InspectOutfile Class Reference

Representation of an Inspect outfile. More...

#include <OpenMS/FORMAT/InspectOutfile.h>

Public Member Functions
	InspectOutfile ()
	default constructor More...
	InspectOutfile (const InspectOutfile &inspect_outfile)
	copy constructor More...
virtual	~InspectOutfile ()
	destructor More...
InspectOutfile &	operator= (const InspectOutfile &inspect_outfile)
	assignment operator More...
bool	operator== (const InspectOutfile &inspect_outfile) const
	equality operator More...
std::vector< Size >	load (const String &result_filename, std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &protein_identification, const double p_value_threshold, const String &database_filename="")
std::vector< Size >	getWantedRecords (const String &result_filename, double p_value_threshold)
void	compressTrieDB (const String &database_filename, const String &index_filename, std::vector< Size > &wanted_records, const String &snd_database_filename, const String &snd_index_filename, bool append=false)
void	generateTrieDB (const String &source_database_filename, const String &database_filename, const String &index_filename, bool append=false, const String species="")
void	getACAndACType (String line, String &accession, String &accession_type)
void	getPrecursorRTandMZ (const std::vector< std::pair< String, std::vector< std::pair< Size, Size > > > > &files_and_peptide_identification_with_scan_number, std::vector< PeptideIdentification > &ids)
void	getLabels (const String &source_database_filename, String &ac_label, String &sequence_start_label, String &sequence_end_label, String &comment_label, String &species_label)
std::vector< Size >	getSequences (const String &database_filename, const std::map< Size, Size > &wanted_records, std::vector< String > &sequences)
void	getExperiment (PeakMap &exp, String &type, const String &in_filename)
bool	getSearchEngineAndVersion (const String &cmd_output, ProteinIdentification &protein_identification)
void	readOutHeader (const String &filename, const String &header_line, Int &spectrum_file_column, Int &scan_column, Int &peptide_column, Int &protein_column, Int &charge_column, Int &MQ_score_column, Int &p_value_column, Int &record_number_column, Int &DB_file_pos_column, Int &spec_file_pos_column, Size &number_of_columns)

Static Protected Attributes
static const Size	db_pos_length_
	length of 1) More...
static const Size	trie_db_pos_length_
	length of 2) More...
static const Size	protein_name_length_
	length of 3) More...
static const Size	record_length_
	length of the whole record More...
static const char	trie_delimiter_
	the sequences in the trie database are delimited by this character More...
static const String	score_type_
	type of score More...

Detailed Description

Representation of an Inspect outfile.

This class serves to read in an Inspect outfile and write an idXML file

Todo:

Handle Modifications (Andreas)

Constructor & Destructor Documentation

InspectOutfile() [1/2]

InspectOutfile

(

)

default constructor

InspectOutfile() [2/2]

InspectOutfile

(

const InspectOutfile &

inspect_outfile

)

copy constructor

~InspectOutfile()

virtual ~InspectOutfile ( )

virtual

destructor

Member Function Documentation

compressTrieDB()

void compressTrieDB	(	const String &	database_filename,
		const String &	index_filename,
		std::vector< Size > &	wanted_records,
		const String &	snd_database_filename,
		const String &	snd_index_filename,
		bool	append = false
	)

generates a trie database from another one, using the wanted records only

Exceptions

Exception::FileNotFound
Exception::ParseError
Exception::UnableToCreateFile

generateTrieDB()

void generateTrieDB	(	const String &	source_database_filename,
		const String &	database_filename,
		const String &	index_filename,
		bool	append = false,
		const String	species = ""
	)

generates a trie database from a given one (the type of database is determined by getLabels)

Exceptions

Exception::FileNotFound
Exception::UnableToCreateFile

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)

getExperiment()

void getExperiment ( PeakMap &  exp, String &  type, const String &  in_filename  )

inline

get the experiment from a file

Exceptions

Exception::ParseError

is thrown if the file could not be parsed or the filetype could not be determined

