Public Member Functions | Static Public Member Functions | Private Attributes
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

List of all members.

Public Member Functions

 SpectrumList_ChargeStateCalculator (const msdata::SpectrumListPtr &inner, bool overrideExistingChargeState=true, int maxMultipleCharge=3, int minMultipleCharge=2, double intensityFractionBelowPrecursorForSinglyCharged=0.9, 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
- Public Member Functions inherited from pwiz::msdata::SpectrumListWrapper
 SpectrumListWrapper (const SpectrumListPtr &inner)
virtual size_t size () const
 returns the number of spectra
virtual bool empty () const
 returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL)
virtual const SpectrumIdentityspectrumIdentity (size_t index) const
 access to a spectrum index
virtual SpectrumPtr spectrum (size_t index, DetailLevel detailLevel) const
 retrieve a spectrum by index
virtual const
boost::shared_ptr< const
dataProcessingPtr () const
 returns the data processing affecting spectra retrieved through this interface
- 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)
virtual IndexList findNameValue (const std::string &name, const std::string &value) const
 find all spectrum indexes with specified name/value pair
virtual IndexList findSpotID (const std::string &spotID) const
 find all spectrum indexes with spotID (returns empty vector on failure)
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
virtual ~SpectrumList ()

Static Public Member Functions

static bool accept (const msdata::SpectrumListPtr &inner)
 accepts any tandem mass spectrum

Private Attributes

bool override_
int maxCharge_
int minCharge_
double fraction_
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

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

Member Function Documentation

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

accepts any tandem mass spectrum

Definition at line 48 of file SpectrumList_ChargeStateCalculator.hpp.

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

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

Implements pwiz::msdata::SpectrumListWrapper.

Member Data Documentation

bool pwiz::analysis::SpectrumList_ChargeStateCalculator::override_

Definition at line 54 of file SpectrumList_ChargeStateCalculator.hpp.

int pwiz::analysis::SpectrumList_ChargeStateCalculator::maxCharge_

Definition at line 55 of file SpectrumList_ChargeStateCalculator.hpp.

int pwiz::analysis::SpectrumList_ChargeStateCalculator::minCharge_

Definition at line 56 of file SpectrumList_ChargeStateCalculator.hpp.

double pwiz::analysis::SpectrumList_ChargeStateCalculator::fraction_

Definition at line 57 of file SpectrumList_ChargeStateCalculator.hpp.

bool pwiz::analysis::SpectrumList_ChargeStateCalculator::makeMS2_

Definition at line 58 of file SpectrumList_ChargeStateCalculator.hpp.

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