AbsoluteQuantitationStandards Class Reference

Bridges sample-level concentration tables with the FeatureMap output of a feature finder, for building calibration curves used in absolute quantitation. More...

#include <OpenMS/METADATA/AbsoluteQuantitationStandards.h>

Classes
struct	featureConcentration
	One target component matched to a feature in the corresponding FeatureMap, paired with its known concentration. More...
struct	runConcentration
	One (sample, target, internal-standard, concentration) entry as provided by the user. More...

Public Member Functions
	AbsoluteQuantitationStandards ()=default
	Default constructor.
	~AbsoluteQuantitationStandards ()=default
	Destructor.
void	mapComponentsToConcentrations (const std::vector< AbsoluteQuantitationStandards::runConcentration > &run_concentrations, const std::vector< FeatureMap > &feature_maps, std::map< std::string, std::vector< AbsoluteQuantitationStandards::featureConcentration > > &components_to_concentrations) const
	Match each runConcentration to a feature in feature_maps and produce one featureConcentration record per match, keyed by component name.
void	getComponentFeatureConcentrations (const std::vector< AbsoluteQuantitationStandards::runConcentration > &run_concentrations, const std::vector< FeatureMap > &feature_maps, const std::string &component_name, std::vector< AbsoluteQuantitationStandards::featureConcentration > &feature_concentrations) const
	Return the featureConcentration records for a single component name.

Private Member Functions
bool	findComponentFeature_ (const FeatureMap &feature_map, const std::string &component_name, Feature &feature_found) const
	Locate a subordinate feature whose "native_id" meta value equals component_name.

Detailed Description

Bridges sample-level concentration tables with the FeatureMap output of a feature finder, for building calibration curves used in absolute quantitation.

The user supplies a list of runConcentration entries – one per (sample, target component, internal-standard) triple with the known concentrations – together with the FeatureMap instances produced for each sample. The class then locates each component (and its internal standard, when given) in the matching FeatureMap and pairs it with the entry's concentration, yielding featureConcentration records that downstream calibration code can consume.

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Class Documentation

OpenMS::AbsoluteQuantitationStandards::featureConcentration

struct OpenMS::AbsoluteQuantitationStandards::featureConcentration

One target component matched to a feature in the corresponding FeatureMap, paired with its known concentration.

Produced by mapComponentsToConcentrations and getComponentFeatureConcentrations.

Collaboration diagram for AbsoluteQuantitationStandards::featureConcentration:

Class Members
double	actual_concentration	Copied from runConcentration::actual_concentration.
string	concentration_units	Copied from runConcentration::concentration_units.
double	dilution_factor	Copied from runConcentration::dilution_factor.
Feature	feature	Subordinate feature found in the matching FeatureMap (see mapComponentsToConcentrations for the match rule).
double	IS_actual_concentration	Copied from runConcentration::IS_actual_concentration.
Feature	IS_feature	Subordinate feature for the internal standard. Default-constructed when runConcentration::IS_component_name was empty or no IS subordinate was found.

OpenMS::AbsoluteQuantitationStandards::runConcentration

struct OpenMS::AbsoluteQuantitationStandards::runConcentration

One (sample, target, internal-standard, concentration) entry as provided by the user.

Typically populated from a calibration-table file before the standards are mapped to feature data.

Collaboration diagram for AbsoluteQuantitationStandards::runConcentration:

Class Members
double	actual_concentration	Known concentration of the target component in this sample.
string	component_name	Identifier of the target component (matched against subordinate-feature meta value "native_id").
string	concentration_units	Units the concentration values are expressed in.
double	dilution_factor	Sample dilution factor.
double	IS_actual_concentration	Known concentration of the internal standard in this sample.
string	IS_component_name	Identifier of the paired internal standard, or empty if there is none.
string	sample_name	Sample identifier; matched against FeatureMap::getPrimaryMSRunPath after stripping a .mzML or .txt suffix.

Constructor & Destructor Documentation

AbsoluteQuantitationStandards()

AbsoluteQuantitationStandards ( )

default

Default constructor.

~AbsoluteQuantitationStandards()

~AbsoluteQuantitationStandards ( )

default

Destructor.

Member Function Documentation

findComponentFeature_()

bool findComponentFeature_ ( const FeatureMap &  feature_map, const std::string &  component_name, Feature &  feature_found  ) const

private

Locate a subordinate feature whose "native_id" meta value equals component_name.

Walks every Feature in feature_map and, for each, its subordinates; the first subordinate whose "native_id" meta value equals component_name is copied into feature_found.

Parameters

[in]	feature_map	Features to search (top-level features and their subordinates).
[in]	component_name	Required value of the subordinate's "native_id" meta value.
[out]	feature_found	The matching subordinate feature; only written on a successful return.

Returns

true if a matching subordinate was found, false otherwise.

getComponentFeatureConcentrations()

void getComponentFeatureConcentrations	(	const std::vector< AbsoluteQuantitationStandards::runConcentration > &	run_concentrations,
		const std::vector< FeatureMap > &	feature_maps,
		const std::string &	component_name,
		std::vector< AbsoluteQuantitationStandards::featureConcentration > &	feature_concentrations
	)		const

Return the featureConcentration records for a single component name.

Equivalent to filtering run_concentrations down to entries whose component_name matches component_name and running mapComponentsToConcentrations on the result; the records for component_name are then written to feature_concentrations. If no matching record is produced, feature_concentrations is left unchanged.

Parameters

[in]	run_concentrations	Calibration entries to filter.
[in]	feature_maps	Feature maps to search.
[in]	component_name	Only entries with this component name are considered.
[out]	feature_concentrations	Result vector; only assigned when at least one match is produced.

mapComponentsToConcentrations()

void mapComponentsToConcentrations	(	const std::vector< AbsoluteQuantitationStandards::runConcentration > &	run_concentrations,
		const std::vector< FeatureMap > &	feature_maps,
		std::map< std::string, std::vector< AbsoluteQuantitationStandards::featureConcentration > > &	components_to_concentrations
	)		const

Match each runConcentration to a feature in feature_maps and produce one featureConcentration record per match, keyed by component name.

For every entry in run_concentrations:

• Entries with an empty sample_name or component_name are skipped.
• A FeatureMap from feature_maps is considered a candidate when its first FeatureMap::getPrimaryMSRunPath entry, with a trailing .mzML or .txt suffix removed, equals the entry's sample_name. When the primary-run-path list is empty the candidate is accepted unconditionally.
• Within the chosen FeatureMap, the target component is located as a subordinate feature whose "native_id" meta value equals component_name. If no such subordinate exists, the entry is skipped.
• When IS_component_name is non-empty, the same subordinate lookup is performed for the internal standard, but the entry is kept even when the IS lookup fails (the resulting featureConcentration::IS_feature is then default-constructed).
• At most one FeatureMap is matched per entry; matching stops at the first hit.

Parameters

[in]	run_concentrations	Calibration entries to consider.
[in]	feature_maps	Feature maps to search.
[out]	components_to_concentrations	Result, keyed by component_name. Cleared at the start of the call.