Search Toolkit Book for CWinMaskCountsGenerator

This class encapsulates the n-mer frequency counts generation functionality of winmasker. More...

#include <algo/winmask/win_mask_gen_counts.hpp>

Collaboration diagram for CWinMaskCountsGenerator:

Classes
class	GenCountsException
	Exceptions that CWinMaskCountsGenerator may throw. More...

Public Member Functions
	CWinMaskCountsGenerator (const string &input, const string &output, const string &infmt, const string &sformat, const string &th, Uint4 mem_avail, Uint1 unit_size, Uint8 genome_size, Uint4 min_count, Uint4 max_count, bool check_duplicates, bool use_list, const CWinMaskUtil::CIdSet ids, const CWinMaskUtil::CIdSet exclude_ids, bool use_ba, string const &metadata, double min_pct=-1.0, double extend_pct=-1.0, double thres_pct=-1.0, double max_pct=-1.0)
	Constructor. More...

	CWinMaskCountsGenerator (const string &input, CNcbiOstream &os, const string &infmt, const string &sformat, const string &th, Uint4 mem_avail, Uint1 unit_size, Uint8 genome_size, Uint4 min_count, Uint4 max_count, bool check_duplicates, bool use_list, const CWinMaskUtil::CIdSet ids, const CWinMaskUtil::CIdSet exclude_ids, bool use_ba, string const &metadata, double min_pct=-1.0, double extend_pct=-1.0, double thres_pct=-1.0, double max_pct=-1.0)
	Constructor. More...

	~CWinMaskCountsGenerator ()
	Object destructor. More...

void	operator() ()
	This function does the actual n-mer counting. More...

Private Member Functions
void	process (Uint4 prefix, Uint1 prefix_size, const vector< string > &input, bool do_output)

Uint8	fastalen (const string &fname) const

Private Attributes
string	input

CRef< CSeqMaskerOstat >	ustat

Uint8	max_mem

Uint4	unit_size

Uint8	genome_size

Uint4	min_count

Uint4	max_count

Uint4	t_high

bool	has_min_count

bool	no_extra_pass

bool	check_duplicates

bool	use_list

Uint4	total_ecodes

vector< Uint4 >	score_counts

double	th [4]

const CWinMaskUtil::CIdSet *	ids

const CWinMaskUtil::CIdSet *	exclude_ids

string	infmt

Detailed Description

This class encapsulates the n-mer frequency counts generation functionality of winmasker.

Definition at line 61 of file win_mask_gen_counts.hpp.

Constructor & Destructor Documentation

◆ CWinMaskCountsGenerator() [1/2]

CWinMaskCountsGenerator::CWinMaskCountsGenerator	(	const string &	input,
		const string &	output,
		const string &	infmt,
		const string &	sformat,
		const string &	th,
		Uint4	mem_avail,
		Uint1	unit_size,
		Uint8	genome_size,
		Uint4	min_count,
		Uint4	max_count,
		bool	check_duplicates,
		bool	use_list,
		const CWinMaskUtil::CIdSet *	ids,
		const CWinMaskUtil::CIdSet *	exclude_ids,
		bool	use_ba,
		string const &	metadata,
		double	min_pct = `-1.0`,
		double	extend_pct = `-1.0`,
		double	thres_pct = `-1.0`,
		double	max_pct = `-1.0`
	)

Constructor.

Creates an instance based on configuration parameters.

Parameters

input	input file name or a name of the file containing a list of input files (one per line) depending on the value of use_list parameter
output	name of the output file (empty means standard output)
infmt	input format
sformat	counts format
th	string describing 4 percentage values (comma separated) used to compute winmask score thresholds
mem_avail	memory (in megabytes) available to the function
unit_size	n-mer size (value of n)
min_count	do not consider n-mers with counts less than the value this parameter
max_count	maximum n-mer count to consider in winmask thresholds computations
check_duplicates	true if input checking for duplicates is requested; false otherwise
use_list	true if input file contains the list of fasta file names; false if input is the name of the fasta file itself
ids	set of ids to consider
exclude_ids	set of ids to ignore
use_ba	use bit array optimization for optimized binary unit counts format
metadata	the metadata string
min_pct	min score as percentage of counts
extend_pct	interval extension score as percentage of counts
thres_pct	masking threshold score as percentage of counts
max_pct	max score as percentage of counts

Definition at line 171 of file win_mask_gen_counts.cpp.

