FASTAFile Class Reference

This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusual symbols (such as translation end (*)), they will be kept! You can use aggregate methods load() and store() to read/write a set of protein sequences at the cost of memory. More...

#include <OpenMS/FORMAT/FASTAFile.h>

Inheritance diagram for FASTAFile:

Classes
struct	FASTAEntry
	FASTA entry type (identifier, description and sequence) The first std::string corresponds to the identifier that is written after the > in the FASTA file. The part after the first whitespace is stored in description and the text from the next line until the next > (exclusive) is stored in sequence. More...

Public Member Functions
	FASTAFile ()=default
	Default constructor.
	~FASTAFile () override=default
	Destructor.
void	readStart (const std::string &filename)
	Prepares a FASTA file given by filename for streamed reading using readNext().
void	readStartWithProgress (const std::string &filename, const std::string &progress_label)
	same as readStart(), but does internal progress logging whenever readNextWithProgress() is called
bool	readNext (FASTAEntry &protein)
	Reads the next FASTA entry from file.
bool	readNextWithProgress (FASTAEntry &protein)
std::streampos	position ()
	current stream position when reading a file
bool	atEnd ()
	is stream at EOF?
bool	setPosition (const std::streampos &pos)
	seek stream to pos
void	writeStart (const std::string &filename)
	Prepares a FASTA file given by 'filename' for streamed writing using writeNext().
void	writeNext (const FASTAEntry &protein)
	Stores the data given by protein. Call writeStart() once before calling writeNext(). Call writeEnd() when done to close the file!
void	writeEnd ()
	Closes the file (flush). Called implicitly when FASTAFile object goes out of scope.
void	load (const std::string &filename, std::vector< FASTAEntry > &data) const
	loads a FASTA file given by 'filename' and stores the information in 'data' This uses more RAM than readStart() and readNext().
void	store (const std::string &filename, const std::vector< FASTAEntry > &data) const
	stores the data given by 'data' at the file 'filename'
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 std::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)

Protected Member Functions
bool	readEntry_ (std::string &id, std::string &description, std::string &seq)
	Reads a protein entry from the current file position and returns the ID and sequence.
std::streampos	progressPosition_ ()
	The position for the progress logger: the file size once the end of the file is reached (tellg() is -1 then)
std::string	errorLocation_ () const
	Where the entry that readEntry_() read last starts: its line if known, otherwise its byte offset.

Protected Attributes
std::fstream	infile_
	filestream for reading; init using FastaFile::readStart()
std::ofstream	outfile_
	filestream for writing; init using FastaFile::writeStart()
Size	entries_read_ {0}
	some internal book-keeping during reading
std::streampos	fileSize_ {}
	total number of characters of filestream
std::string	seq_
	sequence of currently read protein
std::string	id_
	identifier of currently read protein
std::string	description_
	description of currently read protein
std::string	filename_
	name of the file read (readStart())
Size	line_ {0}
	line of the next character read (1-based); 0: unknown, after setPosition()
Size	entry_line_ {0}
	line of the entry read last (0: unknown)
std::streampos	entry_offset_ {}
	byte offset of the entry read last
std::string	error_
	why readEntry_() failed
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 std::atomic< int >	recursion_depth_

Detailed Description

This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusual symbols (such as translation end (*)), they will be kept! 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. Reading from one and writing to another FASTA file can be handled by one single FASTAFile instance.

Constructor & Destructor Documentation

FASTAFile()

FASTAFile ( )

default

Default constructor.

~FASTAFile()

~FASTAFile ( )

overridedefault

Destructor.

Member Function Documentation

atEnd()

bool atEnd

(

)

is stream at EOF?

errorLocation_()

std::string errorLocation_ ( ) const

protected

Where the entry that readEntry_() read last starts: its line if known, otherwise its byte offset.

load()

void load	(	const std::string &	filename,
		std::vector< FASTAEntry > &	data
	)		const

loads a FASTA file given by 'filename' and stores the information in 'data' This uses more RAM than readStart() and readNext().

