XTandemInfile Class Reference

XTandem input file. More...

#include <OpenMS/FORMAT/XTandemInfile.h>

Inheritance diagram for XTandemInfile:

Collaboration diagram for XTandemInfile:

Public Types
enum	ErrorUnit { DALTONS = 0 , PPM }
	error unit, either Da or ppm More...
enum	MassType { MONOISOTOPIC = 0 , AVERAGE }
	Mass type of the precursor, either monoisotopic or average. More...

Public Member Functions
	XTandemInfile ()
	constructor
	~XTandemInfile () override
	constructor
void	setFragmentMassTolerance (double tolerance)
	setter for the fragment mass tolerance
double	getFragmentMassTolerance () const
	returns the fragment mass tolerance
void	setPrecursorMassTolerancePlus (double tol)
	sets the precursor mass tolerance (plus only)
double	getPrecursorMassTolerancePlus () const
	returns the precursor mass tolerance (plus only)
void	setPrecursorMassToleranceMinus (double tol)
	set the precursor mass tolerance (minus only)
double	getPrecursorMassToleranceMinus () const
	returns the precursor mass tolerance (minus only)
void	setPrecursorErrorType (MassType mono_isotopic)
	sets the precursor mass type
MassType	getPrecursorErrorType () const
	returns the precursor mass type
void	setFragmentMassErrorUnit (ErrorUnit unit)
	sets the fragment mass error unit (Da, ppm)
ErrorUnit	getFragmentMassErrorUnit () const
	returns the fragment mass error unit (Da, ppm)
void	setPrecursorMassErrorUnit (ErrorUnit unit)
	sets the precursor mass error unit (Da, ppm)
ErrorUnit	getPrecursorMassErrorUnit () const
	returns the precursor mass error unit (Da, ppm)
void	setNumberOfThreads (UInt threads)
	sets the number of threads used during the identifications
UInt	getNumberOfThreads () const
	returns the number of threads
void	setModifications (const ModificationDefinitionsSet &mods)
	sets the modifications using a modification definitions set
const ModificationDefinitionsSet &	getModifications () const
	returns the modifications set, using a modification definitions set
void	setOutputFilename (const std::string &output)
	sets the output filename
const std::string &	getOutputFilename () const
	returns the output filename
void	setInputFilename (const std::string &input_file)
	sets the input filename
const std::string &	getInputFilename () const
	returns the input filename
void	setTaxonomyFilename (const std::string &filename)
	set the filename of the taxonomy file
const std::string &	getTaxonomyFilename () const
	returns the filename of the taxonomy file
void	setDefaultParametersFilename (const std::string &filename)
	sets the default parameters file
const std::string &	getDefaultParametersFilename () const
	returns the default parameters file
void	setTaxon (const std::string &taxon)
	sets the taxon used in the taxonomy file
const std::string &	getTaxon () const
	returns the taxon used in the taxonomy file
void	setMaxPrecursorCharge (Int max_charge)
	sets the max precursor charge
Int	getMaxPrecursorCharge () const
	returns the max precursor charge
void	setNumberOfMissedCleavages (UInt missed_cleavages)
	sets the number of missed cleavages allowed
UInt	getNumberOfMissedCleavages () const
	returns the number of missed cleavages allowed
void	setOutputResults (const std::string &result)
	sets the output result type ("all", "valid" or "stochastic")
std::string	getOutputResults () const
	returns the output result type ("all", "valid" or "stochastic")
void	setMaxValidEValue (double value)
	sets the max valid E-value allowed in the list
double	getMaxValidEValue () const
	returns the max valid E-value allowed in the list
void	setSemiCleavage (const bool semi_cleavage)
	set state of semi cleavage
void	setAllowIsotopeError (const bool allow_isotope_error)
	set if misassignment of precursor to first and second 13C isotopic peak should also be considered
bool	getNoiseSuppression () const
	get state of noise suppression
void	setNoiseSuppression (const bool noise_suppression)
	set state of noise suppression
void	setCleavageSite (const std::string &cleavage_site)
	set the cleavage site with a X! Tandem conform regex
const std::string &	getCleavageSite () const
	returns the cleavage site regex
void	write (const std::string &filename, bool ignore_member_parameters=false, bool force_default_mods=false)
	Writes the X! Tandem input file to the given filename.
Public Member Functions inherited from XMLFile
	XMLFile ()
	Construct an XMLFile without schema info; schema_location_ remains unset, so isValid cannot be used until derived-class logic initializes schema_location_ before calling isValid.
	XMLFile (const std::string &schema_location, const std::string &version)
	Construct with a schema location for later isValid calls.
virtual	~XMLFile ()
	Virtual destructor — defaulted; allows safe deletion through a base-class pointer.
bool	isValid (const std::string &filename, std::ostream &os)
	Check if filename validates against the bound XML schema.
const std::string &	getVersion () const
	Return the schema version string passed to the parameterised constructor; empty for default-constructed instances.

