Version 4.1.5

PhasedMTDMarkov Member List

This is the complete list of members for PhasedMTDMarkov, including all inherited members.

_containers	PhasedMarkov	[protected]
_jump	PhasedMarkov	[protected]
_Mus	PhasedMarkov	[protected]
_nb_param	PhasedMarkov	[protected]
_nextPhase	PhasedMarkov	[protected]
_nMu	PhasedMarkov	[protected]
_nPi	PhasedMarkov	[protected]
_order	PhasedMarkov	[protected]
_phase	PhasedMarkov	[protected]
_Pis	PhasedMarkov	[protected]
_postloglike	PhasedMarkov	[protected]
_prevPhase	PhasedMarkov	[protected]
_prior_alpha	PhasedMarkov	[protected]
_rank	PhasedMarkov	[protected]
_size	PhasedMarkov	[protected]
_trans	PhasedMarkov	[protected]
AIC(const TSeq &tseq, short initial_phase=0) const	PhasedMarkov	[inline]
BIC(const TSeq &tseq, short initial_phase=0) const	PhasedMarkov	[inline]
compute_init_law(double *MuInit, const SequenceSet &seqset) const	PhasedMarkov
compute_rank()	PhasedMarkov	[virtual]
compute_stat_laws(bool force=false)	PhasedMarkov
draw_markov_matrices(const gsl_rng *r)	PhasedMarkov
estimate(unsigned long **count, bool decal_required, short mkv_order, short phase, short initial_phase, short nbseed, int nbiter_max, double eps, bool log)	PhasedMTDMarkov	[inline]
PhasedMarkov::estimate(const TSeq &tseq, short phase, short initial_phase, unsigned long beg, unsigned long end, bool calc_rank=false, bool count_again=true)	PhasedMarkov	[inline]
PhasedMarkov::estimate(const string &count_file, bool calc_rank=false)	PhasedMarkov	[inline]
PhasedMarkov::estimate(unsigned long **count, bool decal_required, bool calc_rank=false)	PhasedMarkov
file_to_count(const string &src_file, unsigned long **dest_count)	PhasedMarkov
free_markov_matrices()	PhasedMarkov	[inline, virtual]
free_stat_laws()	PhasedMarkov	[inline]
isMus() const	PhasedMarkov	[inline]
isNextPhase() const	PhasedMarkov	[inline, protected]
isPis() const	PhasedMarkov	[inline]
isPrevPhase() const	PhasedMarkov	[inline, protected]
link_to_translator(const Translator &trans)	PhasedMarkov	[inline]
log_likelihood(const SequenceSet &seqset, short initial_phase=0, short numphase=-1) const	PhasedMarkov
log_likelihood(const Sequence &seq, short initial_phase=0, short numphase=-1) const	PhasedMarkov
log_ratio_likelihood(const SequenceSet &seqset, const PhasedMarkov &M, short initial_phase1=0, short initial_phase2=0) const	PhasedMarkov
log_ratio_likelihood(const Sequence &seq, const PhasedMarkov &M, short initial_phase1=0, short initial_phase2=0) const	PhasedMarkov
markov_matrices() const	PhasedMarkov	[inline]
markov_matrix(short numphase) const	PhasedMarkov	[inline]
Mu(int index, int p=0) const	PhasedMarkov	[inline]
nb_parameters() const	PhasedMarkov	[inline, virtual]
new_markov_matrices()	PhasedMarkov	[inline, virtual]
nextPhase(short p) const	PhasedMarkov	[inline]
nMu() const	PhasedMarkov	[inline]
nPi() const	PhasedMarkov	[inline]
operator()(int index, int p=0)	PhasedMarkov	[inline]
PhasedMarkov(const string &markov_file, bool calc_rank=false)	PhasedMarkov
PhasedMarkov(const SequenceSet &seqset, short phase, short initial_phase=0, bool calc_rank=false, const string &prior_alpha_file=string())	PhasedMarkov
PhasedMarkov(const Sequence &seq, short phase, short initial_phase=0, bool calc_rank=false, const string &prior_alpha_file=string())	PhasedMarkov
PhasedMarkov(const PhasedMarkov &phm)	PhasedMarkov
PhasedMarkov()	PhasedMarkov
PhasedMarkov(short size, short order, short phase, bool alloc=true, const string &prior_alpha_file=string())	PhasedMarkov
PhasedMarkov(const PhasedMarkov &M1, const PhasedMarkov &M2, const float p)	PhasedMarkov
PhasedMarkov(const SequenceSet &seqset, const vector< int > &Indseq, short phase, short initial_phase=0, bool calc_rank=false, const string &prior_alpha_file=string())	PhasedMarkov
PhasedMarkov(const gsl_rng *r, short size, short order, short phase, bool calc_rank=false)	PhasedMarkov
PhasedMarkov(unsigned long **count, short size, short order, short phase, short initial_phase=0, bool calc_rank=false, const string &prior_alpha_file=string())	PhasedMarkov
PhasedMTDMarkov(const TSeq &tseq, short mkv_order, short phase, short initial_phase=0, short nbseed=NBSEED, int nbiter_max=NBITERMAX, double eps=EPS, bool log=false)	PhasedMTDMarkov	[inline]
PhasedMTDMarkov(unsigned long **count, short size, short mtd_order, short mkv_order, short phase, short initial_phase=0, short nbseed=NBSEED, int nbiter_max=NBITERMAX, double eps=EPS, bool log=false)	PhasedMTDMarkov	[inline]
Pi(int index, int p=0) const	PhasedMarkov	[inline]
post_log_likelihood(const TSeq1 &tseq_train, const TSeq2 &tseq_eval, bool force=false, short initial_phase_train=0, short initial_phase_eval=0)	PhasedMarkov	[inline]
prevPhase(short p) const	PhasedMarkov	[inline]
print(const string &FileOut)	PhasedMarkov	[inline]
print(ofstream &Out) const	PhasedMarkov
proba(const string &word, Coder &coder, short numphase=0) const	PhasedMarkov
proba(const vector< short > &word, Coder &coder, short numphase=0) const	PhasedMarkov
proba(long word, int lw=-1, long jump=-1, short numphase=0) const	PhasedMarkov
proba(const long *seq, long tbeg, long tend, short numphase=0) const	PhasedMarkov
proba_c(const string &word, Coder &coder, short numphase=0) const	PhasedMarkov
proba_c(const vector< short > &word, Coder &coder, short numphase=0) const	PhasedMarkov
proba_c(long word, int lw=-1, long jump=-1, short numphase=0) const	PhasedMarkov
proba_c(const long *seq, long tbeg, long tend, short numphase=0) const	PhasedMarkov
stat_law(short numphase=0) const	PhasedMarkov	[inline]
Stochasticity()	PhasedMarkov
tell_order() const	PhasedMarkov	[inline]
tell_phase() const	PhasedMarkov	[inline]
tell_rank() const	PhasedMarkov	[inline]
tell_size() const	PhasedMarkov	[inline]
total_variation(const PhasedMarkov &M)	PhasedMarkov
~PhasedMarkov()	PhasedMarkov	[virtual]
~PhasedMTDMarkov()	PhasedMTDMarkov	[inline]

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Contributors : M.Baudry, P.Y.Bourguignon, M.Hoebeke, V.Miele, P.Nicolas, G.Nuel, H.Richard, D.Robelin

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