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:

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Collaboration diagram for FASTAFile:

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Classes
struct	FASTAEntry
	FASTA entry type (identifier, description and sequence) The first 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. More...

	~FASTAFile () override=default
	Destructor. More...

void	readStart (const String &filename)
	Prepares a FASTA file given by 'filename' for streamed reading using readNext(). More...

void	readStartWithProgress (const String &filename, const String &progress_label)
	same as readStart(), but does internal progress logging whenever readNextWithProgress() is called More...

bool	readNext (FASTAEntry &protein)
	Reads the next FASTA entry from file. If you want to read all entries in one go, use load(). More...

bool	readNextWithProgress (FASTAEntry &protein)

std::streampos	position ()
	current stream position when reading a file More...

bool	atEnd ()
	is stream at EOF? More...

bool	setPosition (const std::streampos &pos)
	seek stream to `pos` More...

void	writeStart (const String &filename)
	Prepares a FASTA file given by 'filename' for streamed writing using writeNext(). More...

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! More...

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

void	load (const 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(). More...

void	store (const String &filename, const std::vector< FASTAEntry > &data) const
	stores the data given by 'data' at the file 'filename' More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

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. More...

Protected Attributes
std::fstream	infile_
	filestream for reading; init using FastaFile::readStart() More...

std::ofstream	outfile_
	filestream for writing; init using FastaFile::writeStart() More...

Size	entries_read_ {0}
	some internal book-keeping during reading More...

std::streampos	fileSize_ {}
	total number of characters of filestream More...

std::string	seq_
	sequence of currently read protein More...

std::string	id_
	identifier of currently read protein More...

std::string	description_
	description of currently read protein More...

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 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?

◆ load()

void load	(	const 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

◆ 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.

Returns: Return true if the protein entry was read and saved successfully, false otherwise

◆ readNext()

bool readNext ( FASTAEntry & protein )

Reads the next FASTA entry from file. 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 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 String &	filename,
		const 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 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 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

◆ 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()

◆ outfile_

std::ofstream outfile_

protected

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

◆ seq_

std::string seq_

protected

sequence of currently read protein

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FASTAFile()

◆ ~FASTAFile()

Member Function Documentation

◆ atEnd()

◆ load()

◆ position()

◆ readEntry_()

◆ readNext()

◆ readNextWithProgress()

◆ readStart()

◆ readStartWithProgress()

◆ setPosition()

◆ store()

◆ writeEnd()

◆ writeNext()

◆ writeStart()

Member Data Documentation

◆ description_

◆ entries_read_

◆ fileSize_

◆ id_

◆ infile_

◆ outfile_

◆ seq_