seq::CodingSequence Class Reference

A coding sequence represents a nucleotide sequence that codes for an amino acid sequence (an oligo- or polypeptide). More...

#include <CodingSequence.h>

List of all members.

Public Member Functions
	CodingSequence ()
	Construct a coding sequence with empty nucleotide sequence.
	CodingSequence (const NTSequence &aNtSequence)
	Construct a coding sequence based on the given nucleotide sequence.
const NTSequence &	ntSequence () const
	Get the nucleotide sequence.
const AASequence &	aaSequence () const
	Get the amino acid sequence.
void	changeNucleotide (int pos, Nucleotide value)
	Change a nucleotide at a given position in the nucleotide sequence to a new value.
int	whatIfMutation (int pos, Nucleotide value, AminoAcid &oldAA, AminoAcid &newAA) const
	Investigate the effect of a nucleotide mutation on the amino acid sequence.
bool	isSynonymousMutation (int pos, Nucleotide value) const
	Investigate whether a give nucleotide mutation is synonymous or non-synonymous with respect to the amino acid sequence.
void	allAASequences (std::vector< std::set< AminoAcid > > &result) const
	Get the amino acid sequence possibilities, taking into account all ambiguities.
Protected Member Functions
void	updateAASequence () const

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Detailed Description

A coding sequence represents a nucleotide sequence that codes for an amino acid sequence (an oligo- or polypeptide).

It is useful when one wants to track the effect of changes in the nucleotide sequence for the amino acid sequence, and to investigate properties of nucleotide mutations.

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Constructor & Destructor Documentation

seq::CodingSequence::CodingSequence (   )

Construct a coding sequence with empty nucleotide sequence.

seq::CodingSequence::CodingSequence (  const NTSequence &  aNtSequence  )

Construct a coding sequence based on the given nucleotide sequence. The sequence must be translatable as per AASequence::translate(const NTSequence&).

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Member Function Documentation

const AASequence & seq::CodingSequence::aaSequence (   )  const

Get the amino acid sequence. If needed, the amino acid sequence is updated to reflect changes in the nucleotide sequence.

void seq::CodingSequence::allAASequences (  std::vector< std::set< AminoAcid > > &  result  )  const

Get the amino acid sequence possibilities, taking into account all ambiguities.

void seq::CodingSequence::changeNucleotide (  int  pos, Nucleotide  value )

Change a nucleotide at a given position in the nucleotide sequence to a new value.

bool seq::CodingSequence::isSynonymousMutation (  int  pos, Nucleotide  value )  const

Investigate whether a give nucleotide mutation is synonymous or non-synonymous with respect to the amino acid sequence.

const NTSequence& seq::CodingSequence::ntSequence (   )  const [inline]

Get the nucleotide sequence.

void seq::CodingSequence::updateAASequence (   )  const [protected]

int seq::CodingSequence::whatIfMutation (  int  pos, Nucleotide  value, AminoAcid &  oldAA, AminoAcid &  newAA )  const

Investigate the effect of a nucleotide mutation on the amino acid sequence. This returns both the old (oldAA) and new amino acid (newAA) encoded by the mutation, as well as the position (return value).

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

• src/sequence/CodingSequence.h
• src/sequence/CodingSequence.C

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