OpenMS  2.8.0
Classes | Public Member Functions | Private Attributes | List of all members
IdentificationSummary Class Reference

#include <OpenMS/QC/IdentificationSummary.h>

Inheritance diagram for IdentificationSummary:
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Collaboration diagram for IdentificationSummary:
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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 StringgetName () 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...
 

Class Documentation

◆ OpenMS::IdentificationSummary::UniqueID

struct OpenMS::IdentificationSummary::UniqueID
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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_idsvector with ProteinIdentifications
pep_idsvector 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