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...
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