/**
@brief Similarity pairwise score
This function return the similarity score of two spectra based on SteinScott.
@param s1 const PeakSpectrum Spectrum 1
@param s2 const PeakSpectrum Spectrum 2
@see SteinScottImproveScore()
*/
double SteinScottImproveScore::operator()(const PeakSpectrum & s1, const PeakSpectrum & s2) const
{
const double epsilon = (double)param_.getValue("tolerance");
const double constant = epsilon / 10000;
//const double c(0.0004);
double score(0), sum(0), sum1(0), sum2(0), sum3(0), sum4(0);
/* std::cout << s1 << std::endl;
std::cout << std::endl;
std::cout << s2 << std::endl;*/
for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
{
double temp = it1->getIntensity();
sum1 += temp * temp;
sum3 += temp;
}
for (PeakSpectrum::ConstIterator it1 = s2.begin(); it1 != s2.end(); ++it1)
{
double temp = it1->getIntensity();
sum2 += temp * temp;
sum4 += temp;
}
double z = constant * (sum3 * sum4);
Size j_left(0);
for (Size i = 0; i != s1.size(); ++i)
{
for (Size j = j_left; j != s2.size(); ++j)
{
double pos1(s1[i].getMZ()), pos2(s2[j].getMZ());
if (std::abs(pos1 - pos2) <= 2 * epsilon)
{
sum += s1[i].getIntensity() * s2[j].getIntensity();
}
else
{
if (pos2 > pos1)
{
break;
}
else
{
j_left = j;
}
}
}
}
//std::cout<< sum << " Sum " << z << " z " << std::endl;
score = (sum - z) / (std::sqrt((sum1 * sum2)));
// std::cout<<score<< " score" << std::endl;
if (score < (float)param_.getValue("threshold"))
{
score = 0;
}
return score;
}
double SpectrumAlignmentScore::operator()(const PeakSpectrum & s1, const PeakSpectrum & s2) const
{
const double tolerance = (double)param_.getValue("tolerance");
bool is_relative_tolerance = param_.getValue("is_relative_tolerance").toBool();
bool use_linear_factor = param_.getValue("use_linear_factor").toBool();
bool use_gaussian_factor = param_.getValue("use_gaussian_factor").toBool();
if (use_linear_factor && use_gaussian_factor)
{
cerr << "Warning: SpectrumAlignmentScore, use either 'use_linear_factor' or 'use_gaussian_factor'!" << endl;
}
SpectrumAlignment aligner;
Param p;
p.setValue("tolerance", tolerance);
p.setValue("is_relative_tolerance", (String)param_.getValue("is_relative_tolerance"));
aligner.setParameters(p);
vector<pair<Size, Size> > alignment;
aligner.getSpectrumAlignment(alignment, s1, s2);
double score(0), sum(0), sum1(0), sum2(0);
for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
{
sum1 += it1->getIntensity() * it1->getIntensity();
}
for (PeakSpectrum::ConstIterator it1 = s2.begin(); it1 != s2.end(); ++it1)
{
sum2 += it1->getIntensity() * it1->getIntensity();
}
for (vector<pair<Size, Size> >::const_iterator it = alignment.begin(); it != alignment.end(); ++it)
{
//double factor(0.0);
//factor = (epsilon - fabs(s1[it->first].getPosition()[0] - s2[it->second].getPosition()[0])) / epsilon;
double mz_tolerance(tolerance);
if (is_relative_tolerance)
{
mz_tolerance = mz_tolerance * s1[it->first].getPosition()[0] / 1e6;
}
double mz_difference(fabs(s1[it->first].getPosition()[0] - s2[it->second].getPosition()[0]));
double factor = 1.0;
if (use_linear_factor || use_gaussian_factor)
{
factor = getFactor_(mz_tolerance, mz_difference, use_gaussian_factor);
}
sum += sqrt(s1[it->first].getIntensity() * s2[it->second].getIntensity() * factor);
}
score = sum / (sqrt(sum1 * sum2));
return score;
}
std::vector<PeakSpectrum> AScore::peakPickingPerWindowsInSpectrum_(PeakSpectrum &real_spectrum) const
