SpectralMatch Class Reference

One library-search match record: the observed spectrum, the matching DB spectrum, the score, and the metabolite metadata copied from the hit. More...

#include <OpenMS/ANALYSIS/ID/MetaboliteSpectralMatching.h>

Collaboration diagram for SpectralMatch:

Public Member Functions
	SpectralMatch ()
	Default constructor (zero-initialised numeric fields, empty strings)
	~SpectralMatch ()
	Default destructor.
	SpectralMatch (const SpectralMatch &)
	Copy constructor.
SpectralMatch &	operator= (const SpectralMatch &)
	Assignment operator.
double	getObservedPrecursorMass () const
	Precursor mass (Da) of the experimental MS2 spectrum being matched.
void	setObservedPrecursorMass (const double &)
	Setter for the observed-side precursor mass (Da)
double	getObservedPrecursorRT () const
	Retention time (seconds) at which the observed MS2 spectrum was acquired.
void	setObservedPrecursorRT (const double &)
	Setter for the observed-side precursor RT (seconds)
double	getFoundPrecursorMass () const
	Precursor mass (Da) recorded on the DB-side spectrum that matched.
void	setFoundPrecursorMass (const double &)
	Setter for the DB-side precursor mass (Da)
Int	getFoundPrecursorCharge () const
	Precursor charge recorded on the DB-side spectrum.
void	setFoundPrecursorCharge (const Int &)
	Setter for the DB-side precursor charge.
double	getMatchingScore () const
	Hyperscore (higher is better; 0 if fewer than three peaks matched — see MetaboliteSpectralMatching::computeHyperScore)
void	setMatchingScore (const double &)
	Setter for the hyperscore.
Size	getObservedSpectrumIndex () const
	Index of the observed MS2 spectrum in the input PeakMap passed to MetaboliteSpectralMatching::run.
void	setObservedSpectrumIndex (const Size &)
	Setter for the observed-spectrum index.
Size	getMatchingSpectrumIndex () const
	Index of the matching DB spectrum in the spectral-library PeakMap.
void	setMatchingSpectrumIndex (const Size &)
	Setter for the DB-spectrum index.
std::string	getObservedSpectrumNativeID () const
	Native id (vendor-specific id) of the observed MS2 spectrum.
void	setObservedSpectrumNativeID (const std::string &)
	Setter for the observed-spectrum native id.
std::string	getPrimaryIdentifier () const
	Primary identifier of the matched metabolite. The .cpp populates this via the first available of: GNPS_Spectrum_ID, Massbank_Accession_ID, the metabolite-name meta value, or — as a last fallback — the DB spectrum's native id.
void	setPrimaryIdentifier (const std::string &)
	Setter for the primary metabolite identifier.
std::string	getSecondaryIdentifier () const
	Secondary identifier of the matched metabolite. The .cpp populates this from the HMDB_ID meta value on the DB-side spectrum.
void	setSecondaryIdentifier (const std::string &)
	Setter for the secondary metabolite identifier.
std::string	getCommonName () const
	Common (trivial) name of the matched metabolite.
void	setCommonName (const std::string &)
	Setter for the common name.
std::string	getSumFormula () const
	Chemical sum formula of the matched metabolite (neutral)
void	setSumFormula (const std::string &)
	Setter for the sum formula.
std::string	getInchiString () const
	InChI string of the matched metabolite.
void	setInchiString (const std::string &)
	Setter for the InChI string.
std::string	getSMILESString () const
	SMILES string of the matched metabolite.
void	setSMILESString (const std::string &)
	Setter for the SMILES string.
std::string	getPrecursorAdduct () const
	Adduct annotation recorded on the DB-side precursor (e.g. "[M+H]+")
void	setPrecursorAdduct (const std::string &)
	Setter for the precursor adduct.
double	getObservedCCS () const
	Observed collision cross section (CCS) of the experimental precursor in Angstrom^2; -1.0 if not available.
void	setObservedCCS (const double &)
	Setter for the observed CCS (Angstrom^2); use -1.0 to indicate "not available".
double	getFoundCCS () const
	CCS (Angstrom^2) of the matching DB-side spectrum; -1.0 if not available.
void	setFoundCCS (const double &)
	Setter for the DB-side CCS (Angstrom^2); use -1.0 to indicate "not available".

