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pwiz::analysis::SpectrumList_Demux::Params Struct Reference

User-defined options for demultiplexing. More...

#include <SpectrumList_Demux.hpp>

Public Types

enum  Optimization { Optimization::NONE, Optimization::OVERLAP_ONLY }
 Optimization methods available. More...
 

Public Member Functions

 Params ()
 

Static Public Member Functions

static const std::string & optimizationToString (Optimization opt)
 Converts an optimization enum to a string. More...
 
static Optimization stringToOptimization (const std::string &s)
 Converts a string to an optimization enum (returns NONE enum if no enum matches the string) More...
 

Public Attributes

pwiz::chemistry::MZTolerance massError
 Error scalar for extracting MS/MS peaks. More...
 
double demuxBlockExtra
 Multiplier to expand or reduce the # of spectra considered when demux'ing. More...
 
int nnlsMaxIter
 Maximum iterations for NNLS solve. More...
 
double nnlsEps
 Epsilon value for convergence criterion of NNLS solver. More...
 
bool applyWeighting
 Weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones. More...
 
bool regularizeSums
 After demux solve, scale the sum of the intensities contributed form each of the input windows to match the non-demux'd intensity. More...
 
bool variableFill
 Set to true if fill times are allowed to vary for each scan window. More...
 
Optimization optimization
 Optimizations can be chosen when experimental design is known. More...
 

Detailed Description

User-defined options for demultiplexing.

Definition at line 40 of file SpectrumList_Demux.hpp.

Member Enumeration Documentation

◆ Optimization

Optimization methods available.

Enumerator
NONE 
OVERLAP_ONLY 

Definition at line 43 of file SpectrumList_Demux.hpp.

44  {
45  NONE,
46  OVERLAP_ONLY
47  };

Constructor & Destructor Documentation

◆ Params()

pwiz::analysis::SpectrumList_Demux::Params::Params ( )
inline

Definition at line 55 of file SpectrumList_Demux.hpp.

55  :
57  demuxBlockExtra(0.0),
58  nnlsMaxIter(50),
59  nnlsEps(1e-10),
60  applyWeighting(true),
61  regularizeSums(true),
62  variableFill(false),
64 
65  {}

Member Function Documentation

◆ optimizationToString()

static const std::string& pwiz::analysis::SpectrumList_Demux::Params::optimizationToString ( Optimization  opt)
static

Converts an optimization enum to a string.

◆ stringToOptimization()

static Optimization pwiz::analysis::SpectrumList_Demux::Params::stringToOptimization ( const std::string &  s)
static

Converts a string to an optimization enum (returns NONE enum if no enum matches the string)

Member Data Documentation

◆ massError

pwiz::chemistry::MZTolerance pwiz::analysis::SpectrumList_Demux::Params::massError

Error scalar for extracting MS/MS peaks.

Definition at line 68 of file SpectrumList_Demux.hpp.

◆ demuxBlockExtra

double pwiz::analysis::SpectrumList_Demux::Params::demuxBlockExtra

Multiplier to expand or reduce the # of spectra considered when demux'ing.

If 0, a fully determined system of equation is built. If > 1.0, the number of rows included in the system is extended demuxBlockExtra * (# scans in 1 duty cycle)

Definition at line 74 of file SpectrumList_Demux.hpp.

◆ nnlsMaxIter

int pwiz::analysis::SpectrumList_Demux::Params::nnlsMaxIter

Maximum iterations for NNLS solve.

Definition at line 77 of file SpectrumList_Demux.hpp.

◆ nnlsEps

double pwiz::analysis::SpectrumList_Demux::Params::nnlsEps

Epsilon value for convergence criterion of NNLS solver.

Definition at line 80 of file SpectrumList_Demux.hpp.

◆ applyWeighting

bool pwiz::analysis::SpectrumList_Demux::Params::applyWeighting

Weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones.

Definition at line 84 of file SpectrumList_Demux.hpp.

◆ regularizeSums

bool pwiz::analysis::SpectrumList_Demux::Params::regularizeSums

After demux solve, scale the sum of the intensities contributed form each of the input windows to match the non-demux'd intensity.

Definition at line 88 of file SpectrumList_Demux.hpp.

◆ variableFill

bool pwiz::analysis::SpectrumList_Demux::Params::variableFill

Set to true if fill times are allowed to vary for each scan window.

Definition at line 91 of file SpectrumList_Demux.hpp.

◆ optimization

Optimization pwiz::analysis::SpectrumList_Demux::Params::optimization

Optimizations can be chosen when experimental design is known.

Definition at line 94 of file SpectrumList_Demux.hpp.

Referenced by testOverlapOnly().


The documentation for this struct was generated from the following file:
pwiz::analysis::SpectrumList_Demux::Params::optimization
Optimization optimization
Optimizations can be chosen when experimental design is known.
Definition: SpectrumList_Demux.hpp:94
pwiz::chemistry::MZTolerance::PPM
@ PPM
Definition: MZTolerance.hpp:40
pwiz::analysis::SpectrumList_Demux::Params::variableFill
bool variableFill
Set to true if fill times are allowed to vary for each scan window.
Definition: SpectrumList_Demux.hpp:91
pwiz::analysis::SpectrumList_Demux::Params::regularizeSums
bool regularizeSums
After demux solve, scale the sum of the intensities contributed form each of the input windows to mat...
Definition: SpectrumList_Demux.hpp:88
pwiz::analysis::SpectrumList_Demux::Params::nnlsMaxIter
int nnlsMaxIter
Maximum iterations for NNLS solve.
Definition: SpectrumList_Demux.hpp:77
pwiz::analysis::SpectrumList_Demux::Params::applyWeighting
bool applyWeighting
Weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones.
Definition: SpectrumList_Demux.hpp:84
pwiz::analysis::SpectrumList_Demux::Params::Optimization::NONE
@ NONE
pwiz::analysis::SpectrumList_Demux::Params::massError
pwiz::chemistry::MZTolerance massError
Error scalar for extracting MS/MS peaks.
Definition: SpectrumList_Demux.hpp:68
pwiz::analysis::SpectrumList_Demux::Params::demuxBlockExtra
double demuxBlockExtra
Multiplier to expand or reduce the # of spectra considered when demux'ing.
Definition: SpectrumList_Demux.hpp:74
pwiz::analysis::SpectrumList_Demux::Params::nnlsEps
double nnlsEps
Epsilon value for convergence criterion of NNLS solver.
Definition: SpectrumList_Demux.hpp:80