IdentificationSummary Class Reference

#include <OpenMS/QC/IdentificationSummary.h>

Inheritance diagram for IdentificationSummary:

Collaboration diagram for IdentificationSummary:

Classes
struct	Result
struct	UniqueID

Public Member Functions
	IdentificationSummary ()=default
	Constructor. More...
virtual	~IdentificationSummary ()=default
	Destructor. More...
Result	compute (std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)
	computes a summary of an idXML file More...
const String &	getName () const override
	Returns the name of the metric. 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 Attributes
const String	name_ = "Summary of detected Proteins and Peptides from idXML file"

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...

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Class Documentation

OpenMS::IdentificationSummary::UniqueID

struct OpenMS::IdentificationSummary::UniqueID

Collaboration diagram for IdentificationSummary::UniqueID:

Class Members
UInt	count
float	fdr_threshold

Constructor & Destructor Documentation

IdentificationSummary()

IdentificationSummary ( )

default

Constructor.

~IdentificationSummary()

virtual ~IdentificationSummary ( )

virtualdefault

Destructor.

Member Function Documentation

compute()

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

computes a summary of an idXML file

Parameters

prot_ids	vector with ProteinIdentifications
pep_ids	vector with PeptideIdentifications

Returns

result object with summary values: total number of PSM (peptide_spectrum_matches), number of identified peptides with given FDR threshold (unique_peptides), number of identified proteins with given FDR threshold (unique_proteins), missed cleavages mean (missed_cleavages_mean), identification score mean of protein hits (protein_hit_scores_mean), identified peptide lengths mean (peptide_length_mean)

getName()

const String& getName ( ) const

overridevirtual

Returns the name of the metric.

Implements QCBase.

requires()

QCBase::Status requires ( ) const

overridevirtual

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

Implements QCBase.

Member Data Documentation

name_

const String name_ = "Summary of detected Proteins and Peptides from idXML file"

private