OpenMS  2.8.0
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:
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Collaboration diagram for RTAlignment:
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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 StringgetName () 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
fmFeatureMap to receive the new metavalues
trafoTransformation 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
idsPepIDs to receive the new metavalues
trafoTransformation 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