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pwiz::analysis::SpectrumList_ScanSummer Class Reference

Provides a custom-sorted spectrum list. More...

#include <SpectrumList_ScanSummer.hpp>

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

Public Member Functions

 SpectrumList_ScanSummer (const msdata::SpectrumListPtr &inner, double precursorTol, double rTimeTol, double mobilityTol=0, pwiz::util::IterationListenerRegistry *ilr=0)
 
void pushSpectrum (const msdata::SpectrumIdentity &)
 
double getPrecursorMz (const msdata::Spectrum &) const
 
void sumSubScansNaive (pwiz::util::BinaryData< double > &, pwiz::util::BinaryData< double > &, const precursorGroupPtr &, msdata::DetailLevel) const
 
virtual size_t size () const
 returns the number of spectra More...
 
virtual const msdata::SpectrumIdentityspectrumIdentity (size_t index) const
 access to a spectrum index More...
 
virtual msdata::SpectrumPtr spectrum (size_t index, bool getBinaryData=false) const
 retrieve a spectrum by index More...
 
virtual msdata::SpectrumPtr spectrum (size_t index, msdata::DetailLevel) const
 retrieve a spectrum by 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 Member Functions

 SpectrumList_ScanSummer (SpectrumList_ScanSummer &)
 
SpectrumList_ScanSummeroperator= (SpectrumList_ScanSummer &)
 

Private Attributes

double lowerMZlimit
 
double upperMZlimit
 
double TotalDaltons
 
double precursorTol_
 
double rTimeTol_
 
double mobilityTol_
 
std::vector< msdata::SpectrumIdentityspectrumIdentities
 
std::vector< size_t > indexMap
 
std::vector< precursorGroupPtrprecursorMap
 
std::map< double, precursorGroupPtrprecursorList
 
std::vector< precursorGroupPtrms2RetentionTimes
 

Additional Inherited Members

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

Detailed Description

Provides a custom-sorted spectrum list.

Definition at line 55 of file SpectrumList_ScanSummer.hpp.

Constructor & Destructor Documentation

◆ SpectrumList_ScanSummer() [1/2]

pwiz::analysis::SpectrumList_ScanSummer::SpectrumList_ScanSummer ( const msdata::SpectrumListPtr inner,
double  precursorTol,
double  rTimeTol,
double  mobilityTol = 0,
pwiz::util::IterationListenerRegistry ilr = 0 
)

◆ SpectrumList_ScanSummer() [2/2]

pwiz::analysis::SpectrumList_ScanSummer::SpectrumList_ScanSummer ( SpectrumList_ScanSummer )
private

Member Function Documentation

◆ pushSpectrum()

void pwiz::analysis::SpectrumList_ScanSummer::pushSpectrum ( const msdata::SpectrumIdentity )

◆ getPrecursorMz()

double pwiz::analysis::SpectrumList_ScanSummer::getPrecursorMz ( const msdata::Spectrum ) const

◆ sumSubScansNaive()

void pwiz::analysis::SpectrumList_ScanSummer::sumSubScansNaive ( pwiz::util::BinaryData< double > &  ,
pwiz::util::BinaryData< double > &  ,
const precursorGroupPtr ,
msdata::DetailLevel   
) const

◆ size()

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

returns the number of spectra

Reimplemented from pwiz::msdata::SpectrumListWrapper.

◆ spectrumIdentity()

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

access to a spectrum index

Reimplemented from pwiz::msdata::SpectrumListWrapper.

◆ spectrum() [1/2]

virtual msdata::SpectrumPtr pwiz::analysis::SpectrumList_ScanSummer::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]

virtual msdata::SpectrumPtr pwiz::analysis::SpectrumList_ScanSummer::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.

◆ operator=()

SpectrumList_ScanSummer& pwiz::analysis::SpectrumList_ScanSummer::operator= ( SpectrumList_ScanSummer )
private

Member Data Documentation

◆ lowerMZlimit

double pwiz::analysis::SpectrumList_ScanSummer::lowerMZlimit
private

Definition at line 71 of file SpectrumList_ScanSummer.hpp.

◆ upperMZlimit

double pwiz::analysis::SpectrumList_ScanSummer::upperMZlimit
private

Definition at line 72 of file SpectrumList_ScanSummer.hpp.

◆ TotalDaltons

double pwiz::analysis::SpectrumList_ScanSummer::TotalDaltons
private

Definition at line 73 of file SpectrumList_ScanSummer.hpp.

◆ precursorTol_

double pwiz::analysis::SpectrumList_ScanSummer::precursorTol_
private

Definition at line 74 of file SpectrumList_ScanSummer.hpp.

◆ rTimeTol_

double pwiz::analysis::SpectrumList_ScanSummer::rTimeTol_
private

Definition at line 75 of file SpectrumList_ScanSummer.hpp.

◆ mobilityTol_

double pwiz::analysis::SpectrumList_ScanSummer::mobilityTol_
private

Definition at line 76 of file SpectrumList_ScanSummer.hpp.

◆ spectrumIdentities

std::vector<msdata::SpectrumIdentity> pwiz::analysis::SpectrumList_ScanSummer::spectrumIdentities
private

Definition at line 78 of file SpectrumList_ScanSummer.hpp.

◆ indexMap

std::vector<size_t> pwiz::analysis::SpectrumList_ScanSummer::indexMap
private

Definition at line 79 of file SpectrumList_ScanSummer.hpp.

◆ precursorMap

std::vector<precursorGroupPtr> pwiz::analysis::SpectrumList_ScanSummer::precursorMap
private

Definition at line 80 of file SpectrumList_ScanSummer.hpp.

◆ precursorList

std::map<double, precursorGroupPtr> pwiz::analysis::SpectrumList_ScanSummer::precursorList
private

Definition at line 81 of file SpectrumList_ScanSummer.hpp.

◆ ms2RetentionTimes

std::vector<precursorGroupPtr> pwiz::analysis::SpectrumList_ScanSummer::ms2RetentionTimes
private

Definition at line 82 of file SpectrumList_ScanSummer.hpp.


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