vc1/基因的双序列对比算法(needleman-wunsch)实现.cpp

#include <iostream>
#include <string>
#include <algorithm>
#include <fstream>
#include <windows.h>

using namespace std;

#define INDEL_CHAR '-'
int MATCH = 1, DIS_MATCH = -1, INDEL = -3;
char choice;

class ResUnit  		//һ<><D2BB>˫<EFBFBD><CBAB><EFBFBD>бȶԺ<C8B6><D4BA>Ľ<EFBFBD><C4BD><EFBFBD>
{
	public:
		string str1;	//ԭʼ<D4AD><CABC><EFBFBD><EFBFBD>1
		string str2;	//ԭʼ<D4AD><CABC><EFBFBD><EFBFBD>2
		string res1;	//<2F><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>1
		string res2;	//<2F><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>2
		int score;		//<2F><><EFBFBD><EFBFBD><EFBFBD>ܵ÷֣<C3B7><D6A3><EFBFBD>ӳ<EFBFBD><D3B3><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>е<EFBFBD><D0B5><EFBFBD><EFBFBD>Ƴ̶<C6B3>
		int tag;		//<2F><>ֹ<EFBFBD><D6B9><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
};

class SingleSeq  	//һ<><D2BB><EFBFBD><EFBFBD><EFBFBD>б<EFBFBD><D0B1><EFBFBD><EFBFBD>Ϻ<EFBFBD><CFBA><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
{
	public:
		string str;		//һ<><D2BB><EFBFBD><EFBFBD><EFBFBD>е<EFBFBD>ԭʼ<D4AD><CABC><EFBFBD><EFBFBD>
		string res;		//һ<><D2BB><EFBFBD><EFBFBD><EFBFBD>б<EFBFBD><D0B1><EFBFBD><EFBFBD>Ϻ<EFBFBD><CFBA><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
};

struct BacktrackingUnit {
	int goUp;		//<2F>Ƿ<EFBFBD><C7B7><EFBFBD><EFBFBD>ϻ<EFBFBD><CFBB><EFBFBD>
	int goLeftUp;	//<2F>Ƿ<EFBFBD><C7B7><EFBFBD><EFBFBD><EFBFBD><EFBFBD>ϻ<EFBFBD><CFBB><EFBFBD>
	int goLeft;		//<2F>Ƿ<EFBFBD><C7B7><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
	int score;		//<2F>÷־<C3B7><D6BE><EFBFBD><EFBFBD><EFBFBD>(i, j)<29><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>Ԫ<EFBFBD>ķ<EFBFBD>ֵ
};

typedef struct BacktrackingUnit *unitLine;

struct SequenceUnit {
	string *str1;	//ƥ<><C6A5><EFBFBD><EFBFBD><EFBFBD><EFBFBD>1
	string *str2;	//ƥ<><C6A5><EFBFBD><EFBFBD><EFBFBD><EFBFBD>2
	int score;
};

/*
<EFBFBD>Ƚ<EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>·<EFBFBD><EFBFBD>֮<EFBFBD><EFBFBD>˭<EFBFBD><EFBFBD><EFBFBD><EFBFBD>
f(i-1,j-1),f(i-1,j)+indel,f(i,j-1)+indel
*/

int max3(int a, int b, int c)
{
	return max(max(a, b), c);
}

/*
<EFBFBD>Ƚ<EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>ַ<EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>ʲô<EFBFBD><EFBFBD>match<EFBFBD><EFBFBD>dismatch<EFBFBD><EFBFBD>indel
*/

int myCompare(char a, char b)
{
	if (a == b)
		return MATCH;
	else if (a == ' ' || b == ' ')
		return INDEL;
	return DIS_MATCH;
}

ResUnit traceback(unitLine **item, const int i, const int j, string str1,

                  string str2, string res1, string res2, int n, ResUnit resUnit)


{
	unitLine temp = item[i][j];
	if (resUnit.tag != 1) {
		if (!(i || j)) {   // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>Ԫ(0, 0)<29><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>ʼ<EFBFBD><CABC><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>ַ<EFBFBD><D6B7><EFBFBD><EFBFBD><EFBFBD>ÿ<EFBFBD><C3BF><EFBFBD>ַ<EFBFBD><D6B7><EFBFBD><EFBFBD><EFBFBD><EFBFBD>ȶԵ<C8B6><D4B5><EFBFBD>
			resUnit.str1 = str1;
			resUnit.str2 = str2;
			resUnit.res1 = res1;
			resUnit.res2 = res2;
			resUnit.tag = 1;
			return resUnit;
		}
		if (temp->goUp) {    // <20><><EFBFBD>ϻ<EFBFBD><CFBB><EFBFBD>һ<EFBFBD><D2BB>
			res1 = str1[i - 1] + res1;
			res2 = INDEL_CHAR + res2;
			resUnit = traceback(item, i - 1, j, str1, str2, res1, res2, n + 1, resUnit);
		}
		if (temp->goLeftUp) {    // <20><><EFBFBD><EFBFBD><EFBFBD>ϻ<EFBFBD><CFBB><EFBFBD>һ<EFBFBD><D2BB>
			res1 = str1[i - 1] + res1;
			res2 = str2[j - 1] + res2;
			resUnit = traceback(item, i - 1, j - 1, str1, str2, res1, res2, n + 1, resUnit);
		}
		if (temp->goLeft) {    // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>һ<EFBFBD><D2BB>
			res1 = INDEL_CHAR + res1;
			res2 = str2[j - 1] + res2;
			resUnit = traceback(item, i, j - 1, str1, str2, res1, res2, n + 1, resUnit);
		}
		return resUnit;
	}
	return resUnit;
}

ResUnit NeedlemanWunch(string str1, string str2)
{
	//<2F>ַ<EFBFBD><D6B7><EFBFBD>str1,str2<72><32><EFBFBD><EFBFBD>
	const int m = str1.length();
	const int n = str2.length();
	int m1, m2, m3, mm;
	unitLine **unit;

	// <20><>ʼ<EFBFBD><CABC>
	if ((unit = (unitLine **)malloc(sizeof(unitLine *) * (m + 1))) == NULL) {
		fputs("Error: Out of space!\n", stderr);
		exit(1);
	}

	for (int i = 0; i <= m; i++) {
		if ((unit[i] = (unitLine *)malloc(sizeof(unitLine) * (n + 1))) == NULL) {
			fputs("Error: Out of space!\n", stderr);
			exit(1);
		}
		for (int j = 0; j <= n; j++) {
			if ((unit[i][j] = (unitLine)malloc(sizeof(struct BacktrackingUnit))) == NULL) {
				fputs("Error: Out of space!\n", stderr);
				exit(1);
			}
			unit[i][j]->goUp = 0;
			unit[i][j]->goLeftUp = 0;
			unit[i][j]->goLeft = 0;
		}
	}
	unit[0][0]->score = 0;

	for (int i = 1; i <= m; i++) {
		unit[i][0]->score = INDEL * i;
		unit[i][0]->goUp = 1;
	}

	for (int j = 1; j <= n; j++) {
		unit[0][j]->score = INDEL * j;
		unit[0][j]->goLeft = 1;
	}

