seq::NTSequence Class Reference

A nucleotide sequence. More...

#include <NTSequence.h>

List of all members.

Public Member Functions
	NTSequence ()
	Create an empty nucleotide sequence with emtpy name and empty description.
	NTSequence (unsigned size)
	Create a nucleotide sequence of length size, filled with Nucleotide::N, with empty name and emtpy description.
	NTSequence (const std::string name, const std::string description, const std::string aSeqString, bool sampleAmbiguities=false) throw (ParseException)
	Create a nucleotide sequence with given name and description, and with the given sequence string.
	NTSequence (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[.
void	sampleAmbiguities ()
	Remove ambiguity nucleotide symbols by replacing them by sampling a random non-ambiguous nucleotide that is represented by the ambiguity symbol.
void	nonAmbiguousSequences (std::vector< NTSequence > &result) const
	Add all the possible non-ambiguous sequences possibly represented by this sequence to result.
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.

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Detailed Description

A nucleotide sequence.

The sequence may have a name and a description.

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

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Constructor & Destructor Documentation

seq::NTSequence::NTSequence (   )

Create an empty nucleotide sequence with emtpy name and empty description.

seq::NTSequence::NTSequence (  unsigned  size  )

Create a nucleotide sequence of length size, filled with Nucleotide::N, with empty name and emtpy description.

seq::NTSequence::NTSequence (  const std::string  name, const std::string  description, const std::string  aSeqString, bool  sampleAmbiguities = false )  throw (ParseException)

Create a nucleotide sequence with given name and description, and with the given sequence string. Each character in the sequence string will be interpreted as a Nucleotide using the Nucleotide::Nucleotide(char) constructor. If sampleAmbiguities = true, then sampleAmbiguities() is performed during construction. See also: sampleAmbiguities()

seq::NTSequence::NTSequence (  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::NTSequence::asString (   )  const

Represent the sequence data as a string.

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

Get the description.

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

Get the name.

void seq::NTSequence::nonAmbiguousSequences (  std::vector< NTSequence > &  result  )  const

Add all the possible non-ambiguous sequences possibly represented by this sequence to result.

void seq::NTSequence::sampleAmbiguities (   )

Remove ambiguity nucleotide symbols by replacing them by sampling a random non-ambiguous nucleotide that is represented by the ambiguity symbol. See also: Nucleotide::sampleAmbiguity()

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

Set the description.

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

Set the name.

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

• src/sequence/NTSequence.h

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