Sequence Class Reference

The Sequence class has been designed for Markovian analysis of a single sequence. More...

#include <seqpp/Sequence.h>

Inheritance diagram for Sequence:

List of all members.

Public Member Functions
	Sequence (ifstream &ifile, short order, const Translator &transl, Coder &coder, const string &name_file="noname")
	Constructor from a flow ifile from a fasta file.
	Sequence (short order, unsigned long length, const Translator &transl)
	minimal constructor
	Sequence (const string &name_file, short order, const Translator &transl)
	Constructor from a Fasta or Genbank file containing a single sequence.
	Sequence (const Sequence &seq)
	Copy constructor.
	Sequence (const Sequence &seq, short order)
	Deduction constructor from an order 0-sequence.
virtual	~Sequence ()
	destructor
short	tell_int (unsigned long pos) const
	Returns the int value of the token on position pos.
long	tell_code (unsigned long pos) const
	Returns the code on position pos.
long &	operator() (unsigned long pos) const
	idem "tell_code" Returns the code on position pos
long	tell_code () const
	Returns the code on current position.
const long *	seq () const
	Returns the coded sequence as a vector.
const long *	get_code () const
	Returns the coded sequence as a vector.
void	simule (const double *m_trans, const double *v_init, const gsl_rng *r)
	simulate the observations from a transition matrix and a vector for initial _order-word proba
void	simule (const double *m_trans, const gsl_rng *r)
	simulate the observations from a transition matrix, random initial law
void	simule_under_composition (const double *v_statlaw, long s_statlaw, const gsl_rng *r)
	simulate the observations using the stat law the tokens composition
void	simule_phased (short phase, const double **m_trans, const double *v_init, const gsl_rng *r)
	simulate the observations from a vector of transition matrices and a vector for initial _order word proba
void	simule (unsigned long position, double *proba, const gsl_rng *r)
	simulate the observation on position from a alphabet size vector
Protected Member Functions
virtual unsigned long	tell_max_count () const
	return the max length for the count
virtual void	compute_count (unsigned long **extern_count, short phase, short initial_phase, unsigned long beg, unsigned long end) const
	compute the count

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Detailed Description

The Sequence class has been designed for Markovian analysis of a single sequence.

On each position, the markovian predictor is coded and store (see PrimaryCount):

  Exple with the alphabet AGCT: 
  sequence position  .... 7  8  9 ...
  token              .... A  G  A ...
  code stored        ..........24

Sequence object of integer values corresponding to the code of the word considered on a position t for a Markov model of order _order... this code corresponds to the number of smaller words and the calculus in base |A| of this word, with A the alphabet.
ex : from A to GGG for order 2 with dna alphabet

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Constructor & Destructor Documentation

Sequence::Sequence	(	ifstream &	ifile,
		short	order,
		const Translator &	transl,
		Coder &	coder,
		const string &	name_file = "noname"
	)

Constructor from a flow ifile from a fasta file.

on the position of the char '>', create an object until the next '>' generating his name by the concatenation of the sentence after the char '>'. The flow is or eof or on a '>' at the end.

Parameters:

	ifile	iftream flow
	order	markovian order
	transl	reference to a Translator
	coder	reference to a Coder
	name_file	file name corresponding to ifile

References PrimaryCount::_coder, PrimaryCount::_coder_in, PrimaryCount::_count, PrimaryCount::_count_ok, PrimarySequence::_ipos, PrimarySequence::_length, PrimarySequence::_name, PrimarySequence::_name_file, PrimaryCount::_nbinv, PrimaryCount::_nbvalue, PrimarySequence::_nmodal, PrimarySequence::_obs, PrimaryCount::_order, PrimaryCount::_phase, PrimarySequence::_sizecode, and PrimarySequence::_transl.

Sequence::Sequence	(	short	order,
		unsigned long	length,
		const Translator &	transl
	)

minimal constructor

Parameters:

	order	markovian order
	length	default length
	transl	reference to a Translator

References PrimaryCount::_coder, PrimaryCount::_coder_in, PrimaryCount::_count, PrimaryCount::_count_ok, PrimarySequence::_ipos, PrimarySequence::_length, PrimarySequence::_name, PrimarySequence::_name_file, PrimaryCount::_nbinv, PrimaryCount::_nbvalue, PrimarySequence::_nmodal, PrimarySequence::_obs, PrimaryCount::_order, PrimaryCount::_phase, PrimarySequence::_sizecode, and PrimarySequence::_transl.

Sequence::Sequence	(	const string &	name_file,
		short	order,
		const Translator &	transl
	)

Constructor from a Fasta or Genbank file containing a single sequence.

Parameters:

	name_file	file name to open
	order	markovian order
	transl	reference to a Translator

References PrimaryCount::_coder, PrimaryCount::_coder_in, PrimaryCount::_count, PrimaryCount::_count_ok, PrimarySequence::_ipos, PrimarySequence::_length, PrimarySequence::_name, PrimarySequence::_name_file, PrimaryCount::_nbinv, PrimaryCount::_nbvalue, PrimarySequence::_nmodal, PrimarySequence::_obs, PrimaryCount::_order, PrimaryCount::_phase, PrimarySequence::_sizecode, and PrimarySequence::_transl.

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

• Sequence.h
• Sequence.cc