PepNovoOutfile Class Reference [File IO]

Representation of a PepNovo output file. More...

#include <OpenMS/FORMAT/PepNovoOutfile.h>

List of all members.

Public Types
typedef std::map< Size, std::pair< DoubleReal, DoubleReal > >	IndexPosMappingType
Public Member Functions
	PepNovoOutfile ()
	Constructor.
	PepNovoOutfile (const PepNovoOutfile &pepnovo_outfile)
	copy constructor
virtual	~PepNovoOutfile ()
	destructor
PepNovoOutfile &	operator= (const PepNovoOutfile &pepnovo_outfile)
	assignment operator
bool	operator== (const PepNovoOutfile &pepnovo_outfile) const
	equality operator
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
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

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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.

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Member Typedef Documentation

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

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Constructor & Destructor Documentation

PepNovoOutfile

(

)

Constructor.

PepNovoOutfile

(

const PepNovoOutfile &

pepnovo_outfile

)

copy constructor

virtual ~PepNovoOutfile

(

)

[virtual]

destructor

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Member Function Documentation

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

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

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>

PepNovoOutfile& operator=

(

const PepNovoOutfile &

pepnovo_outfile

)

assignment operator

bool operator==

(

const PepNovoOutfile &

pepnovo_outfile

)

const

equality operator