Abstract base interface for spectral-library scoring strategies consumed by matchSpectrum. More...

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

Inheritance diagram for TargetedSpectraExtractor::Comparator:

Collaboration diagram for TargetedSpectraExtractor::Comparator:

Public Member Functions
virtual	~Comparator ()=default

virtual void	generateScores (const MSSpectrum &spec, std::vector< std::pair< Size, double > > &scores, double min_score) const =0
	Score `spec` against every entry of the cached library; keep only matches `>=` `min_score`.

virtual void	init (const std::vector< MSSpectrum > &library, const std::map< std::string, DataValue > &options)=0
	Load the reference library and (re)configure the comparator.

const std::vector< MSSpectrum > &	getLibrary () const
	Return the reference library passed to the most recent init call.

Protected Attributes
std::vector< MSSpectrum >	library_

Detailed Description

Abstract base interface for spectral-library scoring strategies consumed by matchSpectrum.

Implementations cache a reference library on init and then score query spectra against it via generateScores. The scoring direction is "higher is better" — the matchSpectrum caller sorts the returned pairs by descending score and keeps the top entries. Implementations are free to interpret the options map however they see fit; the caller passes user-supplied parameters through verbatim.

Constructor & Destructor Documentation

◆ ~Comparator()

virtual ~Comparator ( )

virtualdefault

Member Function Documentation

◆ generateScores()

virtual void generateScores	(	const MSSpectrum &	spec,
		std::vector< std::pair< Size, double > > &	scores,
		double	min_score
	)		const

pure virtual

Score spec against every entry of the cached library; keep only matches >= min_score.

Parameters

[in]	spec	Query spectrum.
[out]	scores	(library_index, score) pairs for matches that clear the threshold; unsorted.
[in]	min_score	Lower bound on the kept score (inclusive).

Implemented in TargetedSpectraExtractor::BinnedSpectrumComparator.

◆ getLibrary()

const std::vector< MSSpectrum > & getLibrary ( ) const

inline

Return the reference library passed to the most recent init call.

◆ init()

virtual void init	(	const std::vector< MSSpectrum > &	library,
		const std::map< std::string, DataValue > &	options
	)

pure virtual

Load the reference library and (re)configure the comparator.

Parameters

[in]	library	Reference spectra to score against in subsequent generateScores calls.
[in]	options	Implementation-specific knobs. BinnedSpectrumComparator consults `"bin_size"`, `"peak_spread"`, `"bin_offset"` — see its override for details.

Implemented in TargetedSpectraExtractor::BinnedSpectrumComparator.

Member Data Documentation

◆ library_

std::vector<MSSpectrum> library_

protected

Public Member Functions

Protected Attributes