{
vector<PeakSpectrum> windows_top10;
double spect_lower_bound = floor(real_spectrum.front().getMZ() / 100) * 100;
double spect_upper_bound = ceil(real_spectrum.back().getMZ() / 100) * 100;
Size number_of_windows = static_cast<Size>(ceil((spect_upper_bound - spect_lower_bound) / 100));
windows_top10.resize(number_of_windows);
PeakSpectrum::Iterator it_current_peak = real_spectrum.begin();
Size window_upper_bound(spect_lower_bound + 100);
for (Size current_window = 0; current_window < number_of_windows; ++current_window)
{
PeakSpectrum real_window;
while (((*it_current_peak).getMZ() <= window_upper_bound) && (it_current_peak < real_spectrum.end()))
{
real_window.push_back(*it_current_peak);
++it_current_peak;
}
real_window.sortByIntensity(true);
for (Size i = 0; (i < 10) & (i < real_window.size()); ++i)
{
windows_top10[current_window].push_back(real_window[i]);
}
window_upper_bound += 100;
}
return windows_top10;
}
// s1 should be the original spectrum
DoubleReal CompNovoIdentificationBase::compareSpectra_(const PeakSpectrum & s1, const PeakSpectrum & s2)
{
DoubleReal score(0.0);
PeakSpectrum::ConstIterator it1 = s1.begin();
PeakSpectrum::ConstIterator it2 = s2.begin();
Size num_matches(0);
while (it1 != s1.end() && it2 != s2.end())
{
DoubleReal pos1(it1->getPosition()[0]), pos2(it2->getPosition()[0]);
if (fabs(pos1 - pos2) < fragment_mass_tolerance_)
{
score += it1->getIntensity();
++num_matches;
}
if (pos1 <= pos2)
{
++it1;
}
else
{
++it2;
}
}
if (num_matches == 0)
{
return 0;
}
score /= sqrt((DoubleReal)num_matches);
return score;
}
void SuffixArrayPeptideFinder::getCandidates(vector<vector<pair<SuffixArrayPeptideFinder::FASTAEntry, String> > >& candidates, const String& DTA_file)
{
DTAFile dta_file;
PeakSpectrum s;
dta_file.load(DTA_file, s);
s.sortByPosition();
PeakSpectrum::ConstIterator it(s.begin());
vector<double> spec;
for (; it != s.end(); ++it)
{
spec.push_back(it->getPosition()[0]);
}
const vector<double> specc(spec);
getCandidates(candidates, specc);
return;
}
SqrtMower copy(*e_ptr);
TEST_EQUAL(*e_ptr == copy, true)
END_SECTION
START_SECTION((SqrtMower& operator=(const SqrtMower& source)))
SqrtMower copy;
copy = *e_ptr;
TEST_EQUAL(*e_ptr == copy, true)
END_SECTION
START_SECTION((template<typename SpectrumType> void filterSpectrum(SpectrumType& spectrum)))
DTAFile dta_file;
PeakSpectrum spec;
dta_file.load(OPENMS_GET_TEST_DATA_PATH("Transformers_tests.dta"), spec);
TEST_REAL_SIMILAR((spec.begin() + 40)->getIntensity(), 37.5)
e_ptr->filterSpectrum(spec);
TEST_REAL_SIMILAR((spec.begin() + 40)->getIntensity(), sqrt(37.5))
END_SECTION
START_SECTION((void filterPeakMap(PeakMap& exp)))
DTAFile dta_file;
PeakSpectrum spec;
dta_file.load(OPENMS_GET_TEST_DATA_PATH("Transformers_tests.dta"), spec);
PeakMap pm;
pm.addSpectrum(spec);
TEST_REAL_SIMILAR((pm.begin()->begin() + 40)->getIntensity(), 37.5)
double ZhangSimilarityScore::operator()(const PeakSpectrum & s1, const PeakSpectrum & s2) const
{
const double tolerance = (double)param_.getValue("tolerance");
bool use_linear_factor = param_.getValue("use_linear_factor").toBool();
bool use_gaussian_factor = param_.getValue("use_gaussian_factor").toBool();
double score(0), sum(0), sum1(0), sum2(0) /*, squared_sum1(0), squared_sum2(0)*/;
// TODO remove parameter
if (param_.getValue("is_relative_tolerance").toBool() )
{
throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
}
for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
{
sum1 += it1->getIntensity();
/*
for (PeakSpectrum::ConstIterator it2 = s1.begin(); it2 != s1.end(); ++it2)
{
if (abs(it1->getPosition()[0] - it2->getPosition()[0]) <= 2 * tolerance)
{
squared_sum1 += it1->getIntensity() * it2->getIntensity();
}
}*/
}
/*
UInt i_left(0);
for (Size i = 0; i != s1.size(); ++i)
{
sum1 += s1[i].getIntensity();
for (Size j = i_left; j != s1.size(); ++j)
{
double pos1(s1[i].getPosition()[0]), pos2(s1[j].getPosition()[0]);
if (abs(pos1 - pos2) <= 2 * tolerance)
{
squared_sum1 += s1[i].getIntensity() * s1[j].getIntensity();
}
else
{
if (pos2 > pos1)
{
break;
}
else
{
i_left = i;
}
}
}
}*/
/*
i_left = 0;
for (Size i = 0; i != s2.size(); ++i)
{
sum2 += s2[i].getIntensity();
for (Size j = i_left; j != s2.size(); ++j)
{
double pos1(s2[i].getPosition()[0]), pos2(s2[j].getPosition()[0]);
if (abs(pos1 - pos2) <= 2 * tolerance)
{
squared_sum1 += s2[i].getIntensity() * s2[j].getIntensity();
}
else
{
if (pos2 > pos1)
{
break;
}
else
{
i_left = i;
}
}
}
}*/
for (PeakSpectrum::ConstIterator it1 = s2.begin(); it1 != s2.end(); ++it1)
{
sum2 += it1->getIntensity();
/*
for (PeakSpectrum::ConstIterator it2 = s2.begin(); it2 != s2.end(); ++it2)
{
if (abs(it1->getPosition()[0] - it2->getPosition()[0]) <= 2 * tolerance)
{
squared_sum2 += it1->getIntensity() * it2->getIntensity();
}
}
*/
}
Size j_left(0);
for (Size i = 0; i != s1.size(); ++i)
{
for (Size j = j_left; j != s2.size(); ++j)
{
double pos1(s1[i].getMZ()), pos2(s2[j].getMZ());
if (fabs(pos1 - pos2) < tolerance)
{
//double factor((tolerance - fabs(pos1 - pos2)) / tolerance);
double factor = 1.0;
if (use_linear_factor || use_gaussian_factor)
{
factor = getFactor_(tolerance, fabs(pos1 - pos2), use_gaussian_factor);
}
sum += sqrt(s1[i].getIntensity() * s2[j].getIntensity() * factor);
}
else
{
if (pos2 > pos1)
{
break;
}
else
{
j_left = j;
}
}
}
}
/*
for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
{
for (PeakSpectrum::ConstIterator it2 = s2.begin(); it2 != s2.end(); ++it2)
{
if (abs(it1->getPosition()[0] - it2->getPosition()[0]) <= 2 * tolerance)
{
sum += sqrt(it1->getIntensity() * it2->getIntensity());
}
}
}*/
score = sum / (sqrt(sum1 * sum2));
return score;
}
void CompNovoIonScoring::scoreSpectra(Map<double, IonScore> & ion_scores, PeakSpectrum & CID_spec, PeakSpectrum & ETD_spec, double precursor_weight, Size charge)
{
// adds single charged variants of putative single charged ions
//addSingleChargedIons_(ion_scores, CID_spec);
for (PeakSpectrum::ConstIterator it = CID_spec.begin(); it != CID_spec.end(); ++it)
{
double it_pos(it->getPosition()[0]);
IonScore ion_score;
ion_scores[it_pos] = ion_score;
}
for (PeakSpectrum::ConstIterator it = CID_spec.begin(); it != CID_spec.end(); ++it)
{
ion_scores[it->getPosition()[0]].s_isotope_pattern_1 = scoreIsotopes_(CID_spec, it, ion_scores, 1);
if (it->getPosition()[0] < precursor_weight / 2.0)
{
ion_scores[it->getPosition()[0]].s_isotope_pattern_2 = scoreIsotopes_(CID_spec, it, ion_scores, 2);
}
else
{
ion_scores[it->getPosition()[0]].s_isotope_pattern_2 = -1;
}
}
// find possible supporting ions from ETD spec to CID spec
scoreETDFeatures_(charge, precursor_weight, ion_scores, CID_spec, ETD_spec);
// combine the features and give b-ion scores
scoreWitnessSet_(charge, precursor_weight, ion_scores, CID_spec);
