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20 #ifndef _SPECTRUMLIST_DEMUX_HPP
21 #define _SPECTRUMLIST_DEMUX_HPP
24 #include <boost/smart_ptr/scoped_ptr.hpp>
123 #endif // _SPECTRUMLIST_DEMUX_HPP
static Optimization stringToOptimization(const std::string &s)
Converts a string to an optimization enum (returns NONE enum if no enum matches the string)
Optimization optimization
Optimizations can be chosen when experimental design is known.
boost::shared_ptr< SpectrumList > SpectrumListPtr
SpectrumList decorator implementation that can demultiplex spectra of several precursor windows acqui...
Identifying information for a spectrum.
Inheritable pass-through implementation for wrapping a SpectrumList.
msdata::SpectrumPtr spectrum(size_t index, bool getBinaryData=false) const
retrieve a spectrum by index
SpectrumList_Demux(const msdata::SpectrumListPtr &inner, const Params &p=Params())
Generates an abstract SpectrumList_Demux decorator from inner SpectrumList.
struct for expressing m/z tolerance in either amu or ppm
boost::scoped_ptr< Impl > impl_
static const std::string & optimizationToString(Optimization opt)
Converts an optimization enum to a string.
const msdata::SpectrumIdentity & spectrumIdentity(size_t index) const
access to a spectrum index
bool variableFill
Set to true if fill times are allowed to vary for each scan window.
bool regularizeSums
After demux solve, scale the sum of the intensities contributed form each of the input windows to mat...
int nnlsMaxIter
Maximum iterations for NNLS solve.
bool applyWeighting
Weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones.
boost::shared_ptr< Spectrum > SpectrumPtr
User-defined options for demultiplexing.
pwiz::chemistry::MZTolerance massError
Error scalar for extracting MS/MS peaks.
Optimization
Optimization methods available.
size_t size() const
returns the number of spectra
virtual ~SpectrumList_Demux()
double demuxBlockExtra
Multiplier to expand or reduce the # of spectra considered when demux'ing.
double nnlsEps
Epsilon value for convergence criterion of NNLS solver.
SpectrumList_Demux::Params::Optimization DemuxOptimization
msdata::SpectrumPtr spectrum(size_t index, msdata::DetailLevel detailLevel) const
retrieve a spectrum by index