//!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;
}
//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;
}
//!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;
}