Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options. More...

#include <OpenMS/CHEMISTRY/SpectrumAnnotator.h>

Inheritance diagram for SpectrumAnnotator:

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Collaboration diagram for SpectrumAnnotator:

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Public Member Functions
Constructors and Destructors
	SpectrumAnnotator ()
	default constructor More...

	SpectrumAnnotator (const SpectrumAnnotator &source)
	copy constructor More...

	~SpectrumAnnotator () override
	destructor More...

SpectrumAnnotator &	operator= (const SpectrumAnnotator &tsg)
	assignment operator 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...

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...

Available annotators
bool	basic_statistics_

bool	list_of_ions_matched_

bool	max_series_

bool	SN_statistics_

bool	precursor_statistics_

unsigned	topNmatch_fragmenterrors_

bool	fragmenterror_statistics_

bool	terminal_series_match_ratio_

static const boost::regex	nt_regex_

static const boost::regex	ct_regex_

static const boost::regex	noloss_regex_

static const boost::regex	seriesposition_regex_

void	annotateMatches (PeakSpectrum &spec, const PeptideHit &ph, const TheoreticalSpectrumGenerator &tg, const SpectrumAlignment &sa) const
	Adds ion match annotation to the `spec` input spectrum. More...

void	addIonMatchStatistics (PeptideIdentification &pi, MSSpectrum &spec, const TheoreticalSpectrumGenerator &tg, const SpectrumAlignment &sa) const
	Adds ion match statistics to `pi` PeptideIdentifcation. More...

void	updateMembers_ () override
	overwrite More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

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

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...

Detailed Description

Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
basic_statistics	string	true	true, false	If set, meta values for peak_number, sum_intensity, matched_ion_number, matched_intensity are added
list_of_ions_matched	string	true	true, false	If set, meta values for matched_ions are added
max_series	string	true	true, false	If set, meta values for max_series_type, max_series_size are added
S/N_statistics	string	true	true, false	If set to 1 isotope peaks of the product ion peaks are added
precursor_statistics	string	true	true, false	If set, meta values for precursor_in_ms2 are added
topNmatch_fragmenterrors	int	7		If set n > 0, meta values for topN_meanfragmenterror, topN_MSEfragmenterror, topN_stddevfragmenterror are added
fragmenterror_statistics	string	true	true, false	If set, meta values for median_fragment_error, IQR_fragment_error are added
terminal_series_match_ratio	string	true	true, false	If set, meta values for NTermIonCurrentRatio, CTermIonCurrentRatio are added

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ SpectrumAnnotator() [1/2]

SpectrumAnnotator ( )

default constructor

◆ SpectrumAnnotator() [2/2]

SpectrumAnnotator ( const SpectrumAnnotator & source )

copy constructor

◆ ~SpectrumAnnotator()

~SpectrumAnnotator ( )

override

destructor

Member Function Documentation

◆ addIonMatchStatistics()

void addIonMatchStatistics	(	PeptideIdentification &	pi,
		MSSpectrum &	spec,
		const TheoreticalSpectrumGenerator &	tg,
		const SpectrumAlignment &	sa
	)		const

Adds ion match statistics to pi PeptideIdentifcation.

Parameters

pi	A spectrum identifications to be annotated, looking up matches from a spectrum and the theoretical spectrum inferred from the identifications sequence
spec	A PeakSpectrum containing the peaks from which the `pi` identifications are made
tg	A TheoreticalSpectrumGenerator to infer the theoretical spectrum. Its own parameters define which ion types are referred
sa	A SpectrumAlignment to match the theoretical spectrum with the measured. Its own parameters define the match tolerance

The ion match statistics are added as UserParams to either the PeptideIdentification (parameters of the matching) and PeptideHit. The parameters of the TheoreticalSpectrumGenerator define the comprehensiveness of the available matching. The parameters of SpectrumAlignment define the matching tolerance. See the parameter section of this class for the available statistics.

◆ annotateMatches()

void annotateMatches	(	PeakSpectrum &	spec,
		const PeptideHit &	ph,
		const TheoreticalSpectrumGenerator &	tg,
		const SpectrumAlignment &	sa
	)		const

Adds ion match annotation to the spec input spectrum.

Parameters

spec	A PeakSpectrum containing the peaks from which the `pi` identifications are made
ph	A spectrum identifications to be used for the annotation, looking up matches from a spectrum and the theoretical spectrum inferred from the identifications sequence
tg	A TheoreticalSpectrumGenerator to infer the theoretical spectrum. Its own parameters define which ion types are referred
sa	A SpectrumAlignment to match the theoretical spectrum with the measured. Its own parameters define the match tolerance

The matches are added as DataArrays to the spectrum (Names: IonName and IonMatchError). The parameters of the TheoreticalSpectrumGenerator define the comprehensiveness of the available matching. The parameters of SpectrumAlignment define the matching tolerance. See the parameter section of this class for the available options.

◆ operator=()

SpectrumAnnotator& operator= ( const SpectrumAnnotator & tsg )

assignment operator

◆ updateMembers_()

void updateMembers_ ( )

overridevirtual

overwrite

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ basic_statistics_

bool basic_statistics_

protected

◆ ct_regex_

const boost::regex ct_regex_

staticprotected

◆ fragmenterror_statistics_

bool fragmenterror_statistics_

protected

◆ list_of_ions_matched_

bool list_of_ions_matched_

protected

◆ max_series_

bool max_series_

protected

◆ noloss_regex_

const boost::regex noloss_regex_

staticprotected

◆ nt_regex_

const boost::regex nt_regex_

staticprotected

◆ precursor_statistics_

bool precursor_statistics_

protected

◆ seriesposition_regex_

const boost::regex seriesposition_regex_

staticprotected

◆ SN_statistics_

bool SN_statistics_

protected

◆ terminal_series_match_ratio_

bool terminal_series_match_ratio_

protected

◆ topNmatch_fragmenterrors_

unsigned topNmatch_fragmenterrors_

protected

Public Member Functions

Available annotators

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SpectrumAnnotator() [1/2]

◆ SpectrumAnnotator() [2/2]

◆ ~SpectrumAnnotator()

Member Function Documentation

◆ addIonMatchStatistics()

◆ annotateMatches()

◆ operator=()

◆ updateMembers_()

Member Data Documentation

◆ basic_statistics_

◆ ct_regex_

◆ fragmenterror_statistics_

◆ list_of_ions_matched_

◆ max_series_

◆ noloss_regex_

◆ nt_regex_

◆ precursor_statistics_

◆ seriesposition_regex_

◆ SN_statistics_

◆ terminal_series_match_ratio_

◆ topNmatch_fragmenterrors_