20 #ifndef _PRECURSORMASKCODEC_HPP 21 #define _PRECURSORMASKCODEC_HPP 129 #endif // _PRECURSORMASKCODEC_HPP A method of hashing an isolation window to a unique long value mz is and m/z of a unique point in the...
size_t overlapsPerSpectrum_
Number of overlap windows per multiplexed spectrum.
msdata::ProcessingMethod processingMethod_
Cached processing method to return from GetProcessingMethod()
int GetSpectraPerCycle() const override
Returns the number of spectra required to cover all precursor isolation windows.
void SpectrumToIndices(msdata::Spectrum_const_ptr spectrumPtr, std::vector< size_t > &indices) const override
Identifies the precursor windows within a spectrum and returns the indices to the design matrix colum...
size_t spectraPerCycle_
Number of spectra required to cover all precursor windows.
int GetOverlapsPerCycle() const override
Returns the number of overlap repeats per cycle. So for no overlap, this returns 1. For an overlap that splits each precursor in two, this returns 2. Etc.
A container that wraps DemuxWindow to preserve the full precision window boundaries.
MZHash mzHash
Hashed m/z value for fast and simple comparison operations.
double mz
Full precision m/z value.
Eigen::VectorXd GetMask(msdata::Spectrum_const_ptr sPtr, double weight) const override
Generates a design matrix row describing which precursor isolation windows are present in the given s...
bool operator==(const DemuxBoundary &rhs) const
DemuxBoundaries are equated only by their hashes.
Implementation of the IPrecursorMaskCodec interface that is able to handle both overlapping MSX exper...
msdata::ProcessingMethod GetProcessingMethod() const override
Returns a descriptor of the processing done by this PrecursorMaskCodec.
Interface for generating and accessing precursor masks for a demultiplexing scheme.
IsolationWindow GetIsolationWindow(size_t i) const override
Returns the precursor window for a given index.
Description of the default peak processing method. This element describes the base method used in the...
bool variableFill_
Whether this data acquired with variable fill times or not. This is set by the user.
size_t GetNumDemuxWindows() const override
Returns the total number of demux'd precursor windows. This is the number of possible indices returne...
bool operator<(const DemuxBoundary &rhs) const
DemuxBoundaries are sorted to the precision of their hash.
int GetPrecursorsPerSpectrum() const override
Returns the number of precursor isolations per spectrum. This is verified to be constant for all spec...
void IdentifyOverlap(std::vector< IsolationWindow > &demuxWindows)
Identifies any overlap in a DemuxWindow set and splits any overlapping regions such that a non-overla...
virtual ~PrecursorMaskCodec()
size_t precursorsPerSpectrum_
Number of precursors (or isolation windows) per multiplexed spectrum.
Matrix< DemuxScalar, Dynamic, Dynamic > MatrixType
boost::shared_ptr< const msdata::Spectrum > Spectrum_const_ptr
size_t GetDemuxBlockSize() const override
Returns the number of windows required to demultiplex.
std::vector< IsolationWindow > isolationWindows_
This is effectively the index to isolation window map for translating isolation windows to...
PrecursorMaskCodec(msdata::SpectrumList_const_ptr slPtr, bool variableFill=false)
Construct a PrecursorMaskCodec for interpreting overlapping and MSX experiments for demultiplexing...
void IdentifyCycle(msdata::SpectrumList_const_ptr spectrumList, std::vector< IsolationWindow > &demuxWindows)
Identifies the repeating scan pattern in the experiment and extracts features of the experimental des...
Simple container that is useful for breaking up DemuxWindows into their edges and resolving overlap...
DemuxBoundary(double mz)
Constructs a DemuxBoundary from an m/z floating point value.
boost::shared_ptr< const msdata::SpectrumList > SpectrumList_const_ptr
void ReadDemuxScheme(msdata::SpectrumList_const_ptr spectrumList)
Interpret the experimental design of the multiplexed experiment and cache values for building the des...