seq Namespace Reference

Classes
class	NucleotideSubstitutionModel
	Describes the mutation behaviour of (the whole of) replication enzymes for one replication cycle. More...
class	AASequence
	An amino acid sequence. More...
class	AminoAcid
	An amino acid. More...
class	CodingSequence
	A coding sequence represents a nucleotide sequence that codes for an amino acid sequence (an oligo- or polypeptide). More...
class	Codon
	Utility class that defines the genetic code. More...
class	Mutation
	A mutation in a sequence of type Char. More...
class	NTSequence
	A nucleotide sequence. More...
class	Nucleotide
	A nucleotide, including support for ambiguity codes. More...
class	ParseException
	Exception thrown when an error was encountered while parsing the string representation of an nucleotide, nucleotide sequence, amino acid, amino acid sequence, or a FASTA file. More...
Typedefs
typedef Mutation< Nucleotide >	NTMutation
	A typedef for nucleotide mutations.
typedef Mutation< AminoAcid >	AAMutation
	A typedef for amino acid mutations.
Functions
void	readFastaEntry (std::istream &i, std::string &name, std::string &description, std::string &sequence) throw (ParseException)
void	writeFastaEntry (std::ostream &o, const std::string &name, const std::string &description, const std::string &sequence)
std::istream &	operator>> (std::istream &i, AASequence &sequence) throw (ParseException)
	Read an amino acid sequence in FASTA format from the given stream.
std::ostream &	operator<< (std::ostream &o, const AASequence &sequence)
	Write an amino acid sequence to the given stream in FASTA format.
std::ostream &	operator<< (std::ostream &o, const AminoAcid aa)
	Write the one-letter representation of the amino acid to the stream.
void	printAmbiguousAASequence (std::ostream &out, const CodingSequence &cs)
	Write an amino acid sequence with all possible ambiguities to the stream.
std::set< AAMutation >	readMutations (std::istream &mutationFile, std::string prefix) throw (ParseException)
std::istream &	operator>> (std::istream &i, NTSequence &sequence) throw (ParseException)
	Read a nucleotide sequence in FASTA format from the given stream.
std::ostream &	operator<< (std::ostream &o, const NTSequence &sequence)
	Write a nucleotide sequence to the given stream in FASTA format.
std::ostream &	operator<< (std::ostream &o, const Nucleotide nt)
	Write the character representation of the nucleotide.

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Typedef Documentation

typedef class Mutation< AminoAcid > seq::AAMutation

A typedef for amino acid mutations.

typedef class Mutation< Nucleotide > seq::NTMutation

A typedef for nucleotide mutations.

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Function Documentation

std::ostream & seq::operator<< (  std::ostream &  s, const Nucleotide  nt )

Write the character representation of the nucleotide.

std::ostream& seq::operator<< (  std::ostream &  o, const NTSequence &  sequence )

Write a nucleotide sequence to the given stream in FASTA format.

std::ostream & seq::operator<< (  std::ostream &  s, const AminoAcid  aa )

Write the one-letter representation of the amino acid to the stream.

std::ostream & seq::operator<< (  std::ostream &  o, const AASequence &  sequence )

Write an amino acid sequence to the given stream in FASTA format.

std::istream& seq::operator>> (  std::istream &  i, NTSequence &  sequence )  throw (ParseException)

Read a nucleotide sequence in FASTA format from the given stream.

std::istream & seq::operator>> (  std::istream &  i, AASequence &  sequence )  throw (ParseException)

Read an amino acid sequence in FASTA format from the given stream.

void seq::printAmbiguousAASequence (  std::ostream &  out, const CodingSequence &  cs )

Write an amino acid sequence with all possible ambiguities to the stream. The format is e.g. TW{LM}YS

void seq::readFastaEntry (  std::istream &  i, std::string &  name, std::string &  description, std::string &  sequence )  throw (ParseException)

std::set< AAMutation > seq::readMutations (  std::istream &  mutationFile, std::string  prefix )  throw (ParseException)

void seq::writeFastaEntry (  std::ostream &  o, const std::string &  name, const std::string &  description, const std::string &  sequence )

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