MS2File Class Reference

#include <OpenMS/FORMAT/MS2File.h>

Inheritance diagram for MS2File:

Collaboration diagram for MS2File:

Public Member Functions
	MS2File ()
	constructor More...
	~MS2File () override
	constructor More...
template<typename MapType >
void	load (const String &filename, MapType &exp)
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...
virtual	~ProgressLogger ()
	Destructor. More...
	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...
LogType	getLogType () const
	Returns the type of progress log being used. More...
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. More...
void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...
void	setProgress (SignedSize value) const
	Sets the current progress. More...
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

@brief MS2 input file adapter.

For the format description take a look at:
Rapid Communications in Mass Spectrometry. 2004;18(18):2162-8.

MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the
storage of shotgun proteomic spectra and identifications.

McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, Johnson JR,
Cociorva D, Yates JR 3rd.

PMID: 15317041

Constructor & Destructor Documentation

MS2File()

MS2File

(

)

constructor

~MS2File()

~MS2File ( )

override

constructor

Member Function Documentation

load()

void load ( const String &  filename, MapType &  exp  )

inline

References MSExperiment::addSpectrum(), MSSpectrum::clear(), File::exists(), SpectrumSettings::getPrecursors(), File::readable(), MSExperiment::reset(), Peak1D::setIntensity(), DocumentIdentifier::setLoadedFilePath(), DocumentIdentifier::setLoadedFileType(), MSSpectrum::setMSLevel(), SpectrumSettings::setNativeID(), Peak1D::setPosition(), String::simplify(), String::split(), OpenMS::StringUtils::split(), OpenMS::StringUtils::toDouble(), OpenMS::StringUtils::toFloat(), and String::trim().