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NCBI C++ ToolKit: CWinMaskConfig Class Reference

Search Toolkit Book for CWinMaskConfig

Objects of this class contain winmasker configuration data. More...

#include <algo/winmask/win_mask_config.hpp>

Objects of this class contain winmasker configuration data.

The class is also responsible for validation of command line arguments.

Definition at line 95 of file win_mask_config.hpp.

◆ CIdSet ◆ CIdSet_SeqId ◆ CIdSet_TextMatch ◆ EAppType Enumerator eAny eComputeCounts eConvertCounts eGenerateMasks eGenerateMasksWithDuster

Definition at line 103 of file win_mask_config.hpp.

◆ CWinMaskConfig() [1/2]

Object constructor.

Parameters: args C++ toolkit style command line arguments. type type of application; eAny means application needs to be decided based on args determine_input when false, CWinMaskConfig is not concerned with the input files

Definition at line 319 of file win_mask_config.cpp.

References _TRACE, app_type, eComputeCounts, eConvertCounts, exclude_ids, CArgs::Exist(), FillIdList(), ids, iformatstr, is, kInput, kInputFormat, metadata, NCBI_THROW, reader, set_max_score, set_min_score, text_match, writer, and x_GetWriter().

◆ ~CWinMaskConfig() CWinMaskConfig::~CWinMaskConfig ( ) ◆ CWinMaskConfig() [2/2]

Prohibit copy constructor.

Parameters: rhs object to copy from [in]

◆ AbsMergeCutoffDist() Uint4 CWinMaskConfig::AbsMergeCutoffDist ( ) const inline ◆ AddWinMaskArgs()

Definition at line 50 of file win_mask_config.cpp.

References CArgDescriptions::AddDefaultKey(), CArgDescriptions::AddFlag(), CArgDescriptions::AddKey(), CArgDescriptions::AddOptionalKey(), CArgAllow_Strings::Allow(), eAny, CArgDescriptions::eBoolean, eComputeCounts, eConvertCounts, CArgDescriptions::eDouble, CArgDescriptions::eExcludes, eGenerateMasks, eGenerateMasksWithDuster, CArgDescriptions::eInputFile, CArgDescriptions::eInteger, CArgDescriptions::eOutputFile, CArgDescriptions::eString, i, kInput, kInputFormat, kInputFormats, kMax_Int, kNumInputFormats, kNumOutputFormats, kOutput, kOutputFormat, kOutputFormats, CArgDescriptions::SetConstraint(), and CArgDescriptions::SetCurrentGroup().

Referenced by CWinMaskApplication::Init().

◆ AppType() EAppType CWinMaskConfig::AppType ( ) const inline

Type of application to run.

Returns: eComputeCounts to compute unit counts eConvertCounts to convert unit counts from one format to another eGenerateMasks to generate masks using only WindowMasker eGenerateMasks to generate masks using both WindowMasker and DustMasker

Definition at line 355 of file win_mask_config.hpp.

References app_type.

Referenced by CWinMaskApplication::Run().

◆ CheckDup() bool CWinMaskConfig::CheckDup ( ) const inline ◆ CutoffScore() Uint4 CWinMaskConfig::CutoffScore ( ) const inline ◆ Discontig() bool CWinMaskConfig::Discontig ( ) const inline ◆ DustLevel() Uint4 CWinMaskConfig::DustLevel ( ) const inline ◆ DustLinker() Uint4 CWinMaskConfig::DustLinker ( ) const inline ◆ DustWindow() Uint4 CWinMaskConfig::DustWindow ( ) const inline ◆ ExcludeIds() ◆ ExtendScorePct() double CWinMaskConfig::ExtendScorePct ( ) const inline ◆ FaList() bool CWinMaskConfig::FaList ( ) const inline ◆ FillIdList() ◆ GenomeSize() Uint8 CWinMaskConfig::GenomeSize ( ) const inline ◆ GetMetaData() ◆ Ids() ◆ InFmt() ◆ Input() string CWinMaskConfig::Input ( ) const inline ◆ LStatName() ◆ MatchId() bool CWinMaskConfig::MatchId ( ) const inline ◆ MaxScore() Uint4 CWinMaskConfig::MaxScore ( ) const inline ◆ MaxScorePct() double CWinMaskConfig::MaxScorePct ( ) const inline ◆ MeanMergeCutoffDist() Uint4 CWinMaskConfig::MeanMergeCutoffDist ( ) const inline ◆ Mem() Uint4 CWinMaskConfig::Mem ( ) const inline ◆ MergeCutoffScore() Uint4 CWinMaskConfig::MergeCutoffScore ( ) const inline

Average unit score triggering the interval merging.

For each pair of consequtive mask intervals winmasker that are candidates for merging (see description of CWinMaskConfig::MeanMergeCutoffDist()) winmasker evaluates the mean unit score of all units in the interval starting at the start of the first interval and ending at the end of the second interval. If the result is greater or equal than the value returned by this function the intervals are merged.

Returns: the value of the mean unit score triggering merging of masked intervals which is the value of -mscore command line option to winmasker.

