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PMarkov Member List

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

_containerMarkov [protected]
_containersPhasedMarkov [protected]
_jumpPhasedMarkov [protected]
_MuMarkov [protected]
_MusPhasedMarkov [protected]
_nb_paramPhasedMarkov [protected]
_nextPhasePhasedMarkov [protected]
_nMuPhasedMarkov [protected]
_nPiPhasedMarkov [protected]
_orderPhasedMarkov [protected]
_phasePhasedMarkov [protected]
_PiMarkov [protected]
_PisPhasedMarkov [protected]
_postloglikePhasedMarkov [protected]
_PowPiMarkov [protected]
_prevPhasePhasedMarkov [protected]
_prior_alphaPhasedMarkov [protected]
_rankPhasedMarkov [protected]
_sizePhasedMarkov [protected]
_transPhasedMarkov [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_power()Markov
compute_rank()Markov [virtual]
compute_stat_law(bool force=false)Markov [inline]
compute_stat_laws(bool force=false)PhasedMarkov
draw(unsigned long *count, bool decal_required, gsl_rng *r, const Translator &trans=Translator(), const string &xmlfile=string())PMarkov [inline]
draw(gsl_rng *r, const Translator &trans, const string &xmlfile=string())PMarkov [inline]
draw_markov_matrices(const gsl_rng *r)PhasedMarkov
draw_markov_matrix(const gsl_rng *r)Markov [inline]
estimate(const TSeq &tseq, unsigned long beg, unsigned long end, bool calc_rank)Markov [inline]
estimate(unsigned long *count, bool decal_required, bool calc_rank=false)Markov [inline]
estimate(const string &count_file, bool calc_rank=false)Markov [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(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_markov_matrix()Markov [inline]
free_power()Markov
free_stat_law()Markov [inline]
free_stat_laws()PhasedMarkov [inline]
info_nb_leaves() const PMarkov [inline]
isMu() const Markov [inline]
isMus() const PhasedMarkov [inline]
isNextPhase() const PhasedMarkov [inline, protected]
isPi() const Markov [inline]
isPis() const PhasedMarkov [inline]
isPow() const Markov [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(const char *ConfFile, bool calc_rank=false)Markov
Markov(const SequenceSet &seqset, bool calc_rank=false, const string &prior_alpha_file=string())Markov
Markov(const Sequence &seq, bool calc_rank=false, const string &prior_alpha_file=string())Markov
Markov(const Markov &)Markov
Markov()Markov
Markov(short size, short order, bool alloc=true, const string &prior_alpha_file=string())Markov [inline]
Markov(const Markov &M1, const Markov &M2, const float p)Markov
Markov(const gsl_rng *r, short size, short order, bool calc_rank=false)Markov [inline]
Markov(unsigned long *count, short size, short order, const string &prior_alpha_file=string(), bool calc_rank=false)Markov
markov_matrices() const PhasedMarkov [inline]
markov_matrix() const Markov [inline]
PhasedMarkov::markov_matrix(short numphase) const PhasedMarkov [inline]
mean_post_log_likelihood(const TSeq1 &tseq_train, const TSeq2 &tseq_eval, short initial_phase_train=0, short initial_phase_eval=0)PMarkov [inline]
mean_post_log_likelihood(const TSeq &tseq_eval, short initial_phase_eval=0)PMarkov [inline]
mean_post_log_likelihood(unsigned long *count_train, bool decal_required_t, unsigned long *count_eval, bool decal_required_e)PMarkov [inline]
mean_post_log_likelihood(unsigned long *count_eval, bool decal_required_e)PMarkov [inline]
mean_post_log_likelihood()PMarkov [inline]
Mu(int index) const Markov [inline]
PhasedMarkov::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)Markov [inline]
PhasedMarkov::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
Pi(int index, int p=0) const PhasedMarkov [inline]
PMarkov(Partition &p, const SequenceSet &seqset, const string &prior_alpha_file=string(), bool motif_prior=true, double penalty=0., const string &xmlfile=string())PMarkov [inline]
PMarkov(Partition &p, const Sequence &seq, const string &prior_alpha_file=string(), bool motif_prior=true, double penalty=0., const Translator &trans=Translator(), const string &xmlfile=string())PMarkov [inline]
PMarkov(Partition &p, unsigned long *count, short size, short order, const string &prior_alpha_file=string(), bool motif_prior=true, double penalty=0., const Translator &trans=Translator(), const string &xmlfile=string())PMarkov [inline]
PMarkov(Partition &part, const string &count_file, short size, short order, const string &prior_alpha_file=string(), bool motif_prior=true, double penalty=0., const Translator &trans=Translator(), const string &xmlfile=string())PMarkov [inline]
PMarkov(Partition &part, short size, short order, const string &prior_alpha_file=string(), bool motif_prior=true, double penalty=0., bool alloc=true)PMarkov [inline]
post_log_likelihood(const TSeq &tseq_eval)PMarkov [inline]
post_log_likelihood(unsigned long *count_eval, bool decal_required_e)PMarkov [inline]
Markov::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
proba_step(long w1, long w2, int step)Markov [inline]
select(unsigned long *count, bool decal_required, const Translator &trans=Translator(), const string &xmlfile=string())PMarkov [inline]
stat_law() const Markov [inline]
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
~Markov()Markov [virtual]
~PhasedMarkov()PhasedMarkov [virtual]



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