Protected Member Functions
	XTandemInfile (const XTandemInfile &rhs)
XTandemInfile &	operator= (const XTandemInfile &rhs)
void	writeTo_ (std::ostream &os, bool ignore_member_parameters)
void	writeNote_ (std::ostream &os, const std::string &label, const std::string &value)
void	writeNote_ (std::ostream &os, const std::string &label, const char *value)
void	writeNote_ (std::ostream &os, const std::string &label, bool value)
std::string	convertModificationSet_ (const std::set< ModificationDefinition > &mods, std::map< std::string, double > &affected_origins) const
	Converts the given set of Modifications into a format compatible to X!Tandem.
Protected Member Functions inherited from XMLFile
void	parse_ (const std::string &filename, XMLHandler *handler)
	Parse the XML file at filename through handler.
void	parseBuffer_ (const std::string &buffer, XMLHandler *handler)
	Parse an in-memory XML buffer through handler.
void	save_ (const std::string &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by handler in the file given by filename.
void	enforceEncoding_ (const std::string &encoding)
	Set or clear the XML-encoding override applied to subsequent parse_ / parseBuffer_ calls.

Protected Attributes
double	fragment_mass_tolerance_
double	precursor_mass_tolerance_plus_
double	precursor_mass_tolerance_minus_
ErrorUnit	fragment_mass_error_unit_
ErrorUnit	precursor_mass_error_unit_
MassType	fragment_mass_type_
MassType	precursor_mass_type_
UInt	max_precursor_charge_
double	precursor_lower_mz_
double	fragment_lower_mz_
UInt	number_of_threads_
UInt	batch_size_
ModificationDefinitionsSet	modifications_
std::string	input_filename_
std::string	output_filename_
std::string	taxonomy_file_
std::string	taxon_
std::string	cleavage_site_
bool	semi_cleavage_
	semi cleavage
bool	allow_isotope_error_
UInt	number_of_missed_cleavages_
std::string	default_parameters_file_
std::string	output_results_
double	max_valid_evalue_
bool	force_default_mods_
Protected Attributes inherited from XMLFile
std::string	schema_location_
	Path of the XML schema for validation; empty when the default constructor was used (isValid then throws NotImplemented).
std::string	schema_version_
	Schema version string returned by getVersion.
std::string	enforced_encoding_
	Optional XML encoding override applied to the InputSource in parse_ and parseBuffer_; empty disables the override. Used as a workaround for XTandem output XML which carries an encoding the parser otherwise stumbles on.

Detailed Description

XTandem input file.

This class is able to load/write a X!Tandem configuration file.

These files store parameters within 'note' tags, e.g.,

  <note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
  <note type="input" label="output, proteins">yes</note>

Member Enumeration Documentation

ErrorUnit

enum ErrorUnit

error unit, either Da or ppm

Enumerator
DALTONS
PPM

MassType

enum MassType

Mass type of the precursor, either monoisotopic or average.

Enumerator
MONOISOTOPIC
AVERAGE

Constructor & Destructor Documentation

XTandemInfile() [1/2]

XTandemInfile

(

)

constructor

~XTandemInfile()

~XTandemInfile ( )

override

constructor

XTandemInfile() [2/2]

XTandemInfile ( const XTandemInfile &  rhs )

protected

Member Function Documentation

convertModificationSet_()

std::string convertModificationSet_ ( const std::set< ModificationDefinition > &  mods, std::map< std::string, double > &  affected_origins  ) const

protected

Converts the given set of Modifications into a format compatible to X!Tandem.

