OpenMS
2.4.0
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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... | |
Representation of a PepNovo output file.
This class serves to read in a PepNovo outfile. The information can be retrieved via the load function.
typedef std::map<Size, std::pair<double, double> > IndexPosMappingType |
PepNovoOutfile | ( | ) |
Constructor.
PepNovoOutfile | ( | const PepNovoOutfile & | pepnovo_outfile | ) |
copy constructor
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virtual |
destructor
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.
pepnovo_output_without_parameters_filename | |
protein_identification |
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_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> |
PepNovoOutfile& operator= | ( | const PepNovoOutfile & | pepnovo_outfile | ) |
assignment operator
bool operator== | ( | const PepNovoOutfile & | pepnovo_outfile | ) | const |
equality operator