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pwiz::analysis::SpectrumList_Demux Class Reference

SpectrumList decorator implementation that can demultiplex spectra of several precursor windows acquired in the same scan. More...

#include <SpectrumList_Demux.hpp>

Inheritance diagram for pwiz::analysis::SpectrumList_Demux:
pwiz::msdata::SpectrumListWrapper pwiz::msdata::SpectrumList

Classes

struct  Params
 User-defined options for demultiplexing. More...
 

Public Member Functions

 SpectrumList_Demux (const msdata::SpectrumListPtr &inner, const Params &p=Params())
 Generates an abstract SpectrumList_Demux decorator from inner SpectrumList. More...
 
virtual ~SpectrumList_Demux ()
 
SpectrumList Interface
msdata::SpectrumPtr spectrum (size_t index, bool getBinaryData=false) const
 retrieve a spectrum by index More...
 
msdata::SpectrumPtr spectrum (size_t index, msdata::DetailLevel detailLevel) const
 retrieve a spectrum by index More...
 
size_t size () const
 returns the number of spectra More...
 
const msdata::SpectrumIdentityspectrumIdentity (size_t index) const
 access to a spectrum index More...
 
- Public Member Functions inherited from pwiz::msdata::SpectrumListWrapper
 SpectrumListWrapper (const SpectrumListPtr &inner)
 
virtual bool empty () const
 returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL) More...
 
virtual const boost::shared_ptr< const DataProcessingdataProcessingPtr () const
 returns the data processing affecting spectra retrieved through this interface More...
 
SpectrumListPtr inner () const
 
SpectrumListPtr innermost () const
 
- Public Member Functions inherited from pwiz::msdata::SpectrumList
virtual size_t find (const std::string &id) const
 find id in the spectrum index (returns size() on failure) More...
 
virtual size_t findAbbreviated (const std::string &abbreviatedId, char delimiter='.') const
 find an abbreviated id (e.g. "1.1.123.2" for "sample=1 period=1 cycle=123 experiment=2") in the spectrum index (returns size() on failure) More...
 
virtual IndexList findNameValue (const std::string &name, const std::string &value) const
 find all spectrum indexes with specified name/value pair More...
 
virtual IndexList findSpotID (const std::string &spotID) const
 find all spectrum indexes with spotID (returns empty vector on failure) More...
 
virtual SpectrumPtr spectrum (const SpectrumPtr &seed, bool getBinaryData) const
 get a copy of the seed spectrum, optionally with its binary data populated this is useful for formats like mzML that can delay loading of binary data More...
 
virtual void warn_once (const char *msg) const
 issues a warning once per SpectrumList instance (based on string hash) More...
 
virtual ~SpectrumList ()
 

Private Attributes

boost::scoped_ptr< Impl > impl_
 

Additional Inherited Members

- Protected Attributes inherited from pwiz::msdata::SpectrumListWrapper
SpectrumListPtr inner_
 
DataProcessingPtr dp_
 

Detailed Description

SpectrumList decorator implementation that can demultiplex spectra of several precursor windows acquired in the same scan.

SpectrumList_Demux can separate multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. This method can handle variable fill times, requiring that the user specify whether the fill times have varied.

Definition at line 35 of file SpectrumList_Demux.hpp.

Constructor & Destructor Documentation

◆ SpectrumList_Demux()

pwiz::analysis::SpectrumList_Demux::SpectrumList_Demux ( const msdata::SpectrumListPtr inner,
const Params p = Params() 
)

Generates an abstract SpectrumList_Demux decorator from inner SpectrumList.

Parameters
innerThe inner SpectrumList
pUser-defined options

◆ ~SpectrumList_Demux()

virtual pwiz::analysis::SpectrumList_Demux::~SpectrumList_Demux ( )
virtual

Member Function Documentation

◆ spectrum() [1/2]

msdata::SpectrumPtr pwiz::analysis::SpectrumList_Demux::spectrum ( size_t  index,
bool  getBinaryData = false 
) const
virtual

retrieve a spectrum by index

  • binary data arrays will be provided if (getBinaryData == true);
  • client may assume the underlying Spectrum* is valid

Implements pwiz::msdata::SpectrumListWrapper.

◆ spectrum() [2/2]

msdata::SpectrumPtr pwiz::analysis::SpectrumList_Demux::spectrum ( size_t  index,
msdata::DetailLevel  detailLevel 
) const
virtual

retrieve a spectrum by index

  • detailLevel determines what fields are guaranteed present on the spectrum after the call
  • client may assume the underlying Spectrum* is valid

Reimplemented from pwiz::msdata::SpectrumListWrapper.

◆ size()

size_t pwiz::analysis::SpectrumList_Demux::size ( ) const
virtual

returns the number of spectra

Reimplemented from pwiz::msdata::SpectrumListWrapper.

◆ spectrumIdentity()

const msdata::SpectrumIdentity& pwiz::analysis::SpectrumList_Demux::spectrumIdentity ( size_t  index) const
virtual

access to a spectrum index

Reimplemented from pwiz::msdata::SpectrumListWrapper.

Member Data Documentation

◆ impl_

boost::scoped_ptr<Impl> pwiz::analysis::SpectrumList_Demux::impl_
private

Definition at line 114 of file SpectrumList_Demux.hpp.


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