References FileHandler::getTypeByContent(), FileHandler::loadExperiment(), ProgressLogger::NONE, MSExperiment::reset(), FileTypes::typeToName(), and FileTypes::UNKNOWN.

getLabels()

void getLabels	(	const String &	source_database_filename,
		String &	ac_label,
		String &	sequence_start_label,
		String &	sequence_end_label,
		String &	comment_label,
		String &	species_label
	)

retrieve the labels of a given database (at the moment FASTA and Swissprot)

Exceptions

Exception::FileNotFound
Exception::ParseError

getPrecursorRTandMZ()

void getPrecursorRTandMZ	(	const std::vector< std::pair< String, std::vector< std::pair< Size, Size > > > > &	files_and_peptide_identification_with_scan_number,
		std::vector< PeptideIdentification > &	ids
	)

retrieve the precursor retention time and mz value

Exceptions

Exception::ParseError

getSearchEngineAndVersion()

bool getSearchEngineAndVersion	(	const String &	cmd_output,
		ProteinIdentification &	protein_identification
	)

get the search engine and its version from the output of the InsPecT executable without parameters

returns true on success, false otherwise

getSequences()

std::vector<Size> getSequences	(	const String &	database_filename,
		const std::map< Size, Size > &	wanted_records,
		std::vector< String > &	sequences
	)

retrieve sequences from a trie database

Exceptions

Exception::FileNotFound

getWantedRecords()

std::vector<Size> getWantedRecords	(	const String &	result_filename,
		double	p_value_threshold
	)

loads only results which exceeds a given P-value threshold

Parameters

result_filename	The filename of the results file
p_value_threshold	Only identifications exceeding this threshold are read

Exceptions

FileNotFound	is thrown is the file is not found
FileEmpty	is thrown if the given file is empty

load()

std::vector<Size> load	(	const String &	result_filename,
		std::vector< PeptideIdentification > &	peptide_identifications,
		ProteinIdentification &	protein_identification,
		const double	p_value_threshold,
		const String &	database_filename = ""
	)

load the results of an Inspect search

Parameters

result_filename	Input parameter which is the file name of the input file
peptide_identifications	Output parameter which holds the peptide identifications from the given file
protein_identification	Output parameter which holds the protein identifications from the given file
p_value_threshold
database_filename

Exceptions

FileNotFound	is thrown if the given file could not be found
ParseError	is thrown if the given file could not be parsed
FileEmpty	is thrown if the given file is empty

operator=()

InspectOutfile& operator=

(

const InspectOutfile &

inspect_outfile

)

assignment operator

operator==()

bool operator==

(

const InspectOutfile &

inspect_outfile

)

const

equality operator

readOutHeader()

void readOutHeader	(	const String &	filename,
		const String &	header_line,
		Int &	spectrum_file_column,
		Int &	scan_column,
		Int &	peptide_column,
		Int &	protein_column,
		Int &	charge_column,
		Int &	MQ_score_column,
		Int &	p_value_column,
		Int &	record_number_column,
		Int &	DB_file_pos_column,
		Int &	spec_file_pos_column,
		Size &	number_of_columns
	)

read the header of an inspect output file and retrieve various information

Exceptions

Exception::ParseError

Member Data Documentation

db_pos_length_

const Size db_pos_length_

staticprotected

length of 1)

a record in the index file that belongs to a trie database consists of three parts 1) the protein's position in the original database 2) the protein's position in the trie database 3) the name of the protein (the line with the accession identifier)

protein_name_length_

const Size protein_name_length_

staticprotected

length of 3)

record_length_

const Size record_length_

staticprotected

length of the whole record

score_type_

const String score_type_

staticprotected

type of score

trie_db_pos_length_

const Size trie_db_pos_length_

staticprotected

length of 2)

trie_delimiter_

const char trie_delimiter_

staticprotected

the sequences in the trie database are delimited by this character