Private Attributes
double	observed_precursor_mass_
	Observed-side precursor mass (Da)
double	observed_precursor_rt_
	Observed-side precursor RT (seconds)
double	found_precursor_mass_
	DB-side precursor mass (Da)
Int	found_precursor_charge_
	DB-side precursor charge.
double	matching_score_
	Hyperscore (see MetaboliteSpectralMatching::computeHyperScore)
Size	observed_spectrum_idx_
	Index of the observed spectrum in the input PeakMap.
Size	matching_spectrum_idx_
	Index of the DB spectrum in the spectral-library PeakMap.
std::string	observed_spectrum_native_id_
	Native id (vendor-specific) of the observed spectrum.
std::string	primary_id_
	Primary metabolite identifier.
std::string	secondary_id_
	Secondary metabolite identifier.
std::string	common_name_
	Trivial / common name.
std::string	sum_formula_
	Neutral chemical sum formula.
std::string	inchi_string_
	InChI string.
std::string	smiles_string_
	SMILES string.
std::string	precursor_adduct_
	DB-side precursor adduct annotation.
double	observed_ccs_
	Observed-side collision cross section (Angstrom^2); -1.0 if not available.
double	found_ccs_
	DB-side collision cross section (Angstrom^2); -1.0 if not available.

Detailed Description

One library-search match record: the observed spectrum, the matching DB spectrum, the score, and the metabolite metadata copied from the hit.

Used by MetaboliteSpectralMatching to accumulate all candidate matches before the top-N export step. The fields fall into three groups:

• Observed-side: the index / native id of the experimental MS2 spectrum and its precursor mass / RT.
• DB-side: the index of the matching DB spectrum, the DB precursor mass / charge, and the hyperscore (see MetaboliteSpectralMatching::computeHyperScore).
• Metabolite metadata copied from the DB spectrum: primary/secondary identifier, common name, sum formula, InChI, SMILES, and the precursor adduct.

Constructor & Destructor Documentation

SpectralMatch() [1/2]

SpectralMatch

(

)

Default constructor (zero-initialised numeric fields, empty strings)

~SpectralMatch()

~SpectralMatch

(

)

Default destructor.

SpectralMatch() [2/2]

SpectralMatch

(

const SpectralMatch &

)

Copy constructor.

Member Function Documentation

getCommonName()

std::string getCommonName

(

)

const

Common (trivial) name of the matched metabolite.

getFoundCCS()

double getFoundCCS

(

)

const

CCS (Angstrom^2) of the matching DB-side spectrum; -1.0 if not available.

getFoundPrecursorCharge()

Int getFoundPrecursorCharge

(

)

const

Precursor charge recorded on the DB-side spectrum.

getFoundPrecursorMass()

double getFoundPrecursorMass

(

)

const

Precursor mass (Da) recorded on the DB-side spectrum that matched.

getInchiString()

std::string getInchiString

(

)

const

InChI string of the matched metabolite.

getMatchingScore()

double getMatchingScore

(

)

const

Hyperscore (higher is better; 0 if fewer than three peaks matched — see MetaboliteSpectralMatching::computeHyperScore)

Referenced by SpectralMatchScoreComparator::operator()().

getMatchingSpectrumIndex()

Size getMatchingSpectrumIndex

(

)

const

Index of the matching DB spectrum in the spectral-library PeakMap.

getObservedCCS()

double getObservedCCS

(

)

const

Observed collision cross section (CCS) of the experimental precursor in Angstrom^2; -1.0 if not available.

getObservedPrecursorMass()

double getObservedPrecursorMass

(

)

const

Precursor mass (Da) of the experimental MS2 spectrum being matched.

getObservedPrecursorRT()

double getObservedPrecursorRT

(

)

const

Retention time (seconds) at which the observed MS2 spectrum was acquired.

getObservedSpectrumIndex()

Size getObservedSpectrumIndex

(

)

const

Index of the observed MS2 spectrum in the input PeakMap passed to MetaboliteSpectralMatching::run.

getObservedSpectrumNativeID()

std::string getObservedSpectrumNativeID

(

)

const

Native id (vendor-specific id) of the observed MS2 spectrum.

getPrecursorAdduct()

std::string getPrecursorAdduct

(

)

const

Adduct annotation recorded on the DB-side precursor (e.g. "[M+H]+")

getPrimaryIdentifier()

std::string getPrimaryIdentifier

(

)

const

Primary identifier of the matched metabolite. The .cpp populates this via the first available of: GNPS_Spectrum_ID, Massbank_Accession_ID, the metabolite-name meta value, or — as a last fallback — the DB spectrum's native id.

