MassFeatureTrace Class Reference

Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by SpectralDeconvolution In other words, per spectrum deconvolved masses are converted into deconvolved features Currently only works for MS1 spectra. (Top-down DIA is not yet used much). Every time an MS1 spectrum is deconvolved, the relevant information is stored in this class. This class also comes with tsv, TopFD feature file formats. More...

#include <OpenMS/ANALYSIS/TOPDOWN/MassFeatureTrace.h>

Inheritance diagram for MassFeatureTrace:

Collaboration diagram for MassFeatureTrace:

Public Types
typedef FLASHHelperClasses::PrecalculatedAveragine	PrecalculatedAveragine
typedef FLASHHelperClasses::LogMzPeak	LogMzPeak

Public Member Functions
	MassFeatureTrace ()
	constructor More...
	~MassFeatureTrace () override=default
	destructor More...
	MassFeatureTrace (const MassFeatureTrace &)=default
	copy constructor More...
	MassFeatureTrace (MassFeatureTrace &&other)=default
	move constructor More...
MassFeatureTrace &	operator= (const MassFeatureTrace &fd)=default
	assignment operator More...
MassFeatureTrace &	operator= (MassFeatureTrace &&fd)=default
std::vector< FLASHHelperClasses::MassFeature >	findFeaturesAndUpdateQscore2D (const PrecalculatedAveragine &averagine, std::vector< DeconvolvedSpectrum > &deconvolved_spectra, int ms_level=1, bool is_decoy=false)
	Find mass features. 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...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Attributes
std::map< double, std::map< double, PeakGroup > >	peak_group_map_
	peak group information is stored in here for tracing 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 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

Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by SpectralDeconvolution In other words, per spectrum deconvolved masses are converted into deconvolved features Currently only works for MS1 spectra. (Top-down DIA is not yet used much). Every time an MS1 spectrum is deconvolved, the relevant information is stored in this class. This class also comes with tsv, TopFD feature file formats.

Member Typedef Documentation

LogMzPeak

typedef FLASHHelperClasses::LogMzPeak LogMzPeak

PrecalculatedAveragine

typedef FLASHHelperClasses::PrecalculatedAveragine PrecalculatedAveragine

Constructor & Destructor Documentation

MassFeatureTrace() [1/3]

MassFeatureTrace

(

)

constructor

~MassFeatureTrace()

~MassFeatureTrace ( )

overridedefault

destructor

MassFeatureTrace() [2/3]

MassFeatureTrace ( const MassFeatureTrace &  )

default

copy constructor

MassFeatureTrace() [3/3]

MassFeatureTrace ( MassFeatureTrace &&  other )

default

move constructor

Member Function Documentation

findFeaturesAndUpdateQscore2D()

std::vector<FLASHHelperClasses::MassFeature> findFeaturesAndUpdateQscore2D	(	const PrecalculatedAveragine &	averagine,
		std::vector< DeconvolvedSpectrum > &	deconvolved_spectra,
		int	ms_level = 1,
		bool	is_decoy = false
	)

Find mass features.

Parameters

averagine	precalculated averagine for cosine calculation
deconvolved_spectra	the spectra on which features are found
ms_level	ms level to process
is_decoy	if set, only process decoy spectra. otherwise only target spectra

operator=() [1/2]

MassFeatureTrace& operator= ( const MassFeatureTrace &  fd )

default

assignment operator

operator=() [2/2]

MassFeatureTrace& operator= ( MassFeatureTrace &&  fd )

default

updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

peak_group_map_

std::map<double, std::map<double, PeakGroup> > peak_group_map_

private

peak group information is stored in here for tracing