#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	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 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...

Class Documentation

◆ OpenMS::IdentificationSummary::UniqueID

struct OpenMS::IdentificationSummary::UniqueID

Collaboration diagram for IdentificationSummary::UniqueID:

[legend]

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.

◆ requirements()

QCBase::Status requirements ( ) 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

Classes

Public Member Functions

Private Attributes

Additional Inherited Members