| OpenMS 2.5.0

Classes | Public Member Functions | Private Member Functions | List of all members
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.

## 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.