| alt_scoring_current | StochHMM::trellis | private |
| alt_scoring_previous | StochHMM::trellis | private |
| alt_simple_stochastic_table | StochHMM::trellis | private |
| backward() | StochHMM::trellis | |
| backward(model *h, sequences *sqs) | StochHMM::trellis | |
| backward_score | StochHMM::trellis | private |
| baum_welch() | StochHMM::trellis | |
| complex_emissions | StochHMM::trellis | private |
| complex_transitions | StochHMM::trellis | private |
| dbl_backward_score | StochHMM::trellis | private |
| dbl_baum_welch_score | StochHMM::trellis | private |
| dbl_forward_score | StochHMM::trellis | private |
| dbl_posterior_score | StochHMM::trellis | private |
| dbl_viterbi_score | StochHMM::trellis | private |
| ending_backward_prob | StochHMM::trellis | private |
| ending_forward_prob | StochHMM::trellis | private |
| ending_nth_viterbi | StochHMM::trellis | private |
| ending_viterbi_score | StochHMM::trellis | private |
| ending_viterbi_tb | StochHMM::trellis | private |
| exDef_defined | StochHMM::trellis | private |
| explicit_duration_current | StochHMM::trellis | private |
| explicit_duration_previous | StochHMM::trellis | private |
| export_trellis(std::ifstream &) | StochHMM::trellis | |
| export_trellis(std::string &file) | StochHMM::trellis | |
| fast_complex_backward() | StochHMM::trellis | |
| fast_complex_backward(model *h, sequences *sqs) | StochHMM::trellis | |
| fast_complex_baum_welch() | StochHMM::trellis | |
| fast_complex_baum_welch(model *h, sequences *sqs) | StochHMM::trellis | |
| fast_complex_stochastic_forward() | StochHMM::trellis | |
| fast_complex_stochastic_forward(model *h, sequences *sqs) | StochHMM::trellis | |
| fast_complex_stochastic_viterbi() | StochHMM::trellis | |
| fast_complex_stochastic_viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| fast_complex_viterbi() | StochHMM::trellis | |
| fast_complex_viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| forward() | StochHMM::trellis | |
| forward(model *h, sequences *sqs) | StochHMM::trellis | |
| forward_score | StochHMM::trellis | private |
| get_dbl_posterior() | StochHMM::trellis | inline |
| get_explicit_duration_length(transition *trans, size_t sequencePosition, size_t state_iter, size_t to_state) | StochHMM::trellis | private |
| get_model() | StochHMM::trellis | inline |
| get_naive_backward_scores() | StochHMM::trellis | inline |
| get_naive_forward_scores() | StochHMM::trellis | inline |
| get_naive_viterbi_scores() | StochHMM::trellis | inline |
| getBackwardProbability() | StochHMM::trellis | inline |
| getBackwardTable() | StochHMM::trellis | inline |
| getEndingTransition(size_t) | StochHMM::trellis | private |
| getForwardProbability() | StochHMM::trellis | inline |
| getForwardTable() | StochHMM::trellis | inline |
| getModel() | StochHMM::trellis | inline |
| getPosteriorTable() | StochHMM::trellis | inline |
| getSeq() | StochHMM::trellis | inline |
| getTransition(state *st, size_t trans_to_state, size_t sequencePosition) | StochHMM::trellis | private |
| hmm | StochHMM::trellis | private |
| naive_backward() | StochHMM::trellis | |
| naive_backward(model *h, sequences *sqs) | StochHMM::trellis | |
| naive_baum_welch() | StochHMM::trellis | |
| naive_baum_welch(model *h, sequences *sqs) | StochHMM::trellis | |
| naive_forward() | StochHMM::trellis | |
| naive_forward(model *h, sequences *sqs) | StochHMM::trellis | |
| naive_nth_scores | StochHMM::trellis | private |
| naive_nth_viterbi(size_t n) | StochHMM::trellis | |
| naive_nth_viterbi(model *h, sequences *sqs, size_t n) | StochHMM::trellis | |
| naive_stochastic_forward() | StochHMM::trellis | |
| naive_stochastic_forward(model *h, sequences *sqs) | StochHMM::trellis | |
| naive_stochastic_viterbi() | StochHMM::trellis | |
| naive_stochastic_viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| naive_viterbi() | StochHMM::trellis | |
| naive_viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| nth_scoring_current | StochHMM::trellis | private |
| nth_scoring_previous | StochHMM::trellis | private |
