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Commit bdebd23

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author
werewolf
committed
finish method
1 parent 4d786b9 commit bdebd23

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8 files changed

+275
-228
lines changed

8 files changed

+275
-228
lines changed

‎src/algorithm/DNA_Analyzer.cc‎

Lines changed: 211 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -1,55 +1,237 @@
11
#include "DNA_Analyzer.h"
22

3-
void DNA_Analyzer::RabinKarpAlgorithm(const std::filesystem::path& path_1, const std::filesystem::path& path_2) {
3+
void DNA_Analyzer::RabinKarpAlgorithm(const std::filesystem::path& path_1,
4+
const std::filesystem::path& path_2) {
45
std::ifstream file_a(path_1), file_b(path_2);
56

6-
std::string a((std::istreambuf_iterator<char>(file_a)), std::istreambuf_iterator<char>());
7-
std::string b((std::istreambuf_iterator<char>(file_b)), std::istreambuf_iterator<char>());
7+
std::string a((std::istreambuf_iterator<char>(file_a)),
8+
std::istreambuf_iterator<char>());
9+
std::string b((std::istreambuf_iterator<char>(file_b)),
10+
std::istreambuf_iterator<char>());
811

9-
const int p = 31;// простое число
10-
const int m = 1e9 + 9;// модуль
12+
const int p = 31;
13+
const int m = 1e9 + 9;
1114
int S = a.size(), T = b.size();
12-
13-
std::vector<long long> p_pow(std::max(S, T));// предподсчет степеней числа p
15+
16+
std::vector<long long> p_pow(std::max(S, T));
1417
p_pow[0] = 1;
1518
for (int i = 1; i < (int)p_pow.size(); i++) {
1619
p_pow[i] = (p_pow[i - 1] * p) % m;
1720
}
18-
19-
std::vector<long long> h(S + 1, 0); // хеши от всех префиксов строки text
21+
22+
std::unordered_map<char, int> code_map{
23+
{'A', 1}, {'C', 2}, {'G', 3}, {'T', 4}};
24+
25+
std::vector<long long> h(S + 1, 0);
2026
for (int i = 0; i < S; i++) {
21-
int code;
22-
switch(a[i]) { // перевод из алфавита {A, C, G, T} в числа
23-
case 'A': code = 1; break;
24-
case 'C': code = 2; break;
25-
case 'G': code = 3; break;
26-
case 'T': code = 4; break;
27-
}
27+
char c = a[i];
28+
int code = code_map[c];
2829
h[i + 1] = (h[i] + code * p_pow[i]) % m;
2930
}
30-
31-
long long h_s = 0;// хеш подстроки длины T строки text
31+
32+
long long h_s = 0;
3233
for (int i = 0; i < T; i++) {
33-
int code;
34-
switch(b[i]) { // перевод из алфавита {A, C, G, T} в числа
35-
case 'A': code = 1; break;
36-
case 'C': code = 2; break;
37-
case 'G': code = 3; break;
38-
case 'T': code = 4; break;
39-
}
34+
char c = b[i];
35+
int code = code_map[c];
4036
h_s = (h_s + code * p_pow[i]) % m;
4137
}
42-
43-
std::vector<int> positions;// позиции вхождения подстроки pattern в строку text
38+
39+
std::vector<int> positions;
4440
for (int i = 0; i + T - 1 < S; i++) {
45-
long long cur_h = (h[i + T] + m - h[i]) % m;// вычисление хеша для подстроки
41+
long long cur_h = (h[i + T] + m - h[i]) % m;
4642
if (cur_h == h_s * p_pow[i] % m) {
4743
positions.push_back(i);
4844
}
4945
}
5046

