AbsoluteQuantitationStandards Class Reference

AbsoluteQuantitationStandards is a class to handle the relationship between runs, components, and their actual concentrations. More...

#include <OpenMS/METADATA/AbsoluteQuantitationStandards.h>

Classes
struct	featureConcentration
	Structure to hold a single component and its corresponding known concentration. More...
struct	runConcentration
	Structure to map runs to components to known concentrations. More...

Public Member Functions
	AbsoluteQuantitationStandards ()=default
	Constructor. More...
	~AbsoluteQuantitationStandards ()=default
	Destructor. More...
void	mapComponentsToConcentrations (const std::vector< AbsoluteQuantitationStandards::runConcentration > &run_concentrations, const std::vector< FeatureMap > &feature_maps, std::map< String, std::vector< AbsoluteQuantitationStandards::featureConcentration >> &components_to_concentrations) const
	Method to map runs to components to known concentrations. More...
void	getComponentFeatureConcentrations (const std::vector< AbsoluteQuantitationStandards::runConcentration > &run_concentrations, const std::vector< FeatureMap > &feature_maps, const String &component_name, std::vector< AbsoluteQuantitationStandards::featureConcentration > &feature_concentrations) const
	Get the feature concentrations from a single component. More...

Private Member Functions
bool	findComponentFeature_ (const FeatureMap &feature_map, const String &component_name, Feature &feature_found) const
	Finds a feature for a given component name. More...

Detailed Description

AbsoluteQuantitationStandards is a class to handle the relationship between runs, components, and their actual concentrations.

A mapping between a run, the components in the run, and the actual concentration of the components in the run are required to build a calibration curve that is required for absolute quantitation.

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Class Documentation

OpenMS::AbsoluteQuantitationStandards::featureConcentration

struct OpenMS::AbsoluteQuantitationStandards::featureConcentration

Structure to hold a single component and its corresponding known concentration.

Class Members
double	actual_concentration
String	concentration_units
double	dilution_factor
Feature	feature
double	IS_actual_concentration
Feature	IS_feature

OpenMS::AbsoluteQuantitationStandards::runConcentration

struct OpenMS::AbsoluteQuantitationStandards::runConcentration

Structure to map runs to components to known concentrations.

Class Members
double	actual_concentration
String	component_name
String	concentration_units
double	dilution_factor
double	IS_actual_concentration
String	IS_component_name
String	sample_name

Constructor & Destructor Documentation

AbsoluteQuantitationStandards()

AbsoluteQuantitationStandards ( )

default

Constructor.

~AbsoluteQuantitationStandards()

~AbsoluteQuantitationStandards ( )

default

Destructor.

Member Function Documentation

findComponentFeature_()

bool findComponentFeature_ ( const FeatureMap &  feature_map, const String &  component_name, Feature &  feature_found  ) const

private

Finds a feature for a given component name.

Parameters

[in]	feature_map	The container of features.
[in]	component_name	The feature must have this name as its "native_id".
[out]	feature_found	If found, the feature is saved in this parameter.

getComponentFeatureConcentrations()

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

Get the feature concentrations from a single component.

This method internally calls `mapComponentsToConcentrations()`, but takes in consideration only those elements of `run_concentrations` that have the passed `component_name`.

Warning

The method checks for the FeatureMaps' sample names with FeatureMap::getPrimaryMSRunPath()

Parameters

[in]	run_concentrations	A list of runConcentration structs (e.g., from file upload).
[in]	feature_maps	The method maps to these features.
[in]	component_name	Only runConcentration with this name will be considered.
[out]	feature_concentrations	The list of feature concentrations found.

mapComponentsToConcentrations()

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

Method to map runs to components to known concentrations.

Warning

The method checks for the FeatureMaps' sample names with FeatureMap::getPrimaryMSRunPath()

Parameters

[in]	run_concentrations	A list of runConcentration structs (e.g., from file upload).
[in]	feature_maps	The method maps to these features.
[out]	components_to_concentrations	A map that links run data to feature data.