_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(const TSeq &tseq, short phase, short initial_phase, unsigned long beg, unsigned long end, bool calc_rank=false, bool count_again=true) | PhasedMarkov | [inline] |
estimate(const string &count_file, bool calc_rank=false) | PhasedMarkov | [inline] |
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 | |
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] |