getSecondaryIdentifier()

std::string getSecondaryIdentifier

(

)

const

Secondary identifier of the matched metabolite. The .cpp populates this from the HMDB_ID meta value on the DB-side spectrum.

getSMILESString()

std::string getSMILESString

(

)

const

SMILES string of the matched metabolite.

getSumFormula()

std::string getSumFormula

(

)

const

Chemical sum formula of the matched metabolite (neutral)

operator=()

SpectralMatch & operator=

(

const SpectralMatch &

)

Assignment operator.

setCommonName()

void setCommonName

(

const std::string &

)

Setter for the common name.

setFoundCCS()

void setFoundCCS

(

const double &

)

Setter for the DB-side CCS (Angstrom^2); use -1.0 to indicate "not available".

setFoundPrecursorCharge()

void setFoundPrecursorCharge

(

const Int &

)

Setter for the DB-side precursor charge.

setFoundPrecursorMass()

void setFoundPrecursorMass

(

const double &

)

Setter for the DB-side precursor mass (Da)

setInchiString()

void setInchiString

(

const std::string &

)

Setter for the InChI string.

setMatchingScore()

void setMatchingScore

(

const double &

)

Setter for the hyperscore.

setMatchingSpectrumIndex()

void setMatchingSpectrumIndex

(

const Size &

)

Setter for the DB-spectrum index.

setObservedCCS()

void setObservedCCS

(

const double &

)

Setter for the observed CCS (Angstrom^2); use -1.0 to indicate "not available".

setObservedPrecursorMass()

void setObservedPrecursorMass

(

const double &

)

Setter for the observed-side precursor mass (Da)

setObservedPrecursorRT()

void setObservedPrecursorRT

(

const double &

)

Setter for the observed-side precursor RT (seconds)

setObservedSpectrumIndex()

void setObservedSpectrumIndex

(

const Size &

)

Setter for the observed-spectrum index.

setObservedSpectrumNativeID()

void setObservedSpectrumNativeID

(

const std::string &

)

Setter for the observed-spectrum native id.

setPrecursorAdduct()

void setPrecursorAdduct

(

const std::string &

)

Setter for the precursor adduct.

setPrimaryIdentifier()

void setPrimaryIdentifier

(

const std::string &

)

Setter for the primary metabolite identifier.

setSecondaryIdentifier()

void setSecondaryIdentifier

(

const std::string &

)

Setter for the secondary metabolite identifier.

setSMILESString()

void setSMILESString

(

const std::string &

)

Setter for the SMILES string.

setSumFormula()

void setSumFormula

(

const std::string &

)

Setter for the sum formula.

Member Data Documentation

common_name_

std::string common_name_

private

Trivial / common name.

found_ccs_

double found_ccs_

private

DB-side collision cross section (Angstrom^2); -1.0 if not available.

found_precursor_charge_

Int found_precursor_charge_

private

DB-side precursor charge.

found_precursor_mass_

double found_precursor_mass_

private

DB-side precursor mass (Da)

inchi_string_

std::string inchi_string_

private

InChI string.

matching_score_

double matching_score_

private

Hyperscore (see MetaboliteSpectralMatching::computeHyperScore)

matching_spectrum_idx_

Size matching_spectrum_idx_

private

Index of the DB spectrum in the spectral-library PeakMap.

observed_ccs_

double observed_ccs_

private

Observed-side collision cross section (Angstrom^2); -1.0 if not available.

observed_precursor_mass_

double observed_precursor_mass_

private

Observed-side precursor mass (Da)

observed_precursor_rt_

double observed_precursor_rt_

private

Observed-side precursor RT (seconds)

observed_spectrum_idx_

Size observed_spectrum_idx_

private

Index of the observed spectrum in the input PeakMap.

observed_spectrum_native_id_

std::string observed_spectrum_native_id_

private

Native id (vendor-specific) of the observed spectrum.

precursor_adduct_

std::string precursor_adduct_

private

DB-side precursor adduct annotation.

primary_id_

std::string primary_id_

private

Primary metabolite identifier.

secondary_id_

std::string secondary_id_

private

Secondary metabolite identifier.

smiles_string_

std::string smiles_string_

private

SMILES string.

sum_formula_

std::string sum_formula_

private

Neutral chemical sum formula.