ProteoWizard
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Interface for generating and accessing precursor masks for a demultiplexing scheme. More...
#include <IPrecursorMaskCodec.hpp>
Public Types | |
typedef boost::shared_ptr< IPrecursorMaskCodec > | ptr |
Shared pointer definition. More... | |
typedef boost::shared_ptr< const IPrecursorMaskCodec > | const_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 () |
Interface for generating and accessing precursor masks for a demultiplexing scheme.
Definition at line 191 of file IPrecursorMaskCodec.hpp.
typedef boost::shared_ptr<IPrecursorMaskCodec> pwiz::analysis::IPrecursorMaskCodec::ptr |
Shared pointer definition.
Definition at line 196 of file IPrecursorMaskCodec.hpp.
typedef boost::shared_ptr<const IPrecursorMaskCodec> pwiz::analysis::IPrecursorMaskCodec::const_ptr |
Constant shared pointer definition.
Definition at line 199 of file IPrecursorMaskCodec.hpp.
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inlinevirtual |
Definition at line 249 of file IPrecursorMaskCodec.hpp.
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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.
[in] | sPtr | Multiplexed spectrum from which to extract precursor windows. |
[in] | weight | Scalar value by which to weight the resulting design matrix vector. This weighting is a simple scalar multiplication of the vector. |
Implemented in pwiz::analysis::PrecursorMaskCodec.
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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.
[in] | sPtr | Multiplexed spectrum from which to extract precursor windows. |
[out] | m | Matrix in which to place the design vector. |
[in] | rowNum | Row of the matrix in which to place the design vector corresponding to the given spectrum. |
[in] | weight | Scalar value by which to weight the resulting design matrix vector. This weighting is a simple scalar multiplication of the vector. |
Implemented in pwiz::analysis::PrecursorMaskCodec.
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pure virtual |
Identifies the precursor windows within a spectrum and returns the indices to the design matrix columns corresponding to those windows.
[in] | sPtr | Multiplexed spectrum from which to extract precursor windows. |
[out] | indices | Indices of the design matrix columns that correspond to the precursor windows in the given spectrum. |
Implemented in pwiz::analysis::PrecursorMaskCodec.
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pure virtual |
Returns the precursor window for a given index.
[in] | i | Index of the column of the design matrix corresponding to the precursor window. |
Implemented in pwiz::analysis::PrecursorMaskCodec.
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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.
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pure virtual |
Returns the number of spectra required to cover all precursor isolation windows.
Implemented in pwiz::analysis::PrecursorMaskCodec.
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pure virtual |
Returns the number of precursor isolations per spectrum. This is verified to be constant for all spectra.
Implemented in pwiz::analysis::PrecursorMaskCodec.
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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.
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pure virtual |
Returns the number of windows required to demultiplex.
Implemented in pwiz::analysis::PrecursorMaskCodec.
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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.
Implemented in pwiz::analysis::PrecursorMaskCodec.