/////////////////////////////////////////////////////////////////////////////////////
// Realign hits: compute F/B/MAC and MAC-backtrace algorithms
/////////////////////////////////////////////////////////////////////////////////////
void PosteriorDecoder::realign(HMM &q, HMM &t, Hit &hit,
PosteriorMatrix &p_mm, ViterbiMatrix &viterbi_matrix,
std::vector<PosteriorDecoder::MACBacktraceResult> alignment_to_exclude,
char * exclstr, char* template_exclstr, int par_min_overlap, float shift, float mact, float corr) {
HMM & curr_q_hmm = q;
HMM & curr_t_hmm = t;
memorizeHitValues(hit);
initializeForAlignment(curr_q_hmm, curr_t_hmm, hit, viterbi_matrix, 0, t.L, par_min_overlap);
for (size_t ibt = 0; ibt < alignment_to_exclude.size(); ibt++) {
// Mask out previous found MAC alignments
excludeMACAlignment(q.L, hit.L, viterbi_matrix, 0, alignment_to_exclude.at(ibt));
}
if(exclstr) {
// Mask excluded regions
exclude_regions(exclstr, curr_q_hmm, curr_t_hmm, viterbi_matrix);
}
if(template_exclstr) {
// Mask excluded regions
exclude_template_regions(template_exclstr, curr_q_hmm, curr_t_hmm, viterbi_matrix);
}
forwardAlgorithm(curr_q_hmm, curr_t_hmm, hit, p_mm, viterbi_matrix, shift, 0);
//std::cout << hit->score << hit[elem]->Pforward << std::endl;
backwardAlgorithm(curr_q_hmm, curr_t_hmm, hit, p_mm, viterbi_matrix, shift, 0);
macAlgorithm(curr_q_hmm, curr_t_hmm, hit, p_mm, viterbi_matrix, mact, 0);
backtraceMAC(curr_q_hmm, curr_t_hmm, p_mm, viterbi_matrix, 0, hit, corr);
restoreHitValues(hit);
writeProfilesToHits(curr_q_hmm, curr_t_hmm, p_mm, viterbi_matrix, hit);
// add result to exclution paths (needed to align 2nd, 3rd, ... best alignment)
}
std::vector<Hit> ViterbiRunner::alignment(Parameters& par, HMMSimd * q_simd,
std::vector<HHEntry*> dbfiles, const float qsc, float* pb,
const float S[20][20], const float Sim[20][20], const float R[20][20], const int ssm_mode,
const float S73[NDSSP][NSSPRED][MAXCF], const float S33[NSSPRED][MAXCF][NSSPRED][MAXCF],
const float S37[NSSPRED][MAXCF][NDSSP]) {
HMM * q = q_simd->GetHMM(0);
// Initialize memory
std::vector<HMM*> t_hmm;
for(size_t i = 0; i < HMMSimd::VEC_SIZE * thread_count; i++) {
HMM* t = new HMM(MAXSEQDIS, par.maxres);
t_hmm.push_back(t);
}
HMMSimd** t_hmm_simd = new HMMSimd*[thread_count];
std::vector<ViterbiConsumerThread *> threads;
for (int thread_id = 0; thread_id < thread_count; thread_id++) {
t_hmm_simd[thread_id] = new HMMSimd(par.maxres);
ViterbiConsumerThread * thread = new ViterbiConsumerThread(thread_id, par, q_simd, t_hmm_simd[thread_id],viterbiMatrix[thread_id], ssm_mode, S73, S33, S37);
threads.push_back(thread);
}
std::vector<Hit> ret_hits;
std::vector<HHEntry*> dbfiles_to_align;
std::map<std::string, std::vector<Viterbi::BacktraceResult> > excludeAlignments;
// For all the databases comming through prefilter
std::copy(dbfiles.begin(), dbfiles.end(), std::back_inserter(dbfiles_to_align));
// loop to detect second/thrid/... best alignemtns
for (int alignment = 0; alignment < par.altali; alignment++) {
HH_LOG(INFO) << "Alternative alignment: " << alignment << std::endl;
unsigned int allElementToAlignCount = dbfiles_to_align.size();
unsigned int seqBlockSize = allElementToAlignCount;
if(alignment == 0 && par.early_stopping_filter){
seqBlockSize = 2000;
}
for(unsigned int seqJunkStart = 0; seqJunkStart < allElementToAlignCount; seqJunkStart += seqBlockSize ){
//sort by length to improve performance.
