SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user-specified format. More...

#include <SpectrumList_TitleMaker.hpp>

Inheritance diagram for pwiz::analysis::SpectrumList_TitleMaker:

List of all members.

Public Member Functions
	SpectrumList_TitleMaker (const msdata::MSData &msd, const std::string &format)
	The format string recognizes some keywords to replace with the appropriate field: <RunId> - Run::id <Index> - SpectrumIdentity::index <Id> - SpectrumIdentity::id (nativeID) <ScanNumber> - if the nativeID can be represented as a single number, that number, else index <ActivationType> - for the first precursor, Activation::cvParamChild("dissociation method") <IsolationMz> - for the first precursor, IsolationWindow::cvParam("isolation target m/z") <SelectedIonMz> - for the first selected ion of the first precursor, SelectedIon::cvParam("selected ion m/z") <ChargeState> - for the first selected ion of the first precursor, SelectedIon::cvParam("charge state") <SpectrumType> - Spectrum::cvParamChild("spectrum type") <ScanStartTimeInSeconds> - for the first scan, Scan::cvParam("scan start time") converted to seconds <ScanStartTimeInMinutes> - for the first scan, Scan::cvParam("scan start time") converted to minutes <BasePeakMz> - Spectrum::cvParam("base peak m/z") <BasePeakIntensity> - Spectrum::cvParam("base peak intensity") <TotalIonCurrent> - Spectrum::cvParam("total ion current")
virtual msdata::SpectrumPtr	spectrum (size_t index, bool getBinaryData=false) const
	retrieve a spectrum by index
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)

Private Attributes
const msdata::MSData &	msd_
const std::string	format_
cv::CVID	nativeIdFormat_

Additional Inherited Members
Protected Attributes inherited from pwiz::msdata::SpectrumListWrapper
SpectrumListPtr	inner_
DataProcessingPtr	dp_

Detailed Description

SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user-specified format.

Definition at line 37 of file SpectrumList_TitleMaker.hpp.

Constructor & Destructor Documentation

pwiz::analysis::SpectrumList_TitleMaker::SpectrumList_TitleMaker	(	const msdata::MSData &	msd,
		const std::string &	format
	)

The format string recognizes some keywords to replace with the appropriate field: <RunId> - Run::id <Index> - SpectrumIdentity::index <Id> - SpectrumIdentity::id (nativeID) <ScanNumber> - if the nativeID can be represented as a single number, that number, else index <ActivationType> - for the first precursor, Activation::cvParamChild("dissociation method") <IsolationMz> - for the first precursor, IsolationWindow::cvParam("isolation target m/z") <SelectedIonMz> - for the first selected ion of the first precursor, SelectedIon::cvParam("selected ion m/z") <ChargeState> - for the first selected ion of the first precursor, SelectedIon::cvParam("charge state") <SpectrumType> - Spectrum::cvParamChild("spectrum type") <ScanStartTimeInSeconds> - for the first scan, Scan::cvParam("scan start time") converted to seconds <ScanStartTimeInMinutes> - for the first scan, Scan::cvParam("scan start time") converted to minutes <BasePeakMz> - Spectrum::cvParam("base peak m/z") <BasePeakIntensity> - Spectrum::cvParam("base peak intensity") <TotalIonCurrent> - Spectrum::cvParam("total ion current")