The set affected_origins can be used to avoid duplicate modifications, which are not supported in X! Tandem. Currently, a warning message is printed. Also, if a fixed mod is already given, a corresponding variable mods needs to have its delta mass reduced by the fixed modifications mass. This is also done automatically here.

Parameters

[in]	mods	The modifications to convert
[in]	affected_origins	Set of origins, which were used previously. Will be augmented with the current mods.

Returns

An X! Tandem compatible string representation.

getCleavageSite()

const std::string & getCleavageSite

(

)

const

returns the cleavage site regex

getDefaultParametersFilename()

const std::string & getDefaultParametersFilename

(

)

const

returns the default parameters file

getFragmentMassErrorUnit()

ErrorUnit getFragmentMassErrorUnit

(

)

const

returns the fragment mass error unit (Da, ppm)

getFragmentMassTolerance()

double getFragmentMassTolerance

(

)

const

returns the fragment mass tolerance

getInputFilename()

const std::string & getInputFilename

(

)

const

returns the input filename

getMaxPrecursorCharge()

Int getMaxPrecursorCharge

(

)

const

returns the max precursor charge

getMaxValidEValue()

double getMaxValidEValue

(

)

const

returns the max valid E-value allowed in the list

getModifications()

const ModificationDefinitionsSet & getModifications

(

)

const

returns the modifications set, using a modification definitions set

getNoiseSuppression()

bool getNoiseSuppression

(

)

const

get state of noise suppression

getNumberOfMissedCleavages()

UInt getNumberOfMissedCleavages

(

)

const

returns the number of missed cleavages allowed

getNumberOfThreads()

UInt getNumberOfThreads

(

)

const

returns the number of threads

getOutputFilename()

const std::string & getOutputFilename

(

)

const

returns the output filename

getOutputResults()

std::string getOutputResults

(

)

const

returns the output result type ("all", "valid" or "stochastic")

getPrecursorErrorType()

MassType getPrecursorErrorType

(

)

const

returns the precursor mass type

getPrecursorMassErrorUnit()

ErrorUnit getPrecursorMassErrorUnit

(

)

const

returns the precursor mass error unit (Da, ppm)

getPrecursorMassToleranceMinus()

double getPrecursorMassToleranceMinus

(

)

const

returns the precursor mass tolerance (minus only)

getPrecursorMassTolerancePlus()

double getPrecursorMassTolerancePlus

(

)

const

returns the precursor mass tolerance (plus only)

getTaxon()

const std::string & getTaxon

(

)

const

returns the taxon used in the taxonomy file

getTaxonomyFilename()

const std::string & getTaxonomyFilename

(

)

const

returns the filename of the taxonomy file

operator=()

XTandemInfile & operator= ( const XTandemInfile &  rhs )

protected

setAllowIsotopeError()

void setAllowIsotopeError

(

const bool

allow_isotope_error

)

set if misassignment of precursor to first and second 13C isotopic peak should also be considered

setCleavageSite()

void setCleavageSite

(

const std::string &

cleavage_site

)

set the cleavage site with a X! Tandem conform regex

setDefaultParametersFilename()

void setDefaultParametersFilename

(

const std::string &

filename

)

sets the default parameters file

setFragmentMassErrorUnit()

void setFragmentMassErrorUnit

(

ErrorUnit

unit

)

sets the fragment mass error unit (Da, ppm)

setFragmentMassTolerance()

void setFragmentMassTolerance

(

double

tolerance

)

setter for the fragment mass tolerance

setInputFilename()

void setInputFilename

(

const std::string &

input_file

)

sets the input filename

setMaxPrecursorCharge()

void setMaxPrecursorCharge

(

Int

max_charge

)

sets the max precursor charge

setMaxValidEValue()

void setMaxValidEValue

(

double

value

)

sets the max valid E-value allowed in the list

setModifications()

void setModifications

(

const ModificationDefinitionsSet &

mods

)

sets the modifications using a modification definitions set

setNoiseSuppression()

void setNoiseSuppression

(

const bool

noise_suppression

)

