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pwiz::analysis::SpectrumList_PeakPicker Class Reference

SpectrumList implementation to replace peak profiles with picked peaks. More...

#include <SpectrumList_PeakPicker.hpp>

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

Public Member Functions

 SpectrumList_PeakPicker (const msdata::SpectrumListPtr &inner, PeakDetectorPtr algorithm, bool preferVendorPeakPicking, const util::IntegerSet &msLevelsToPeakPick)
 
virtual msdata::SpectrumPtr spectrum (size_t index, msdata::DetailLevel detailLevel) const
 retrieve a spectrum by index More...
 
virtual msdata::SpectrumPtr spectrum (size_t index, bool getBinaryData=false) const
 retrieve a spectrum by index More...
 
- Public Member Functions inherited from pwiz::msdata::SpectrumListWrapper
 SpectrumListWrapper (const SpectrumListPtr &inner)
 
virtual size_t size () const
 returns the number of spectra More...
 
virtual bool empty () const
 returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL) More...
 
virtual const SpectrumIdentityspectrumIdentity (size_t index) const
 access to a spectrum index 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 ()
 

Static Public Member Functions

static bool accept (const msdata::SpectrumListPtr &inner)
 

Private Attributes

PeakDetectorPtr algorithm_
 
const util::IntegerSet msLevelsToPeakPick_
 
int mode_
 

Additional Inherited Members

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

Detailed Description

SpectrumList implementation to replace peak profiles with picked peaks.

Definition at line 39 of file SpectrumList_PeakPicker.hpp.

Constructor & Destructor Documentation

§ SpectrumList_PeakPicker()

pwiz::analysis::SpectrumList_PeakPicker::SpectrumList_PeakPicker ( const msdata::SpectrumListPtr inner,
PeakDetectorPtr  algorithm,
bool  preferVendorPeakPicking,
const util::IntegerSet msLevelsToPeakPick 
)

Member Function Documentation

§ accept()

static bool pwiz::analysis::SpectrumList_PeakPicker::accept ( const msdata::SpectrumListPtr inner)
static

§ spectrum() [1/2]

virtual msdata::SpectrumPtr pwiz::analysis::SpectrumList_PeakPicker::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.

§ spectrum() [2/2]

virtual msdata::SpectrumPtr pwiz::analysis::SpectrumList_PeakPicker::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.

Member Data Documentation

§ algorithm_

PeakDetectorPtr pwiz::analysis::SpectrumList_PeakPicker::algorithm_
private

Definition at line 55 of file SpectrumList_PeakPicker.hpp.

§ msLevelsToPeakPick_

const util::IntegerSet pwiz::analysis::SpectrumList_PeakPicker::msLevelsToPeakPick_
private

Definition at line 56 of file SpectrumList_PeakPicker.hpp.

§ mode_

int pwiz::analysis::SpectrumList_PeakPicker::mode_
private

Definition at line 57 of file SpectrumList_PeakPicker.hpp.


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