One small-molecule hit produced by AccurateMassSearchEngine. More...

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

Collaboration diagram for AccurateMassSearchResult:

Public Member Functions
	AccurateMassSearchResult ()
	Default constructor; all numeric fields zero, strings and vectors empty.

	~AccurateMassSearchResult ()
	Default destructor.

	AccurateMassSearchResult (const AccurateMassSearchResult &other)
	Copy constructor.

AccurateMassSearchResult &	operator= (const AccurateMassSearchResult &other)
	Copy-assignment operator.

double	getObservedMZ () const
	Observed m/z of the source feature (Th).

void	setObservedMZ (const double &mz)
	Set the observed m/z of the source feature.

double	getCalculatedMZ () const
	Theoretical m/z of the matched compound + adduct (Th).

void	setCalculatedMZ (const double &mz)
	Set the theoretical m/z of the matched compound + adduct.

double	getQueryMass () const
	Neutral mass used to query the database (Dalton), back- calculated from getObservedMZ assuming getFoundAdduct and getCharge.

void	setQueryMass (const double &mass)
	Set the neutral mass used to query the database.

double	getFoundMass () const
	Neutral mass of the matched database compound (Dalton).

void	setFoundMass (const double &mass)
	Set the neutral mass of the matched database compound.

Int	getCharge () const
	Ion charge under which this match was attempted (positive for cations, negative for anions).

void	setCharge (const Int &ch)
	Set the ion charge under which this match was attempted.

double	getMZErrorPPM () const
	Signed m/z error in ppm: (observed − theoretical) / theoretical · 1e6.

void	setMZErrorPPM (const double ppm)
	Set the signed m/z error in ppm.

double	getObservedRT () const
	Retention time of the source feature (seconds).

void	setObservedRT (const double &rt)
	Set the retention time of the source feature (seconds).

double	getObservedIntensity () const
	Intensity of the source feature (consensus-aggregated when the input was a ConsensusMap).

void	setObservedIntensity (const double &intensity)
	Set the intensity of the source feature.

std::vector< double >	getIndividualIntensities () const
	Per-sample intensities of the source feature when the input is a ConsensusMap; empty otherwise.

void	setIndividualIntensities (const std::vector< double > &indiv_ints)
	Set the per-sample intensities of the source feature.

Size	getMatchingIndex () const
	Index of this hit in the engine's internal candidate list for the source feature. Useful when reconstructing scoring details after export.

void	setMatchingIndex (const Size &idx)
	Set the candidate-list index.

Size	getSourceFeatureIndex () const
	Index of the source feature in the input map (back- reference to the raw observation).

void	setSourceFeatureIndex (const Size &idx)
	Set the source feature index.

const std::string &	getFoundAdduct () const
	Adduct that produced the match, in AdductInfo notation (e.g. `"M+H;1+"`, `"M-H2O+H;1+"`).

void	setFoundAdduct (const std::string &add)
	Set the adduct that produced the match.

const std::string &	getFormulaString () const
	Empirical formula of the matched database compound.

void	setEmpiricalFormula (const std::string &ep)
	Set the empirical formula of the matched database compound.

const std::vector< std::string > &	getMatchingHMDBids () const
	All database identifiers (HMDB-style) that share the matched compound's formula and mass; can be empty when no identifier mapping is available.

void	setMatchingHMDBids (const std::vector< std::string > &ids)
	Set the matched database identifiers.

const std::vector< double > &	getMasstraceIntensities () const
	Per-isotopologue intensities of the underlying feature's mass traces; used as the empirical isotope pattern when computing getIsotopesSimScore.

void	setMasstraceIntensities (const std::vector< double > &intensities)
	Set the underlying feature's per-isotopologue intensities.

double	getIsotopesSimScore () const
	Similarity between the observed isotope pattern (from getMasstraceIntensities) and the theoretical pattern of the matched compound. Higher values indicate a better match.

void	setIsotopesSimScore (const double &score)
	Set the isotope-pattern similarity score.

