| OpenMS 2.5.0

Public Member Functions | Private Attributes | List of all members
RTAlignment Class Reference

Take the original retention time before map alignment and use the alignment's trafoXML for calculation of the new alignment retention times. More...

`#include <OpenMS/QC/RTAlignment.h>`

Inheritance diagram for RTAlignment:

## Public Member Functions

| RTAlignment ()=default
| Constructor. More...
virtual | ~RTAlignment ()=default
| Destructor. More...
void | compute (FeatureMap &fm, const TransformationDescription &trafo) const
| Calculates retention time after map alignment and sets meta values "rt_raw" and "rt_align" in all PepIDs (on features and all unassigned PepIDs) More...
void | compute (std::vector< PeptideIdentification > &ids, const TransformationDescription &trafo) const
| Calculates retention time after map alignment and sets meta values "rt_raw" and "rt_align" in all PepIDs. More...
const String & | getName () const override
| returns the name of the metric More...
Status | requires () const override
| define the required input file: featureXML before map alignment (=POSTFDRFEAT), trafoXML after map alignment (=TRAFOALIGN) More...

## Private Attributes

const String | name_ = "RTAlignment"
| name of the metric More...

## Additional Inherited Members

Public Types inherited from QCBase
enum | Requires : UInt64 { FAIL, RAWMZML, POSTFDRFEAT, PREFDRFEAT, CONTAMINANTS, TRAFOALIGN, SIZE_OF_REQUIRES }
| Enum to encode a file type as a bit. More...
Static Public Member Functions inherited from QCBase
template<typename MAP , typename T >
static void | iterateFeatureMap (MAP &fmap, T lambda)
| function, which iterates through all PeptideIdentifications of a given FeatureMap and applies a given lambda function More...
Static Public Attributes inherited from QCBase
static const std::string | names_of_requires []
| strings corresponding to enum Requires More...

## Detailed Description

Take the original retention time before map alignment and use the alignment's trafoXML for calculation of the new alignment retention times.

Sets meta values "rt_raw" and "rt_align" in PeptideIdentifications of the featureMap's PepIDs. It does not change the RT of the features.

## Constructor & Destructor Documentation

## ◆ RTAlignment()

RTAlignment | ( |  | ) |

default

Constructor.

## ◆ ~RTAlignment()

virtual ~RTAlignment | ( |  | ) |

virtual default

Destructor.

## Member Function Documentation

## ◆ compute() [1/2]

void compute | ( | FeatureMap & | fm,
|  | const TransformationDescription & | trafo
| ) |  | const

Calculates retention time after map alignment and sets meta values "rt_raw" and "rt_align" in all PepIDs (on features and all unassigned PepIDs)

Parameters

  fm | FeatureMap to receive the new metavalues
  trafo | Transformation information to get needed data from

## ◆ compute() [2/2]

void compute | ( | std::vector< PeptideIdentification > & | ids,
|  | const TransformationDescription & | trafo
| ) |  | const

Calculates retention time after map alignment and sets meta values "rt_raw" and "rt_align" in all PepIDs.

Parameters

  ids | PepIDs to receive the new metavalues
  trafo | Transformation information to get needed data from

## ◆ getName()

const String& getName | ( |  | ) | const

override virtual

returns the name of the metric

Implements QCBase.

## ◆ requires()

Status requires | ( |  | ) | const

override virtual

define the required input file: featureXML before map alignment (=POSTFDRFEAT), trafoXML after map alignment (=TRAFOALIGN)

Implements QCBase.

## Member Data Documentation

## ◆ name_

const String name_ = "RTAlignment"

private

name of the metric