AP_filter Class Reference

#include <AP_filter.hxx>

Public Member Functions
	AP_filter (size_t size)
	AP_filter (const char *filter, const char *zerobases, size_t size)
	AP_filter (const AP_filter &other)
	AP_filter (AF_Not, const AP_filter &other)
	AP_filter (const AP_filter &f1, AF_Combine comb, const AP_filter &f2)
	~AP_filter ()
	DECLARE_ASSIGNMENT_OPERATOR (AP_filter)
long	get_timestamp () const
size_t	get_filtered_length () const
size_t	get_length () const
bool	use_position (size_t pos) const
const size_t *	get_filterpos_2_seqpos () const
void	enable_simplify (AWT_FILTER_SIMPLIFY type)
const uchar *	get_simplify_table () const
void	enable_bootstrap ()
bool	does_bootstrap () const
size_t	bootstrapped_seqpos (size_t bpos) const
char *	to_string () const
char *	blowup_string (const char *filtered_string, char insert) const
char *	filter_string (const char *fulllen_string) const
GB_ERROR	is_invalid () const
bool	was_checked_for_validity () const

Detailed Description

Definition at line 38 of file AP_filter.hxx.

Constructor & Destructor Documentation

AP_filter::AP_filter

(

size_t

size

)

Definition at line 63 of file AP_filter.cxx.

AP_filter::AP_filter	(	const char *	filter,
		const char *	zerobases,
		size_t	size
	)

Definition at line 93 of file AP_filter.cxx.

AP_filter::AP_filter

(

const AP_filter &

other

)

Definition at line 67 of file AP_filter.cxx.

AP_filter::AP_filter	(	AF_Not	,
		const AP_filter &	other
	)

Definition at line 102 of file AP_filter.cxx.

References get_length().

AP_filter::AP_filter	(	const AP_filter &	f1,
		AF_Combine	comb,
		const AP_filter &	f2
	)

Definition at line 112 of file AP_filter.cxx.

References af_assert, AND, get_length(), OR, and XOR.

AP_filter::~AP_filter

(

)

Definition at line 140 of file AP_filter.cxx.

Member Function Documentation

AP_filter::DECLARE_ASSIGNMENT_OPERATOR

(

AP_filter

)

long AP_filter::get_timestamp ( ) const

inline

Definition at line 81 of file AP_filter.hxx.

Referenced by AP_rates::init().

size_t AP_filter::get_filtered_length ( ) const

inline

Definition at line 82 of file AP_filter.hxx.

Referenced by AP_weights::AP_weights(), ColumnStat::calculate(), ST_ML::get_filtered_length(), AliView::get_length(), AP_rates::init(), InsertDatainGDE(), is_invalid(), SQ_helix::SQ_calc_helix_layout(), SQ_fetch_filtered_sequence(), SQ_pass1(), SQ_pass1_no_tree(), and st_ml_add_quality_string_to_species().

size_t AP_filter::get_length ( ) const

inline

Definition at line 83 of file AP_filter.hxx.

Referenced by AP_filter(), AP_weights::AP_weights(), ColumnStat::calculate(), export_sequence_data::export_sequence_data(), ST_ML::get_alignment_length(), InsertDatainGDE(), and is_invalid().

bool AP_filter::use_position ( size_t  pos ) const

inline

Definition at line 85 of file AP_filter.hxx.

References af_assert.

Referenced by AP_weights::AP_weights(), blowup_string(), ColumnStat::calculate(), AP_rates::init(), and InsertDatainGDE().

const size_t* AP_filter::get_filterpos_2_seqpos ( ) const

inline

Definition at line 91 of file AP_filter.hxx.

Referenced by bootstrapped_seqpos(), filter_string(), SQ_helix::SQ_calc_helix_layout(), and SQ_fetch_filtered_sequence().

void AP_filter::enable_simplify

(

AWT_FILTER_SIMPLIFY

type

)

Definition at line 160 of file AP_filter.cxx.

References af_assert, AWT_FILTER_SIMPLIFY_DNA, AWT_FILTER_SIMPLIFY_NONE, AWT_FILTER_SIMPLIFY_PROTEIN, and type.

Referenced by awt_get_filter(), and get_simplify_table().

const uchar* AP_filter::get_simplify_table ( ) const

inline

Definition at line 100 of file AP_filter.hxx.

References AWT_FILTER_SIMPLIFY_NONE, AWT_FILTER_SIMPLIFY_NOT_INITIALIZED, and enable_simplify().

Referenced by InsertDatainGDE().

void AP_filter::enable_bootstrap

(

)

Definition at line 206 of file AP_filter.cxx.

References af_assert, and GB_random().

Referenced by di_calculate_matrix().

bool AP_filter::does_bootstrap ( ) const

inline

Definition at line 109 of file AP_filter.hxx.

size_t AP_filter::bootstrapped_seqpos ( size_t  bpos ) const

inline

Definition at line 111 of file AP_filter.hxx.

References af_assert, and get_filterpos_2_seqpos().

char * AP_filter::to_string

(

)

const

Definition at line 146 of file AP_filter.cxx.

References af_assert.

Referenced by InsertDatainGDE().

char * AP_filter::blowup_string	(	const char *	filtered_string,
		char	insert
	)		const

blow up 'filtered_string' to unfiltered length by inserting 'fillChar' at filtered positions

Definition at line 222 of file AP_filter.cxx.

References af_assert, and use_position().

Referenced by st_ml_add_quality_string_to_species().

char * AP_filter::filter_string

(

const char *

fulllen_string

)

const

filter given 'fulllen_string'

Definition at line 239 of file AP_filter.cxx.

References af_assert, and get_filterpos_2_seqpos().

GB_ERROR AP_filter::is_invalid ( ) const

inline

returns error

• if filter is based on an empty alignment (i.e. no alignment is selected)
• if all positions are filtered out (i.e. filtered sequences will be empty)

Definition at line 123 of file AP_filter.hxx.

References af_assert, get_filtered_length(), get_length(), and NULp.

Referenced by awt_invalid_filter(), ST_ML::calc_st_ml(), ColumnStat::calculate(), WeightedFilter::create_aliview(), di_autodetect_callback(), SEQIO::export_by_format(), export_sequence_data::export_sequence_data(), and InsertDatainGDE().

bool AP_filter::was_checked_for_validity ( ) const

inline

Definition at line 140 of file AP_filter.hxx.

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

• SL/FILTER/AP_filter.hxx
• SL/FILTER/AP_filter.cxx