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pwiz::analysis::ThresholdFilter Struct Reference

#include <ThresholdFilter.hpp>

Inheritance diagram for pwiz::analysis::ThresholdFilter:
pwiz::analysis::SpectrumDataFilter

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

§ 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.

41  {
42  /// keep the <threshold> [most|least] intense data points
43  /// - <threshold> is rounded to the nearest integer
44  /// - if the <threshold> falls within equally intense data points, all data points with that intensity are removed
46 
47  /// keep the <threshold> [most|least] intense data points
48  /// - <threshold> is rounded to the nearest integer
49  /// - if the <threshold> falls within equally intense data points, all data points with that intensity are kept
51 
52  /// keep data points ranked [better|worse] than <threshold>
53  /// - <threshold> is rounded to the nearest integer
54  /// - rank 1 is the most intense
55  // TODO: By_CompetitionRank,
56 
57  /// keep data points ranked [better|worse] than <threshold>
58  /// - rank 1 is the most intense
59  // TODO: By_FractionalRank,
60 
61  /// keep data points [more|less] absolutely intense than <threshold>
63 
64  /// keep data points [more|less] relatively intense than <threshold>
65  /// - <threshold> is each data point's fraction of the base peak intensity (in the range [0,1])
67 
68  /// keep data points [more|less] relatively intense than <threshold>
69  /// - <threshold> is each data point's fraction of the total intensity, aka total ion current (in the range [0,1])
71 
72  /// keep data points that are part of the <threshold> [most|least] intense fraction
73  /// - <threshold> is the fraction of TIC to keep, i.e. the TIC of the kept data points is <threshold> * original TIC
75  };
keep the <threshold> [most|least] intense data points
keep data points [more|less] relatively intense than <threshold>
keep data points [more|less] relatively intense than <threshold>
keep data points that are part of the <threshold> [most|least] intense fraction
keep the <threshold> [most|least] intense data points
keep data points ranked [better|worse] than <threshold>

§ 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.

79  {
80  Orientation_MostIntense, /// thresholder removes the least intense data points
81  Orientation_LeastIntense /// thresholder removes the most intense data points
82  };
thresholder removes the least intense data points

Constructor & Destructor Documentation

§ ThresholdFilter()

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

§ operator()()

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

§ describe()

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

Member Data Documentation

§ byType

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

Definition at line 92 of file ThresholdFilter.hpp.

§ threshold

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

Definition at line 93 of file ThresholdFilter.hpp.

§ orientation

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

Definition at line 94 of file ThresholdFilter.hpp.

§ msLevelsToThreshold

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

Definition at line 95 of file ThresholdFilter.hpp.

§ byTypeMostIntenseName

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

Definition at line 98 of file ThresholdFilter.hpp.

§ byTypeLeastIntenseName

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: