Read/write Mascot generic files (MGF). More...

#include <OpenMS/FORMAT/MascotGenericFile.h>

Inheritance diagram for MascotGenericFile:

Public Member Functions
	MascotGenericFile ()
	constructor More...

	~MascotGenericFile () override
	destructor More...

void	updateMembers_ () override
	docu in base class More...

void	store (const String &filename, const PeakMap &experiment, bool compact=false)
	stores the experiment data in a MascotGenericFile that can be used as input for MASCOT shell execution (optionally a compact format is used: no zero-intensity peaks, limited number of decimal places) More...

void	store (std::ostream &os, const String &filename, const PeakMap &experiment, bool compact=false)
	store the experiment data in a MascotGenericFile; the output is written to the given stream, the filename will be noted in the file (optionally a compact format is used: no zero-intensity peaks, limited number of decimal places) More...

template<typename MapType >
void	load (const String &filename, MapType &exp)
	loads a Mascot Generic File into a PeakMap More...

std::pair< String, String >	getHTTPPeakListEnclosure (const String &filename) const
	enclosing Strings of the peak list body for HTTP submission More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

	~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	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 () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Protected Member Functions
void	writeParameterHeader_ (const String &name, std::ostream &os)
	writes a parameter header More...

void	writeModifications_ (const std::vector< String > &mods, std::ostream &os, bool variable_mods=false)
	write a list of (fixed or variable) modifications More...

void	writeHeader_ (std::ostream &os)
	writes the full header More...

void	writeSpectrum_ (std::ostream &os, const PeakSpectrum &spec, const String &filename, const String &native_id_type_accession)
	writes the spectrum More...

void	writeMSExperiment_ (std::ostream &os, const String &filename, const PeakMap &experiment)
	writes the MSExperiment More...

template<typename SpectrumType >
bool	getNextSpectrum_ (std::ifstream &is, SpectrumType &spectrum, Size &line_number, const Size &spectrum_number)
	reads a spectrum block, the section between 'BEGIN IONS' and 'END IONS' of a MGF file More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
bool	store_compact_
	use a compact format for storing (no zero-intensity peaks, limited number of decimal places)? More...

std::map< String, String >	mod_group_map_
	mapping of modifications with specificity groups, that have to be treated specially (e.g. "Deamidated (NQ)") More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Read/write Mascot generic files (MGF).

For details of the format, see http://www.matrixscience.com/help/data_file_help.html#GEN.

Constructor & Destructor Documentation

◆ MascotGenericFile()

MascotGenericFile ( )

constructor

◆ ~MascotGenericFile()

~MascotGenericFile ( )

override

destructor

Member Function Documentation

◆ getHTTPPeakListEnclosure()

std::pair<String, String> getHTTPPeakListEnclosure ( const String & filename ) const

enclosing Strings of the peak list body for HTTP submission

Can be used to embed custom content into HTTP submission (when writing only the MGF header in HTTP format and then adding the peaks (in whatever format, e.g. mzXML) enclosed in this body. The filename can later be found in the Mascot response.

◆ getNextSpectrum_()

bool getNextSpectrum_	(	std::ifstream &	is,
		SpectrumType &	spectrum,
		Size &	line_number,
		const Size &	spectrum_number
	)

inlineprotected

reads a spectrum block, the section between 'BEGIN IONS' and 'END IONS' of a MGF file

References SpectrumSettings::getPrecursors(), String::hasPrefix(), String::hasSubstring(), MetaInfoInterface::metaValueExists(), String::remove(), MetaInfoInterface::removeMetaValue(), Peak1D::setIntensity(), MetaInfoInterface::setMetaValue(), SpectrumSettings::setNativeID(), Peak1D::setPosition(), MSSpectrum::setRT(), String::simplify(), String::split(), String::substitute(), String::substr(), String::toDouble(), String::toInt(), and String::trim().

◆ load()

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

inline

loads a Mascot Generic File into a PeakMap

Parameters

filename	file name which the map should be read from
exp	the map which is filled with the data from the given file

Exceptions

FileNotFound is thrown if the given file could not be found

References MSExperiment::addSpectrum(), File::exists(), SpectrumSettings::getPrecursors(), MSExperiment::reset(), and MSSpectrum::setMSLevel().

◆ store() [1/2]

void store	(	const String &	filename,
		const PeakMap &	experiment,
		bool	compact = `false`
	)

stores the experiment data in a MascotGenericFile that can be used as input for MASCOT shell execution (optionally a compact format is used: no zero-intensity peaks, limited number of decimal places)

◆ store() [2/2]

void store	(	std::ostream &	os,
		const String &	filename,
		const PeakMap &	experiment,
		bool	compact = `false`
	)

store the experiment data in a MascotGenericFile; the output is written to the given stream, the filename will be noted in the file (optionally a compact format is used: no zero-intensity peaks, limited number of decimal places)

◆ updateMembers_()

void updateMembers_ ( )

overridevirtual

docu in base class

Reimplemented from DefaultParamHandler.

◆ writeHeader_()

void writeHeader_ ( std::ostream & os )

protected

writes the full header

◆ writeModifications_()

void writeModifications_	(	const std::vector< String > &	mods,
		std::ostream &	os,
		bool	variable_mods = `false`
	)

protected

write a list of (fixed or variable) modifications

◆ writeMSExperiment_()

void writeMSExperiment_	(	std::ostream &	os,
		const String &	filename,
		const PeakMap &	experiment
	)

protected

writes the MSExperiment

◆ writeParameterHeader_()

void writeParameterHeader_	(	const String &	name,
		std::ostream &	os
	)

protected

writes a parameter header

◆ writeSpectrum_()

void writeSpectrum_	(	std::ostream &	os,
		const PeakSpectrum &	spec,
		const String &	filename,
		const String &	native_id_type_accession
	)

protected

writes the spectrum

Member Data Documentation

◆ mod_group_map_

std::map<String, String> mod_group_map_

protected

mapping of modifications with specificity groups, that have to be treated specially (e.g. "Deamidated (NQ)")

◆ store_compact_

bool store_compact_

protected

use a compact format for storing (no zero-intensity peaks, limited number of decimal places)?

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MascotGenericFile()

◆ ~MascotGenericFile()

Member Function Documentation

◆ getHTTPPeakListEnclosure()

◆ getNextSpectrum_()

◆ load()

◆ store() [1/2]

◆ store() [2/2]

◆ updateMembers_()

◆ writeHeader_()

◆ writeModifications_()

◆ writeMSExperiment_()

◆ writeParameterHeader_()

◆ writeSpectrum_()

Member Data Documentation

◆ mod_group_map_

◆ store_compact_