#include <OpenMS/FORMAT/InspectOutfile.h>

Collaboration diagram for InspectOutfile:

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

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 More...

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

@brief Representation of an Inspect outfile

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

Todo:: Handle Modifications (Andreas)

@ingroup FileIO

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

@throw Exception::FileNotFound
@throw Exception::ParseError
@throw 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(), 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)

@throw Exception::FileNotFound
@throw 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

@throw 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

@throw 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

@param result_filename The filename of the results file
@param p_value_threshold Only identifications exceeding this threshold are read
@throw FileNotFound is thrown is the file is not found
@throw 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

@param result_filename Input parameter which is the file name of the input file
@param peptide_identifications Output parameter which holds the peptide identifications from the given file
@param protein_identification Output parameter which holds the protein identifications from the given file
@param p_value_threshold
@param database_filename
@throw FileNotFound is thrown if the given file could not be found
@throw ParseError is thrown if the given file could not be parsed
@throw 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

Public Member Functions

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ InspectOutfile() [1/2]

◆ InspectOutfile() [2/2]

◆ ~InspectOutfile()

Member Function Documentation

◆ compressTrieDB()

◆ generateTrieDB()

◆ getACAndACType()

◆ getExperiment()

◆ getLabels()

◆ getPrecursorRTandMZ()

◆ getSearchEngineAndVersion()

◆ getSequences()

◆ getWantedRecords()

◆ load()

◆ operator=()

◆ operator==()

◆ readOutHeader()

Member Data Documentation

◆ db_pos_length_

◆ protein_name_length_

◆ record_length_

◆ score_type_

◆ trie_db_pos_length_

◆ trie_delimiter_