![]() |
Version 4.1.5 |
#include <seqpp/Markov.h>
Inheritance diagram for Markov:
Public Member Functions | |
Markov (const char *ConfFile, bool calc_rank=false) | |
Constructor 1 : read a configuration file. | |
Markov (const SequenceSet &seqset, bool calc_rank=false, const string &prior_alpha_file=string()) | |
Constructor 2 : Estimate the transition matrices on the sequences of seqset. | |
Markov (const Sequence &seq, bool calc_rank=false, const string &prior_alpha_file=string()) | |
Constructor 3 : Estimate the transition matrices on the sequence seq. | |
Markov (const Markov &) | |
Constructor 4 : Copy constructor. | |
Markov () | |
Constructor 5 : Default constructor. | |
Markov (short size, short order, bool alloc=true, const string &prior_alpha_file=string()) | |
Constructor 6 : Minimal Constructor. | |
Markov (const Markov &M1, const Markov &M2, const float p) | |
Constructor 7 : Creation of a "mixed" Markov chain M = p*M1 + (1-p)*M2 */. | |
Markov (const gsl_rng *r, short size, short order, bool calc_rank=false) | |
Constructor 8 : random markov matrices. | |
Markov (unsigned long *count, short size, short order, const string &prior_alpha_file=string(), bool calc_rank=false) | |
Constructor 9 : Estimate the transition matrices on a word-count. | |
virtual | ~Markov () |
Destructor. | |
template<class TSeq> | |
void | estimate (const TSeq &tseq, unsigned long beg, unsigned long end, bool calc_rank) |
Estimate the transition matrices on the sequence/sequenceset tseq. | |
void | estimate (unsigned long *count, bool decal_required, bool calc_rank=false) |
Estimate the transition matrices from a word count. | |
void | estimate (const string &count_file, bool calc_rank=false) |
Estimate the transition matrices from a file containing the count. | |
const double * | markov_matrix () const |
access to the markov matrix | |
void | draw_markov_matrix (const gsl_rng *r) |
draw at random the markov matrix | |
void | free_markov_matrix () |
free the memory allocated for markov matrix | |
void | compute_stat_law (bool force=false) |
Compute the stationnary laws. | |
void | free_stat_law () |
free the memory allocated for stationnary law | |
const double * | stat_law () const |
access to the stationnary distrib | |
virtual int | compute_rank () |
Computes the rank of convergence of the Markov Chain. | |
void | compute_power () |
Initialisation the _rank powers of the markov matrix. | |
int | free_power () |
free the memory allocated for the power | |
double | proba_step (long w1, long w2, int step) |
transition from word w1 to word w2 in step steps | |
bool | isPi () const |
bool | isPow () const |
bool | isMu () const |
double & | operator() (int index) |
() operator for Markov matrix Pi elements | |
double | Mu (int index) const |
Access to stationnary vector Mu elements. | |
Protected Attributes | |
double * | _Pi |
Pointer to "Matrix" (in a vector format) of transition probabilities (=_Pis[0]). | |
double * | _container |
Container of "Matrix" (in a vector format) of transition probabilities (=_containers[0]). | |
double * | _Mu |
Vector of stationnary probabilities (=_Mus[0]). | |
double *** | _PowPi |
Power of the _Pi matrix. |
This is a special case of a phased Markov [PhasedMarkov] model when only one phase is considered.
|
Constructor 2 : Estimate the transition matrices on the sequences of seqset.
|
|
Constructor 3 : Estimate the transition matrices on the sequence seq.
|
|
Constructor 6 : Minimal Constructor. Initialises the constants of the model but not the matrix nor the stat law
|
|
Constructor 7 : Creation of a "mixed" Markov chain M = p*M1 + (1-p)*M2 */.
|
|
Constructor 8 : random markov matrices.
|
|
Constructor 9 : Estimate the transition matrices on a word-count.
|
|
draw at random the markov matrix
const gsl_rng_type * T; // Choice a default generator and seed // from environment variables gsl_rng_env_setup(); // New created instance of the generator T = gsl_rng_default; gsl_rng * r = gsl_rng_alloc (T); // Initialize/Seeds the random number generator gsl_rng_set( r, (long)(time( NULL )) ); ... ... gsl_rng_free( r ); |
|
Estimate the transition matrices from a file containing the count.
Reimplemented from PhasedMarkov. |
|
Estimate the transition matrices from a word count.
|
|
Estimate the transition matrices on the sequence/sequenceset tseq.
|
|
_Mu == NULL ? |
|
_Pi == NULL ? |
|
_PowPi == NULL ? |
|
Access to stationnary vector Mu elements.
|
|
() operator for Markov matrix Pi elements
|
|
transition from word w1 to word w2 in step steps if step > _rank, give stat_law(w2). You must have w1-jump, w2-jump < _nMu |
Download seq++ 4.1.5 |
Download previous versions |
Statistique & Genome Home |
Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin |