mgf::MgfHeader Class Reference

Mascot Generic Format file header (global parameters) information. More...

#include <MgfHeader.h>

Public Member Functions
std::string	getCLE (void) const
	Get the name of the enzyme used for digestion.
void	setCLE (const std::string &cle)
	Set the name of the enzyme used for digestion.
std::string	getCOM (void) const
	Get the search title.
void	setCOM (const std::string &com)
	Set the search title.
std::string	getDB (void) const
	Get the database name agains which Mascot should search.
void	setDB (const std::string &db)
	Set the sequence database name that specifies the database against which searches should be carreid out.
std::string	getFORMAT (void) const
	Get the MS/MS data file format.
void	setFORMAT (const std::string &format)
	Set the MS/MS data file format.
std::string	getINSTRUMENT (void) const
	Get the instrument type/fragmentation rules.
void	setINSTRUMENT (const std::string &instrument)
	Set the instrument type/fragementation rules.
std::string	getIT_MODS (void) const
	Get the string representation of the variable modifications.
void	setIT_MODS (const std::string &it_mods)
	Set the variable modification string.
std::string	getITOLU (void) const
	Get the unit used to specify the fragmentation ion tolerance.
void	setITOLU (const std::string &itolu)
	Set the unit used to specify the fragmentation ion tolerance.
std::string	getMASS (void) const
	Get the type of mass reported for the parent ion: monoisotopic or average.
void	setMASS (const std::string &mass)
	Set the parent io mass type: monoisotopic or average.
std::string	getMODS (void) const
	Get the string representation of fixed modifications.
void	setMODS (const std::string &mods)
	Set the string representation of fixed modifications.
std::string	getQUANTITATION (void) const
	Get the strign that identifies the quantitation method.
void	setQUANTITATION (const std::string &quantitation)
	Set the strign that identifies the quantitation method.
std::string	getREPORT (void) const
	Get the maximum number of hits that are being reported in the results.
void	setREPORT (const std::string &report)
	Set the maximum number of hits that are being reported in the results.
std::string	getREPTYPE (void) const
	Get the report type identifier.
void	setREPTYPE (const std::string &reptype)
	Get the report type identifier.
std::string	getSEARCH (void) const
	Get the type of search specified for the underlying MgfFile object.
void	setSEARCH (const std::string &search)
	Set the type of search specified for the underlying MgfFile object.
std::string	getTAXONOMY (void) const
	Get the taxonomy (as specified in Mascot's taxonomy file).
void	setTAXONOMY (const std::string &taxonomy)
	Set the taxonomy (as specified in Mascot's taxonomy file).
std::string	getTOLU (void) const
	Get the unit in which the tolerance is specified.
void	setTOLU (const std::string &tolu)
	Set the unit in which the tolerance is specified.
std::string	getUSEREMAIL (void) const
	Get the user email address.
void	setUSEREMAIL (const std::string &useremail)
	Set the user email address.
std::string	getUSERNAME (void) const
	Get the name of the user submitting the search.
void	setUSERNAME (const std::string &username)
	Set the name of the user submitting the search.
int	getPFA (void) const
	Get the number of allowed missed cleavages.
void	setPFA (const int pfa)
	Set the number of allowed missed cleavages.
int	getDECOY (void) const
	Get the decoy search flag (0=false, 1=true).
void	setDECOY (const int decoy)
	Set the decoy search flag (0=false, 1=true).
int	getERRORTOLERANT (void) const
	Get the status of the error-tolerant search flag.
void	setERRORTOLERANT (const int errortolerant)
	Set the status of the error-tolerant search flag.
double	getPEP_ISOTOPE_ERROR (void) const
	Get the status of the isotope error correction flag.
void	setPEP_ISOTOPE_ERROR (const double pep_isotope_error)
	Set/unset the peptide isotope error correction flag.
double	getITOL (void) const
	Get the fragment ion tolerance.
void	setITOL (const double itol)
	Set the fragment ion tolerance.
double	getPRECURSOR (void) const
	Get the scan precursor mass (in m/z).
void	setPRECURSOR (const double precursor)
	Set the precursor mass (in m/z).
double	getSEG (void) const
	Get the mass of the intact protein.
void	setSEG (const double seg)
	Set the mass of the intact protein.
double	getTOL (void) const
	Get the search tolerance.
void	setTOL (const double tol)
	Set the search tolerance.
void	getCHARGE (std::vector< int > &charges) const
	Get the precursor charges for which a search is requested.
void	setCHARGE (const std::vector< int > &charges)
	Set the precursor charges for which a search is requested.
void	getFRAMES (std::vector< int > &frames) const
	Get the type of NA translation.
void	setFRAMES (const std::vector< int > &frames)
	Get the type of NA translation.
void	clear ()
	Clear all information from the current MgfHeader object.
Friends
std::ostream &	operator<< (std::ostream &os, const MgfHeader &mgf)
	Output operator.

Detailed Description

Mascot Generic Format file header (global parameters) information.

MGF files hold global and local parameters. Whereas local parameters are stored with the respective MgfSpectrum, MgfHeader is where the global variables reside. The description and values of the variables are taken from the official MatrixScience format information page at http://www.matrixscience.com/help/data_file_help.html#GEN..

Member Function Documentation

void mgf::MgfHeader::clear ( )

Clear all information from the current MgfHeader object.

void mgf::MgfHeader::getCHARGE ( std::vector< int > & charges ) const

Get the precursor charges for which a search is requested.

See also:: http://www.matrixscience.com/help/search_field_help.html#TWO

Parameters:

[out] charges The charge vector.

std::string mgf::MgfHeader::getCLE ( void ) const

Get the name of the enzyme used for digestion.

See also:: http://www.matrixscience.com/help/search_field_help.html#CLE

Returns:: The enzyme name (e.g. Trypsin).

std::string mgf::MgfHeader::getCOM ( void ) const

Get the search title.

See also:: http://www.matrixscience.com/help/search_field_help.html#COM

Returns:: The search title.

std::string mgf::MgfHeader::getDB ( void ) const

Get the database name agains which Mascot should search.

See also:: http://www.matrixscience.com/help/search_field_help.html#DB

Returns:: The database name.

int mgf::MgfHeader::getDECOY ( void ) const

Get the decoy search flag (0=false, 1=true).

Returns:: The decoy search flag.

int mgf::MgfHeader::getERRORTOLERANT ( void ) const

Get the status of the error-tolerant search flag.

Returns:: The flag value (0=no error-tolerant search, 1=error-tolerant search)

std::string mgf::MgfHeader::getFORMAT ( void ) const

Get the MS/MS data file format.

Valid values are Mascot generic (the default), Sequest (.DTA), Finnigan (.ASC), Micromass (.PKL), PerSeptive (.PKS), Sciex API III, Bruker (.XML), mzData (.XML).

Returns:: The data file format.

void mgf::MgfHeader::getFRAMES ( std::vector< int > & frames ) const

Get the type of NA translation.

The default value is an array of [1, 2, 3, 4, 5, 6]. Documentation on this parameter and its exact use is sparse.

See also:: http://www.matrixscience.com/help/data_file_help.html#PARAMS

Returns:: The list of translations (?).

std::string mgf::MgfHeader::getINSTRUMENT ( void ) const

Get the instrument type/fragmentation rules.

Based on the definitions in the Mascot fragmentation_rules configuration files, this defines the type of instrument Mascot expects and the fragmentation scheme used to derive the theoretical fragementation spectra.

Returns:: The.

std::string mgf::MgfHeader::getIT_MODS ( void ) const

Get the string representation of the variable modifications.

The modification string specifies which variable post-translational modifications are searched in a Mascot query.

Returns:: A string of variable modifications.

double mgf::MgfHeader::getITOL ( void ) const

Get the fragment ion tolerance.

Keep in mind that the value is unit dependent and the unit is available via getITOLU().

See also:: http://www.matrixscience.com/help/search_field_help.html#ITOL

Returns:: The fragment ion tolerance.

std::string mgf::MgfHeader::getITOLU ( void ) const

Get the unit used to specify the fragmentation ion tolerance.

Valid values are mmu and Da.

Returns:: The.

std::string mgf::MgfHeader::getMASS ( void ) const

Get the type of mass reported for the parent ion: monoisotopic or average.

Returns:: The

std::string mgf::MgfHeader::getMODS ( void ) const

Get the string representation of fixed modifications.

The modification string specifies which fixed post-translational modifications are searched in all Mascot queries in the MgfFile object. The setting may be overridden in individual MgfSpectrum instances.

Returns:: A string representation of the fixed modifications specified for the current MgfFile.

double mgf::MgfHeader::getPEP_ISOTOPE_ERROR ( void ) const

Get the status of the isotope error correction flag.

The flag controls whether Mascot also attempts to find peptide-spectral matches for a precursor mass -1m/z. This counters situations in which the instrument picks the second isotope as parent mass.

Returns:: The.isotope error correction flag value (0=off, 1=on)

int mgf::MgfHeader::getPFA ( void ) const

Get the number of allowed missed cleavages.

The range allowed by Mascot is [0-9], defaults to 1.

See also:: http://www.matrixscience.com/help/search_field_help.html#PFA

Returns:: The number of missed cleavages used for the current MgfFile.

double mgf::MgfHeader::getPRECURSOR ( void ) const

Get the scan precursor mass (in m/z).

See also:: http://www.matrixscience.com/help/search_field_help.html#PRECURSOR

Returns:: The.mass of the precursor.

std::string mgf::MgfHeader::getQUANTITATION ( void ) const

Get the strign that identifies the quantitation method.

Method strings are defined in Mascot's quantitation.xml file. Defined for MIS only.

Returns:: The quantitation identificatn string.

std::string mgf::MgfHeader::getREPORT ( void ) const

Get the maximum number of hits that are being reported in the results.

Vaild values are AUTO or an integer.

Returns:: The maximum number of hits, as a string.

std::string mgf::MgfHeader::getREPTYPE ( void ) const

Get the report type identifier.

Valid values are

protein
peptide (Default for MIS)
archive (MIS only)
concise (Default for PMF)
select (MIS only)
unassigned (MIS only)
See also:
http://www.matrixscience.com/help/results_help.html

Returns:
A report identifier string.

std::string mgf::MgfHeader::getSEARCH ( void ) const

Get the type of search specified for the underlying MgfFile object.

Valid values are PMF, SQ, MIS.

Returns:: The search type string.

double mgf::MgfHeader::getSEG ( void ) const

Get the mass of the intact protein.

The intacat mass is in Da, applied as a sliding windows. Follow the link for more information.

See also:: http://www.matrixscience.com/help/search_field_help.html#SEG

Returns:: The protein mass in Da.

std::string mgf::MgfHeader::getTAXONOMY ( void ) const

Get the taxonomy (as specified in Mascot's taxonomy file).

See also:: http://www.matrixscience.com/help/search_field_help.html#TAXONOMY

Returns:: The taxonomy.

double mgf::MgfHeader::getTOL ( void ) const

Get the search tolerance.

The return value is unit-dependent. The unit is available via getTOLU().

See also:: http://www.matrixscience.com/help/search_field_help.html#TOL

Returns:: The search tolerance.

std::string mgf::MgfHeader::getTOLU ( void ) const

Get the unit in which the tolerance is specified.

Valid values are %, ppm, mmu and Da).

Returns:: A string specifying the tolerance unit.

std::string mgf::MgfHeader::getUSEREMAIL ( void ) const

Get the user email address.

Returns:: A user email address string.

std::string mgf::MgfHeader::getUSERNAME ( void ) const

Get the name of the user submitting the search.

Returns:: The.username.

void mgf::MgfHeader::setCHARGE ( const std::vector< int > & charges )

Set the precursor charges for which a search is requested.

See also:: http://www.matrixscience.com/help/search_field_help.html#TWO

Parameters:

[in] charges The charge vector.

void mgf::MgfHeader::setCLE ( const std::string & cle )

Set the name of the enzyme used for digestion.

If the MGF file is to be searched, then the name needs to correspond to an enzyme name specified in the Mascot enzyme file. Because there is no way for mgfp to check the validity of the string, the responsibility for valid enzyme names lies with the user.

See also:: http://www.matrixscience.com/help/search_field_help.html#CLE

Parameters:

[in] cle The enzyme string (e.g. Trypsin).

void mgf::MgfHeader::setCOM ( const std::string & com )

Set the search title.

See also:: http://www.matrixscience.com/help/search_field_help.html#COM

Parameters:

[in] com The search title.

void mgf::MgfHeader::setDB ( const std::string & db )

Set the sequence database name that specifies the database against which searches should be carreid out.

See also:: http://www.matrixscience.com/help/search_field_help.html#DB

Parameters:

[in] db The database name.

void mgf::MgfHeader::setDECOY ( const int decoy )

Set the decoy search flag (0=false, 1=true).

Parameters:

[in] decoy The decoy search flag.

void mgf::MgfHeader::setERRORTOLERANT ( const int errortolerant )

Set the status of the error-tolerant search flag.

Error-tolerant searchs are not available for PMF queries.

Parameters:

[in] errortolerant The desired value of the error-tolerant search flag (0=off, 1=on).

void mgf::MgfHeader::setFORMAT ( const std::string & format )

Set the MS/MS data file format.

Valid values are Mascot generic (the default), Sequest (.DTA), Finnigan (.ASC), Micromass (.PKL), PerSeptive (.PKS), Sciex API III, Bruker (.XML), mzData (.XML).

Parameters:

[in] format Data file format string.

void mgf::MgfHeader::setFRAMES ( const std::vector< int > & frames )

Get the type of NA translation.

The default value is an array of [1, 2, 3, 4, 5, 6]. Documentation on this parameter and its exact use is sparse.

See also:: http://www.matrixscience.com/help/data_file_help.html#PARAMS

Parameters:

[in] frames The list of translations (?).

void mgf::MgfHeader::setINSTRUMENT ( const std::string & instrument )

Set the instrument type/fragementation rules.

Valid values are defined in the Mascot fragmentation_rules configuration file. There is no way for mgfp to validate the user input, hence the responsibility lies with the user.

Parameters:

[in] instrument The

void mgf::MgfHeader::setIT_MODS ( const std::string & it_mods )

Set the variable modification string.

The modfication string specifies which variable post-translational modifications are searched in a Mascot query. Strings should conform to UniMod standards.

Parameters:

[in] it_mods The modification string.

void mgf::MgfHeader::setITOL ( const double itol )

Set the fragment ion tolerance.

Also make sure to use setITOLU() to specify the correct fragment ion tolerance unit.

See also:: http://www.matrixscience.com/help/search_field_help.html#ITOL

Parameters:

[in] itol The fragment ion tolerance.

void mgf::MgfHeader::setITOLU ( const std::string & itolu )

Set the unit used to specify the fragmentation ion tolerance.

Valid values are mmu and Da. Currently, the responsibility for valid input lies with the user.

Parameters:

[in] itolu The fragmentation ion tolerance unit.

void mgf::MgfHeader::setMASS ( const std::string & mass )

Set the parent io mass type: monoisotopic or average.

Parameters:

[in] mass The

void mgf::MgfHeader::setMODS ( const std::string & mods )

Set the string representation of fixed modifications.

The modification string specifies which fixed post-translational modifications are searched in all Mascot queries in the MgfFile object. The setting may be overridden in individual MgfSpectrum instances. The modification string mus conform to UniMod standards.

Parameters:

[in] mods A string representation of fixed modifications used for all spectra in the cuffrrent MfgFile object (may be overridden in particular MgfSpectrum objects).

void mgf::MgfHeader::setPEP_ISOTOPE_ERROR ( const double pep_isotope_error )

Set/unset the peptide isotope error correction flag.

