//!Perform traceback through trellis //!\return [out] path trackback_path void simpleTrellis::traceback(traceback_path& path) { if (ending.viti!=-INFINITY) { path.setScore(ending.viti); int pointer=ending.ptr; path.push_back(ending.ptr); size_t seq_length = seq->getLength(); if (seq_length==0) { return; } for(size_t position=seq_length -1 ; position>0; position--) { pointer=trell[position][pointer].ptr; path.push_back(pointer); if (pointer==-2) { path.clear(); return; } } } return; }
//!Perform traceback through trellis //!\return [out] path trackback_path void simpleTrellis::traceback(traceback_path& path,size_t n) { if (n<=ending.nth_viterbi_scores->size()) { if (ending.viti!=-INFINITY) { path.setScore((*ending.nth_viterbi_scores)[n].viterbi_score); int state_pointer=(*ending.nth_viterbi_scores)[n].traceback_state; size_t score_pointer = (*ending.nth_viterbi_scores)[n].traceback_state_score; path.push_back(state_pointer); size_t seq_length = seq->getLength(); if (seq_length==0) { return; } for(size_t position=seq_length -1 ; position>0; position--) { state_pointer = (*trell[position][state_pointer].nth_viterbi_scores)[score_pointer].traceback_state; score_pointer = (*trell[position][state_pointer].nth_viterbi_scores)[score_pointer].traceback_state_score; path.push_back(state_pointer); if (state_pointer==-2) { path.clear(); return; } } } } return; }
//!Perform traceback through trellis //!\return path trackback_path void trellis::traceback(traceback_path& path){ if (seq_size==0 || traceback_table == NULL){ return; } if (ending_viterbi_score == -INFINITY){ return; } else{ path.setScore(ending_viterbi_score); path.push_back(ending_viterbi_tb); int16_t pointer = ending_viterbi_tb; for( size_t position = seq_size -1 ; position>0 ; position--){ pointer = (*traceback_table)[position][pointer]; if (pointer == -1){ std::cerr << "No valid path at Position: " << position << std::endl; return; } path.push_back(pointer); } } return; }
//!Perform a traceback starting at position and state given //! \param [out] traceback_path //! \param position Position to start traceback //! \param state State to begin traceback void trellis::traceback(traceback_path& path, size_t position, size_t state){ if (seq_size == 0 || traceback_table == NULL){ return; } if (path.getModel() == NULL){ path.setModel(hmm); } int16_t pointer = (*traceback_table)[position][state]; if (pointer == -1){ std::cerr << "No valid path at State: " << state << " from Position: " << position << std::endl; return; } for( size_t pos = position - 1 ; pos>0 ; pos--){ pointer = (*traceback_table)[pos][pointer]; if (pointer == -1){ std::cerr << "No valid path at State: " << state << " from Position: " << position << std::endl; return; } path.push_back(pointer); } return; }
//!Tracing posterior not currently supported on simpleTrellis void basicTrellis::tracePosterior(traceback_path& path){ size_t seq_length = seq->getLength(); if (seq_length==0){ return; } for (size_t position = seq_length-1;position!=SIZE_MAX;--position){ path.push_back((*posterior_pointer)[position]); } return; }
void basicTrellis::traceStochPosterior(traceback_path& path){ size_t states = hmm->state_size(); size_t seq_length = seq->getLength(); if (seq_length==0){ return; } for (size_t position = seq_length-1;position!=SIZE_MAX;--position){ double random=((double)rand()/((double)(RAND_MAX)+(double)(1))); double cumulative_prob(0.0); for (int state = 0; state<states ; ++state){ cumulative_prob+=(*posterior)[position][state]; if (random<cumulative_prob){ path.push_back(state); break; } } } return; }
//TODO: Finish nth traceback function void trellis::traceback_nth(traceback_path& path, size_t n){ if (seq_size == 0 || n > nth_size || (nth_traceback_table == NULL && naive_nth_scores == NULL)){ return; } if (nth_traceback_table != NULL){ int16_t st_pointer = (*ending_nth_viterbi)[n].st_tb; int16_t sc_pointer = (*ending_nth_viterbi)[n].score_tb; path.setScore((*ending_nth_viterbi)[n].score); path.push_back(st_pointer); for( size_t position = seq_size -1 ; position>0 ; position--){ (*nth_traceback_table)[position].get(st_pointer,sc_pointer); if (st_pointer == -1){ std::cerr << "No valid path at Position: " << position << std::endl; return; } path.push_back(st_pointer); } } else{ int16_t st_pointer = (*ending_nth_viterbi)[n].st_tb; int16_t sc_pointer = (*ending_nth_viterbi)[n].score_tb; path.setScore((*ending_nth_viterbi)[n].score); path.push_back(st_pointer); for( size_t position = seq_size -1 ; position>0 ; position--){ nthScore& temp = (*(*naive_nth_scores)[position][st_pointer])[sc_pointer]; st_pointer = temp.st_tb; sc_pointer = temp.score_tb; if (st_pointer == -1){ std::cerr << "No valid path at Position: " << position << std::endl; return; } path.push_back(st_pointer); } } return; }