MissedCleavages Class Reference

This class is a metric for the QualityControl TOPP Tool. More...

#include <OpenMS/QC/MissedCleavages.h>

Inheritance diagram for MissedCleavages:

Collaboration diagram for MissedCleavages:

Public Member Functions
	MissedCleavages ()=default
	constructor More...
virtual	~MissedCleavages ()=default
	destructor More...
void	compute (FeatureMap &fmap)
	Counts the number of MissedCleavages per PeptideIdentification. More...
void	compute (std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)
const String &	getName () const override
	returns the name of the metric More...
const std::vector< std::map< UInt32, UInt32 > > &	getResults () const
	returns the result as maps of #missed_cleavages –> counts; one map for each call to compute(...) More...
QCBase::Status	requires () const override
	Returns the input data requirements of the compute(...) function. More...
Public Member Functions inherited from QCBase
bool	isRunnable (const Status &s) const

Private Types
typedef std::map< UInt32, UInt32 >	MapU32

Private Member Functions
void	get_missed_cleavages_from_peptide_identification_ (const ProteaseDigestion &digestor, MapU32 &result, const UInt32 &max_mc, PeptideIdentification &pep_id)
	collects number of missed cleavages from PeptideIdentification in a result map (missed cleavages: occurences) More...

Private Attributes
std::vector< std::map< UInt32, UInt32 > >	mc_result_
	container that stores results 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

This class is a metric for the QualityControl TOPP Tool.

This class counts the number of MissedCleavages per PeptideIdentification given a FeatureMap and returns an agglomeration statistic (observed counts). Additionally the PeptideHits in the FeatureMap are augmented with MetaInformation:

• 'missed_cleavages'
• 'FWHM' (from feature's 'FWHM' or 'model_FWHM')
• 'mass' (experimental mass of peptide)

Member Typedef Documentation

MapU32

typedef std::map<UInt32, UInt32> MapU32

private

Constructor & Destructor Documentation

MissedCleavages()

MissedCleavages ( )

default

constructor

~MissedCleavages()

virtual ~MissedCleavages ( )

virtualdefault

destructor

Member Function Documentation

compute() [1/2]

void compute

(

FeatureMap &

fmap

)

Counts the number of MissedCleavages per PeptideIdentification.

The result is a key/value map: #missed_cleavages –> counts Additionally the first PeptideHit in each PeptideIdentification of the FeatureMap is annotated with metavalue 'missed_cleavages'. The protease and digestion parameters are taken from the first ProteinIdentication (and SearchParameter therein) within the FeatureMap itself.

Parameters

fmap	FeatureMap with Peptide and ProteinIdentifications

compute() [2/2]

void compute	(	std::vector< ProteinIdentification > &	prot_ids,
		std::vector< PeptideIdentification > &	pep_ids
	)

get_missed_cleavages_from_peptide_identification_()

void get_missed_cleavages_from_peptide_identification_ ( const ProteaseDigestion &  digestor, MapU32 &  result, const UInt32 &  max_mc, PeptideIdentification &  pep_id  )

private

collects number of missed cleavages from PeptideIdentification in a result map (missed cleavages: occurences)

getName()

const String& getName ( ) const

overridevirtual

returns the name of the metric

Implements QCBase.

getResults()

const std::vector<std::map<UInt32, UInt32> >& getResults

(

)

const

returns the result as maps of #missed_cleavages –> counts; one map for each call to compute(...)

requires()

QCBase::Status requires ( ) const

overridevirtual

Returns the input data requirements of the compute(...) function.

Returns

Status for POSTFDRFEAT;

Implements QCBase.

Member Data Documentation

mc_result_

std::vector<std::map<UInt32, UInt32> > mc_result_

private

container that stores results