set state of noise suppression

setNumberOfMissedCleavages()

void setNumberOfMissedCleavages

(

UInt

missed_cleavages

)

sets the number of missed cleavages allowed

setNumberOfThreads()

void setNumberOfThreads

(

UInt

threads

)

sets the number of threads used during the identifications

setOutputFilename()

void setOutputFilename

(

const std::string &

output

)

sets the output filename

setOutputResults()

void setOutputResults

(

const std::string &

result

)

sets the output result type ("all", "valid" or "stochastic")

setPrecursorErrorType()

void setPrecursorErrorType

(

MassType

mono_isotopic

)

sets the precursor mass type

setPrecursorMassErrorUnit()

void setPrecursorMassErrorUnit

(

ErrorUnit

unit

)

sets the precursor mass error unit (Da, ppm)

setPrecursorMassToleranceMinus()

void setPrecursorMassToleranceMinus

(

double

tol

)

set the precursor mass tolerance (minus only)

setPrecursorMassTolerancePlus()

void setPrecursorMassTolerancePlus

(

double

tol

)

sets the precursor mass tolerance (plus only)

setSemiCleavage()

void setSemiCleavage

(

const bool

semi_cleavage

)

set state of semi cleavage

setTaxon()

void setTaxon

(

const std::string &

taxon

)

sets the taxon used in the taxonomy file

setTaxonomyFilename()

void setTaxonomyFilename

(

const std::string &

filename

)

set the filename of the taxonomy file

write()

void write	(	const std::string &	filename,
		bool	ignore_member_parameters = false,
		bool	force_default_mods = false
	)

Writes the X! Tandem input file to the given filename.

If ignore_member_parameters is true, only a very limited number of tags fed by member variables (i.e. in, out, database/taxonomy) is written.

Parameters

[out]	filename	the name of the file which is written
[in]	ignore_member_parameters	Do not write tags for class members
[in]	force_default_mods	Force writing of mods covered by special parameters

Exceptions

UnableToCreateFile

is thrown if the given file could not be created

writeNote_() [1/3]

void writeNote_ ( std::ostream &  os, const std::string &  label, bool  value  )

protected

writeNote_() [2/3]

void writeNote_ ( std::ostream &  os, const std::string &  label, const char *  value  )

protected

writeNote_() [3/3]

void writeNote_ ( std::ostream &  os, const std::string &  label, const std::string &  value  )

protected

writeTo_()

void writeTo_ ( std::ostream &  os, bool  ignore_member_parameters  )

protected

Member Data Documentation

allow_isotope_error_

bool allow_isotope_error_

protected

batch_size_

UInt batch_size_

protected

cleavage_site_

std::string cleavage_site_

protected

default_parameters_file_

std::string default_parameters_file_

protected

force_default_mods_

bool force_default_mods_

protected

fragment_lower_mz_

double fragment_lower_mz_

protected

fragment_mass_error_unit_

ErrorUnit fragment_mass_error_unit_

protected

fragment_mass_tolerance_

double fragment_mass_tolerance_

protected

fragment_mass_type_

MassType fragment_mass_type_

protected

input_filename_

std::string input_filename_

protected

max_precursor_charge_

UInt max_precursor_charge_

protected

max_valid_evalue_

double max_valid_evalue_

protected

modifications_

ModificationDefinitionsSet modifications_

protected

number_of_missed_cleavages_

UInt number_of_missed_cleavages_

protected

number_of_threads_

UInt number_of_threads_

protected

output_filename_

std::string output_filename_

protected

output_results_

std::string output_results_

protected

precursor_lower_mz_

double precursor_lower_mz_

protected

precursor_mass_error_unit_

ErrorUnit precursor_mass_error_unit_

protected

precursor_mass_tolerance_minus_

double precursor_mass_tolerance_minus_

protected

precursor_mass_tolerance_plus_

double precursor_mass_tolerance_plus_

protected

precursor_mass_type_

MassType precursor_mass_type_

protected

semi_cleavage_

bool semi_cleavage_

protected

semi cleavage

taxon_

std::string taxon_

protected

taxonomy_file_

std::string taxonomy_file_

protected