seq::AASequence Class Reference

An amino acid sequence. More...

#include <AASequence.h>

List of all members.

Public Member Functions
	AASequence ()
	Create an empty amino acid sequence with emtpy name and empty description.
	AASequence (unsigned size)
	Create an amino acid sequence of length size, filled with AminoAcid::X, with empty name and emtpy description.
	AASequence (const std::string name, const std::string description, const std::string aSeqString) throw (ParseException)
	Create an amino acid sequence with given name and description, and with the given sequence string.
	AASequence (const const_iterator first, const const_iterator last)
	Create a nucleotide sequence with empty name and emtpy description, and copy the sequence data from the range [first, last[.
std::string	asString () const
	Represent the sequence data as a string.
std::string	name () const
	Get the name.
std::string	description () const
	Get the description.
void	setName (std::string name)
	Set the name.
void	setDescription (std::string description)
	Set the description.
Static Public Member Functions
static AASequence	translate (const NTSequence &ntSequence)
	Translate a nucleotide sequence to an amino acid sequence.
static AASequence	translate (const NTSequence::const_iterator begin, const NTSequence::const_iterator end)
	Translate a nucleotide sequence, defined by the range begin to end, to an amino acid sequence.

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Detailed Description

An amino acid sequence.

The sequence may have a name and a description.

The sequence data is stored by publicly inheriting std::vector<AminoAcid>, so you can use all std::vector manipulations to access the amino acid data.

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Constructor & Destructor Documentation

seq::AASequence::AASequence (   )

Create an empty amino acid sequence with emtpy name and empty description.

seq::AASequence::AASequence (  unsigned  size  )

Create an amino acid sequence of length size, filled with AminoAcid::X, with empty name and emtpy description.

seq::AASequence::AASequence (  const std::string  name, const std::string  description, const std::string  aSeqString )  throw (ParseException)

Create an amino acid sequence with given name and description, and with the given sequence string. Each character in the sequence string will be interpreted as an AminoAcid using the AminoAcid::AminoAcid(char) constructor.

seq::AASequence::AASequence (  const const_iterator  first, const const_iterator  last )

Create a nucleotide sequence with empty name and emtpy description, and copy the sequence data from the range [first, last[.

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Member Function Documentation

std::string seq::AASequence::asString (   )  const

Represent the sequence data as a string.

std::string seq::AASequence::description (   )  const [inline]

Get the description.

std::string seq::AASequence::name (   )  const [inline]

Get the name.

void seq::AASequence::setDescription (  std::string  description  )  [inline]

Set the description.

void seq::AASequence::setName (  std::string  name  )  [inline]

Set the name.

AASequence seq::AASequence::translate (  const NTSequence::const_iterator  begin, const NTSequence::const_iterator  end )  [static]

Translate a nucleotide sequence, defined by the range begin to end, to an amino acid sequence. The nucleotide sequence must have a length that is a multiple of three. The resulting amino acid sequence will contain an amino acid for every triplet of nucleotides in the nucleotide sequence, and will have an empty name and empty description. See also: translate(const NTSequence&), Codon::translate(const NTSequence::const_iterator)

AASequence seq::AASequence::translate (  const NTSequence &  ntSequence  )  [static]

Translate a nucleotide sequence to an amino acid sequence. The nucleotide sequence must have a length that is a multiple of three. The resulting amino acid sequence will contain an amino acid for every triplet of nucleotides in the nucleotide sequence. The amino acid sequence will have the same name and description as the nucleotide sequence. See also: translate(const NTSequence::const_iterator, const NTSequence::const_iterator), Codon::translate(const NTSequence::const_iterator)

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

• src/sequence/AASequence.h
• src/sequence/AASequence.C

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