//desc sort (for better utilisation ofthreads)
unsigned int seqJunkSize = imin(allElementToAlignCount - (seqJunkStart), seqBlockSize);
sort(dbfiles_to_align.begin() + seqJunkStart,
dbfiles_to_align.begin() + (seqJunkStart + seqJunkSize),
HHDatabaseEntryCompare());
// read in data for thread
#pragma omp parallel for schedule(dynamic, 1)
for (unsigned int idb = seqJunkStart; idb < (seqJunkStart + seqJunkSize); idb += HMMSimd::VEC_SIZE) {
int current_thread_id = 0;
#ifdef OPENMP
current_thread_id = omp_get_thread_num();
#endif
const int current_t_index = (current_thread_id * HMMSimd::VEC_SIZE);
std::vector<HMM *> templates_to_align;
// read in alignment
int maxResElem = imin((seqJunkStart + seqJunkSize) - (idb),
HMMSimd::VEC_SIZE);
for (int i = 0; i < maxResElem; i++) {
HHEntry* entry = dbfiles_to_align.at(idb + i);
int format_tmp = 0;
char wg = 1; // performance reason
entry->getTemplateHMM(par, wg, qsc, format_tmp, pb, S, Sim, t_hmm[current_t_index + i]);
t_hmm[current_t_index + i]->entry = entry;
PrepareTemplateHMM(par, q, t_hmm[current_t_index + i], format_tmp, false, pb, R);
templates_to_align.push_back(t_hmm[current_t_index + i]);
}
t_hmm_simd[current_thread_id]->MapHMMVector(templates_to_align);
exclude_alignments(maxResElem, q_simd, t_hmm_simd[current_thread_id],
excludeAlignments, viterbiMatrix[current_thread_id]);
if(par.exclstr) {
// Mask excluded regions
exclude_regions(par.exclstr, maxResElem, q_simd, t_hmm_simd[current_thread_id], viterbiMatrix[current_thread_id]);
}
if(par.template_exclstr) {
// Mask excluded regions
exclude_template_regions(par.template_exclstr, maxResElem, q_simd, t_hmm_simd[current_thread_id], viterbiMatrix[current_thread_id]);
}
// start next job
threads[current_thread_id]->align(maxResElem, par.nseqdis, par.smin);
} // idb loop
// merge thread results
// search hits for next alignment
HH_LOG(INFO) << (seqJunkStart + seqJunkSize) << " alignments done" << std::endl;
merge_thread_results(ret_hits, dbfiles_to_align, excludeAlignments, threads, alignment, par.smin);
for (unsigned int thread = 0; thread < threads.size(); thread++) {
threads[thread]->clear();
}
if ( alignment == 0 && par.early_stopping_filter )
{
float early_stopping_sum = calculateEarlyStop(par, q, ret_hits, seqJunkStart);
float filter_cutoff = seqJunkSize * par.filter_thresh;
if( early_stopping_sum < filter_cutoff){
HH_LOG(INFO) << "Stop after DB-HHM: " << (seqJunkStart + seqJunkSize) << " because early stop "
<< early_stopping_sum << " < filter cutoff " << filter_cutoff << "\n";
break; // stop junk loop and just find alternative alignments
}
}
} // junk loop
// earse first elements. These are the elements from alignment run before,
// new elements are after + elementToAlignCount
dbfiles_to_align.erase(dbfiles_to_align.begin(), dbfiles_to_align.begin() + allElementToAlignCount);
} // Alignment loop
// clean memory
for (int thread_id = 0; thread_id < thread_count; thread_id++) {
delete t_hmm_simd[thread_id];
delete threads[thread_id];
}
threads.clear();
delete[] t_hmm_simd;
for(size_t i = 0; i < HMMSimd::VEC_SIZE * thread_count; i++) {
delete t_hmm[i];
}
t_hmm.clear();
return ret_hits;
}
