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pwiz::analysis::IPrecursorMaskCodec Class Referenceabstract

Interface for generating and accessing precursor masks for a demultiplexing scheme. More...

#include <IPrecursorMaskCodec.hpp>

Inheritance diagram for pwiz::analysis::IPrecursorMaskCodec:
pwiz::analysis::PrecursorMaskCodec

Public Types

typedef boost::shared_ptr< IPrecursorMaskCodecptr
 Shared pointer definition. More...
 
typedef boost::shared_ptr< const IPrecursorMaskCodecconst_ptr
 Constant shared pointer definition. More...
 

Public Member Functions

virtual Eigen::VectorXd GetMask (msdata::Spectrum_const_ptr sPtr, double weight=1.0) const =0
 Generates a design matrix row describing which precursor isolation windows are present in the given spectrum. More...
 
virtual void GetMask (msdata::Spectrum_const_ptr sPtr, DemuxTypes::MatrixType &m, size_t rowNum, double weight=1.0) const =0
 Generates a design matrix row describing which precursor isolation windows are present in the given spectrum and places it into the specified row of the user-provided matrix. More...
 
virtual void SpectrumToIndices (msdata::Spectrum_const_ptr sPtr, std::vector< size_t > &indices) const =0
 Identifies the precursor windows within a spectrum and returns the indices to the design matrix columns corresponding to those windows. More...
 
virtual IsolationWindow GetIsolationWindow (size_t i) const =0
 Returns the precursor window for a given index. More...
 
virtual size_t GetNumDemuxWindows () const =0
 Returns the total number of demux'd precursor windows. This is the number of possible indices returned by SpectrumToIndices(). More...
 
virtual int GetSpectraPerCycle () const =0
 Returns the number of spectra required to cover all precursor isolation windows. More...
 
virtual int GetPrecursorsPerSpectrum () const =0
 Returns the number of precursor isolations per spectrum. This is verified to be constant for all spectra. More...
 
virtual int GetOverlapsPerCycle () const =0
 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. More...
 
virtual size_t GetDemuxBlockSize () const =0
 Returns the number of windows required to demultiplex. More...
 
virtual msdata::ProcessingMethod GetProcessingMethod () const =0
 Returns a descriptor of the processing done by this PrecursorMaskCodec. More...
 
virtual ~IPrecursorMaskCodec ()
 

Detailed Description

Interface for generating and accessing precursor masks for a demultiplexing scheme.

Definition at line 191 of file IPrecursorMaskCodec.hpp.

Member Typedef Documentation

◆ ptr

Shared pointer definition.

Definition at line 196 of file IPrecursorMaskCodec.hpp.

◆ const_ptr

Constant shared pointer definition.

Definition at line 199 of file IPrecursorMaskCodec.hpp.

Constructor & Destructor Documentation

◆ ~IPrecursorMaskCodec()

virtual pwiz::analysis::IPrecursorMaskCodec::~IPrecursorMaskCodec ( )
inlinevirtual

Definition at line 249 of file IPrecursorMaskCodec.hpp.

249 {}

Member Function Documentation

◆ GetMask() [1/2]

virtual Eigen::VectorXd pwiz::analysis::IPrecursorMaskCodec::GetMask ( msdata::Spectrum_const_ptr  sPtr,
double  weight = 1.0 
) const
pure virtual

Generates a design matrix row describing which precursor isolation windows are present in the given spectrum.

This row can be weighted by a given scalar.

Parameters
[in]sPtrMultiplexed spectrum from which to extract precursor windows.
[in]weightScalar value by which to weight the resulting design matrix vector. This weighting is a simple scalar multiplication of the vector.
Returns
Design matrix row describing which precursor isolation windows are present in the given spectrum.

Implemented in pwiz::analysis::PrecursorMaskCodec.

◆ GetMask() [2/2]

virtual void pwiz::analysis::IPrecursorMaskCodec::GetMask ( msdata::Spectrum_const_ptr  sPtr,
DemuxTypes::MatrixType m,
size_t  rowNum,
double  weight = 1.0 
) const
pure virtual

Generates a design matrix row describing which precursor isolation windows are present in the given spectrum and places it into the specified row of the user-provided matrix.

Parameters
[in]sPtrMultiplexed spectrum from which to extract precursor windows.
[out]mMatrix in which to place the design vector.
[in]rowNumRow of the matrix in which to place the design vector corresponding to the given spectrum.
[in]weightScalar value by which to weight the resulting design matrix vector. This weighting is a simple scalar multiplication of the vector.
Precondition
Out array must be same size as GetDemuxBlockSize()

Implemented in pwiz::analysis::PrecursorMaskCodec.

◆ SpectrumToIndices()

virtual void pwiz::analysis::IPrecursorMaskCodec::SpectrumToIndices ( msdata::Spectrum_const_ptr  sPtr,
std::vector< size_t > &  indices 
) const
pure virtual

Identifies the precursor windows within a spectrum and returns the indices to the design matrix columns corresponding to those windows.

Parameters
[in]sPtrMultiplexed spectrum from which to extract precursor windows.
[out]indicesIndices of the design matrix columns that correspond to the precursor windows in the given spectrum.

Implemented in pwiz::analysis::PrecursorMaskCodec.

◆ GetIsolationWindow()

virtual IsolationWindow pwiz::analysis::IPrecursorMaskCodec::GetIsolationWindow ( size_t  i) const
pure virtual

Returns the precursor window for a given index.

Parameters
[in]iIndex of the column of the design matrix corresponding to the precursor window.
Returns
A DemuxWindow describing the m/z range of the precursor window.

Implemented in pwiz::analysis::PrecursorMaskCodec.

◆ GetNumDemuxWindows()

virtual size_t pwiz::analysis::IPrecursorMaskCodec::GetNumDemuxWindows ( ) const
pure virtual

Returns the total number of demux'd precursor windows. This is the number of possible indices returned by SpectrumToIndices().

Implemented in pwiz::analysis::PrecursorMaskCodec.

◆ GetSpectraPerCycle()

virtual int pwiz::analysis::IPrecursorMaskCodec::GetSpectraPerCycle ( ) const
pure virtual

Returns the number of spectra required to cover all precursor isolation windows.

Implemented in pwiz::analysis::PrecursorMaskCodec.

◆ GetPrecursorsPerSpectrum()

virtual int pwiz::analysis::IPrecursorMaskCodec::GetPrecursorsPerSpectrum ( ) const
pure virtual

Returns the number of precursor isolations per spectrum. This is verified to be constant for all spectra.

Implemented in pwiz::analysis::PrecursorMaskCodec.

◆ GetOverlapsPerCycle()

virtual int pwiz::analysis::IPrecursorMaskCodec::GetOverlapsPerCycle ( ) const
pure virtual

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.

Implemented in pwiz::analysis::PrecursorMaskCodec.

◆ GetDemuxBlockSize()

virtual size_t pwiz::analysis::IPrecursorMaskCodec::GetDemuxBlockSize ( ) const
pure virtual

Returns the number of windows required to demultiplex.

Implemented in pwiz::analysis::PrecursorMaskCodec.

◆ GetProcessingMethod()

virtual msdata::ProcessingMethod pwiz::analysis::IPrecursorMaskCodec::GetProcessingMethod ( ) const
pure virtual

Returns a descriptor of the processing done by this PrecursorMaskCodec.

WARNING: It is important that this gives a string containing "Demultiplexing" in order for SpectrumWorkerThreads.cpp to handle demultiplexing properly.

Returns
The processing method performed by this PrecursorMaskCodec

Implemented in pwiz::analysis::PrecursorMaskCodec.


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