Private Attributes
double	observed_mz_
	Stored information/results of DB query.

double	theoretical_mz_
	theoretical m/z of matched compound + adduct (Th)

double	searched_mass_
	neutral mass used to query the database (Da)

double	db_mass_
	neutral mass of the matched database compound (Da)

Int	charge_
	charge assumed for this match (positive for cations)

double	mz_error_ppm_
	signed m/z error (observed − theoretical), ppm

double	observed_rt_
	RT of source feature (s)

double	observed_intensity_
	intensity of source feature

std::vector< double >	individual_intensities_
	per-sample intensities (ConsensusMap input)

Size	matching_index_
	index in the engine's internal candidate list

Size	source_feature_index_
	index in the input feature/peak map

std::string	found_adduct_
	adduct in AdductInfo notation (e.g. "M+H;1+")

std::string	empirical_formula_
	empirical formula of matched compound

std::vector< std::string >	matching_hmdb_ids_
	zero or more DB IDs (multiple isobars share a formula)

std::vector< double >	mass_trace_intensities_
	per-isotopologue intensities from the feature

double	isotopes_sim_score_
	observed vs. theoretical isotope-pattern similarity

Friends
std::ostream &	operator<< (std::ostream &os, const AccurateMassSearchResult &amsr)
	Diagnostic stream output of all fields (not a parseable serialization).

Detailed Description

One small-molecule hit produced by AccurateMassSearchEngine.

Represents a single (observed feature/peak) — (database compound + adduct) match. AccurateMassSearchEngine emits one of these per accepted (feature, adduct, candidate-compound) combination, so the same input feature can appear in several results if it is consistent with more than one adduct or matches multiple isobaric compounds in the database.

Lifecycle

Each result is built up incrementally by the search engine via the setters and exposed read-only to consumers via the getters. The class holds no logic of its own — it is a plain value object grouping the observable, the database hit, and the diagnostics that explain why the two were matched.

Field semantics

Observed quantities (from the spectrum / feature):

observed_mz : observed m/z of the feature.
observed_rt : retention time of the feature.
observed_intensity: intensity of the feature.
individual_intensities : per-FeatureHandle intensities, populated only on the ConsensusMap overload of AccurateMassSearchEngine::run; stays empty when the engine is invoked on a plain FeatureMap.
mass_trace_intensities : per-isotopologue intensities of the underlying mass traces (used for the isotope-pattern similarity score).

Match-derived quantities:

searched_mass : neutral mass back-calculated from observed_mz under the assumption of found_adduct and charge. Used as the database query.
db_mass : neutral mass of the matched database compound (the "ground truth" for this hit).
theoretical_mz: m/z that the matched compound + adduct would produce; differs from observed_mz by mz_error_ppm.
mz_error_ppm : signed m/z error in ppm, observed vs. theoretical.
charge : ion charge under which the match was attempted (positive for cations, negative for anions).

Compound annotation:

found_adduct : adduct that produced the match, in the notation used by AdductInfo (e.g. "M+H;1+", "M-H2O+H;1+").
empirical_formula : empirical formula of the matched compound.
matching_hmdb_ids : zero or more database IDs that share the formula and mass (multiple isobars are common in HMDB-style databases).

Back-references:

matching_index : index of the hit within the engine's internal candidate list (useful when reconstructing scoring details after export).
source_feature_index: index of the source feature/peak in the input map (lets callers traceback to the raw observation).

Quality score:

isotopes_sim_score : isotope-pattern similarity between the feature's observed mass-trace intensities and the theoretical pattern of the candidate compound. Higher = better.

See also: AccurateMassSearchEngine; AdductInfo

Constructor & Destructor Documentation

◆ AccurateMassSearchResult() [1/2]

AccurateMassSearchResult ( )

Default constructor; all numeric fields zero, strings and vectors empty.

◆ ~AccurateMassSearchResult()

~AccurateMassSearchResult ( )

Default destructor.

◆ AccurateMassSearchResult() [2/2]

AccurateMassSearchResult ( const AccurateMassSearchResult & other )

Copy constructor.

Parameters

[in] other Source result to copy from.

Member Function Documentation

◆ getCalculatedMZ()

double getCalculatedMZ ( ) const

Theoretical m/z of the matched compound + adduct (Th).

◆ getCharge()

Int getCharge ( ) const

Ion charge under which this match was attempted (positive for cations, negative for anions).

◆ getFormulaString()

const std::string & getFormulaString ( ) const

Empirical formula of the matched database compound.

◆ getFoundAdduct()

const std::string & getFoundAdduct ( ) const

Adduct that produced the match, in AdductInfo notation (e.g. "M+H;1+", "M-H2O+H;1+").

◆ getFoundMass()

double getFoundMass ( ) const

Neutral mass of the matched database compound (Dalton).