| nth_size | StochHMM::trellis | private |
| nth_swap_ptr | StochHMM::trellis | private |
| nth_traceback_table | StochHMM::trellis | private |
| nth_viterbi() | StochHMM::trellis | |
| nth_viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| posterior() | StochHMM::trellis | |
| posterior(model *h, sequences *sqs) | StochHMM::trellis | |
| posterior_score | StochHMM::trellis | private |
| print() | StochHMM::trellis | |
| reset() | StochHMM::trellis | |
| scoring_current | StochHMM::trellis | private |
| scoring_previous | StochHMM::trellis | private |
| seq_size | StochHMM::trellis | private |
| seqs | StochHMM::trellis | private |
| simple_backward() | StochHMM::trellis | |
| simple_backward(model *h, sequences *sqs) | StochHMM::trellis | |
| simple_baum_welch() | StochHMM::trellis | |
| simple_baum_welch(model *h, sequences *sqs) | StochHMM::trellis | |
| simple_forward() | StochHMM::trellis | |
| simple_forward(model *h, sequences *sqs) | StochHMM::trellis | |
| simple_nth_viterbi(size_t n) | StochHMM::trellis | |
| simple_nth_viterbi(model *h, sequences *sqs, size_t n) | StochHMM::trellis | |
| simple_posterior() | StochHMM::trellis | |
| simple_posterior(model *h, sequences *sqs) | StochHMM::trellis | |
| simple_simple_stochastic_viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| simple_stochastic_forward() | StochHMM::trellis | |
| simple_stochastic_forward(model *h, sequences *sqs) | StochHMM::trellis | |
| simple_stochastic_viterbi() | StochHMM::trellis | |
| simple_stochastic_viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| simple_viterbi() | StochHMM::trellis | |
| simple_viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| sparse_complex_backward() | StochHMM::trellis | |
| sparse_complex_backward(model *h, sequences *sqs) | StochHMM::trellis | |
| sparse_complex_baum_welch() | StochHMM::trellis | |
| sparse_complex_baum_welch(model *h, sequences *sqs) | StochHMM::trellis | |
| sparse_complex_stochastic_forward() | StochHMM::trellis | |
| sparse_complex_stochastic_forward(model *h, sequences *sqs) | StochHMM::trellis | |
| sparse_complex_viterbi() | StochHMM::trellis | |
| sparse_complex_viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| state_size | StochHMM::trellis | private |
| stochastic_forward() | StochHMM::trellis | |
| stochastic_forward(model *h, sequences *sqs) | StochHMM::trellis | |
| stochastic_table | StochHMM::trellis | private |
| stochastic_traceback(traceback_path &path) | StochHMM::trellis | |
| stochastic_traceback(multiTraceback &, size_t) | StochHMM::trellis | |
| stochastic_viterbi() | StochHMM::trellis | |
| stochastic_viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| store() | StochHMM::trellis | inline |
| store(bool val) | StochHMM::trellis | inline |
| store_values | StochHMM::trellis | private |
| stringify() | StochHMM::trellis | |
| swap_ptr | StochHMM::trellis | private |
| swap_ptr_duration | StochHMM::trellis | private |
| traceback(traceback_path &path) | StochHMM::trellis | |
| traceback(traceback_path &path, size_t position, size_t state) | StochHMM::trellis | |
| traceback_nth(traceback_path &path, size_t n) | StochHMM::trellis | |
| traceback_nth_viterbi(multiTraceback &) | StochHMM::trellis | |
| traceback_posterior(traceback_path &path) | StochHMM::trellis | |
| traceback_stoch_posterior(traceback_path &path) | StochHMM::trellis | |
| traceback_stoch_posterior(multiTraceback &paths, size_t reps) | StochHMM::trellis | |
| traceback_table | StochHMM::trellis | private |
| transitionFuncTraceback(state *st, size_t position, transitionFuncParam *func) | StochHMM::trellis | private |
| trellis() | StochHMM::trellis | |
| trellis(model *h, sequences *sqs) | StochHMM::trellis | |
| type | StochHMM::trellis | private |
| update_emissions() | StochHMM::trellis | |
| update_transitions() | StochHMM::trellis | |
| viterbi() | StochHMM::trellis | |
| viterbi(model *h, sequences *sqs) | StochHMM::trellis | |
| viterbi_score | StochHMM::trellis | private |
| ~trellis() | StochHMM::trellis | |
1.8.1