Definition at line 246 of file win_mask_config.hpp.

References merge_cutoff_score.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ MergePass() bool CWinMaskConfig::MergePass ( ) const inline ◆ MergeUnitStep() Uint1 CWinMaskConfig::MergeUnitStep ( ) const inline ◆ MinScore() Uint4 CWinMaskConfig::MinScore ( ) const inline ◆ MinScorePct() double CWinMaskConfig::MinScorePct ( ) const inline ◆ operator=()

Prohibit assignment operator.

Parameters: rhs object to copy from [in]

◆ Output() string CWinMaskConfig::Output ( ) const inline ◆ Pattern() Uint4 CWinMaskConfig::Pattern ( ) const inline ◆ Reader() ◆ s_DetermineAppType() ◆ SetMaxScore() Uint4 CWinMaskConfig::SetMaxScore ( ) const inline ◆ SetMinScore() Uint4 CWinMaskConfig::SetMinScore ( ) const inline ◆ SFormat() ◆ Textend() Uint4 CWinMaskConfig::Textend ( ) const inline ◆ Th() string CWinMaskConfig::Th ( ) const inline

Percentage thresholds.

Comma separated list of floating point numbers between 0.0 and 100.0 used to compute winmask score thresholds. The corresponding score thresholds will be added as comments to the end of the output. For each number the program finds the score such that the corresponding fraction of different n-mers has the lower score.

Returns: comma separated list of values

Definition at line 420 of file win_mask_config.hpp.

References th.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ ThresScorePct() double CWinMaskConfig::ThresScorePct ( ) const inline ◆ TMin_Count() Uint1 CWinMaskConfig::TMin_Count ( ) const inline ◆ Trigger() ◆ UnitSize() Uint1 CWinMaskConfig::UnitSize ( ) const inline ◆ UnitStep() Uint1 CWinMaskConfig::UnitStep ( ) const inline ◆ UseBA() bool CWinMaskConfig::UseBA ( ) const inline ◆ WindowSize() Uint1 CWinMaskConfig::WindowSize ( ) const inline ◆ WindowStep() Uint4 CWinMaskConfig::WindowStep ( ) const inline ◆ Writer() ◆ x_GetWriter() ◆ abs_merge_cutoff_dist Uint4 CWinMaskConfig::abs_merge_cutoff_dist private ◆ app_type ◆ checkdup bool CWinMaskConfig::checkdup private ◆ cutoff_score Uint4 CWinMaskConfig::cutoff_score private ◆ discontig bool CWinMaskConfig::discontig private ◆ dust_level Uint4 CWinMaskConfig::dust_level private ◆ dust_linker Uint4 CWinMaskConfig::dust_linker private ◆ dust_window Uint4 CWinMaskConfig::dust_window private ◆ exclude_ids CIdSet* CWinMaskConfig::exclude_ids private ◆ fa_list bool CWinMaskConfig::fa_list private ◆ genome_size Uint8 CWinMaskConfig::genome_size private ◆ ids ◆ iformatstr string CWinMaskConfig::iformatstr private ◆ input ◆ is ◆ lstat_name string CWinMaskConfig::lstat_name private ◆ max_score Uint4 CWinMaskConfig::max_score private ◆ mean_merge_cutoff_dist Uint4 CWinMaskConfig::mean_merge_cutoff_dist private ◆ mem Uint4 CWinMaskConfig::mem private ◆ merge_cutoff_score Uint4 CWinMaskConfig::merge_cutoff_score private ◆ merge_pass bool CWinMaskConfig::merge_pass private ◆ merge_unit_step Uint1 CWinMaskConfig::merge_unit_step private ◆ metadata string CWinMaskConfig::metadata private ◆ min_score Uint4 CWinMaskConfig::min_score private ◆ output ◆ pattern Uint4 CWinMaskConfig::pattern private ◆ reader ◆ set_max_score Uint4 CWinMaskConfig::set_max_score private ◆ set_min_score Uint4 CWinMaskConfig::set_min_score private ◆ sformat string CWinMaskConfig::sformat private ◆ smem Uint4 CWinMaskConfig::smem private ◆ t_extend_pct double CWinMaskConfig::t_extend_pct private ◆ t_high_pct double CWinMaskConfig::t_high_pct private ◆ t_low_pct double CWinMaskConfig::t_low_pct private ◆ t_thres_pct double CWinMaskConfig::t_thres_pct private ◆ text_match bool CWinMaskConfig::text_match private ◆ textend Uint4 CWinMaskConfig::textend private ◆ th ◆ tmin_count Uint1 CWinMaskConfig::tmin_count private ◆ trigger string CWinMaskConfig::trigger private ◆ unit_size Uint1 CWinMaskConfig::unit_size private ◆ unit_step Uint1 CWinMaskConfig::unit_step private ◆ use_ba bool CWinMaskConfig::use_ba private ◆ window_size Uint1 CWinMaskConfig::window_size private ◆ window_step Uint4 CWinMaskConfig::window_step private ◆ writer

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

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

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