Sequence Class Reference

#include <sequence.hpp>

Inheritance diagram for Sequence:

List of all members.

Classes
class	ParseError
Public Types
typedef std::vector< int >	parent_t
Public Member Functions
const Alphabet &	GetAlphabet () const
Sequence &	operator+= (const char ch)
void	Append (const char *str, int len)
Sequence &	operator/= (int mask)
Sequence	operator/ (int mask) const
bool	CString (char *str, int max_length) const
constructors
	Sequence (const Alphabet &a)
	Sequence (const Sequence &seq)
	Sequence (const Alphabet &a, const std::string &str)
	Sequence (const Alphabet &a, const_iterator begin, const_iterator end)
	Sequence (const Alphabet &a, const char *str)
	Sequence (const Alphabet &a, char c)
assignment operators
Sequence &	operator= (const char *str)
Sequence &	operator= (const std::string &str)
Sequence &	operator= (const Sequence &seq)
Sequence &	operator+= (const char *str)
Sequence &	operator+= (const std::string &str)
Sequence &	operator+= (const Sequence &seq)
Sequence &	operator+= (const int i)
Sequence &	operator+= (const unsigned int i)
Friends
bool	operator== (const Sequence &a, const Sequence &b)
bool	operator== (char a, const Sequence &b)
bool	operator== (const std::string &a, const Sequence &b)
bool	operator== (int a, const Sequence &b)
bool	operator== (unsigned int a, const Sequence &b)
bool	operator== (const Sequence &a, char b)
bool	operator== (const Sequence &a, const std::string &b)
bool	operator== (const Sequence &a, int b)
bool	operator== (const Sequence &a, unsigned int b)
bool	operator!= (const Sequence &a, const Sequence &b)
bool	operator!= (char a, const Sequence &b)
bool	operator!= (const std::string &a, const Sequence &b)
bool	operator!= (int a, const Sequence &b)
bool	operator!= (unsigned int a, const Sequence &b)
bool	operator!= (const Sequence &a, char b)
bool	operator!= (const Sequence &a, const std::string &b)
bool	operator!= (const Sequence &a, int b)
bool	operator!= (const Sequence &a, unsigned int b)
std::ostream &	operator<< (std::ostream &ost, const Sequence &s)
std::istream &	operator>> (std::istream &ist, Sequence &s)
concatenation operators
Sequence	operator+ (const Sequence &a, const Sequence &b)
Sequence	operator+ (char a, const Sequence &b)
Sequence	operator+ (const std::string &a, const Sequence &b)
Sequence	operator+ (int a, const Sequence &b)
Sequence	operator+ (unsigned int a, const Sequence &b)
Sequence	operator+ (const Sequence &a, char b)
Sequence	operator+ (const Sequence &a, const std::string &b)
Sequence	operator+ (const Sequence &a, int b)
Sequence	operator+ (const Sequence &a, unsigned int b)

---

Detailed Description

class for molecular sequences. One can use the + and += operators in a natural way. When a character does not fit into the provided alphabet an exception is thrown. Sequence::operator/ and Sequence::operator/= can be used to resrict the sequence on a subalphabet

Definition at line 38 of file sequence.hpp.

---

Constructor & Destructor Documentation

Sequence::Sequence

(

const Alphabet &

a

)

[inline]

construct an empty sequence over alphabet a.

Definition at line 68 of file sequence.hpp.

---

Member Function Documentation

void Sequence::Append	(	const char *	str,
		int	len
	)

Encode a string of length l and append the sequence.

Parameters:

	str	input string
	len	number of characters to be read

bool Sequence::CString	(	char *	str,
		int	max_length
	)			const

convert the sequence into a c-string.

Parameters:

	str
	max_length	(max. length of str, including the termination charakter), to copy the complete sequence at least size()+1 bytes have to be allocated

Returns:

true if the complete sequence was copied

Sequence& Sequence::operator+=

(

const char

ch

)

[inline]

Encode letter and add it to the sequence

Definition at line 142 of file sequence.hpp.

Sequence Sequence::operator/

(

int

mask

)

const [inline]

Restrict the sequence to a subalphabet The sub-alphabet is given a or'ed combination of SubAlphabetMask

Remarks:

is slower than Restrict(int mask,self_t & s) const;

Parameters:

mask

or encoded subalphabet combination

Definition at line 273 of file sequence.hpp.

Sequence& Sequence::operator/=

(

int

mask

)

[inline]

Restrict the sequence to a subalphabet The sub-alphabet is given a or'ed combination of SubAlphabetMask

Parameters:

mask

or encoded subalphabet combination

Definition at line 253 of file sequence.hpp.

---

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

• src/sequence.hpp