SequestOutfile Class Reference

Representation of a Sequest output file. More...

#include <OpenMS/FORMAT/SequestOutfile.h>

Collaboration diagram for SequestOutfile:

Public Member Functions
	SequestOutfile ()
	Constructor. More...
	SequestOutfile (const SequestOutfile &sequest_outfile)
	copy constructor More...
virtual	~SequestOutfile ()
	destructor More...
SequestOutfile &	operator= (const SequestOutfile &sequest_outfile)
	assignment operator More...
bool	operator== (const SequestOutfile &sequest_outfile) const
	equality operator More...
void	load (const String &result_filename, std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &protein_identification, const double p_value_threshold, std::vector< double > &pvalues, const String &database="", const bool ignore_proteins_per_peptide=false)
	loads data from a Sequest outfile More...
bool	getColumns (const String &line, std::vector< String > &substrings, Size number_of_columns, Size reference_column)
	retrieve columns from a Sequest outfile line More...
void	getSequences (const String &database_filename, const std::map< String, Size > &ac_position_map, std::vector< String > &sequences, std::vector< std::pair< String, Size > > &found, std::map< String, Size > &not_found)
void	getACAndACType (String line, String &accession, String &accession_type)
void	readOutHeader (const String &result_filename, DateTime &datetime, double &precursor_mz_value, Int &charge, Size &precursor_mass_type, Size &ion_mass_type, Size &displayed_peptides, String &sequest, String &sequest_version, String &database_type, Int &number_column, Int &rank_sp_column, Int &id_column, Int &mh_column, Int &delta_cn_column, Int &xcorr_column, Int &sp_column, Int &sf_column, Int &ions_column, Int &reference_column, Int &peptide_column, Int &score_column, Size &number_of_columns)

Static Private Attributes
static double	const_weights_ []
static double	xcorr_weights_ []
static double	delta_cn_weights_ []
static double	rank_sp_weights_ []
static double	delta_mass_weights_ []
static Size	max_pep_lens_ []
static Size	num_frags_ []

Detailed Description

Representation of a Sequest output file.

This class serves to read in a Sequest outfile. The information can be retrieved via the load function.

Todo:

Handle Modifications (Andreas)

Complete rewrite of the parser (and those of InsPecT and PepNovo), the code is bullshit... (Andreas)

Constructor & Destructor Documentation

SequestOutfile() [1/2]

SequestOutfile

(

)

Constructor.

SequestOutfile() [2/2]

SequestOutfile

(

const SequestOutfile &

sequest_outfile

)

copy constructor

~SequestOutfile()

virtual ~SequestOutfile ( )

virtual

destructor

Member Function Documentation

getACAndACType()

void getACAndACType	(	String	line,
		String &	accession,
		String &	accession_type
	)

retrieve the accession type and accession number from a protein description line (e.g. from FASTA line: >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus], get ac:AAD44166.1 ac type: GenBank)

getColumns()

bool getColumns	(	const String &	line,
		std::vector< String > &	substrings,
		Size	number_of_columns,
		Size	reference_column
	)

retrieve columns from a Sequest outfile line

getSequences()

void getSequences	(	const String &	database_filename,
		const std::map< String, Size > &	ac_position_map,
		std::vector< String > &	sequences,
		std::vector< std::pair< String, Size > > &	found,
		std::map< String, Size > &	not_found
	)

retrieve sequences from a FASTA database

Parameters

database_filename
ac_position_map
sequences
found
not_found

Exceptions

Exception::FileNotFound

is thrown if the database file could not be found

load()

void load	(	const String &	result_filename,
		std::vector< PeptideIdentification > &	peptide_identifications,
		ProteinIdentification &	protein_identification,
		const double	p_value_threshold,
		std::vector< double > &	pvalues,
		const String &	database = "",
		const bool	ignore_proteins_per_peptide = false
	)

loads data from a Sequest outfile

Parameters

result_filename	the file to be loaded
peptide_identifications	the identifications
protein_identification	the protein identifications
p_value_threshold	the significance level (for the peptide hit scores)
pvalues	a list with the pvalues of the peptides (pvalues computed with peptide prophet)
database	the database used for the search
ignore_proteins_per_peptide	this is a hack to deal with files that use a suffix like "+1" in column "Reference", but do not actually list extra protein references in subsequent lines

Exceptions

Exception::FileNotFound	is thrown if the given result file could not be found
Exception::ParseError	is thrown if the given result file could not be parsed
Exception::IllegalArgument	This class serves to read in a Sequest outfile. The information can be retrieved via the load function.

operator=()

SequestOutfile& operator=

(

const SequestOutfile &

sequest_outfile

)

assignment operator

operator==()

bool operator==

(

const SequestOutfile &

sequest_outfile

)

const

equality operator

readOutHeader()

void readOutHeader	(	const String &	result_filename,
		DateTime &	datetime,
		double &	precursor_mz_value,
		Int &	charge,
		Size &	precursor_mass_type,
		Size &	ion_mass_type,
		Size &	displayed_peptides,
		String &	sequest,
		String &	sequest_version,
		String &	database_type,
		Int &	number_column,
		Int &	rank_sp_column,
		Int &	id_column,
		Int &	mh_column,
		Int &	delta_cn_column,
		Int &	xcorr_column,
		Int &	sp_column,
		Int &	sf_column,
		Int &	ions_column,
		Int &	reference_column,
		Int &	peptide_column,
		Int &	score_column,
		Size &	number_of_columns
	)

read the header of an out file and retrieve various information

Exceptions

Exception::FileNotFound	is thrown if the results file could not be found
Exception::ParseError	is thrown if the results file could not be parsed

Member Data Documentation

const_weights_

double const_weights_[]

staticprivate

delta_cn_weights_

double delta_cn_weights_[]

staticprivate

delta_mass_weights_

double delta_mass_weights_[]

staticprivate

max_pep_lens_

Size max_pep_lens_[]

staticprivate

num_frags_

Size num_frags_[]

staticprivate

rank_sp_weights_

double rank_sp_weights_[]

staticprivate

xcorr_weights_

double xcorr_weights_[]

staticprivate