PEFFFile Class Reference

This class serves for reading and writing PEFF (PSI Extended FASTA Format) files. More...

#include <OpenMS/FORMAT/PEFFFile.h>

Inheritance diagram for PEFFFile:

Collaboration diagram for PEFFFile:

Public Member Functions
	PEFFFile ()=default
	Default constructor.
	~PEFFFile () override=default
	Destructor.
void	load (const String &filename, std::vector< PEFFEntry > &entries, std::vector< PEFFDatabaseMetadata > &headers) const
	Loads a PEFF file and stores entries and headers.
void	store (const String &filename, const std::vector< PEFFEntry > &entries, const PEFFDatabaseMetadata &header) const
	Stores entries to a PEFF file with the given header.
void	store (const String &filename, const std::vector< PEFFEntry > &entries, const std::vector< PEFFDatabaseMetadata > &headers) const
	Stores entries to a PEFF file with multiple database headers.
void	readStart (const String &filename)
	Prepares a PEFF file for streamed reading using readNext().
bool	readNext (PEFFEntry &entry)
	Reads the next PEFF entry from the file.
const std::vector< PEFFDatabaseMetadata > &	getHeaders () const
	Returns the headers parsed during readStart().
bool	atEnd () const
	Returns true if the end of the file has been reached.
void	writeStart (const String &filename, const PEFFDatabaseMetadata &header)
	Prepares a PEFF file for streamed writing using writeNext().
void	writeStart (const String &filename, const std::vector< PEFFDatabaseMetadata > &headers)
	Prepares a PEFF file for streamed writing using writeNext(), with multiple headers.
void	writeNext (const PEFFEntry &entry)
	Writes the next PEFF entry to the file.
void	writeEnd ()
	Closes the output file (called automatically in destructor)
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.
virtual	~ProgressLogger ()
	Destructor.
	ProgressLogger (const ProgressLogger &other)
	Copy constructor.
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!
LogType	getLogType () const
	Returns the type of progress log being used.
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.
void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display.
void	setProgress (SignedSize value) const
	Sets the current progress.
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end)

Static Public Member Functions
static bool	isPEFFFile (const String &filename)
	Checks if a file appears to be a PEFF file (by checking for # PEFF header).
static String	toProForma (const PEFFEntry &entry)
	Converts a PEFF entry to ProForma notation.

Protected Member Functions
void	parseHeaderLine_ (const String &line, PEFFDatabaseMetadata &header, bool &new_db)
	Parse a header line (# Key=Value or # //)
void	parseAnnotations_ (const String &description, PEFFEntry &entry)
	Parse annotations from the description line.
PEFFModification	parseModification_ (const String &tuple)
	Parse a single modification tuple.
PEFFVariantSimple	parseVariantSimple_ (const String &tuple)
	Parse a simple variant tuple.
PEFFVariantComplex	parseVariantComplex_ (const String &tuple)
	Parse a complex variant tuple.
PEFFProcessedRegion	parseProcessedRegion_ (const String &tuple)
	Parse a processed region tuple.
PEFFDisulfideBond	parseDisulfideBond_ (const String &tuple)
	Parse a disulfide bond tuple.
std::vector< String >	parseParenList_ (const String &value)
	Parse a parenthesized list of values.
String	formatHeader_ (const PEFFDatabaseMetadata &header) const
	Format the header section for output.
String	formatHeader_ (const std::vector< PEFFDatabaseMetadata > &headers) const
	Format the header section for output (multiple database blocks)
String	formatEntry_ (const PEFFEntry &entry) const
	Format a single entry for output.
bool	readEntry_ (std::string &id, std::string &description, std::string &seq)
	Read entry data (identifier, description, sequence)

Protected Attributes
std::fstream	infile_
	Input file stream.
std::ofstream	outfile_
	Output file stream.
std::vector< PEFFDatabaseMetadata >	headers_
	Parsed headers.
Size	entries_read_ {0}
	Number of entries read.
std::streampos	fileSize_ {0}
	File size for progress.
std::string	seq_
	Current sequence buffer.
std::string	id_
	Current identifier buffer.
std::string	description_
	Current description buffer.
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class serves for reading and writing PEFF (PSI Extended FASTA Format) files.

PEFF extends FASTA with rich annotations for modifications, variants, processed regions, and proteoforms. See https://github.com/HUPO-PSI/PEFF for the specification.

You can use aggregate methods load() and store() to read/write a set of protein sequences at the cost of memory.

Or use single read/write of protein sequences using readStart(), readNext() and writeStart(), writeNext(), writeEnd() for more memory efficiency.

Constructor & Destructor Documentation

PEFFFile()

PEFFFile ( )

default

Default constructor.

~PEFFFile()

~PEFFFile ( )

overridedefault

Destructor.

Member Function Documentation

atEnd()

bool atEnd

(

)

const

Returns true if the end of the file has been reached.

formatEntry_()

String formatEntry_ ( const PEFFEntry &  entry ) const

protected

Format a single entry for output.

formatHeader_() [1/2]

String formatHeader_ ( const PEFFDatabaseMetadata &  header ) const

protected

Format the header section for output.

formatHeader_() [2/2]

String formatHeader_ ( const std::vector< PEFFDatabaseMetadata > &  headers ) const

protected

Format the header section for output (multiple database blocks)

getHeaders()

const std::vector< PEFFDatabaseMetadata > & getHeaders

(

)

const

Returns the headers parsed during readStart().

Headers are available after calling readStart().

isPEFFFile()

static bool isPEFFFile ( const String &  filename )

static

Checks if a file appears to be a PEFF file (by checking for # PEFF header).

Parameters

filename

The file to check

Returns

true if the file starts with PEFF headers

load()

void load	(	const String &	filename,
		std::vector< PEFFEntry > &	entries,
		std::vector< PEFFDatabaseMetadata > &	headers
	)		const

Loads a PEFF file and stores entries and headers.

Parameters

filename	The PEFF file to load
entries	Output vector for PEFF entries
headers	Output vector for database metadata (one per database in file)

Exceptions

Exception::FileNotFound	is thrown if the file does not exist.
Exception::ParseError	is thrown if the file format is invalid.

parseAnnotations_()

void parseAnnotations_ ( const String &  description, PEFFEntry &  entry  )

protected

Parse annotations from the description line.

parseDisulfideBond_()

PEFFDisulfideBond parseDisulfideBond_ ( const String &  tuple )

protected

Parse a disulfide bond tuple.

parseHeaderLine_()

void parseHeaderLine_ ( const String &  line, PEFFDatabaseMetadata &  header, bool &  new_db  )

protected

Parse a header line (# Key=Value or # //)

parseModification_()

PEFFModification parseModification_ ( const String &  tuple )

protected

Parse a single modification tuple.

parseParenList_()

std::vector< String > parseParenList_ ( const String &  value )

protected

Parse a parenthesized list of values.

parseProcessedRegion_()

PEFFProcessedRegion parseProcessedRegion_ ( const String &  tuple )

protected

Parse a processed region tuple.

parseVariantComplex_()

PEFFVariantComplex parseVariantComplex_ ( const String &  tuple )

protected

Parse a complex variant tuple.

parseVariantSimple_()

PEFFVariantSimple parseVariantSimple_ ( const String &  tuple )

protected

Parse a simple variant tuple.

readEntry_()

bool readEntry_ ( std::string &  id, std::string &  description, std::string &  seq  )

protected

Read entry data (identifier, description, sequence)

readNext()

bool readNext

(

PEFFEntry &

entry

)

Reads the next PEFF entry from the file.

Parameters

entry

Output for the next entry

Returns

true if an entry was read, false if EOF was reached

Exceptions

Exception::ParseError

is thrown if parsing fails.

readStart()

void readStart

(

const String &

filename

)

Prepares a PEFF file for streamed reading using readNext().

Parameters

filename

The PEFF file to read

Exceptions

Exception::FileNotFound	is thrown if the file does not exist.
Exception::FileNotReadable	is thrown if the file cannot be read.

store() [1/2]

void store	(	const String &	filename,
		const std::vector< PEFFEntry > &	entries,
		const PEFFDatabaseMetadata &	header
	)		const

Stores entries to a PEFF file with the given header.

Parameters

filename	The output file path
entries	The entries to store
header	The database metadata header

Exceptions

Exception::UnableToCreateFile

is thrown if the file cannot be created.

store() [2/2]

void store	(	const String &	filename,
		const std::vector< PEFFEntry > &	entries,
		const std::vector< PEFFDatabaseMetadata > &	headers
	)		const

Stores entries to a PEFF file with multiple database headers.

Writes a single file description block followed by one sequence database description block per provided header, then all entries.

Parameters

filename	The output file path
entries	The entries to store
headers	The database metadata headers (one per database in file)

Exceptions

Exception::UnableToCreateFile	is thrown if the file cannot be created.
Exception::InvalidParameter	is thrown if headers is empty.

toProForma()

static String toProForma ( const PEFFEntry &  entry )

static

Converts a PEFF entry to ProForma notation.

Parameters

entry

The PEFF entry to convert

Returns

ProForma string representation

writeEnd()

void writeEnd

(

)

Closes the output file (called automatically in destructor)

writeNext()

void writeNext

(

const PEFFEntry &

entry

)

Writes the next PEFF entry to the file.

Parameters

entry

The entry to write

writeStart() [1/2]

void writeStart	(	const String &	filename,
		const PEFFDatabaseMetadata &	header
	)

Prepares a PEFF file for streamed writing using writeNext().

Parameters

filename	The output file path
header	The database metadata header

Exceptions

Exception::UnableToCreateFile

is thrown if the file cannot be created.

writeStart() [2/2]

void writeStart	(	const String &	filename,
		const std::vector< PEFFDatabaseMetadata > &	headers
	)

Prepares a PEFF file for streamed writing using writeNext(), with multiple headers.

Writes a single file description block followed by one database description block per header.

Parameters

filename	The output file path
headers	The database metadata headers (one per database in file)

Exceptions

Exception::UnableToCreateFile	is thrown if the file cannot be created.
Exception::InvalidParameter	is thrown if headers is empty.

Member Data Documentation

description_

std::string description_

protected

Current description buffer.

entries_read_

Size entries_read_ {0}

protected

Number of entries read.

fileSize_

std::streampos fileSize_ {0}

protected

File size for progress.

headers_

std::vector<PEFFDatabaseMetadata> headers_

protected

Parsed headers.

id_

std::string id_

protected

Current identifier buffer.

infile_

std::fstream infile_

protected

Input file stream.

outfile_

std::ofstream outfile_

protected

Output file stream.

seq_

std::string seq_

protected

Current sequence buffer.