| OpenMS 2.5.0

Public Types | Public Member Functions | List of all members
PepNovoOutfile Class Reference
Format » File IO

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...
PepNovoOutfile & | operator= (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 | ( |  | ) |

Constructor.

## ◆ PepNovoOutfile() [2/2]

PepNovoOutfile | ( | const PepNovoOutfile & | pepnovo_outfile | ) |

copy constructor

## ◆ ~PepNovoOutfile()

virtual ~PepNovoOutfile | ( |  | ) |

virtual

destructor

## 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.

Parameters

  pepnovo_output_without_parameters_filename |
  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

Parameters

  result_filename | the file to be loaded
  peptide_identifications | the peptide identifications
  protein_identification | the protein identification
  score_threshold | cutoff threshold for the PepNovo score (PnvScr)
  id_rt_mz | map 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_map | map 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