DiaPrescore Class Reference

Scoring of an spectrum given library intensities of a transition group. More...

#include <OpenMS/ANALYSIS/OPENSWATH/DIAPrescoring.h>

Inheritance diagram for DiaPrescore:

Collaboration diagram for DiaPrescore:

Classes
struct	TransitionGroupTheoreticalSpectrumCache
	Cached transition-group-specific theoretical spectrum used by the DIA prescore. More...

Public Member Functions
	DiaPrescore ()
	DiaPrescore (double dia_extract_window, int nr_isotopes=4, int nr_charges=4)
void	defineDefaults ()
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method.
void	score (const SpectrumSequence &spec, const std::vector< OpenSwath::LightTransition > &lt, const RangeMobility &im_range, double &dotprod, double &manhattan) const
	Score one or more observed spectra for a transition group.
void	buildTheoreticalSpectrum (const std::vector< OpenSwath::LightTransition > &lt, TransitionGroupTheoreticalSpectrumCache &theoretical_spectrum_cache) const
	Build the theoretical DIA isotope spectrum cache for repeated scoring.
void	operator() (const OpenSwath::SpectrumAccessPtr &swath_ptr, OpenSwath::LightTargetedExperiment &transition_exp_used, const RangeMobility &range_im, OpenSwath::IDataFrameWriter *ivw) const
	Compute Manhattan and dot-product scores for all spectra accessible through the SpectrumAccessPtr.
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.
virtual	~DefaultParamHandler ()
	Destructor.
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.
void	setParameters (const Param &param)
	Sets the parameters.
const Param &	getParameters () const
	Non-mutable access to the parameters.
const Param &	getDefaults () const
	Non-mutable access to the default parameters.
const std::string &	getName () const
	Non-mutable access to the name.
void	setName (const std::string &name)
	Mutable access to the name.
const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Static Public Member Functions
static void	scorePrepared (const SpectrumSequence &spec, const TransitionGroupTheoreticalSpectrumCache &theoretical_spectrum_cache, double dia_extract_window, const RangeMobility &im_range, double &dotprod, double &manhattan)
	Score an observed spectrum sequence against a precomputed theoretical DIA spectrum.
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.

Private Attributes
double	dia_extract_window_
int	nr_isotopes_
int	nr_charges_

Additional Inherited Members
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!
std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
std::string	error_name_
	Name that is displayed in error messages during the parameter checking.
bool	check_defaults_
	If this member is set to false no checking if parameters in done;.
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Detailed Description

Scoring of an spectrum given library intensities of a transition group.

In DIA (data independent acquisition) / SWATH analysis, at each chromatographic point a full MS2 spectrum is recorded. This class allows to compute a number of scores based on the full MS2 spectrum available. The scores are the following:

See also class DIAScoring.

Simulate theoretical spectrum from library intensities of transition group and compute manhattan distance and dotprod score between spectrum intensities and simulated spectrum.

Constructor & Destructor Documentation

DiaPrescore() [1/2]

DiaPrescore

(

)

DiaPrescore() [2/2]

DiaPrescore	(	double	dia_extract_window,
		int	nr_isotopes = 4,
		int	nr_charges = 4
	)

Member Function Documentation

buildTheoreticalSpectrum()

void buildTheoreticalSpectrum	(	const std::vector< OpenSwath::LightTransition > &	lt,
		TransitionGroupTheoreticalSpectrumCache &	theoretical_spectrum_cache
	)		const

Build the theoretical DIA isotope spectrum cache for repeated scoring.

The transition-group-specific theoretical spectrum cache depends only on the transition group and DiaPrescore parameters, not on the observed spectrum.

Parameters

[in]	lt	Library transitions for the transition group
[out]	theoretical_spectrum_cache	Precomputed theoretical spectrum cache

defineDefaults()

void defineDefaults

(

)

operator()()

void operator()	(	const OpenSwath::SpectrumAccessPtr &	swath_ptr,
		OpenSwath::LightTargetedExperiment &	transition_exp_used,
		const RangeMobility &	range_im,
		OpenSwath::IDataFrameWriter *	ivw
	)		const

Compute Manhattan and dot-product scores for all spectra accessible through the SpectrumAccessPtr.

Scores all transition groups in the LightTargetedExperiment against the spectra provided by swath_ptr and writes the per-spectrum score vectors to ivw.

score()

void score	(	const SpectrumSequence &	spec,
		const std::vector< OpenSwath::LightTransition > &	lt,
		const RangeMobility &	im_range,
		double &	dotprod,
		double &	manhattan
	)		const

Score one or more observed spectra for a transition group.

Builds the transition-group-specific theoretical spectrum cache from the library intensities and compares it against the observed spectrum sequence. The input may contain multiple adjacent MS2 spectra / frames around the apex or a single pre-merged spectrum, depending on the upstream merge mode.

scorePrepared()

static void scorePrepared ( const SpectrumSequence &  spec, const TransitionGroupTheoreticalSpectrumCache &  theoretical_spectrum_cache, double  dia_extract_window, const RangeMobility &  im_range, double &  dotprod, double &  manhattan  )

static

Score an observed spectrum sequence against a precomputed theoretical DIA spectrum.

The observed input may be a single merged spectrum or multiple spectra / frames around the feature apex, depending on the configured spectrum addition mode.

Parameters

[in]	spec	Observed spectrum sequence around the feature apex
[in]	theoretical_spectrum_cache	Precomputed theoretical spectrum cache
[in]	dia_extract_window	DIA extraction window in Th
[in]	im_range	Ion mobility extraction range
[out]	dotprod	Dot product score
[out]	manhattan	Manhattan distance score

updateMembers_()

void updateMembers_ ( )

overridevirtual

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

dia_extract_window_

double dia_extract_window_

private

nr_charges_

int nr_charges_

private

nr_isotopes_

int nr_isotopes_

private