51-
for (auto &it: positions) {
47+
for (auto& it : positions) {
5248
std::cout << it << " ";
5349
}
5450
std::cout << std::endl;
5551
}
52+
53+
void DNA_Analyzer::NWAlgorithm(const std::filesystem::path& path) {
54+
std::ifstream file(path);
55+
56+
Score score(0, 0, 0);
57+
file >> score.match >> score.mismatch >> score.gap;
58+
std::string a, b;
59+
file >> a >> b;
60+
61+
std::cout << optimalScore(score, a, b);
62+
63+
auto k = optimalAlignment(score, a, b);
64+
std::cout << k.first << std::endl;
65+
std::cout << k.second.first << std::endl;
66+
std::cout << k.second.second << std::endl;
67+
}
68+
69+
int DNA_Analyzer::optimalScore(Score score, std::string s1, std::string s2) {
70+
int n = s1.size(), m = s2.size();
71+
std::vector<std::vector<int>> dp(n + 1, std::vector<int>(m + 1));
72+
for (int i = 1; i <= n; i++) dp[i][0] = dp[i - 1][0] + score.gap;
73+
for (int i = 1; i <= m; i++) dp[0][i] = dp[0][i - 1] + score.gap;
74+
for (int i = 1; i <= n; i++) {
75+
for (int j = 1; j <= m; j++) {
76+
int match = dp[i - 1][j - 1] +
77+
(s1[i - 1] == s2[j - 1] ? score.match : score.mismatch);
78+
int ins = dp[i][j - 1] + score.gap;
79+
int del = dp[i - 1][j] + score.gap;
80+
dp[i][j] = std::max({match, ins, del});
81+
}
82+
}
83+
return dp[n][m];
84+
}
85+
86+
std::pair<int, std::pair<std::string, std::string>>
87+
DNA_Analyzer::optimalAlignment(Score score, std::string s1, std::string s2) {
88+
int n = s1.size(), m = s2.size();
89+
std::vector<std::vector<int>> dp(n + 1, std::vector<int>(m + 1));
90+
std::vector<std::vector<int>> p(
91+
n + 1, std::vector<int>(m + 1)); // 0-diag, 1-up, 2-left
92+
93+
for (int i = 1; i <= n; i++) dp[i][0] = dp[i - 1][0] + score.gap, p[i][0] = 1;
94+
for (int i = 1; i <= m; i++) dp[0][i] = dp[0][i - 1] + score.gap, p[0][i] = 2;
95+
for (int i = 1; i <= n; i++) {
96+
for (int j = 1; j <= m; j++) {
97+
int match = dp[i - 1][j - 1] +
98+
(s1[i - 1] == s2[j - 1] ? score.match : score.mismatch);
99+
int ins = dp[i][j - 1] + score.gap;
100+
int del = dp[i - 1][j] + score.gap;
101+
if (match >= ins && match >= del) {
102+
dp[i][j] = match;
103+
p[i][j] = 0;
104+
} else if (ins >= match && ins >= del) {
105+
dp[i][j] = ins;
106+
p[i][j] = 2;
107+
} else {
108+
dp[i][j] = del;
109+
p[i][j] = 1;
110+
}
111+
}
112+
}
113+
114+
int i = n, j = m;
115+
std::string res1, res2;
116+
while (i > 0 || j > 0) {
117+
if (p[i][j] == 0) {
118+
res1 += s1[i - 1];
119+
res2 += s2[j - 1];
120+
i--;
121+
j--;
122+
} else if (p[i][j] == 1) {
123+
res1 += s1[i - 1];
124+
res2 += '-';
125+
i--;
126+
} else {
127+
res1 += '-';
128+
res2 += s2[j - 1];
129+
j--;
130+
}
131+
}
132+
reverse(res1.begin(), res1.end());
133+
reverse(res2.begin(), res2.end());
134+
135+
return {dp[n][m], {res1, res2}};
136+
}
137+
138+
void DNA_Analyzer::RegexAlgorithm(const std::filesystem::path& path) {
139+
std::ifstream file(path);
140+
std::string s, p;
141+
file >> s >> p;
142+
std::cout << isMatch(s, p) << std::endl;
143+
}
144+
145+
bool DNA_Analyzer::isMatch(std::string s, std::string p) {
146+
int m = p.size(), n = s.size();
147+
std::vector<std::vector<bool>> dp(m + 1, std::vector<bool>(n + 1));
148+
dp[0][0] = true;
149+
for (int i = 1; i <= m; i++) {
150+
if (p[i - 1] == '*') dp[i][0] = dp[i - 2][0];
151+
}
152+
for (int i = 1; i <= m; i++) {
153+
for (int j = 1; j <= n; j++) {
154+
if (s[j - 1] == p[i - 1] || p[i - 1] == '.')
155+
dp[i][j] = dp[i - 1][j - 1];
156+
else if (p[i - 1] == '*') {
157+
dp[i][j] = dp[i - 2][j] ||
158+
(dp[i][j - 1] && (s[j - 1] == p[i - 2] || p[i - 2] == '.'));
159+
} else if (p[i - 1] == '?') {
160+
dp[i][j] = dp[i - 1][j - 1] || dp[i - 1][j] || dp[i][j - 1];
161+
}
162+
}
163+
}
164+
return dp[m][n];
165+
}
166+
167+
void DNA_Analyzer::KSimilarAlgorithm(const std::filesystem::path& path) {
168+
std::ifstream file(path);
169+
std::string s, p;
170+
file >> s >> p;
171+
std::cout << kSimilarity(s, p) << std::endl;
172+
}
173+
174+
int DNA_Analyzer::kSimilarity(std::string s1, std::string s2) {
175+
if (s1.size() != s2.size()) return -1;
176+
std::unordered_set<std::string> visited;
177+
std::queue<std::pair<std::string, int>> q;
178+
q.push({s1, 0});
179+
visited.insert(s1);
180+
while (!q.empty()) {
181+
std::string curr = q.front().first;
182+
int swaps = q.front().second;
183+
q.pop();
184+
if (curr == s2) return swaps;
185+
int i = 0;
186+
while (curr[i] == s2[i]) i++;
187+
for (int j = i + 1; j < curr.size(); j++) {
188+
if (curr[j] == s2[i] && curr[j] != s2[j]) {
189+
std::swap(curr[i], curr[j]);
190+
if (visited.count(curr) == 0) {
191+
q.push({curr, swaps + 1});
192+
visited.insert(curr);
193+
}
194+
std::swap(curr[i], curr[j]);
195+
}
196+
}
197+
}
198+
return -1;
199+
}
200+
201+
void DNA_Analyzer::WindowAlgorithm(const std::filesystem::path& path) {
202+
std::ifstream file(path);
203+
std::string s, p;
204+
file >> s >> p;
205+
std::cout << minWindowSubstring(s, p) << std::endl;
206+
}
207+
208+
std::string DNA_Analyzer::minWindowSubstring(std::string s, std::string t) {
209+
std::unordered_map<char, int> mp;
210+
for (char c : t) mp[c]++;
211+
int cnt = mp.size(), left = 0, right = 0, ansL = -1, ansR = -1,
212+
minLen = INT_MAX;
213+
while (right < s.size()) {
214+
if (mp.count(s[right])) {
215+
mp[s[right]]--;
216+
if (mp[s[right]] == 0) cnt--;
217+
}
218+
right++;
219+
220+
while (cnt == 0) {
221+
if (right - left < minLen) {
222+
minLen = right - left;
223+
ansL = left;
224+
ansR = right;
225+
}
226+
if (mp.count(s[left])) {
227+
mp[s[left]]++;
228+
if (mp[s[left]] > 0) cnt++;
229+
}
230+
left++;
231+
}
232+
}
233+
if (ansL == -1)
234+
return "";
235+
else
236+
return s.substr(ansL, ansR - ansL);
237+
}

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