#include <ThresholdFilter.hpp>

Inheritance diagram for pwiz::analysis::ThresholdFilter:

Public Types
enum	ThresholdingBy_Type { ThresholdingBy_Count, ThresholdingBy_CountAfterTies, ThresholdingBy_AbsoluteIntensity, ThresholdingBy_FractionOfBasePeakIntensity, ThresholdingBy_FractionOfTotalIntensity, ThresholdingBy_FractionOfTotalIntensityCutoff }
	determines the method of thresholding and the meaning of the threshold value More...
enum	ThresholdingOrientation { Orientation_MostIntense, Orientation_LeastIntense }
	determines the orientation of the thresholding More...

Public Member Functions
	ThresholdFilter (ThresholdingBy_Type byType_=ThresholdingBy_Count, double threshold_=1.0, ThresholdingOrientation orientation_=Orientation_MostIntense, const pwiz::util::IntegerSet &msLevelsToThreshold=pwiz::util::IntegerSet(1, INT_MAX))
virtual void	operator() (const pwiz::msdata::SpectrumPtr) const
virtual void	describe (pwiz::msdata::ProcessingMethod &) const
Public Member Functions inherited from pwiz::analysis::SpectrumDataFilter
virtual	~SpectrumDataFilter ()

Public Attributes
const ThresholdingBy_Type	byType
const double	threshold
const ThresholdingOrientation	orientation
const pwiz::util::IntegerSet	msLevelsToThreshold

Static Private Attributes
static const char *	byTypeMostIntenseName []
static const char *	byTypeLeastIntenseName []

Detailed Description

Definition at line 37 of file ThresholdFilter.hpp.

Member Enumeration Documentation

enum pwiz::analysis::ThresholdFilter::ThresholdingBy_Type

determines the method of thresholding and the meaning of the threshold value

Enumerator:

ThresholdingBy_Count	keep the <threshold> [most\|least] intense data points <threshold> is rounded to the nearest integer if the <threshold> falls within equally intense data points, all data points with that intensity are removed
ThresholdingBy_CountAfterTies	keep the <threshold> [most\|least] intense data points <threshold> is rounded to the nearest integer if the <threshold> falls within equally intense data points, all data points with that intensity are kept
ThresholdingBy_AbsoluteIntensity	keep data points ranked [better\|worse] than <threshold> <threshold> is rounded to the nearest integer rank 1 is the most intense keep data points ranked [better\|worse] than <threshold> rank 1 is the most intense keep data points [more\|less] absolutely intense than <threshold>
ThresholdingBy_FractionOfBasePeakIntensity	keep data points [more\|less] relatively intense than <threshold> <threshold> is each data point's fraction of the base peak intensity (in the range [0,1])
ThresholdingBy_FractionOfTotalIntensity	keep data points [more\|less] relatively intense than <threshold> <threshold> is each data point's fraction of the total intensity, aka total ion current (in the range [0,1])
ThresholdingBy_FractionOfTotalIntensityCutoff	keep data points that are part of the <threshold> [most\|least] intense fraction <threshold> is the fraction of TIC to keep, i.e. the TIC of the kept data points is <threshold> * original TIC

Definition at line 40 of file ThresholdFilter.hpp.

    {
        /// keep the <threshold> [most|least] intense data points
        /// - <threshold> is rounded to the nearest integer
        /// - if the <threshold> falls within equally intense data points, all data points with that intensity are removed
        ThresholdingBy_Count,
        /// keep the <threshold> [most|least] intense data points
        /// - <threshold> is rounded to the nearest integer
        /// - if the <threshold> falls within equally intense data points, all data points with that intensity are kept
        ThresholdingBy_CountAfterTies,
        /// keep data points ranked [better|worse] than <threshold>
        /// - <threshold> is rounded to the nearest integer
        /// - rank 1 is the most intense
        // TODO: By_CompetitionRank,
        /// keep data points ranked [better|worse] than <threshold>
        /// - rank 1 is the most intense
        // TODO: By_FractionalRank,
        /// keep data points [more|less] absolutely intense than <threshold>
        ThresholdingBy_AbsoluteIntensity,
        /// keep data points [more|less] relatively intense than <threshold>
        /// - <threshold> is each data point's fraction of the base peak intensity (in the range [0,1])
        ThresholdingBy_FractionOfBasePeakIntensity,
        /// keep data points [more|less] relatively intense than <threshold>
        /// - <threshold> is each data point's fraction of the total intensity, aka total ion current (in the range [0,1])
        ThresholdingBy_FractionOfTotalIntensity,
        /// keep data points that are part of the <threshold> [most|least] intense fraction
        /// - <threshold> is the fraction of TIC to keep, i.e. the TIC of the kept data points is <threshold> * original TIC
        ThresholdingBy_FractionOfTotalIntensityCutoff
    };

enum pwiz::analysis::ThresholdFilter::ThresholdingOrientation

determines the orientation of the thresholding

Enumerator:

Orientation_MostIntense

Orientation_LeastIntense

thresholder removes the least intense data points

thresholder removes the most intense data points

Definition at line 78 of file ThresholdFilter.hpp.

    {
        Orientation_MostIntense, /// thresholder removes the least intense data points
        Orientation_LeastIntense /// thresholder removes the most intense data points
    };

Constructor & Destructor Documentation

pwiz::analysis::ThresholdFilter::ThresholdFilter	(	ThresholdingBy_Type	byType_ = `ThresholdingBy_Count`,
		double	threshold_ = `1.0`,
		ThresholdingOrientation	orientation_ = `Orientation_MostIntense`,
		const pwiz::util::IntegerSet &	msLevelsToThreshold = `pwiz::util::IntegerSet(1, INT_MAX)`
	)

Member Function Documentation

virtual void pwiz::analysis::ThresholdFilter::operator() ( const pwiz::msdata::SpectrumPtr ) const

virtual

Implements pwiz::analysis::SpectrumDataFilter.

virtual void pwiz::analysis::ThresholdFilter::describe ( pwiz::msdata::ProcessingMethod & ) const

virtual

Implements pwiz::analysis::SpectrumDataFilter.

Member Data Documentation

const ThresholdingBy_Type pwiz::analysis::ThresholdFilter::byType

Definition at line 92 of file ThresholdFilter.hpp.

const double pwiz::analysis::ThresholdFilter::threshold

Definition at line 93 of file ThresholdFilter.hpp.

const ThresholdingOrientation pwiz::analysis::ThresholdFilter::orientation

Definition at line 94 of file ThresholdFilter.hpp.

const pwiz::util::IntegerSet pwiz::analysis::ThresholdFilter::msLevelsToThreshold

Definition at line 95 of file ThresholdFilter.hpp.

const char* pwiz::analysis::ThresholdFilter::byTypeMostIntenseName[]

staticprivate

Definition at line 98 of file ThresholdFilter.hpp.

const char* pwiz::analysis::ThresholdFilter::byTypeLeastIntenseName[]

staticprivate

Definition at line 99 of file ThresholdFilter.hpp.

The documentation for this struct was generated from the following file:

/Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/analysis/spectrum_processing/ThresholdFilter.hpp

Public Types

Public Member Functions

Public Attributes

Static Private Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation