition at line 186 of file ST_ml.cxx.

References AP_sequence::bind_to_species(), error(), GB_add_callback(), GB_CB_CHANGED, GB_CB_DELETE, get_bound_species_data(), st_assert, st_sequence_callback(), and st_sequence_del_callback().

void MostLikelySeq::unbind_from_species

(

bool

remove_callbacks

)

Definition at line 197 of file ST_ml.cxx.

References GB_CB_CHANGED, GB_CB_DELETE, GB_remove_callback(), get_bound_species_data(), st_sequence_callback(), st_sequence_del_callback(), and AP_sequence::unbind_from_species().

Referenced by st_sequence_del_callback().

GBDATA* MostLikelySeq::get_bound_species_data ( ) const

inline

Definition at line 70 of file MostLikelySeq.hxx.

References AP_sequence::get_bound_species_data().

Referenced by bind_to_species(), ST_ML::get_color_string(), print(), set_sequence(), st_ml_add_sequence_part_to_stat(), and unbind_from_species().

void MostLikelySeq::sequence_change

(

)

Definition at line 209 of file ST_ml.cxx.

References ST_ML::clear_all().

Referenced by st_sequence_callback().

void MostLikelySeq::set_sequence

(

)

Transform the sequence from character to vector for current range [ST_ML::first_pos .. ST_ML::last_pos]

Definition at line 224 of file ST_ml.cxx.

References GB_read_char_pntr(), GB_read_string_count(), get_bound_species_data(), ST_ML::get_first_pos(), ST_ML::get_inv_base_frequencies(), ST_ML::get_last_pos(), min, and st_assert.

void MostLikelySeq::calculate_ancestor	(	const MostLikelySeq *	lefts,
		double	leftl,
		const MostLikelySeq *	rights,
		double	rightl
	)

Definition at line 247 of file ST_ml.cxx.

References ST_base_vector::check_overflow(), ST_ML::get_first_pos(), ST_ML::get_last_pos(), ST_ML::get_matrix_for(), ST_ML::get_rate_at(), ST_ML::get_step_size(), ST_base_vector::lik, st_assert, and ST_rate_matrix::transform().

void MostLikelySeq::forget_sequence ( )

inline

Definition at line 76 of file MostLikelySeq.hxx.

Referenced by ST_ML::get_ml_vectors().

void MostLikelySeq::calc_out	(	const MostLikelySeq *	sequence_of_brother,
		double	dist
	)

Definition at line 281 of file ST_ml.cxx.

References ST_base_vector::b, ST_ML::get_base_frequency_at(), ST_ML::get_first_pos(), ST_ML::get_last_pos(), ST_ML::get_matrix_for(), ST_ML::get_rate_at(), ST_ML::get_step_size(), ST_A, ST_MAX_BASE, tmp_out, and ST_rate_matrix::transform().

Referenced by ST_ML::get_ml_vectors().

void MostLikelySeq::print

(

)

Definition at line 303 of file ST_ml.cxx.

References GB_read_char_pntr(), get_bound_species_data(), and ST_MAX_SEQ_PART.

Member Data Documentation

ST_base_vector * MostLikelySeq::tmp_out = NULp

static

contains existing sequence or ancestor sequence as max. likelihood vectors

Definition at line 44 of file MostLikelySeq.hxx.

Referenced by calc_out(), ST_ML::cleanup(), ST_ML::get_color_string(), st_ml_add_sequence_part_to_stat(), and ST_ML::update_ml_likelihood().

ST_ML_Color* MostLikelySeq::color_out

Definition at line 52 of file MostLikelySeq.hxx.

Referenced by ST_ML::get_color_string(), and ~MostLikelySeq().

int* MostLikelySeq::color_out_valid_till

Definition at line 53 of file MostLikelySeq.hxx.

Referenced by ST_ML::get_color_string(), and ~MostLikelySeq().

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

• STAT/MostLikelySeq.hxx
• STAT/ST_ml.cxx