References count, and th.

◆ CWinMaskCountsGenerator() [2/2]

CWinMaskCountsGenerator::CWinMaskCountsGenerator	(	const string &	input,
		CNcbiOstream &	os,
		const string &	infmt,
		const string &	sformat,
		const string &	th,
		Uint4	mem_avail,
		Uint1	unit_size,
		Uint8	genome_size,
		Uint4	min_count,
		Uint4	max_count,
		bool	check_duplicates,
		bool	use_list,
		const CWinMaskUtil::CIdSet *	ids,
		const CWinMaskUtil::CIdSet *	exclude_ids,
		bool	use_ba,
		string const &	metadata,
		double	min_pct = `-1.0`,
		double	extend_pct = `-1.0`,
		double	thres_pct = `-1.0`,
		double	max_pct = `-1.0`
	)

Constructor.

Creates an instance based on configuration parameters.

Parameters

input	input file name or a name of the file containing a list of input files (one per line) depending on the value of use_list parameter
os	the output stream
infmt	input format
sformat	counts format
th	string describing 4 percentage values (comma separated) used to compute winmask score thresholds
mem_avail	memory (in megabytes) available to the function
unit_size	n-mer size (value of n)
min_count	do not consider n-mers with counts less than the value this parameter
max_count	maximum n-mer count to consider in winmask thresholds computations
check_duplicates	true if input checking for duplicates is requested; false otherwise
use_list	true if input file contains the list of fasta file names; false if input is the name of the fasta file itself
ids	set of ids to consider
exclude_ids	set of ids to ignore
use_ba	use bit array optimization for optimized binary unit counts format
metadata	the metadata string
min_pct	min score as percentage of counts
extend_pct	interval extension score as percentage of counts
thres_pct	masking threshold score as percentage of counts
max_pct	max score as percentage of counts

Definition at line 124 of file win_mask_gen_counts.cpp.

References count, and th.

◆ ~CWinMaskCountsGenerator()

CWinMaskCountsGenerator::~CWinMaskCountsGenerator ( )

Object destructor.

Definition at line 223 of file win_mask_gen_counts.cpp.

Member Function Documentation

◆ fastalen()

Uint8 CWinMaskCountsGenerator::fastalen ( const string & fname ) const

private

Definition at line 104 of file win_mask_gen_counts.cpp.

References CWinMaskUtil::consider(), exclude_ids, CBioseq_Handle::GetBioseqLength(), ids, infmt, and result.

Referenced by operator()().

◆ operator()()

void CWinMaskCountsGenerator::operator() ( void )

This function does the actual n-mer counting.

Determines the prefix length based on the available memory and calls process for each prefix to compute partial counts.

Definition at line 226 of file win_mask_gen_counts.cpp.

References _TRACE, check_duplicates, CheckDuplicates(), exclude_ids, fastalen(), CSeqMaskerOstat::finalize(), genome_size, has_min_count, i, ids, infmt, input, LOG_POST, max_count, max_mem, min_count, NCBI_ASSERT, NCBI_THROW, no_extra_pass, offset, process(), score_counts, CSeqMaskerOstat::setComment(), CSeqMaskerOstat::SetCount(), CSeqMaskerOstat::SetMaxCount(), CSeqMaskerOstat::setParam(), CSeqMaskerOstat::setUnitSize(), NStr::Split(), t_high, th, total_ecodes, unit_size, use_list, and ustat.

◆ process()

void CWinMaskCountsGenerator::process	(	Uint4	prefix,
		Uint1	prefix_size,
		const vector< string > &	input,
		bool	do_output
	)

private

Definition at line 409 of file win_mask_gen_counts.cpp.

References _TRACE, ambig(), CWinMaskUtil::consider(), count, data, CBioseq_Handle::eCoding_Iupac, exclude_ids, CObjectManager::GetInstance(), i, ids, infmt, letter(), max_count, min_count, om, reverse_complement(), score_counts, CSeqMaskerOstat::setUnitCount(), t_high, total_ecodes, unit_size, and ustat.