for (Map<double, IonScore>::iterator it = ion_scores.begin(); it != ion_scores.end(); ++it)
{
it->second.score = it->second.s_witness;
}
MassDecompositionAlgorithm decomp_algo;
// check whether a PRMNode_ can be decomposed into amino acids
// rescore the peaks that cannot be possible y-ion candidates
double max_decomp_weight((double)param_.getValue("max_decomp_weight"));
for (Map<double, IonScore>::iterator it = ion_scores.begin(); it != ion_scores.end(); ++it)
{
if (it->first > 19.0 && (it->first - 19.0) < max_decomp_weight)
{
vector<MassDecomposition> decomps;
decomp_algo.getDecompositions(decomps, it->first - 19.0);
#ifdef ION_SCORING_DEBUG
cerr << "Decomps: " << it->first << " " << it->first - 19.0 << " " << decomps.size() << " " << it->second.score << endl;
#endif
if (decomps.empty())
{
it->second.score = 0;
}
}
if (it->first < precursor_weight && precursor_weight - it->first < max_decomp_weight)
{
vector<MassDecomposition> decomps;
decomp_algo.getDecompositions(decomps, precursor_weight - it->first);
#ifdef ION_SCORING_DEBUG
cerr << "Decomps: " << it->first << " " << precursor_weight - it->first << " " << decomps.size() << " " << it->second.score << endl;
#endif
if (decomps.empty())
{
it->second.score = 0;
}
}
}
ion_scores[CID_spec.begin()->getPosition()[0]].score = 1;
ion_scores[(CID_spec.end() - 1)->getPosition()[0]].score = 1;
}
void CompNovoIonScoring::scoreETDFeatures_(Size /*charge*/, double precursor_weight, Map<double, IonScore> & ion_scores, const PeakSpectrum & CID_spec, const PeakSpectrum & ETD_spec)
{
//double fragment_mass_tolerance((double)param_.getValue("fragment_mass_tolerance"));
Size max_isotope_to_score(param_.getValue("max_isotope_to_score"));
for (PeakSpectrum::ConstIterator it1 = CID_spec.begin(); it1 != CID_spec.end(); ++it1)
{
double pos1(it1->getPosition()[0]);
double b_sum(0.0), y_sum(0.0);
// score a-ions
for (PeakSpectrum::ConstIterator it2 = CID_spec.begin(); it2 != CID_spec.end(); ++it2)
{
double pos2(it2->getPosition()[0]);
if (fabs(pos1 - pos2 - 28.0) < fragment_mass_tolerance_)
{
double factor((fragment_mass_tolerance_ - fabs(pos1 - pos2 - 28.0)) / fragment_mass_tolerance_);
#ifdef SCORE_ETDFEATURES_DEBUG
cerr << "scoreETDFeatures: found a-ion " << pos1 << " (" << pos2 << ") (factor=" << factor << ") " << b_sum << " -> ";
#endif
b_sum += it2->getIntensity() * factor;
#ifdef SCORE_ETDFEATURES_DEBUG
cerr << endl;
#endif
}
}
for (PeakSpectrum::ConstIterator it2 = ETD_spec.begin(); it2 != ETD_spec.end(); ++it2)
{
double pos2(it2->getPosition()[0]);
// check if pos2 is precursor doubly charged, which has not fragmented
double pre_diff_lower = (precursor_weight + Constants::PROTON_MASS_U) / 2.0 - fragment_mass_tolerance_;
double pre_diff_upper = (precursor_weight + 4.0 * Constants::PROTON_MASS_U) / 2.0 + fragment_mass_tolerance_;
if (pos2 > pre_diff_lower && pos2 < pre_diff_upper)
{
#ifdef SCORE_ETDFEATURES_DEBUG
cerr << "scoreETDFeatures: pre-range: " << pos2 << " is in precursor peak range: " << pre_diff_lower << " <-> " << pre_diff_upper << endl;
#endif
continue;
}
//double diff(pos2 - pos1);
// pos1 is CID ion; pos2 is ETD ion
// pos1 b-ion, pos2 c-ion
if (fabs(pos1 + 17.0 - pos2) < fragment_mass_tolerance_)
{
// now test if the ETD peak has "isotope" pattern
double factor((fragment_mass_tolerance_ - fabs(pos1 + 17.0 - pos2)) / fragment_mass_tolerance_);
