OpenMS
MissedCleavages Class Reference

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

#include <OpenMS/QC/MissedCleavages.h>

Inheritance diagram for MissedCleavages:
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Collaboration diagram for MissedCleavages:
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Public Member Functions

 MissedCleavages ()=default
 constructor More...
 
virtual ~MissedCleavages ()=default
 destructor More...
 
void compute (FeatureMap &fmap)
 Counts the number of missed cleavages per PeptideIdentification. More...
 
void compute (std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)
 
const StringgetName () const override
 returns the name of the metric More...
 
const std::vector< std::map< UInt32, UInt32 > > & getResults () const
 returns the result as maps of number of missed_cleavages to counts; one map for each call to compute(...) More...
 
QCBase::Status requirements () 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, UInt32MapU32
 

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 missed cleavages 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
fmapFeatureMap 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 number of missed_cleavages to counts; one map for each call to compute(...)

◆ requirements()

QCBase::Status requirements ( ) 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