◆ getIndividualIntensities()

std::vector< double > getIndividualIntensities ( ) const

Per-sample intensities of the source feature when the input is a ConsensusMap; empty otherwise.

◆ getIsotopesSimScore()

double getIsotopesSimScore ( ) const

Similarity between the observed isotope pattern (from getMasstraceIntensities) and the theoretical pattern of the matched compound. Higher values indicate a better match.

◆ getMasstraceIntensities()

const std::vector< double > & getMasstraceIntensities ( ) const

Per-isotopologue intensities of the underlying feature's mass traces; used as the empirical isotope pattern when computing getIsotopesSimScore.

◆ getMatchingHMDBids()

const std::vector< std::string > & getMatchingHMDBids ( ) const

All database identifiers (HMDB-style) that share the matched compound's formula and mass; can be empty when no identifier mapping is available.

◆ getMatchingIndex()

Size getMatchingIndex ( ) const

Index of this hit in the engine's internal candidate list for the source feature. Useful when reconstructing scoring details after export.

◆ getMZErrorPPM()

double getMZErrorPPM ( ) const

Signed m/z error in ppm: (observed − theoretical) / theoretical · 1e6.

◆ getObservedIntensity()

double getObservedIntensity ( ) const

Intensity of the source feature (consensus-aggregated when the input was a ConsensusMap).

◆ getObservedMZ()

double getObservedMZ ( ) const

Observed m/z of the source feature (Th).

◆ getObservedRT()

double getObservedRT ( ) const

Retention time of the source feature (seconds).

◆ getQueryMass()

double getQueryMass ( ) const

Neutral mass used to query the database (Dalton), back- calculated from getObservedMZ assuming getFoundAdduct and getCharge.

◆ getSourceFeatureIndex()

Size getSourceFeatureIndex ( ) const

Index of the source feature in the input map (back- reference to the raw observation).

◆ operator=()

AccurateMassSearchResult & operator= ( const AccurateMassSearchResult & other )

Copy-assignment operator.

Parameters

[in] other Source result to copy from.

◆ setCalculatedMZ()

void setCalculatedMZ ( const double & mz )

Set the theoretical m/z of the matched compound + adduct.

Parameters

[in] mz Theoretical m/z of compound + adduct (Th).

◆ setCharge()

void setCharge ( const Int & ch )

Set the ion charge under which this match was attempted.

Parameters

[in] ch Signed ion charge (positive for cations).

◆ setEmpiricalFormula()

void setEmpiricalFormula ( const std::string & ep )

Set the empirical formula of the matched database compound.

Parameters

[in] ep Empirical formula of the matched compound.

◆ setFoundAdduct()

void setFoundAdduct ( const std::string & add )

Set the adduct that produced the match.

Parameters

[in] add Adduct in AdductInfo notation (e.g. "M+H;1+").

◆ setFoundMass()

void setFoundMass ( const double & mass )

Set the neutral mass of the matched database compound.

Parameters

[in] mass Neutral mass of the matched compound (Da).

◆ setIndividualIntensities()

void setIndividualIntensities ( const std::vector< double > & indiv_ints )

Set the per-sample intensities of the source feature.

Parameters

[in] indiv_ints Per-sample intensities (ConsensusMap input).

◆ setIsotopesSimScore()

void setIsotopesSimScore ( const double & score )

Set the isotope-pattern similarity score.

Parameters

[in] score Isotope-pattern similarity score (higher = better.

◆ setMasstraceIntensities()

void setMasstraceIntensities ( const std::vector< double > & intensities )

Set the underlying feature's per-isotopologue intensities.

Parameters

[in] intensities Per-isotopologue intensities from the feature.

◆ setMatchingHMDBids()

void setMatchingHMDBids ( const std::vector< std::string > & ids )

Set the matched database identifiers.

Parameters

[in] ids Database identifiers (HMDB-style).

◆ setMatchingIndex()

void setMatchingIndex ( const Size & idx )

Set the candidate-list index.

Parameters

[in] idx Index in the engine's internal candidate list.

◆ setMZErrorPPM()

void setMZErrorPPM ( const double ppm )

Set the signed m/z error in ppm.

Parameters

[in] ppm Signed m/z error (observed − theoretical) in ppm.

◆ setObservedIntensity()

void setObservedIntensity ( const double & intensity )

Set the intensity of the source feature.

Parameters

[in] intensity Intensity of the source feature.

◆ setObservedMZ()

void setObservedMZ ( const double & mz )

Set the observed m/z of the source feature.