Referenced by operator()().

Member Data Documentation

◆ check_duplicates

bool CWinMaskCountsGenerator::check_duplicates

private

Definition at line 248 of file win_mask_gen_counts.hpp.

Referenced by operator()().

◆ exclude_ids

const CWinMaskUtil::CIdSet* CWinMaskCountsGenerator::exclude_ids

private

Definition at line 256 of file win_mask_gen_counts.hpp.

Referenced by fastalen(), operator()(), and process().

◆ genome_size

Uint8 CWinMaskCountsGenerator::genome_size

private

Definition at line 242 of file win_mask_gen_counts.hpp.

Referenced by operator()().

◆ has_min_count

bool CWinMaskCountsGenerator::has_min_count

private

Definition at line 246 of file win_mask_gen_counts.hpp.

Referenced by operator()().

◆ ids

const CWinMaskUtil::CIdSet* CWinMaskCountsGenerator::ids

private

Definition at line 255 of file win_mask_gen_counts.hpp.

Referenced by fastalen(), operator()(), and process().

◆ infmt

string CWinMaskCountsGenerator::infmt

private

Definition at line 258 of file win_mask_gen_counts.hpp.

Referenced by fastalen(), operator()(), and process().

◆ input

string CWinMaskCountsGenerator::input

private

Definition at line 238 of file win_mask_gen_counts.hpp.

Referenced by operator()().

◆ max_count

Uint4 CWinMaskCountsGenerator::max_count

private

Definition at line 244 of file win_mask_gen_counts.hpp.

Referenced by operator()(), and process().

◆ max_mem

Uint8 CWinMaskCountsGenerator::max_mem

private

Definition at line 240 of file win_mask_gen_counts.hpp.

Referenced by operator()().

◆ min_count

Uint4 CWinMaskCountsGenerator::min_count

private

Definition at line 243 of file win_mask_gen_counts.hpp.

Referenced by operator()(), and process().

◆ no_extra_pass

bool CWinMaskCountsGenerator::no_extra_pass

private

Definition at line 247 of file win_mask_gen_counts.hpp.

Referenced by operator()().

◆ score_counts

vector< Uint4 > CWinMaskCountsGenerator::score_counts

private

Definition at line 252 of file win_mask_gen_counts.hpp.

Referenced by operator()(), and process().

◆ t_high

Uint4 CWinMaskCountsGenerator::t_high

private

Definition at line 245 of file win_mask_gen_counts.hpp.

Referenced by operator()(), and process().

◆ th

double CWinMaskCountsGenerator::th[4]

private

Definition at line 253 of file win_mask_gen_counts.hpp.

Referenced by CWinMaskCountsGenerator(), and operator()().

◆ total_ecodes

Uint4 CWinMaskCountsGenerator::total_ecodes

private

Definition at line 251 of file win_mask_gen_counts.hpp.

Referenced by operator()(), and process().

◆ unit_size

Uint4 CWinMaskCountsGenerator::unit_size

private

Definition at line 241 of file win_mask_gen_counts.hpp.

Referenced by operator()(), and process().

◆ use_list

bool CWinMaskCountsGenerator::use_list

private

Definition at line 249 of file win_mask_gen_counts.hpp.

Referenced by operator()().

◆ ustat

CRef< CSeqMaskerOstat > CWinMaskCountsGenerator::ustat

private

Definition at line 239 of file win_mask_gen_counts.hpp.

Referenced by operator()(), and process().

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

include/algo/winmask/win_mask_gen_counts.hpp
src/algo/winmask/win_mask_gen_counts.cpp

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CWinMaskCountsGenerator() [1/2]

◆ CWinMaskCountsGenerator() [2/2]

◆ ~CWinMaskCountsGenerator()

Member Function Documentation

◆ fastalen()

◆ operator()()

◆ process()

Member Data Documentation

◆ check_duplicates

◆ exclude_ids

◆ genome_size

◆ has_min_count

◆ ids

◆ infmt

◆ input

◆ max_count

◆ max_mem

◆ min_count

◆ no_extra_pass

◆ score_counts

◆ t_high

◆ th

◆ total_ecodes

◆ unit_size

◆ use_list

◆ ustat