, including all inherited members.
| _container | Markov | [protected] |
| _containers | PhasedMarkov | [protected] |
| _jump | PhasedMarkov | [protected] |
| _Mu | Markov | [protected] |
| _Mus | PhasedMarkov | [protected] |
| _nb_param | PhasedMarkov | [protected] |
| _nextPhase | PhasedMarkov | [protected] |
| _nMu | PhasedMarkov | [protected] |
| _nPi | PhasedMarkov | [protected] |
| _order | PhasedMarkov | [protected] |
| _phase | PhasedMarkov | [protected] |
| _Pi | Markov | [protected] |
| _Pis | PhasedMarkov | [protected] |
| _postloglike | PhasedMarkov | [protected] |
| _PowPi | Markov | [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_power() | Markov | |
| compute_rank() | Markov | [virtual] |
| compute_stat_law(bool force=false) | Markov | [inline] |
| compute_stat_laws(bool force=false) | PhasedMarkov | |
| 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] |
| 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] |
| 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] |
| 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(const Sequence &seq, long tbeg, long tend, short numphase=0) const | PhasedMarkov | [inline] |
| 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_c(const Sequence &seq, long tbeg, long tend, short numphase=0) const | PhasedMarkov | [inline] |
| proba_step(long w1, long w2, int step) | Markov | [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] |
1.5.6