Parameters

[in] mz Observed m/z (Th).

◆ setObservedRT()

void setObservedRT ( const double & rt )

Set the retention time of the source feature (seconds).

Parameters

[in] rt Retention time of the source feature (s).

◆ setQueryMass()

void setQueryMass ( const double & mass )

Set the neutral mass used to query the database.

Parameters

[in] mass Neutral mass used to query the database (Da).

◆ setSourceFeatureIndex()

void setSourceFeatureIndex ( const Size & idx )

Set the source feature index.

Parameters

[in] idx Index in the input feature/peak map.

Friends And Related Symbol Documentation

◆ operator<<

std::ostream & operator<<	(	std::ostream &	os,
		const AccurateMassSearchResult &	amsr
	)

friend

Diagnostic stream output of all fields (not a parseable serialization).

Member Data Documentation

◆ charge_

Int charge_

private

charge assumed for this match (positive for cations)

◆ db_mass_

double db_mass_

private

neutral mass of the matched database compound (Da)

◆ empirical_formula_

std::string empirical_formula_

private

empirical formula of matched compound

◆ found_adduct_

std::string found_adduct_

private

adduct in AdductInfo notation (e.g. "M+H;1+")

◆ individual_intensities_

std::vector<double> individual_intensities_

private

per-sample intensities (ConsensusMap input)

◆ isotopes_sim_score_

double isotopes_sim_score_

private

observed vs. theoretical isotope-pattern similarity

◆ mass_trace_intensities_

std::vector<double> mass_trace_intensities_

private

per-isotopologue intensities from the feature

◆ matching_hmdb_ids_

std::vector<std::string> matching_hmdb_ids_

private

zero or more DB IDs (multiple isobars share a formula)

◆ matching_index_

Size matching_index_

private

index in the engine's internal candidate list

◆ mz_error_ppm_

double mz_error_ppm_

private

signed m/z error (observed − theoretical), ppm

◆ observed_intensity_

double observed_intensity_

private

intensity of source feature

◆ observed_mz_

double observed_mz_

private

Stored information/results of DB query.

observed m/z of source feature (Th)

◆ observed_rt_

double observed_rt_

private

RT of source feature (s)

◆ searched_mass_

double searched_mass_

private

neutral mass used to query the database (Da)

◆ source_feature_index_

Size source_feature_index_

private

index in the input feature/peak map

◆ theoretical_mz_

double theoretical_mz_

private

theoretical m/z of matched compound + adduct (Th)

Public Member Functions

Private Attributes

Friends

Detailed Description

Lifecycle

Field semantics

Constructor & Destructor Documentation

◆ AccurateMassSearchResult() [1/2]

◆ ~AccurateMassSearchResult()

◆ AccurateMassSearchResult() [2/2]

Member Function Documentation

◆ getCalculatedMZ()

◆ getCharge()

◆ getFormulaString()

◆ getFoundAdduct()

◆ getFoundMass()

◆ getIndividualIntensities()

◆ getIsotopesSimScore()

◆ getMasstraceIntensities()

◆ getMatchingHMDBids()

◆ getMatchingIndex()

◆ getMZErrorPPM()

◆ getObservedIntensity()

◆ getObservedMZ()

◆ getObservedRT()

◆ getQueryMass()

◆ getSourceFeatureIndex()

◆ operator=()

◆ setCalculatedMZ()

◆ setCharge()

◆ setEmpiricalFormula()

◆ setFoundAdduct()

◆ setFoundMass()

◆ setIndividualIntensities()

◆ setIsotopesSimScore()

◆ setMasstraceIntensities()

◆ setMatchingHMDBids()

◆ setMatchingIndex()

◆ setMZErrorPPM()

◆ setObservedIntensity()

◆ setObservedMZ()

◆ setObservedRT()

◆ setQueryMass()

◆ setSourceFeatureIndex()

Friends And Related Symbol Documentation

◆ operator<<

Member Data Documentation

◆ charge_

◆ db_mass_

◆ empirical_formula_

◆ found_adduct_

◆ individual_intensities_

◆ isotopes_sim_score_

◆ mass_trace_intensities_

◆ matching_hmdb_ids_

◆ matching_index_

◆ mz_error_ppm_

◆ observed_intensity_

◆ observed_mz_

◆ observed_rt_

◆ searched_mass_

◆ source_feature_index_

◆ theoretical_mz_