FASTAFile Class Reference

This class serves for reading in and writing FASTA files. More...

#include <OpenMS/FORMAT/FASTAFile.h>

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

Public Member Functions
	FASTAFile ()
	Default constructor. More...
virtual	~FASTAFile ()
	Destructor. More...
void	readStart (const String &filename)
	Prepares a FASTA file given by 'filename' for streamed reading using readNext(). More...
bool	readNext (FASTAEntry &protein)
	Reads the next FASTA entry from file. More...
std::streampos	position () const
	current stream position More...
bool	atEnd () const
	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(). More...
void	writeEnd ()
	Closes the file (flush). Called implicitly when FASTAFile object does out of scope. More...

Static Public Member Functions
static void	load (const String &filename, std::vector< FASTAEntry > &data)
	loads a FASTA file given by 'filename' and stores the information in 'data' More...
static void	store (const String &filename, const std::vector< FASTAEntry > &data)
	stores the data given by 'data' at the file 'filename' 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...
std::unique_ptr< void, std::function< void(void *) > >	reader_
	filestream for reading; init using FastaFile::readStart(); needs to be a pointer, since its not copy-constructable; we use void* here, to avoid pulling in seqan includes More...
Size	entries_read_
	some internal book-keeping during reading More...

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 constructor.

~FASTAFile()

virtual ~FASTAFile ( )

virtual

Destructor.

Member Function Documentation

atEnd()

bool atEnd

(

)

const

is stream at EOF?

load()

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

static

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 TOPPOpenPepXLLF::main_(), SimpleSearchEngine::main_(), TOPPOpenPepXL::main_(), RNPxlSearch::main_(), and TOPPMetaProSIP::main_().

position()

std::streampos position

(

)

const

current stream position

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.

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.

setPosition()

bool setPosition

(

const std::streampos &

pos

)

seek stream to pos

store()

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

static

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 does 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

entries_read_

Size entries_read_

protected

some internal book-keeping during reading

infile_

std::fstream infile_

protected

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

outfile_

std::ofstream outfile_

protected

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

reader_

std::unique_ptr<void, std::function<void(void*) > > reader_

protected

filestream for reading; init using FastaFile::readStart(); needs to be a pointer, since its not copy-constructable; we use void* here, to avoid pulling in seqan includes