#ifdef SCORE_ETDFEATURES_DEBUG
cerr << "scoreETDFeatures: is b-ion: " << pos1 << " (" << pos2 << ") (factor=" << factor << ") " << b_sum << " -> ";
#endif
vector<double> iso_pattern;
iso_pattern.push_back(it1->getIntensity());
double actual_pos = it1->getPosition()[0];
for (PeakSpectrum::ConstIterator it3 = it2; it3 != ETD_spec.end(); ++it3)
{
double it3_pos(it3->getPosition()[0]);
if (fabs(fabs(actual_pos - it3_pos) - Constants::NEUTRON_MASS_U) < fragment_mass_tolerance_)
{
iso_pattern.push_back(it3->getIntensity());
actual_pos = it3_pos;
}
if (iso_pattern.size() == max_isotope_to_score)
{
break;
}
}
if (ion_scores[it1->getPosition()[0]].is_isotope_1_mono != -1)
{
b_sum += it2->getIntensity() * iso_pattern.size() * factor;
}
#ifdef SCORE_ETDFEATURES_DEBUG
cerr << b_sum << endl;
#endif
}
// pos1 z-ion, pos2 y-ion
if (fabs(pos2 + 16.0 - pos1) < fragment_mass_tolerance_)
{
double factor((fragment_mass_tolerance_ - fabs(pos2 + 16.0 - pos1)) / fragment_mass_tolerance_);
// now test if the ETD peak has "isotope" pattern
#ifdef SCORE_ETDFEATURES_DEBUG
cerr << "scoreETDFeatures: is y-ion: " << pos1 << " (" << pos2 << ") (factor=" << factor << ") " << y_sum << " -> ";
#endif
vector<double> iso_pattern;
iso_pattern.push_back(it1->getIntensity());
double actual_pos = it1->getPosition()[0];
for (PeakSpectrum::ConstIterator it3 = it2; it3 != ETD_spec.end(); ++it3)
{
double it3_pos(it3->getPosition()[0]);
if (fabs(fabs(actual_pos - it3_pos) - Constants::NEUTRON_MASS_U) < fragment_mass_tolerance_)
{
iso_pattern.push_back(it3->getIntensity());
actual_pos = it3_pos;
}
if (iso_pattern.size() == max_isotope_to_score)
{
break;
}
}
#ifdef SCORE_ETDFEATURES_DEBUG
cerr << ion_scores[it1->getPosition()[0]].is_isotope_1_mono << " ";
#endif
if (ion_scores[it1->getPosition()[0]].is_isotope_1_mono != -1)
{
y_sum += it2->getIntensity() * iso_pattern.size() * factor;
}
#ifdef SCORE_ETDFEATURES_DEBUG
cerr << y_sum << endl;
#endif
}
}
ion_scores[it1->getPosition()[0]].s_bion = b_sum;
ion_scores[it1->getPosition()[0]].s_yion = y_sum;
}
return;
}
void CompNovoIonScoring::scoreWitnessSet_(Size charge, double precursor_weight, Map<double, IonScore> & ion_scores, const PeakSpectrum & CID_spec)
{
vector<double> diffs;
//diffs.push_back(28.0);
diffs.push_back(17.0);
diffs.push_back(18.0);
// witnesses of CID spec (diffs)
for (PeakSpectrum::ConstIterator it1 = CID_spec.begin(); it1 != CID_spec.end(); ++it1)
{
//Size num_wit(0);
double wit_score(0.0);
double pos1(it1->getPosition()[0]);
wit_score += it1->getIntensity();
for (PeakSpectrum::ConstIterator it2 = CID_spec.begin(); it2 != CID_spec.end(); ++it2)
{
double pos2(it2->getPosition()[0]);
// direct ++
if (charge > 1)
{
if (fabs(pos2 * 2 - Constants::PROTON_MASS_U - pos1) < fragment_mass_tolerance_)
{
double factor((fragment_mass_tolerance_ - fabs(pos2 * 2 - Constants::PROTON_MASS_U - pos1)) / fragment_mass_tolerance_);
// pos1 is ion, pos2 is ++ion
#ifdef SCORE_WITNESSSET_DEBUG
cerr << "scoreWitnessSet: ++ion " << pos1 << " " << pos2 << " (factor=" << factor << ") " << wit_score << " -> ";
#endif
if (ion_scores[it2->getPosition()[0]].s_isotope_pattern_2 < 0.2)
{
wit_score += it2->getIntensity() * /* 0.2 */ factor;
}
else
{
wit_score += it2->getIntensity() * ion_scores[it2->getPosition()[0]].s_isotope_pattern_2 * factor;
}
#ifdef SCORE_WITNESSSET_DEBUG
cerr << wit_score << endl;
#endif
}
}
// diffs?
