ProteoWizard
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Interface for calculating demultiplexing scheme. More...
#include <IDemultiplexer.hpp>
Public Types | |
typedef boost::shared_ptr< IDemultiplexer > | ptr |
Shared pointer definition. More... | |
typedef boost::shared_ptr< const IDemultiplexer > | const_ptr |
Constant shared pointer definition. More... | |
Public Member Functions | |
virtual void | Initialize (msdata::SpectrumList_const_ptr slc, IPrecursorMaskCodec::const_ptr pmc)=0 |
Initializes the demultiplexer using the demux scheme provided by an IPrecursorMaskCodec. More... | |
virtual void | BuildDeconvBlock (size_t index, const std::vector< size_t > &muxIndices, DemuxTypes::MatrixPtr &masks, DemuxTypes::MatrixPtr &signal)=0 |
Translates a spectrum into a set of matrices to be solved by NNLS. More... | |
virtual void | GetMatrixBlockIndices (size_t indexToDemux, std::vector< size_t > &muxIndices, double demuxBlockExtra=0.0) const =0 |
Figures out which spectra to include in the system of equations to demux. More... | |
virtual const std::vector< size_t > & | SpectrumIndices () const =0 |
Returns the indices to the demultiplexed windows in the solution matrix corresponding to the windows extracted from the spectrum whose index was provided to BuildDeconvBlock() More... | |
virtual | ~IDemultiplexer () |
Interface for calculating demultiplexing scheme.
Definition at line 29 of file IDemultiplexer.hpp.
typedef boost::shared_ptr<IDemultiplexer> pwiz::analysis::IDemultiplexer::ptr |
Shared pointer definition.
Definition at line 34 of file IDemultiplexer.hpp.
typedef boost::shared_ptr<const IDemultiplexer> pwiz::analysis::IDemultiplexer::const_ptr |
Constant shared pointer definition.
Definition at line 37 of file IDemultiplexer.hpp.
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inlinevirtual |
Definition at line 69 of file IDemultiplexer.hpp.
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pure virtual |
Initializes the demultiplexer using the demux scheme provided by an IPrecursorMaskCodec.
Implemented in pwiz::analysis::MSXDemultiplexer, and pwiz::analysis::OverlapDemultiplexer.
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pure virtual |
Translates a spectrum into a set of matrices to be solved by NNLS.
[in] | index | Index of the requested spectrum to be demultiplexed |
[in] | muxIndices | The indices to mulitplexed spectra to use for demultiplexing. These spectra should be near in time to the spectrum to demultiplex and there should be enough to provide a unique solution. |
[out] | masks | The design matrix with rows corresponding to individual spectra and columns corresponding to MS1 isolation windows |
[out] | signal | A transition (MS1 isolation -> MS2 point/centroid) to be deconvolved formatted as a column vector (or a set of transitions formatted as a matrix) |
Implemented in pwiz::analysis::MSXDemultiplexer, and pwiz::analysis::OverlapDemultiplexer.
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pure virtual |
Figures out which spectra to include in the system of equations to demux.
This skips over MS1 spectra and returns the indices of a range of MS2 spectra that can be used to demultiplex the chosen spectrum. This handles the case where the chosen spectrum is at the beginning or end of a file and chooses a sufficient number of nearby MS2 spectra accordingly. More indices will be included if the user has chosen to add additional demux blocks.
[in] | indexToDemux | Index of the requested spectrum |
[out] | muxIndices | Indices of the multiplexed MS2 spectra to be used for demultiplexing |
[in] | demuxBlockExtra | Amount to pad the block size by |
Implemented in pwiz::analysis::MSXDemultiplexer, and pwiz::analysis::OverlapDemultiplexer.
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pure virtual |
Returns the indices to the demultiplexed windows in the solution matrix corresponding to the windows extracted from the spectrum whose index was provided to BuildDeconvBlock()
Implemented in pwiz::analysis::MSXDemultiplexer, and pwiz::analysis::OverlapDemultiplexer.