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

#include <SpectrumList_ChargeStateCalculator.hpp>

Inheritance diagram for pwiz::analysis::SpectrumList_ChargeStateCalculator:

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 SpectrumIdentity &	spectrumIdentity (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 DataProcessing >	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`
	)