Fasta Class Reference

Fasta parser/formatter. More...

#include <Fasta.hpp>

Static Public Member Functions
static Container	parsef (const char *fname, bool importGroupLabels=false)
	Imports a fasta file. More...
static void	parsef (const char *fname, Container &container, bool importGroupLabels=false)
	Imports a fasta file. More...
static Container	parse (const std::string &str, bool importGroupLabels=false)
	Imports a fasta file. More...
static void	parse (const std::string &str, Container &container, bool importGroupLabels=false)
	Imports a fasta file. More...
static Container	parse (std::istream &stream, bool importGroupLabels=false)
	Imports a fasta file from an open stream. More...
static void	parse (std::istream &stream, Container &container, bool importGroupLabels=false)
	Imports a fasta file from an open stream. More...
static void	formatf (const char *fname, const Container &container, bool exportGroupLabels=false, unsigned int lineLength=50)
	Export sequences as fasta. More...
static void	format (std::ostream &file, const Container &container, bool exportGroupLabels=false, unsigned int lineLength=50)
	Export sequences as fasta. More...
static std::string	format (const Container &container, bool exportGroupLabels=false, unsigned int lineLength=50)
	Export sequences as fasta. More...

Protected Member Functions
	Fasta ()
	This class cannot be instantiated.
	Fasta (const Fasta &source)
	This class cannot be instantiated.
Fasta &	operator= (const Fasta &source)
	This class cannot be or copied.
virtual	~Fasta ()
	This class cannot be instantiated.

Detailed Description

Fasta parser/formatter.

Reads a multifasta sequence file from a string, a stream or a file and returns a Container. See the description of the format below. Formats a fasta string from a sequence container object and places it in a string, a stream of a file. All methods are static and the class cannot be instantiated. The methods parsef and formatf will open the file for you while the others will read/write directly in a string.

Specifications of the fasta format:

• The number of sequences is not limited.
• Each sequence is preceded by a header limited to a single line and starting by a ">" character.
• The header length is not limited and all characters are allowed but white spaces and special characters are discouraged.
• Group indices are specified by @0, @1, @2... strings appearing at the end of the header string (just before the carriage return). Note that group labels are ignored by default.
• Group indices are ignored unless specifically specified in a parser's options.
• The sequence itself continues on following lines until the next ">" character or the end of the file.
• White spaces, tab and carriage returns are allowed at any position There is no limitation in length and different sequences can have different lengths.
• Although the standard is lower case characters, Fasta assumes upper case characters and only supports lower case characters (and converts them to upper case characters). Information coded by change in case is lost.

Member Function Documentation

void format ( std::ostream &  file, const Container &  container, bool  exportGroupLabels = false, unsigned int  lineLength = 50  )

static

Export sequences as fasta.

Parameters

file	an open stream.
container	Container object to export.
exportGroupLabels	if set to true, exports group indices as a @x at the end of the sequence name, where x is the group index. Otherwise, this information is discarded.
lineLength	the number of characters to place on a single line. If zero, no newlines are inserted within sequences.

std::string format ( const Container &  container, bool  exportGroupLabels = false, unsigned int  lineLength = 50  )

static

Export sequences as fasta.

This medod creates internally an ostringstream, calls the method format(ostream, container, bool) and returns the resulting string.

Parameters

container	Container object to export.
exportGroupLabels	if set to true, exports group indices as a @x at the end of the sequence name, where x is the group index. Otherwise, this information is discarded.
lineLength	the number of characters to place on a single line. If zero, no newlines are inserted within sequences.

Returns

The formatted string.

void formatf ( const char *  fname, const Container &  container, bool  exportGroupLabels = false, unsigned int  lineLength = 50  )

static

Export sequences as fasta.

Parameters

fname	the name of the file where to place the result.
container	Container object to export.
exportGroupLabels	if set to true, exports group indices as a @x at the end of the sequence name, where x is the group index. Otherwise, this information is discarded.
lineLength	the number of characters to place on a single line. If zero, no newlines are inserted within sequences.

Container parse ( const std::string &  str, bool  importGroupLabels = false  )

static

Imports a fasta file.

Imports the content of the file as is. Calls the method pase(std::istream*, bool) by creating its own istream.

Parameters

str	a string containing the data.
importGroupLabels	if set to true, scan automatically for groups. The format is @ followed by an integer, placed at the end of the header string(sequences without labels will be treated as @0).

Returns

A Container object containing the sequences.

void parse ( const std::string &  str, Container &  container, bool  importGroupLabels = false  )

static

Imports a fasta file.

Imports the content of the file as is. Calls the method pase(std::istream*, bool) by creating its own istream. This method expects a reference to a Container to which the sequences will be appended.

Parameters

str	a string containing the data.
container	a Container instance, empty or not.
importGroupLabels	if set to true, scan automatically for groups. The format is @ followed by an integer, placed at the end of the header string(sequences without labels will be treated as @0).

Returns

Nothing: new sequences are appended to the Container passed as argument.

Container parse ( std::istream &  stream, bool  importGroupLabels = false  )

static

Imports a fasta file from an open stream.

Imports the content of the file as is.

Parameters

stream	an open stream (file or string) containing the data.
importGroupLabels	if set to true, scan automatically for groups. The format is @ followed by an integer, placed at the end of the header string(sequences without labels will be treated as @0).

Returns

A Container object containing the sequences.

void parse ( std::istream &  stream, Container &  container, bool  importGroupLabels = false  )

static

Imports a fasta file from an open stream.

Imports the content of the file as is. This method expects a reference to a Container to which the sequences will be appended.

Parameters

stream	an open stream (file or string) containing the data.
container	a Container instance, empty or not.
importGroupLabels	if set to true, scan automatically for groups. The format is @ followed by an integer, placed at the end of the header string(sequences without labels will be treated as @0).

Returns

Nothing: the new sequences are appended to the Container passed as argument.

Container parsef ( const char *  fname, bool  importGroupLabels = false  )

static

Imports a fasta file.

Imports the content of the file as is. Calls the method pase(std::istream*, bool) by creating its own istream.

Parameters

fname	the name of a fasta file.
importGroupLabels	if set to true, scan automatically for groups. The format is @ followed by an integer, placed at the end of the header string(sequences without labels will be treated as @0).

Returns

A Container object containing the sequences.

void parsef ( const char *  fname, Container &  container, bool  importGroupLabels = false  )

static

Imports a fasta file.

Imports the content of the file as is. Calls the method pase(std::istream*, bool) by creating its own istream. This method expects a reference to a Container to which the sequences will be appended.

Parameters

fname	the name of a fasta file.
container	a Container instance, empty or not.
importGroupLabels	if set to true, scan automatically for groups. The format is @ followed by an integer, placed at the end of the header string(sequences without labels will be treated as @0).

Returns

Nothings: the new sequences are appended to the Container passed as argument.

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The documentation for this class was generated from the following files:

• /home/stephane/Documents/devel/egglib2/egglib-cpp/Fasta.hpp
• /home/stephane/Documents/devel/egglib2/egglib-cpp/Fasta.cpp