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pwiz::analysis::SpectrumList_ChargeStateCalculator Class Reference

SpectrumList implementation that assigns (probable) charge states to tandem mass spectra. More...

#include <SpectrumList_ChargeStateCalculator.hpp>

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

Public Member Functions

 SpectrumList_ChargeStateCalculator (const msdata::SpectrumListPtr &inner, bool overrideExistingChargeState=true, int maxMultipleCharge=3, int minMultipleCharge=2, double intensityFractionBelowPrecursorForSinglyCharged=0.9, int maxKnownCharge=0, bool makeMS2=false)
 
virtual msdata::SpectrumPtr spectrum (size_t index, bool getBinaryData=true) const
 charge calculation requires binary data to function, so returned spectra will always provide the binary data 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 SpectrumPtr spectrum (size_t index, DetailLevel detailLevel) const
 retrieve a spectrum by 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)
 accepts any tandem mass spectrum More...
 

Private Attributes

bool override_
 
int maxCharge_
 
int minCharge_
 
double fraction_
 
int maxKnownCharge_
 
bool makeMS2_
 

Additional Inherited Members

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

Detailed Description

SpectrumList implementation that assigns (probable) charge states to tandem mass spectra.

Definition at line 37 of file SpectrumList_ChargeStateCalculator.hpp.

Constructor & Destructor Documentation

§ SpectrumList_ChargeStateCalculator()

pwiz::analysis::SpectrumList_ChargeStateCalculator::SpectrumList_ChargeStateCalculator ( const msdata::SpectrumListPtr inner,
bool  overrideExistingChargeState = true,
int  maxMultipleCharge = 3,
int  minMultipleCharge = 2,
double  intensityFractionBelowPrecursorForSinglyCharged = 0.9,
int  maxKnownCharge = 0,
bool  makeMS2 = false 
)

Member Function Documentation

§ accept()

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

accepts any tandem mass spectrum

Definition at line 49 of file SpectrumList_ChargeStateCalculator.hpp.

49 {return true;}

§ spectrum()

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

charge calculation requires binary data to function, so returned spectra will always provide the binary data

Implements pwiz::msdata::SpectrumListWrapper.

Member Data Documentation

§ override_

bool pwiz::analysis::SpectrumList_ChargeStateCalculator::override_
private

Definition at line 55 of file SpectrumList_ChargeStateCalculator.hpp.

§ maxCharge_

int pwiz::analysis::SpectrumList_ChargeStateCalculator::maxCharge_
private

Definition at line 56 of file SpectrumList_ChargeStateCalculator.hpp.

§ minCharge_

int pwiz::analysis::SpectrumList_ChargeStateCalculator::minCharge_
private

Definition at line 57 of file SpectrumList_ChargeStateCalculator.hpp.

§ fraction_

double pwiz::analysis::SpectrumList_ChargeStateCalculator::fraction_
private

Definition at line 58 of file SpectrumList_ChargeStateCalculator.hpp.

§ maxKnownCharge_

int pwiz::analysis::SpectrumList_ChargeStateCalculator::maxKnownCharge_
private

Definition at line 59 of file SpectrumList_ChargeStateCalculator.hpp.

§ makeMS2_

bool pwiz::analysis::SpectrumList_ChargeStateCalculator::makeMS2_
private

Definition at line 60 of file SpectrumList_ChargeStateCalculator.hpp.


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