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Version 4.0.0 |
#include <seqpp/Sequence.h>
Inheritance diagram for Sequence:
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 | 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_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 |
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 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.
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minimal constructor
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Constructor from a Fasta or Genbank file containing a single sequence.
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total length case Implements PrimaryCount. |
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Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin |