PepNovoOutfile Class Reference

Representation of a PepNovo output file. More...

#include <OpenMS/FORMAT/PepNovoOutfile.h>

Public Types

typedef std::map< Size, std::pair< double, double > > IndexPosMappingType

Public Member Functions

 PepNovoOutfile ()
 Constructor. More...
 PepNovoOutfile (const PepNovoOutfile &pepnovo_outfile)
 copy constructor More...
virtual ~PepNovoOutfile ()
 destructor More...
PepNovoOutfileoperator= (const PepNovoOutfile &pepnovo_outfile)
 assignment operator More...
bool operator== (const PepNovoOutfile &pepnovo_outfile) const
 equality operator More...
void load (const std::string &result_filename, std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &protein_identification, const double &score_threshold, const IndexPosMappingType &id_rt_mz, const std::map< String, String > &mod_id_map)
 loads data from a PepNovo outfile More...
void getSearchEngineAndVersion (const String &pepnovo_output_without_parameters_filename, ProteinIdentification &protein_identification)
 get the search engine version and search parameters from a PepNovo output file More...

Detailed Description

Representation of a PepNovo output file.

This class serves to read in a PepNovo outfile. The information can be retrieved via the load function.

Member Typedef Documentation

◆ IndexPosMappingType

typedef std::map<Size, std::pair<double, double> > IndexPosMappingType

Constructor & Destructor Documentation

◆ PepNovoOutfile() [1/2]


◆ PepNovoOutfile() [2/2]

PepNovoOutfile ( const PepNovoOutfile pepnovo_outfile)

copy constructor

◆ ~PepNovoOutfile()

virtual ~PepNovoOutfile ( )


Member Function Documentation

◆ getSearchEngineAndVersion()

void getSearchEngineAndVersion ( const String pepnovo_output_without_parameters_filename,
ProteinIdentification protein_identification 

get the search engine version and search parameters from a PepNovo output file

search parameters (precursor tolerance, peak mass tolerance, allowed modifications)are stored in the protein_identification.


◆ load()

void load ( const std::string &  result_filename,
std::vector< PeptideIdentification > &  peptide_identifications,
ProteinIdentification protein_identification,
const double &  score_threshold,
const IndexPosMappingType id_rt_mz,
const std::map< String, String > &  mod_id_map 

loads data from a PepNovo outfile

result_filenamethe file to be loaded
peptide_identificationsthe peptide identifications
protein_identificationthe protein identification
score_thresholdcutoff threshold for the PepNovo score (PnvScr)
id_rt_mzmap the spectrum identifiers returned by PepNovo to the rt and mz values of the spectrum (used to map the identifications back to the spectra). key= <PepNovo Id>, value= <pair<rt,mz> >. For spectra not present in this map identifications cannot be mapped back.
mod_id_mapmap the OpenMS id for modifications (FullId) to the ids returned by PepNovo key= <PepNovo_key>, value= <OpenMS FullId>

◆ operator=()

PepNovoOutfile& operator= ( const PepNovoOutfile pepnovo_outfile)

assignment operator

◆ operator==()

bool operator== ( const PepNovoOutfile pepnovo_outfile) const

equality operator