Utilitary methods working on raw string objects. More...

#include <Bpp/Seq/StringSequenceTools.h>

Public Member Functions
	StringSequenceTools ()
	~StringSequenceTools ()
Static Public Member Functions
static std::string	subseq (const std::string &sequence, int begin, int end) throw (Exception)
	Get a subsequence.
static std::string	setToSizeR (const std::string &sequence, int size)
	Set up the size of a sequence from the right side.
static std::string	setToSizeL (const std::string &sequence, int size)
	Set up the size of a sequence from the left side.
static std::string	deleteChar (const std::string &sequence, char chars)
	Delete all occurence of a character in the sequence.
static std::string	deleteChar (const std::string &sequence, std::string chars)
	Delete all occurence of several characters in the sequence.
static std::string *	reverse (const std::string &sequence)
	Reverse the sequence.
static std::string *	complement (const std::string &sequence)
	Get the complement of a sequence.
static double	getGCcontent (const std::string &sequence, size_t pos, size_t window) throw (BadIntegerException, Exception)
	Calculate the local GC content of a sequence.
static std::vector< int >	codeSequence (const std::string &sequence, const Alphabet *alphabet) throw (BadCharException)
	Convert a string sequence to a vector of int.
static std::string	decodeSequence (const std::vector< int > &sequence, const Alphabet *alphabet) throw (BadIntException)
	Convert a sequence to its string representation.
static Alphabet *	getAlphabetFromSequence (const std::string &sequence) throw (EmptySequenceException, SequenceException, AlphabetException)
	Parse a sequence and try to guess the correct alphabet to use.

Detailed Description

Utilitary methods working on raw string objects.

Sequences may be stored as strings, but this approach is not as powerful as using true sequence objects. Consider using the Sequence and SequenceTools classes for more methods.

Some of the methods implemented here are internally used by the Sequence object.

See also:: Sequence, Site, SequenceTools, SiteTools

Definition at line 66 of file StringSequenceTools.h.

Constructor & Destructor Documentation

bpp::StringSequenceTools::StringSequenceTools ( ) [inline]

Definition at line 69 of file StringSequenceTools.h.

bpp::StringSequenceTools::~StringSequenceTools ( ) [inline]

Definition at line 70 of file StringSequenceTools.h.

Member Function Documentation

vector< int > StringSequenceTools::codeSequence	(	const std::string &	sequence,
		const Alphabet *	alphabet
	)		throw (BadCharException) `[static]`

Convert a string sequence to a vector of int.

This method is used in the sequence constructor. This deals with the most simple cases: the sequence (string) contains a succession of all characters. This is indeed the case for simple alphabets, but may be more complicated if the alphabet is coded with variable code length.

Parameters:

sequence	The sequence to parse.
alphabet	The alphabet to use to code the sequence.

Returns:: A vector of int codes.

Exceptions:

BarCharException If some character does not match the specified alphabet.

Definition at line 272 of file StringSequenceTools.cpp.

References bpp::AlphabetTools::getAlphabetCodingSize().

Referenced by bpp::SequenceWithAnnotation::append(), bpp::BasicSequence::append(), bpp::SequenceWithAnnotation::setContent(), and bpp::BasicSequence::setContent().

string * StringSequenceTools::complement ( const std::string & sequence ) [static]

Get the complement of a sequence.

Deprecated:: Consider working with sequence objects and translators.

For this method, sequence is supposed to be of type DNA.

Parameters:

sequence The sequence to complement.

Returns:: The complementary sequence.

See also:: Sequence; NucleicAcidsReplication

Definition at line 148 of file StringSequenceTools.cpp.

string StringSequenceTools::decodeSequence	(	const std::vector< int > &	sequence,
		const Alphabet *	alphabet
	)		throw (BadIntException) `[static]`

Convert a sequence to its string representation.

Parameters:

sequence	The sequence object to convert.
alphabet	The alphabet to use to decode the sequence.

Returns:: A string representation of the sequence.

Exceptions:

BarIntException If some value does not match the specified alphabet.

Definition at line 290 of file StringSequenceTools.cpp.

Referenced by bpp::BasicSymbolList::toString(), and bpp::EdSymbolList::toString().

string StringSequenceTools::deleteChar	(	const std::string &	sequence,
		char	chars
	)		`[static]`

Delete all occurence of a character in the sequence.

Parameters:

sequence	The sequence to parse.
chars	The character to remove.

Returns:: The sequence with all specified characters removed.

Definition at line 92 of file StringSequenceTools.cpp.

string StringSequenceTools::deleteChar	(	const std::string &	sequence,
		std::string	chars
	)		`[static]`

Delete all occurence of several characters in the sequence.

Parameters:

sequence	The sequence to parse.
chars	The characters to remove.

Returns:: The sequence with all specified characters removed.

Definition at line 109 of file StringSequenceTools.cpp.

Alphabet * StringSequenceTools::getAlphabetFromSequence ( const std::string & sequence ) throw (EmptySequenceException, SequenceException, AlphabetException) [static]

Parse a sequence and try to guess the correct alphabet to use.

Parameters:

sequence The sequence to parse.

Returns:: A pointer toward a new Alphabet object.

Exceptions:

EmptySequenceException	if the sequence is empty.
SequenceException	if their is an ambiguity between several alphabet.
AlphabetException	if the sequence does not match any alphabet.

Definition at line 302 of file StringSequenceTools.cpp.

References bpp::AlphabetTools::getType().

double StringSequenceTools::getGCcontent	(	const std::string &	sequence,
		size_t	pos,
		size_t	window
	)		throw (BadIntegerException, Exception) `[static]`

Calculate the local GC content of a sequence.

GC contents are calculated using a window of specified size around the given position. Note : Calculus for last nucleotides (sequence's size - window size) will return the last possible rate calculated.

Parameters:

sequence	The sequence to analyse.
pos	The position where to compute the GC content.
window	The size of the window to use.

Returns:: The GC content as a ratio (# of GC / window).

Exceptions:

BadIntException	If the sequence is not of type DNA or RNA.
Exception	Error in calculus (if the sequence contain gaps for instance).

Definition at line 194 of file StringSequenceTools.cpp.

string * StringSequenceTools::reverse ( const std::string & sequence ) [static]

Reverse the sequence.

Parameters:

sequence The sequence to reverse.

Returns:: The reversed sequence.

Definition at line 130 of file StringSequenceTools.cpp.

string StringSequenceTools::setToSizeL	(	const std::string &	sequence,
		int	size
	)		`[static]`

Set up the size of a sequence from the left side.

All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.

Parameters:

sequence	The input sequence.
size	The new size of the sequence.

Definition at line 85 of file StringSequenceTools.cpp.

References bpp::TextTools::resizeLeft().

string StringSequenceTools::setToSizeR	(	const std::string &	sequence,
		int	size
	)		`[static]`

Set up the size of a sequence from the right side.

All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.

Parameters:

sequence	The input sequence.
size	The new size of the sequence.

Definition at line 80 of file StringSequenceTools.cpp.

References bpp::TextTools::resizeRight().

string StringSequenceTools::subseq	(	const std::string &	sequence,
		int	begin,
		int	end
	)		throw (Exception) `[static]`

Get a subsequence.

Parameters:

sequence	The input sequence.
begin	The begining position (included).
end	The ending position (included).

Returns:: A string with the subsequence.

Exceptions:

Exception If position does not not match the interval [0, length].

Definition at line 61 of file StringSequenceTools.cpp.

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

Bpp/Seq/StringSequenceTools.h
Bpp/Seq/StringSequenceTools.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation