FragmentMassError Class Reference

#include <OpenMS/QC/FragmentMassError.h>

Inheritance diagram for FragmentMassError:

Collaboration diagram for FragmentMassError:

Classes
struct	FMEStatistics
	Structure for storing results: average and variance of all FragmentMassErrors in ppm. More...

Public Types
enum	ToleranceUnit { AUTO, PPM, DA, SIZE_OF_TOLERANCEUNIT }
Public Types inherited from QCBase
enum	Requires : UInt64 {   NOTHING, RAWMZML, POSTFDRFEAT, PREFDRFEAT,   CONTAMINANTS, TRAFOALIGN, SIZE_OF_REQUIRES }
	Enum to encode a file type as a bit. More...

Public Member Functions
	FragmentMassError ()=default
	Default constructor. More...
virtual	~FragmentMassError ()=default
	Destructor. More...
void	compute (FeatureMap &fmap, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum, ToleranceUnit tolerance_unit=ToleranceUnit::AUTO, double tolerance=20)
	computes FragmentMassError in ppm and Dalton (only of the first PeptideHit of each PepID) More...
const String &	getName () const override
	returns the name of the metric More...
const std::vector< FMEStatistics > &	getResults () const
	returns results More...
QCBase::Status	requires () const override
	Returns the input data requirements of the compute(...) function. More...
Public Member Functions inherited from QCBase
bool	isRunnable (const Status &s) const

Static Public Attributes
static const std::string	names_of_toleranceUnit []
	strings corresponding to enum ToleranceUnit More...
Static Public Attributes inherited from QCBase
static const std::string	names_of_requires []
	strings corresponding to enum Requires More...

Private Attributes
std::vector< FMEStatistics >	results_ {}
	container that stores results More...

Additional Inherited Members
Static Public Member Functions inherited from QCBase
static bool	isLabeledExperiment (const ConsensusMap &cm)
	check if the IsobaricAnalyzer TOPP tool was used to create this ConsensusMap More...
template<typename MAP >
static bool	hasPepID (const MAP &fmap)
	does the container have a PeptideIdentification in its members or as unassignedPepID ? More...

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Class Documentation

OpenMS::FragmentMassError::FMEStatistics

struct OpenMS::FragmentMassError::FMEStatistics

Structure for storing results: average and variance of all FragmentMassErrors in ppm.

Collaboration diagram for FragmentMassError::FMEStatistics:

Class Members
double	average_ppm
double	variance_ppm

Member Enumeration Documentation

ToleranceUnit

enum ToleranceUnit

strong

Enumerator
AUTO
PPM
DA
SIZE_OF_TOLERANCEUNIT

Constructor & Destructor Documentation

FragmentMassError()

FragmentMassError ( )

default

Default constructor.

~FragmentMassError()

virtual ~FragmentMassError ( )

virtualdefault

Destructor.

Member Function Documentation

compute()

void compute	(	FeatureMap &	fmap,
		const MSExperiment &	exp,
		const QCBase::SpectraMap &	map_to_spectrum,
		ToleranceUnit	tolerance_unit = ToleranceUnit::AUTO,
		double	tolerance = 20
	)

computes FragmentMassError in ppm and Dalton (only of the first PeptideHit of each PepID)

Stores average and variance of FragmentMassErrors in ppm as a struct in a vector. Each FragmentMassError (in ppm) is stored in the first PeptideHit of the corresponding PeptideIdentification as metavalue "fragment_mass_error_ppm". Each FragmentMassError (in Da) is stored in the first PeptideHit of the corresponding PeptideIdentification as metavalue "fragment_mass_error_da".

Parameters

fmap	Input FeatureMap for annotation and data for theoretical spectra
exp	Input MSExperiment for MS2 spectra; spectra should be sorted (ascending RT)
map_to_spectrum	Map to find index of spectrum given by meta value at PepID
tolerance	Search window for matching peaks; distance has to be lower than tolerance value
tolerance_unit	Tolerance in ppm or Dalton (if auto was chosen, the unit and value will taken from FeatureMap metadata)

Exceptions

Exceptions::MissingInformation	If fragment mass tolerance is missing in metadata of FeatureMap
Exception::InvalidParameter	PeptideID is missing meta value 'spectrum_reference'
Exception::IllegalArgument	Spectrum for a PepID has ms-level of 1
Exception::MissingInformation	If no fragmentation method given in a MS2 precursor
Exception::InvalidParameter	If the fragmentation method is not ECD, ETD, CID or HCD

getName()

const String& getName ( ) const

overridevirtual

returns the name of the metric

Implements QCBase.

getResults()

const std::vector<FMEStatistics>& getResults

(

)

const

returns results

requires()

QCBase::Status requires ( ) const

overridevirtual

Returns the input data requirements of the compute(...) function.

Returns

Status for RAWMZML and POSTFDRFEAT

Implements QCBase.

Member Data Documentation

names_of_toleranceUnit

const std::string names_of_toleranceUnit[]

static

strings corresponding to enum ToleranceUnit

results_

std::vector<FMEStatistics> results_ {}

private

container that stores results