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:

Collaboration 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...
Public Member Functions inherited from QCBase
bool	isRunnable (const Status &s) const

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

Additional Inherited Members
Public Types inherited from QCBase
enum class	Requires : UInt64 {   NOTHING , RAWMZML , POSTFDRFEAT , PREFDRFEAT ,   CONTAMINANTS , TRAFOALIGN , ID , SIZE_OF_REQUIRES }
	Enum to encode a file type as a bit. More...
enum class	ToleranceUnit { AUTO , PPM , DA , SIZE_OF_TOLERANCEUNIT }
using	Status = FlagSet< Requires >
Static Public Member Functions inherited from QCBase
static bool	isLabeledExperiment (const ConsensusMap &cm)
	check if the IsobaricAnalyzer TOPP tool was used to create this ConsensusMap More...
template<typename MAP >
static bool	hasPepID (const MAP &fmap)
	does the container have a PeptideIdentification in its members or as unassignedPepID ? More...
Static Public Attributes inherited from QCBase
static const std::string	names_of_requires []
	strings corresponding to enum Requires More...
static const std::string	names_of_toleranceUnit []
	strings corresponding to enum ToleranceUnit 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 ( )

virtualdefault

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

overridevirtual

returns the name of the metric

Implements QCBase.

requires()

Status requires ( ) const

overridevirtual

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