Mascot input file adapter. More...

#include <OpenMS/FORMAT/MascotInfile.h>

Inheritance diagram for MascotInfile:

Collaboration diagram for MascotInfile:

Public Member Functions
	MascotInfile ()
	constructor More...

	~MascotInfile () override
	constructor More...

void	store (const String &filename, const PeakSpectrum &spec, double mz, double retention_time, String search_title)
	stores the peak list in a MascotInfile that can be used as input for MASCOT shell execution More...

void	store (const String &filename, const PeakMap &experiment, String search_title)
	stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution More...

template<typename MapType >
void	load (const String &filename, MapType &exp)

const String &	getBoundary ()
	returns the boundary used for the MIME format More...

void	setBoundary (const String &boundary)
	sets the boundary used for the MIME format. By default a 22 character random string is used More...

const String &	getDB ()
	returns the DB to use More...

void	setDB (const String &db)
	sets the DB to use (default: MSDB). See <mascot path>/config/mascot.dat in "Databases" section for possible settings More...

const String &	getSearchType ()
	returns the search type More...

void	setSearchType (const String &search_type)
	sets the search type (default: MIS). So far only MIS is supported! Valid types are "MIS" (MS/MS Ion Search), "PMF" (Peptide Mass Fingerprint) , "SQ" (Sequence Query) More...

const String &	getHits ()
	returns the number of hits to report back More...

void	setHits (const String &hits)
	sets the number of hits to report back (default: 20) More...

const String &	getCleavage ()
	returns the enzyme used for cleavage More...

void	setCleavage (const String &cleavage)
	sets the enzyme used for cleavage (default: Trypsin). See <mascot path>/config/enzymes for possible settings. More...

const String &	getMassType ()
	returns the used mass type ("Monoisotopic" or "Average") More...

void	setMassType (const String &mass_type)
	sets the used mass type "Monoisotopic" or "Average" (default: Monoisotopic) More...

const std::vector< String > &	getModifications ()
	returns a vector containing the fixed modifications (default: none) More...

void	setModifications (const std::vector< String > &mods)
	sets the fixed modifications (default: none). See <mascot path>/config/mod_file for possible settings. More...

const std::vector< String > &	getVariableModifications ()
	returns a vector containing the variable modifications (default: none) More...

void	setVariableModifications (const std::vector< String > &mods)
	sets the fixed modifications (default: none). See <mascot path>/config/mod_file for possible settings. More...

const String &	getInstrument ()
	returns the instrument type More...

void	setInstrument (const String &instrument)
	sets the instrument type (Default: Default). Possible instruments: ESI-QUAD-TOF, MALDI-TOF-PSD, ESI-TRAP, ESI-QUAD, ESI-FTICR, MALDI-TOF-TOF, ESI-4SECTOR, FTMS-ECD, MALDI-QUAD-TOF, MALDI-QIT-TOF More...

UInt	getMissedCleavages () const
	returns the number of allowed missed cleavages More...

void	setMissedCleavages (UInt missed_cleavages)
	sets the number of allowed missed cleavages (default: 1) More...

float	getPrecursorMassTolerance () const
	returns the precursor mass tolerance More...

void	setPrecursorMassTolerance (float precursor_mass_tolerance)
	sets the precursor mass tolerance in Da (default: 2.0) More...

float	getPeakMassTolerance () const
	returns the peak mass tolerance in Da More...

void	setPeakMassTolerance (float ion_mass_tolerance)
	sets the peak mass tolerance in Da (default: 1.0) More...

const String &	getTaxonomy ()
	returns the taxonomy More...

void	setTaxonomy (const String &taxonomy)
	sets the taxonomy (default: All entries). See <mascot path>/config/taxonomy for possible settings. More...

const String &	getFormVersion ()
	returns the Mascot form version More...

void	setFormVersion (const String &form_version)
	sets the Mascot form version (default: 1.01) More...

const String &	getCharges ()
	returns the charges More...

void	setCharges (std::vector< Int > &charges)
	sets the charges (default: 1+, 2+ and 3+) More...

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	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...

Protected Member Functions
void	writeParameterHeader_ (const String &name, FILE *fp, bool line_break=true)
	writes a parameter header More...

void	writeHeader_ (FILE *fp)
	writes the full header More...

void	writeSpectrum_ (FILE *fp, const String &filename, const PeakSpectrum &peaks)
	writes the spectrum More...

void	writeMSExperiment_ (FILE *fp, const String &filename, const PeakMap &experiment)
	writes the MSExperiment More...

bool	getNextSpectrum_ (std::istream &is, std::vector< std::pair< double, double > > &spectrum, UInt &charge, double &precursor_mz, double &precursor_int, double &rt, String &title)

Protected Attributes
double	mz_
	parent mass More...

String	charges_
	charge states to use More...

String	search_title_
	the search title of the mascot search More...

String	db_
	the DB to search in More...