for (vector<double>::const_iterator it = diffs.begin(); it != diffs.end(); ++it)
{
// pos1 is ion, pos2 loss peak
if (fabs(pos1 - pos2 - *it) < fragment_mass_tolerance_)
{
double factor((fragment_mass_tolerance_ - fabs(pos1 - pos2 - *it)) / fragment_mass_tolerance_);
#ifdef SCORE_WITNESSSET_DEBUG
cerr << "scoreWitnessSet: diff " << pos1 << " (" << pos2 << ") " << *it << " (factor=" << factor << ") " << wit_score << " -> ";
#endif
wit_score += it2->getIntensity() /* / 5.0*/ * factor;
#ifdef SCORE_WITNESSSET_DEBUG
cerr << wit_score << endl;
#endif
}
}
// is there a b-ion?; pos1 is ion, pos2 complementary ion
if (fabs(pos1 + pos2 - 1 * Constants::PROTON_MASS_U - precursor_weight) < fragment_mass_tolerance_)
{
double factor((fragment_mass_tolerance_ - fabs(pos1 + pos2 - Constants::PROTON_MASS_U - precursor_weight)) / fragment_mass_tolerance_);
/*factor *= 0.2;*/
#ifdef SCORE_WITNESSSET_DEBUG
cerr << "scoreWitnessSet: complementary " << pos1 << " (" << pos2 << ") (factor=" << factor << ") " << wit_score << " -> ";
#endif
// found complementary ion
if (ion_scores[it2->getPosition()[0]].s_isotope_pattern_1 < 0.5 || ion_scores[it2->getPosition()[0]].is_isotope_1_mono != 1)
{
wit_score += it2->getIntensity() /* * 0.5*/ * factor;
}
else
{
wit_score += it2->getIntensity() * ion_scores[it2->getPosition()[0]].s_isotope_pattern_1 * factor;
}
#ifdef SCORE_WITNESSSET_DEBUG
cerr << wit_score << endl;
#endif
if (ion_scores[it2->getPosition()[0]].s_bion != 0)
{
#ifdef SCORE_WITNESSSET_DEBUG
cerr << "scoreWitnessSet: complementary is b-ion " << pos1 << "(" << pos2 << ")" << wit_score << " -> ";
#endif
wit_score += ion_scores[it2->getPosition()[0]].s_bion * factor;
#ifdef SCORE_WITNESSSET_DEBUG
cerr << wit_score << endl;
#endif
}
}
}
// isotope pattern ok?
if (ion_scores[it1->getPosition()[0]].s_isotope_pattern_1 > 0 && ion_scores[it1->getPosition()[0]].is_isotope_1_mono == 1)
{
#ifdef SCORE_WITNESSSET_DEBUG
cerr << "scoreWitnessSet: isotope pattern: " << pos1 << " " << wit_score << " -> ";
#endif
wit_score += ion_scores[it1->getPosition()[0]].s_isotope_pattern_1 * wit_score;
#ifdef SCORE_WITNESSSET_DEBUG
cerr << wit_score << endl;
#endif
}
if (ion_scores[it1->getPosition()[0]].s_yion > 0)
{
#ifdef SCORE_WITNESSSET_DEBUG
cerr << "scoreWitnessSet: is y-ion: " << pos1 << " " << wit_score << " -> ";
#endif
wit_score += ion_scores[it1->getPosition()[0]].s_yion;
#ifdef SCORE_WITNESSSET_DEBUG
cerr << wit_score << endl;
#endif
}
if (ion_scores[it1->getPosition()[0]].s_bion > 0)
{
#ifdef SCORE_WITNESSSET_DEBUG
cerr << "scoreWitnessSet: is b-ion: " << pos1 << " " << wit_score << " -> ";
#endif
if (ion_scores[it1->getPosition()[0]].s_bion < wit_score)
{
wit_score -= ion_scores[it1->getPosition()[0]].s_bion;
}
else
{
wit_score = 0;
}
}
ion_scores[it1->getPosition()[0]].s_witness = wit_score;
}
return;
}
