Representation of a PepNovo output file. More...
#include <OpenMS/FORMAT/PepNovoOutfile.h>
Public Types | |
| typedef std::map< Size, std::pair< DoubleReal, DoubleReal > > | 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 DoubleReal &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<DoubleReal, DoubleReal> > IndexPosMappingType |
| PepNovoOutfile | ( | ) |
Constructor.
| PepNovoOutfile | ( | const PepNovoOutfile & | pepnovo_outfile | ) |
copy constructor
|
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 DoubleReal & | 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
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |