seq::Nucleotide Class Reference

A nucleotide, including support for ambiguity codes. More...

#include <Nucleotide.h>

List of all members.

Public Member Functions
	Nucleotide ()
	Create a nucleotide with value Nucleotide::N (any).
	Nucleotide (char c) throw (ParseException)
	Create a nucleotide by parsing a character.
char	toChar () const
	Get the uppercase character representation for this nucleotide.
int	intRep () const
	Get the internal representation.
bool	operator== (const Nucleotide &other) const
	Are two nucleotides identical ?
bool	operator!= (const Nucleotide &other) const
	Are two nucleotides different ?
bool	isAmbiguity () const
	Is the nucleotide ambiguous ? Only A,C,G,T are considered non-ambiguous.
void	sampleAmbiguity ()
	Replace the (ambiguos) nucleotide with a random non-ambigiuos nucleotide that is represented by the ambiguity symbol.
void	nonAmbiguousNucleotides (std::vector< Nucleotide > &result) const
	Get all non ambiguous nucleotides represented by this nucleotide.
bool	operator< (const Nucleotide other) const
	So that you can use it as a key for STL containers.
Static Public Member Functions
static Nucleotide	fromRep (int rep)
	Create a nucleotide using the internal representation directly.
Static Public Attributes
Constants used in the internal representation.
See also: intRep() and fromRep(int).
static const int	NT_A = 0
static const int	NT_C = 1
static const int	NT_G = 2
static const int	NT_T = 3
static const int	NT_M = 4
static const int	NT_R = 5
static const int	NT_W = 6
static const int	NT_S = 7
static const int	NT_Y = 8
static const int	NT_K = 9
static const int	NT_V = 10
static const int	NT_H = 11
static const int	NT_D = 12
static const int	NT_B = 13
static const int	NT_N = 14
static const int	NT_GAP = 15
Nucleotide constants.
static const Nucleotide	A
static const Nucleotide	C
static const Nucleotide	G
static const Nucleotide	T
static const Nucleotide	M
static const Nucleotide	R
static const Nucleotide	W
static const Nucleotide	S
static const Nucleotide	Y
static const Nucleotide	K
static const Nucleotide	V
static const Nucleotide	H
static const Nucleotide	D
static const Nucleotide	B
static const Nucleotide	N
static const Nucleotide	GAP

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Detailed Description

A nucleotide, including support for ambiguity codes.

The nucleotide is represented internally using an integer representation. This may be helpful for e.g. indexing into a table. Therefore, it is possible to both retrieve this internal representation with intRep() and construct a Nucleotide from an internal representation directly with fromRep(int).

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Constructor & Destructor Documentation

seq::Nucleotide::Nucleotide (   )

Create a nucleotide with value Nucleotide::N (any).

seq::Nucleotide::Nucleotide (  char  c  )  throw (ParseException)

Create a nucleotide by parsing a character. Accepted are the characters from the FASTA file definition. See also: toChar()

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Member Function Documentation

static Nucleotide seq::Nucleotide::fromRep (  int  rep  )  [inline, static]

Create a nucleotide using the internal representation directly. Only valid representations are accepted, see the NT_* constants. Illegal representations are fenced off by an assert() statement. See also: intRep()

int seq::Nucleotide::intRep (   )  const [inline]

Get the internal representation. See also: fromRep(int)

bool seq::Nucleotide::isAmbiguity (   )  const [inline]

Is the nucleotide ambiguous ? Only A,C,G,T are considered non-ambiguous. See also: sampleAmbiguity()

void seq::Nucleotide::nonAmbiguousNucleotides (  std::vector< Nucleotide > &  result  )  const

Get all non ambiguous nucleotides represented by this nucleotide.

bool seq::Nucleotide::operator!= (  const Nucleotide &  other  )  const [inline]

Are two nucleotides different ?

bool seq::Nucleotide::operator< (  const Nucleotide  other  )  const [inline]

So that you can use it as a key for STL containers.

bool seq::Nucleotide::operator== (  const Nucleotide &  other  )  const [inline]

Are two nucleotides identical ?

void seq::Nucleotide::sampleAmbiguity (   )

Replace the (ambiguos) nucleotide with a random non-ambigiuos nucleotide that is represented by the ambiguity symbol. See also: isAmbiguity()

char seq::Nucleotide::toChar (   )  const [inline]

Get the uppercase character representation for this nucleotide. See also: Nucleotide(char)

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Member Data Documentation

const Nucleotide seq::Nucleotide::A [static]

const Nucleotide seq::Nucleotide::B [static]

const Nucleotide seq::Nucleotide::C [static]

const Nucleotide seq::Nucleotide::D [static]

const Nucleotide seq::Nucleotide::G [static]

const Nucleotide seq::Nucleotide::GAP [static]

const Nucleotide seq::Nucleotide::H [static]

const Nucleotide seq::Nucleotide::K [static]

const Nucleotide seq::Nucleotide::M [static]

const Nucleotide seq::Nucleotide::N [static]

const int seq::Nucleotide::NT_A = 0 [static]

const int seq::Nucleotide::NT_B = 13 [static]

const int seq::Nucleotide::NT_C = 1 [static]

const int seq::Nucleotide::NT_D = 12 [static]

const int seq::Nucleotide::NT_G = 2 [static]

const int seq::Nucleotide::NT_GAP = 15 [static]

const int seq::Nucleotide::NT_H = 11 [static]

const int seq::Nucleotide::NT_K = 9 [static]

const int seq::Nucleotide::NT_M = 4 [static]

const int seq::Nucleotide::NT_N = 14 [static]

const int seq::Nucleotide::NT_R = 5 [static]

const int seq::Nucleotide::NT_S = 7 [static]

const int seq::Nucleotide::NT_T = 3 [static]

const int seq::Nucleotide::NT_V = 10 [static]

const int seq::Nucleotide::NT_W = 6 [static]

const int seq::Nucleotide::NT_Y = 8 [static]

const Nucleotide seq::Nucleotide::R [static]

const Nucleotide seq::Nucleotide::S [static]

const Nucleotide seq::Nucleotide::T [static]

const Nucleotide seq::Nucleotide::V [static]

const Nucleotide seq::Nucleotide::W [static]

const Nucleotide seq::Nucleotide::Y [static]

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

• src/sequence/Nucleotide.h
• src/sequence/Nucleotide.C

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