String	search_type_
	search type: MIS, SQ or PMF More...

String	hits_
	number of hits to report More...

String	cleavage_
	Enzyme used for cleavage. More...

String	mass_type_
	Monoisotopic/average mass. More...

std::vector< String >	mods_
	fixed Modifications More...

std::vector< String >	variable_mods_
	variable Modifications More...

String	instrument_
	the used instrument More...

UInt	missed_cleavages_
	number of missed cleavages More...

float	precursor_mass_tolerance_
	precursor mass tolerance in Da More...

float	ion_mass_tolerance_
	m/z tolerance of ions in Da More...

String	taxonomy_
	taxonomy More...

String	form_version_
	form version More...

String	boundary_
	the boundary used for the MIME format More...

double	retention_time_
	the retention time More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

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

Mascot input file adapter.

Deprecated:: Use MascotGenericFile.h instead, which uses DefaultParamHandler, is more up to date and avoids weird behaviors of this class (especially in terms of MIME boundaries when writing MGF. This class is currently only used by MascotAdapter.cpp.

Creates a file that can be used for Mascot search from a peak list or a whole experiment.

Constructor & Destructor Documentation

◆ MascotInfile()

MascotInfile ( )

constructor

◆ ~MascotInfile()

~MascotInfile ( )

override

constructor

Member Function Documentation

◆ getBoundary()

const String& getBoundary ( )

returns the boundary used for the MIME format

◆ getCharges()

const String& getCharges ( )

returns the charges

◆ getCleavage()

const String& getCleavage ( )

returns the enzyme used for cleavage

◆ getDB()

const String& getDB ( )

returns the DB to use

◆ getFormVersion()

const String& getFormVersion ( )

returns the Mascot form version

◆ getHits()

const String& getHits ( )

returns the number of hits to report back

◆ getInstrument()

const String& getInstrument ( )

returns the instrument type

◆ getMassType()

const String& getMassType ( )

returns the used mass type ("Monoisotopic" or "Average")

◆ getMissedCleavages()

UInt getMissedCleavages ( ) const

returns the number of allowed missed cleavages

◆ getModifications()

const std::vector<String>& getModifications ( )

returns a vector containing the fixed modifications (default: none)

◆ getNextSpectrum_()

bool getNextSpectrum_	(	std::istream &	is,
		std::vector< std::pair< double, double > > &	spectrum,
		UInt &	charge,
		double &	precursor_mz,
		double &	precursor_int,
		double &	rt,
		String &	title
	)

protected

◆ getPeakMassTolerance()

float getPeakMassTolerance ( ) const

returns the peak mass tolerance in Da

◆ getPrecursorMassTolerance()

float getPrecursorMassTolerance ( ) const

returns the precursor mass tolerance

◆ getSearchType()

const String& getSearchType ( )

returns the search type

◆ getTaxonomy()

const String& getTaxonomy ( )

returns the taxonomy

◆ getVariableModifications()

const std::vector<String>& getVariableModifications ( )

returns a vector containing the variable modifications (default: none)

◆ 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(), Peak1D::setIntensity(), MetaInfoInterface::setMetaValue(), MSSpectrum::setMSLevel(), Peak1D::setPosition(), and MSSpectrum::setRT().

◆ setBoundary()

void setBoundary ( const String & boundary )

sets the boundary used for the MIME format.
By default a 22 character random string is used

◆ setCharges()

void setCharges ( std::vector< Int > & charges )

sets the charges (default: 1+, 2+ and 3+)

◆ setCleavage()

void setCleavage ( const String & cleavage )

sets the enzyme used for cleavage (default: Trypsin).
See <mascot path>/config/enzymes for possible settings.

◆ setDB()

void setDB ( const String & db )

sets the DB to use (default: MSDB). See <mascot path>/config/mascot.dat in "Databases" section for possible settings

◆ setFormVersion()

void setFormVersion ( const String & form_version )

sets the Mascot form version (default: 1.01)

◆ setHits()

void setHits ( const String & hits )

sets the number of hits to report back (default: 20)

◆ setInstrument()

void setInstrument ( const String & instrument )

sets the instrument type (Default: Default).
Possible instruments: ESI-QUAD-TOF, MALDI-TOF-PSD, ESI-TRAP, ESI-QUAD, ESI-FTICR, MALDI-TOF-TOF, ESI-4SECTOR, FTMS-ECD, MALDI-QUAD-TOF, MALDI-QIT-TOF

◆ setMassType()

void setMassType ( const String & mass_type )

sets the used mass type "Monoisotopic" or "Average" (default: Monoisotopic)

◆ setMissedCleavages()

void setMissedCleavages ( UInt missed_cleavages )

sets the number of allowed missed cleavages (default: 1)

◆ setModifications()

void setModifications ( const std::vector< String > & mods )

sets the fixed modifications (default: none).
See <mascot path>/config/mod_file for possible settings.

