InspectOutfile Class Reference [File IO]

Representation of an Inspect outfile. More...

#include <OpenMS/FORMAT/InspectOutfile.h>

List of all members.

Public Member Functions
	InspectOutfile ()
	default constructor
	InspectOutfile (const InspectOutfile &inspect_outfile)
	copy constructor
virtual	~InspectOutfile ()
	destructor
InspectOutfile &	operator= (const InspectOutfile &inspect_outfile)
	assignment operator
bool	operator== (const InspectOutfile &inspect_outfile) const
	equality operator
std::vector< Size >	load (const String &result_filename, std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &protein_identification, const DoubleReal p_value_threshold, const String &database_filename="")
std::vector< Size >	getWantedRecords (const String &result_filename, DoubleReal 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)
template<typename PeakT >
void	getExperiment (MSExperiment< PeakT > &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)
static const Size	trie_db_pos_length_
	length of 2)
static const Size	protein_name_length_
	length of 3)
static const Size	record_length_
	length of the whole record
static const char	trie_delimiter_
	the sequences in the trie database are delimited by this character
static const String	score_type_
	type of score

---

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)

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Constructor & Destructor Documentation

InspectOutfile

(

)

default constructor

InspectOutfile

(

const InspectOutfile &

inspect_outfile

)

copy constructor

virtual ~InspectOutfile

(

)

[virtual]

destructor

---

Member Function Documentation

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

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

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)

void getExperiment	(	MSExperiment< PeakT > &	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< PeakT, ChromatogramPeakT >::reset(), FileTypes::typeToName(), and FileTypes::UNKNOWN.

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

Exceptions:

	Exception::FileNotFound
	Exception::ParseError

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

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

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

std::vector<Size> getWantedRecords	(	const String &	result_filename,
		DoubleReal	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

std::vector<Size> load	(	const String &	result_filename,
		std::vector< PeptideIdentification > &	peptide_identifications,
		ProteinIdentification &	protein_identification,
		const DoubleReal	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
	FileEmptry	is thrown if the given file is empty

InspectOutfile& operator=

(

const InspectOutfile &

inspect_outfile

)

assignment operator

bool operator==

(

const InspectOutfile &

inspect_outfile

)

const

equality operator

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 informations

Exceptions:

Exception::ParseError

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Member Data Documentation

const Size db_pos_length_ [static, protected]

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 proteins's position in the trie database 3) the name of the protein (the line with the accession identifier)

const Size protein_name_length_ [static, protected]

length of 3)

const Size record_length_ [static, protected]

length of the whole record

const String score_type_ [static, protected]

type of score

const Size trie_db_pos_length_ [static, protected]

length of 2)

const char trie_delimiter_ [static, protected]

the sequences in the trie database are delimited by this character