The flag controls whether Mascot also attempts to find peptide-spectral matches for a precursor mass -1m/z. This counters situations in which the instrument picks the second isotope as parent mass.

Parameters:

[in] pep_isotope_error The desired value of the peptide isotope error flag.

void mgf::MgfHeader::setPFA ( const int pfa )

Set the number of allowed missed cleavages.

The range allowd by Mascot is [0-9], defaults to 1.

See also:: http://www.matrixscience.com/help/search_field_help.html#PFA

Parameters:

[in] pfa The number of missed cleavages.

void mgf::MgfHeader::setPRECURSOR ( const double precursor )

Set the precursor mass (in m/z).

See also:: http://www.matrixscience.com/help/search_field_help.html#PRECURSOR

Parameters:

[in] precursor The mass value of the precursor (in m/z).

void mgf::MgfHeader::setQUANTITATION ( const std::string & quantitation )

Set the strign that identifies the quantitation method.

Method strings are defined in Mascot's quantitation.xml file. Defined for MIS only.

Parameters:

[in] quantitation The quantitation identification string.

void mgf::MgfHeader::setREPORT ( const std::string & report )

Set the maximum number of hits that are being reported in the results.

Vaild values are AUTO or an integer.

Parameters:

[in] report The maximum number of hits (as a std::string).

void mgf::MgfHeader::setREPTYPE ( const std::string & reptype )

Get the report type identifier.

Valid values are

protein
peptide (Default for MIS)
archive (MIS only)
concise (Default for PMF)
select (MIS only)
unassigned (MIS only)

It is the user's responsibility to supply valid identifiers.

See also:: http://www.matrixscience.com/help/results_help.html

Parameters:

[in] reptype The report type identifier.

void mgf::MgfHeader::setSEARCH ( const std::string & search )

Set the type of search specified for the underlying MgfFile object.

Valid values are PMF, SQ, MIS. It is the user's responsibility to supply a valid string.

Parameters:

[in] search The search type string.

void mgf::MgfHeader::setSEG ( const double seg )

Set the mass of the intact protein.

The intacat mass is in Da, applied as a sliding windows. Follow the link for more information and information on how to set the parameter correctly.

See also:: http://www.matrixscience.com/help/search_field_help.html#SEG; http://www.matrixscience.com/help/pmf_help.html#SEG

Parameters:

[in] seg The

void mgf::MgfHeader::setTAXONOMY ( const std::string & taxonomy )

Set the taxonomy (as specified in Mascot's taxonomy file).

See also:: http://www.matrixscience.com/help/search_field_help.html#TAXONOMY

Parameters:

[in] taxonomy The taxonomy.

void mgf::MgfHeader::setTOL ( const double tol )

Set the search tolerance.

The tolerance value depends on the tolerance unit which can be set using setTOLU().

See also:: http://www.matrixscience.com/help/search_field_help.html#TOL

Parameters:

[in] tol The

void mgf::MgfHeader::setTOLU ( const std::string & tolu )

Set the unit in which the tolerance is specified.

Valid values are %, ppm, mmu and Da).

Parameters:

[in] tolu The tolerance unit.

void mgf::MgfHeader::setUSEREMAIL ( const std::string & useremail )

Set the user email address.

Parameters:

[in] useremail The user email address as abc@example.org.

void mgf::MgfHeader::setUSERNAME ( const std::string & username )

Set the name of the user submitting the search.

Parameters:

[in] username The username.

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const MgfHeader &	mgf
	)			`[friend]`

Output operator.

Defining the stream operator as a friend keeps the header elements accessible. This allows us to iterate over the elemtents instead of calling the get function for each entry and checking the return value.

The documentation for this class was generated from the following files:

include/mgfp/MgfHeader.h
src/MgfHeader.cpp

mgf::MgfHeader Class Reference

Public Member Functions

Friends

Detailed Description

Member Function Documentation

Friends And Related Function Documentation