Exceptions

Exception::FileNotFound	is thrown if the file does not exists.
Exception::ParseError	is thrown if the file does not suit to the standard.

Referenced by NucleicAcidSearchEngine::main_().

position()

std::streampos position

(

)

current stream position when reading a file

progressPosition_()

std::streampos progressPosition_ ( )

protected

The position for the progress logger: the file size once the end of the file is reached (tellg() is -1 then)

readEntry_()

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

protected

Reads a protein entry from the current file position and returns the ID and sequence.

A header line that is followed by the next header line or the end of the file gives an entry without sequence.

Returns

Return true if the protein entry was read and saved successfully, false otherwise (error_ says why)

readNext()

bool readNext

(

FASTAEntry &

protein

)

Reads the next FASTA entry from file.

An entry without sequence (a header followed by the next header or the end of the file) is skipped with a warning. The errors name the file and the line (or, after setPosition(), the byte offset) of the entry that could not be read.

If you want to read all entries in one go, use load().

Returns

true if entry was read; false if EOF was reached

Exceptions

Exception::FileNotFound	is thrown if the file does not exists.
Exception::ParseError	is thrown if the file does not suit to the standard.

readNextWithProgress()

bool readNextWithProgress

(

FASTAEntry &

protein

)

same as readNext(), but does internal progress logging; use readStartWithProgress() to enable this Calls progressEnd() when EOF is reached (i.e. when returning false)

readStart()

void readStart

(

const std::string &

filename

)

Prepares a FASTA file given by filename for streamed reading using readNext().

Exceptions

Exception::FileNotFound	is thrown if the file does not exists.
Exception::ParseError	is thrown if the file does not suit to the standard.

readStartWithProgress()

void readStartWithProgress	(	const std::string &	filename,
		const std::string &	progress_label
	)

same as readStart(), but does internal progress logging whenever readNextWithProgress() is called

setPosition()

bool setPosition

(

const std::streampos &

pos

)

seek stream to pos

store()

void store	(	const std::string &	filename,
		const std::vector< FASTAEntry > &	data
	)		const

stores the data given by 'data' at the file 'filename'

This uses more RAM than writeStart() and writeNext().

Exceptions

Exception::UnableToCreateFile

is thrown if the process is not able to write the file.

writeEnd()

void writeEnd

(

)

Closes the file (flush). Called implicitly when FASTAFile object goes out of scope.

writeNext()

void writeNext

(

const FASTAEntry &

protein

)

Stores the data given by protein. Call writeStart() once before calling writeNext(). Call writeEnd() when done to close the file!

Exceptions

Exception::UnableToCreateFile

is thrown if the process is not able to write the file.

writeStart()

void writeStart

(

const std::string &

filename

)

Prepares a FASTA file given by 'filename' for streamed writing using writeNext().

Exceptions

Exception::UnableToCreateFile

is thrown if the process is not able to write to the file (disk full?).

Member Data Documentation

description_

std::string description_

protected

description of currently read protein

entries_read_

Size entries_read_ {0}

protected

some internal book-keeping during reading

entry_line_

Size entry_line_ {0}

protected

line of the entry read last (0: unknown)

entry_offset_

std::streampos entry_offset_ {}

protected

byte offset of the entry read last

error_

std::string error_

protected

why readEntry_() failed

filename_

std::string filename_

protected

name of the file read (readStart())

fileSize_

std::streampos fileSize_ {}

protected

total number of characters of filestream

id_

std::string id_

protected

identifier of currently read protein

infile_

std::fstream infile_

protected

filestream for reading; init using FastaFile::readStart()

line_

Size line_ {0}

protected

line of the next character read (1-based); 0: unknown, after setPosition()

outfile_

std::ofstream outfile_

protected

filestream for writing; init using FastaFile::writeStart()

seq_

std::string seq_

protected

sequence of currently read protein