int main() {
Punkt pierwszy(1, 5), drugi(1, 8), trzeci(4, 5), czwarty(4, 8);
Kwadrat figura(pierwszy, drugi, trzeci, czwarty);
figura.obwod();
figura.pole();
double szukana;
DTab ala(0);
ala.print();
ala.add(3.6);
ala.print();
ala.add(4.9);
ala.print();
ala.add(4.9);
ala.print();
szukana = ala.get(6);
cout << szukana << endl;
ala.set(3.999, 3);
ala.print();
Zespolona pierwsza(1, 2);
Zespolona druga(3, 4);
Zespolona wynik;
wynik.add(pierwsza, druga);
wynik.Wypisz();
wynik.sub(pierwsza, druga);
wynik.Wypisz();
wynik.mul(pierwsza, druga);
wynik.Wypisz();
wynik.div(pierwsza, druga);
wynik.Wypisz();
wynik.pow(pierwsza);
wynik.Wypisz();
return 0;
}
fasta::SequenceList ScoringMatrix::backtrace_alignment_path(
const fasta::Sequence& sequence, const profile::ProfileMap& profile,
const FeatureScores& f_profile,
int codon_length) {
//creating polyA pseudoSequence representing the profile,
//to know later where are the gaps in the profile
fasta::Residue ala('A' + std::string(codon_length - 1, 'A'), {});
fasta::Residue gap_residue('-' + std::string(codon_length - 1, 'A'), {});
fasta::Sequence new_s1;
fasta::Sequence new_s2;
const size_t profile_length = profile.begin()->second.size();
// TODO: i and j aren't great names...are they?
size_t i = profile_length;
size_t j = sequence.residues.size();
//if bestScore isn't in the lower right corner, then add gaps
//to new_s1 or new_s2
ValueCoords best_score = find_best_score();
// TODO: comparing value to size of something? fishy!
if (best_score[0] != (signed)m_matrix_v.size()-1
|| best_score[1] != (signed)m_matrix_v[0].size()-1) {
i = best_score[0];
j = best_score[1];
for (size_t k = profile_length; k > i; --k) {
new_s1.residues.push_back(ala);
new_s2.residues.push_back(gap_residue);
}
for (size_t k = sequence.residues.size(); k > j; --k) {
new_s2.residues.push_back(sequence.residues[k - 1]);
new_s1.residues.push_back(gap_residue);
}
}
std::string current_matrix = "V";
assert(m_matrix_v.size() == m_matrix_g.size());
assert(m_matrix_v.size() == m_matrix_h.size());
fasta::Residue new_res1;
fasta::Residue new_res2;
//trace back the matrix
while (i > 0 || j > 0) {
if (i > 0 && j > 0 && current_matrix == "V") { //match/mismatch
new_res1 = ala;
new_res2 = sequence.residues[j - 1];
// double profile_score = profile.at(
// sequence.residues[j - 1].codon[0])[i - 1];
double profile_score = profile::get_score(profile, i - 1,
sequence.residues[j - 1].codon[0]);
double feature_score = 0;
if (!m_no_feat) {
for (auto& feat_name : sequence.residues[j - 1].features) {
feature_score += f_profile.get_score(feat_name, i - 1);
}
}
double final_score = profile_score + feature_score;
if (m_matrix_v[i][j] != m_matrix_v[i-1][j-1] + final_score) {
if (i > 0 && j > 0
&& compare_doubles::is_equal(m_matrix_v[i][j],
m_matrix_g[i-1][j-1] + final_score)) {
current_matrix = "G";
} else if (i > 0 && j > 0
&& compare_doubles::is_equal(m_matrix_v[i][j],
m_matrix_h[i-1][j-1]
+ final_score)) {
current_matrix = "H";
}
}
--i;
--j;
} else if (j > 0 && current_matrix == "G") { //gap in seq2
new_res1 = gap_residue;
new_res2 = sequence.residues[j - 1];
if (compare_doubles::is_equal(m_matrix_g[i][j],
m_matrix_v[i][j - 1] + m_gap_opening)) {
current_matrix = "V";
}
else if (compare_doubles::is_equal(m_matrix_g[i][j],
m_matrix_h[i][j - 1]
+ m_gap_opening)) {
current_matrix = "H";
}
--j;
} else if (i > 0 && current_matrix == "H") { //gap in profile
new_res1 = ala;
new_res2 = gap_residue;
if (compare_doubles::is_equal(m_matrix_h[i][j],
m_matrix_v[i - 1][j] + m_gap_opening)) {
current_matrix = "V";
}
else if (compare_doubles::is_equal(m_matrix_h[i][j],
m_matrix_g[i - 1][j]
+ m_gap_opening)) {
current_matrix = "G";
}
--i;
}
new_s1.residues.push_back(new_res1);
new_s2.residues.push_back(new_res2);
}
//need to reverse the sequences, because tracing back the alignment goes
//from the end to the beginning
std::reverse(new_s1.residues.begin(), new_s1.residues.end());
std::reverse(new_s2.residues.begin(), new_s2.residues.end());
return {new_s1, new_s2};
}
