NASE-specific selection of precursor hypotheses and competing envelope evidence. More...

#include <NucleicAcidSearchEngine/include/RNADirectedDeconvolution.h>

Inheritance diagram for RNADirectedDeconvolution:

Public Member Functions
void	deconvolve (const MSSpectrum &spectrum, int scan_number, const std::vector< std::pair< double, int > > &queries)
	Deconvolve queries against complete parent MS1 evidence. Queries do not protect candidates from ordinary FLASH filtering. Empty queries run ordinary FLASH. Query state is cleared after every call. Competition uses the union of query/evidence intervals within the batch; subset-invariant callers must retain the same batch or use ordinary FLASH.

Public Member Functions inherited from SpectralDeconvolution
	SpectralDeconvolution ()
	default constructor

	SpectralDeconvolution (const SpectralDeconvolution &)=default
	copy constructor

	SpectralDeconvolution (SpectralDeconvolution &&other)=default
	move constructor

SpectralDeconvolution &	operator= (const SpectralDeconvolution &fd)=default
	assignment operator

SpectralDeconvolution &	operator= (SpectralDeconvolution &&fd)=default
	move assignment operator

	~SpectralDeconvolution ()=default
	destructor

void	performSpectrumDeconvolution (const MSSpectrum &spec, int scan_number, const PeakGroup &precursor_peak_group)
	main deconvolution function that generates the deconvolved target and dummy spectrum based on the original spectrum.

DeconvolvedSpectrum &	getDeconvolvedSpectrum ()
	return deconvolved spectrum

const PrecalculatedAveragine &	getAveragine ()
	get calculated averagine. Call after calculateAveragine is called.

void	setAveragine (const PrecalculatedAveragine &avg)
	set calculated averagine

void	setTargetMasses (const std::vector< double > &masses, bool exclude=false)
	set targeted or excluded masses for targeted deconvolution. Masses are targeted or excluded in all ms levels.

void	calculateAveragine (bool use_RNA_averagine)
	precalculate averagine (for predefined mass bins) to speed up averagine generation

void	setToleranceEstimation ()
	when estimating tolerance, max_mass_dalton_tolerance_ should be large

void	setTargetDecoyType (PeakGroup::TargetDecoyType target_decoy_type, const DeconvolvedSpectrum &target_dspec_for_decoy_calcualtion)

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.

Private Member Functions
std::optional< MassRanges >	selectCandidateMassRanges_ (const CandidateSelectionContext &context, const DeconvolvedSpectrum *evidence_groups, const std::vector< Size > &valid) const override
	Optionally restrict construction, without protecting candidates from filtering. The default returns nullopt for ordinary full-spectrum deconvolution. An override returning initial intervals is called again with scored seed groups to refine those intervals. Seed bins remain included. All passes use the complete spectrum and the ordinary shared construction/scoring.

Private Attributes
std::vector< Precursor >	queries_

Additional Inherited Members
Public Types inherited from SpectralDeconvolution
typedef FLASHHelperClasses::PrecalculatedAveragine	PrecalculatedAveragine

typedef FLASHHelperClasses::LogMzPeak	LogMzPeak

Static Public Member Functions inherited from SpectralDeconvolution
static int	getNominalMass (double mass)
	convert double to nominal mass

static float	getCosine (const std::vector< float > &a, int a_start, int a_end, const IsotopeDistribution &b, int offset, int min_iso_len)

static float	getIsotopeCosineAndIsoOffset (double mono_mass, const std::vector< float > &per_isotope_intensities, int &offset, const PrecalculatedAveragine &avg, int iso_int_shift, int window_width, const std::vector< double > &excluded_masses)
	Examine intensity distribution over isotope indices. Also determines the most plausible isotope index or, monoisotopic mono_mass.

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.

Static Public Attributes inherited from SpectralDeconvolution
static const int	min_iso_size = 2
	minimum isotopologue count in a peak group

Protected Types inherited from SpectralDeconvolution
using	MassRanges = std::vector< std::pair< double, double > >
	Neutral apex-mass intervals used to restrict candidate construction.

Protected Member Functions inherited from SpectralDeconvolution
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method.

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

NASE-specific selection of precursor hypotheses and competing envelope evidence.

Member Function Documentation

◆ deconvolve()

void deconvolve	(	const MSSpectrum &	spectrum,
		int	scan_number,
		const std::vector< std::pair< double, int > > &	queries
	)

Deconvolve queries against complete parent MS1 evidence. Queries do not protect candidates from ordinary FLASH filtering. Empty queries run ordinary FLASH. Query state is cleared after every call. Competition uses the union of query/evidence intervals within the batch; subset-invariant callers must retain the same batch or use ordinary FLASH.

Parameters

[in]	spectrum	Complete parent MS1 spectrum.
[in]	scan_number	Parent scan number.
[in]	queries	Selected-ion m/z and signed charge; zero charge considers all charges.

Exceptions

Exception::IllegalArgument For nonempty non-MS1 queries or invalid m/z.

References MSSpectrum::getMSLevel(), SpectralDeconvolution::performSpectrumDeconvolution(), RNADirectedDeconvolution::queries_, Precursor::setCharge(), and Peak1D::setMZ().

Referenced by RNAPrecursorCorrector::correct().

◆ selectCandidateMassRanges_()

std::optional< SpectralDeconvolution::MassRanges > selectCandidateMassRanges_	(	const CandidateSelectionContext &	context,
		const DeconvolvedSpectrum *	evidence,
		const std::vector< Size > &	valid
	)		const

overrideprivatevirtual

Optionally restrict construction, without protecting candidates from filtering. The default returns nullopt for ordinary full-spectrum deconvolution. An override returning initial intervals is called again with scored seed groups to refine those intervals. Seed bins remain included. All passes use the complete spectrum and the ordinary shared construction/scoring.

Parameters

[in]	context	Read-only construction settings.
[in]	evidence	Null for the initial pass; scored seed groups for refinement.
[in]	valid	Indices of seed groups passing the shared scoring step.

Returns: Candidate mass intervals, or nullopt to retain all candidate bins.

Reimplemented from SpectralDeconvolution.

References SpectralDeconvolution::CandidateSelectionContext::averagine, FLASHHelperClasses::PrecalculatedAveragine::getApexIndex(), FLASHHelperClasses::getChargeMass(), FLASHHelperClasses::PrecalculatedAveragine::getLastIndex(), FLASHHelperClasses::PrecalculatedAveragine::getLeftCountFromApex(), FLASHHelperClasses::PrecalculatedAveragine::getMaxIsotopeIndex(), FLASHHelperClasses::PrecalculatedAveragine::getRightCountFromApex(), SpectralDeconvolution::CandidateSelectionContext::isotope_distance, SpectralDeconvolution::CandidateSelectionContext::max_charge, SpectralDeconvolution::CandidateSelectionContext::max_mass, SpectralDeconvolution::CandidateSelectionContext::min_charge, SpectralDeconvolution::CandidateSelectionContext::positive, RNADirectedDeconvolution::queries_, and SpectralDeconvolution::CandidateSelectionContext::tolerance.

Member Data Documentation

◆ queries_

std::vector<Precursor> queries_

private

Referenced by RNADirectedDeconvolution::deconvolve(), and RNADirectedDeconvolution::selectCandidateMassRanges_().

Public Member Functions

Private Member Functions