◆ setPeakMassTolerance()

void setPeakMassTolerance ( float ion_mass_tolerance )

sets the peak mass tolerance in Da (default: 1.0)

◆ setPrecursorMassTolerance()

void setPrecursorMassTolerance ( float precursor_mass_tolerance )

sets the precursor mass tolerance in Da (default: 2.0)

◆ setSearchType()

void setSearchType ( const String & search_type )

sets the search type (default: MIS). So far only MIS is supported!
Valid types are "MIS" (MS/MS Ion Search), "PMF" (Peptide Mass Fingerprint) , "SQ" (Sequence Query)

◆ setTaxonomy()

void setTaxonomy ( const String & taxonomy )

sets the taxonomy (default: All entries).
See <mascot path>/config/taxonomy for possible settings.

◆ setVariableModifications()

void setVariableModifications ( const std::vector< String > & mods )

sets the fixed modifications (default: none).
See <mascot path>/config/mod_file for possible settings.

◆ store() [1/2]

void store	(	const String &	filename,
		const PeakMap &	experiment,
		String	search_title
	)

stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution

◆ store() [2/2]

void store	(	const String &	filename,
		const PeakSpectrum &	spec,
		double	mz,
		double	retention_time,
		String	search_title
	)

stores the peak list in a MascotInfile that can be used as input for MASCOT shell execution

◆ writeHeader_()

void writeHeader_ ( FILE * fp )

protected

writes the full header

◆ writeMSExperiment_()

void writeMSExperiment_	(	FILE *	fp,
		const String &	filename,
		const PeakMap &	experiment
	)

protected

writes the MSExperiment

◆ writeParameterHeader_()

void writeParameterHeader_	(	const String &	name,
		FILE *	fp,
		bool	line_break = `true`
	)

protected

writes a parameter header

◆ writeSpectrum_()

void writeSpectrum_	(	FILE *	fp,
		const String &	filename,
		const PeakSpectrum &	peaks
	)

protected

writes the spectrum

Member Data Documentation

◆ boundary_

String boundary_

protected

the boundary used for the MIME format

◆ charges_

String charges_

protected

charge states to use

◆ cleavage_

String cleavage_

protected

Enzyme used for cleavage.

◆ db_

String db_

protected

the DB to search in

◆ form_version_

String form_version_

protected

form version

◆ hits_

String hits_

protected

number of hits to report

◆ instrument_

String instrument_

protected

the used instrument

◆ ion_mass_tolerance_

float ion_mass_tolerance_

protected

m/z tolerance of ions in Da

◆ mass_type_

String mass_type_

protected

Monoisotopic/average mass.

◆ missed_cleavages_

UInt missed_cleavages_

protected

number of missed cleavages

◆ mods_

std::vector<String> mods_

protected

fixed Modifications

◆ mz_

double mz_

protected

parent mass

◆ precursor_mass_tolerance_

float precursor_mass_tolerance_

protected

precursor mass tolerance in Da

◆ retention_time_

double retention_time_

protected

the retention time

◆ search_title_

String search_title_

protected

the search title of the mascot search

◆ search_type_

String search_type_

protected

search type: MIS, SQ or PMF

◆ taxonomy_

String taxonomy_

protected

taxonomy

◆ variable_mods_

std::vector<String> variable_mods_

protected

variable Modifications

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MascotInfile()

◆ ~MascotInfile()

Member Function Documentation

◆ getBoundary()

◆ getCharges()

◆ getCleavage()

◆ getDB()

◆ getFormVersion()

◆ getHits()

◆ getInstrument()

◆ getMassType()

◆ getMissedCleavages()

◆ getModifications()

◆ getNextSpectrum_()

◆ getPeakMassTolerance()

◆ getPrecursorMassTolerance()

◆ getSearchType()

◆ getTaxonomy()

◆ getVariableModifications()

◆ load()

◆ setBoundary()

◆ setCharges()

◆ setCleavage()

◆ setDB()

◆ setFormVersion()

◆ setHits()

◆ setInstrument()

◆ setMassType()

◆ setMissedCleavages()

◆ setModifications()

◆ setPeakMassTolerance()

◆ setPrecursorMassTolerance()

◆ setSearchType()

◆ setTaxonomy()

◆ setVariableModifications()

◆ store() [1/2]

◆ store() [2/2]

◆ writeHeader_()

◆ writeMSExperiment_()

◆ writeParameterHeader_()

◆ writeSpectrum_()

Member Data Documentation

◆ boundary_

◆ charges_

◆ cleavage_

◆ db_

◆ form_version_

◆ hits_

◆ instrument_

◆ ion_mass_tolerance_

◆ mass_type_

◆ missed_cleavages_

◆ mods_

◆ mz_

◆ precursor_mass_tolerance_

◆ retention_time_

◆ search_title_

◆ search_type_

◆ taxonomy_

◆ variable_mods_