ColumnStat Class Reference

#include <ColumnStat.hxx>

Inheritance diagram for ColumnStat:

Collaboration diagram for ColumnStat:

Public Member Functions
	ColumnStat (GBDATA *gb_main_, AW_root *awr_, const char *awar_template, AW_awar *awar_used_alignment)
	~ColumnStat ()
__ATTR__USERESULT GB_ERROR	calculate (AP_filter *filter)
void	forget ()
GBDATA *	get_gb_main () const
bool	has_valid_alignment () const
const char *	get_awar_smooth () const
const char *	get_awar_enable_helix () const
const char *	get_type_path () const
bool	has_rates () const
void	weight_by_inverseRates () const
size_t	get_length () const
const GB_UINT4 *	get_weights () const
const float *	get_rates () const
const float *	get_ttratio () const
const bool *	get_is_helix () const
const float *	get_frequencies (unsigned char c) const
void	create_sai_selection_list (AW_window *aww)
void	refresh_sai_selection_list ()
void	print ()

Detailed Description

Definition at line 40 of file ColumnStat.hxx.

Constructor & Destructor Documentation

ColumnStat::ColumnStat	(	GBDATA *	gb_main_,
		AW_root *	awr_,
		const char *	awar_template,
		AW_awar *	awar_used_alignment
	)

Definition at line 44 of file ColumnStat.cxx.

References AW_awar::add_callback(), ARRAY_ELEMS, AW_root::awar(), AW_root::awar_int(), AW_root::awar_string(), ga_assert, GBS_string_eval(), AW_awar::map(), refresh_columnstat_selection(), refresh_sai_selection_list(), SRT_AWARCOLSTAT_ALIGNMENT, SRT_AWARCOLSTAT_ENABLE_HELIX, SRT_AWARCOLSTAT_NAME, and SRT_AWARCOLSTAT_SMOOTH.

ColumnStat::~ColumnStat

(

)

Definition at line 99 of file ColumnStat.cxx.

References forget().

Member Function Documentation

GB_ERROR ColumnStat::calculate

(

AP_filter *

filter

)

Definition at line 107 of file ColumnStat.cxx.

References aw_message(), AW_root::awar(), DIST_MIN_SEQ, error(), forget(), GB_append_exportedError(), GB_await_error(), GB_child(), GB_entry(), GB_nextChild(), GB_read_ints(), GB_read_key(), GBS_global_string(), GBT_find_SAI(), GBT_get_alignment_len(), AP_filter::get_filtered_length(), AP_filter::get_length(), BI_helix::init(), AP_filter::is_invalid(), BI_helix::is_pairpos(), NULp, AW_awar::read_int(), AW_awar::read_string(), ta, and AP_filter::use_position().

Referenced by ST_ML::calc_st_ml(), colstat_2_gnuplot_cb(), and WeightedFilter::create_weights().

void ColumnStat::forget

(

)

Definition at line 83 of file ColumnStat.cxx.

References NULp.

Referenced by calculate(), WeightedFilter::create_weights(), and ~ColumnStat().

GBDATA* ColumnStat::get_gb_main ( ) const

inline

Definition at line 76 of file ColumnStat.hxx.

References gb_main.

Referenced by COLSTAT_create_selection_window().

bool ColumnStat::has_valid_alignment ( ) const

inline

Definition at line 78 of file ColumnStat.hxx.

Referenced by filter_columnstat_SAIs(), and get_type_path().

const char* ColumnStat::get_awar_smooth ( ) const

inline

Definition at line 80 of file ColumnStat.hxx.

Referenced by COLSTAT_create_selection_window().

const char* ColumnStat::get_awar_enable_helix ( ) const

inline

Definition at line 81 of file ColumnStat.hxx.

Referenced by COLSTAT_create_selection_window().

const char* ColumnStat::get_type_path ( ) const

inline

Definition at line 82 of file ColumnStat.hxx.

References arb_assert, and has_valid_alignment().

Referenced by filter_columnstat_SAIs().

bool ColumnStat::has_rates ( ) const

inline

Definition at line 84 of file ColumnStat.hxx.

Referenced by WeightedFilter::create_weights().

void ColumnStat::weight_by_inverseRates

(

)

const

Definition at line 306 of file ColumnStat.cxx.

Referenced by WeightedFilter::create_weights().

size_t ColumnStat::get_length ( ) const

inline

Definition at line 87 of file ColumnStat.hxx.

Referenced by colstat_2_gnuplot_cb(), WeightedFilter::create_weights(), and SortedFreq::SortedFreq().

const GB_UINT4* ColumnStat::get_weights ( ) const

inline

Definition at line 89 of file ColumnStat.hxx.

References weights.

Referenced by colstat_2_gnuplot_cb(), and WeightedFilter::create_weights().

const float* ColumnStat::get_rates ( ) const

inline

Definition at line 90 of file ColumnStat.hxx.

Referenced by ST_ML::calc_st_ml(), and colstat_2_gnuplot_cb().

const float* ColumnStat::get_ttratio ( ) const

inline

Definition at line 91 of file ColumnStat.hxx.

References ttratio.

Referenced by ST_ML::calc_st_ml(), and colstat_2_gnuplot_cb().

const bool* ColumnStat::get_is_helix ( ) const

inline

Definition at line 92 of file ColumnStat.hxx.

Referenced by colstat_2_gnuplot_cb().

const float* ColumnStat::get_frequencies ( unsigned char  c ) const

inline

Definition at line 93 of file ColumnStat.hxx.

Referenced by colstat_2_gnuplot_cb(), and SortedFreq::SortedFreq().

void ColumnStat::create_sai_selection_list

(

AW_window *

aww

)

Definition at line 367 of file ColumnStat.cxx.

References awt_create_SAI_selection_list(), filter_columnstat_SAIs(), and ta.

Referenced by COLSTAT_create_selection_list().

void ColumnStat::refresh_sai_selection_list

(

)

Definition at line 31 of file ColumnStat.cxx.

References AW_root::awar(), GBS_string_eval(), AW_awar::read_string(), AW_selection::refresh(), and ta.

Referenced by ColumnStat(), and refresh_columnstat_selection().

void ColumnStat::print

(

)

Definition at line 316 of file ColumnStat.cxx.

References fputc().

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

• SL/GUI_ALIVIEW/ColumnStat.hxx
• SL/GUI_ALIVIEW/ColumnStat.cxx