	// <20><>̬<EFBFBD>滮<EFBFBD>㷨<EFBFBD><E3B7A8><EFBFBD><EFBFBD><EFBFBD>÷־<C3B7><D6BE><EFBFBD>ÿ<EFBFBD><C3BF><EFBFBD><EFBFBD>Ԫ<EFBFBD>ķ<EFBFBD>ֵ
	for (int i = 1; i <= m; i++) {
		for (int j = 1; j <= n; j++) {
			m1 = unit[i - 1][j]->score + INDEL;
			m2 = unit[i - 1][j - 1]->score + myCompare(str1[i - 1], str2[j - 1]);
			m3 = unit[i][j - 1]->score + INDEL;
			mm = max3(m1, m2, m3);
			unit[i][j]->score = mm;
			//<2F>ж<EFBFBD>·<EFBFBD><C2B7><EFBFBD><EFBFBD>Դ
			if (m1 == mm)
				unit[i][j]->goUp = 1;
			if (m2 == mm)
				unit[i][j]->goLeftUp = 1;
			if (m3 == mm)
				unit[i][j]->goLeft = 1;
		}
	}

	//<2F><>ʼ<EFBFBD><CABC><EFBFBD><EFBFBD>
	ResUnit res;
	res.tag = 0;
	res = traceback(unit, m, n, str1, str2, "", "", 0, res);
	res.score = unit[m][n]->score;

	//<2F>ͷ<EFBFBD><CDB7>ڴ<EFBFBD>
	for (int i = 0; i <= m; i++) {
		for (int j = 0; j <= n; j++) {
			free(unit[i][j]);
		}
		free(unit[i]);
	}
	free(unit);
	//<2F><><EFBFBD><EFBFBD>ֵ
	return res;
}

bool legal_string(string s)
{
	for (unsigned i = 0; i < s.size(); i++) {
		if (s[i] != 'A' && s[i] != 'T' && s[i] != 'C' && s[i] != 'G')
			return false;
	}
	return true;
}

void read(string &a, string &b)
{
	char c;
	if (!choice) {
		while (true) {
			cout << "<EFBFBD><EFBFBD>ѡ<EFBFBD><EFBFBD><EFBFBD><EFBFBD>\n1.<2E><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>ʾ<EFBFBD><CABE>\n2.<2E><><EFBFBD><EFBFBD>Ϊ<EFBFBD>ı<EFBFBD>\n";
			cin >> choice;
			if (choice != '1' && choice != '2') {
				cout << "#<23><>ѡ<EFBFBD><D1A1><EFBFBD>Ϸ<EFBFBD><CFB7><EFBFBD>ѡ<EFBFBD>\n";
				Sleep(1000);
			} else
				break;
		}
	}

	while (true) {
		cout << "<EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>Ҫ<EFBFBD>ȶԵĻ<EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>У<EFBFBD>\n<EFBFBD><EFBFBD><EFBFBD><EFBFBD>һ:";
		cin >> a;
		if (legal_string(a))
			break;
		else {
			cout << "#<23><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>Ϸ<EFBFBD><CFB7>Ļ<EFBFBD><C4BB><EFBFBD><EFBFBD><EFBFBD><EFBFBD>У<EFBFBD>\n";
			Sleep(1000);
		}
	}

	while (true) {
		cout << "<EFBFBD><EFBFBD><EFBFBD>ж<EFBFBD>:";
		cin >> b;
		if (legal_string(b))
			break;
		else {
			cout << "#<23><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>Ϸ<EFBFBD><CFB7>Ļ<EFBFBD><C4BB><EFBFBD><EFBFBD><EFBFBD><EFBFBD>У<EFBFBD>\n";
			Sleep(1000);
		}
	}

	while (true) {
		cout << "<EFBFBD><EFBFBD>ѡ<EFBFBD><EFBFBD><EFBFBD>ȶԹ<EFBFBD><EFBFBD><EFBFBD>:\n1.<2E><>ȱ<EFBFBD><C8B1><EFBFBD>ȣ<EFBFBD>Ĭ<EFBFBD>ϣ<EFBFBD>\n2.<2E><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>\n3.û<><C3BB><EFBFBD><EFBFBD><EFBFBD><EFBFBD>\n";
		cin >> c;
		if (c != '1' && c != '2' && c != '3') {
			cout << "#<23><>ѡ<EFBFBD><D1A1><EFBFBD>Ϸ<EFBFBD><CFB7><EFBFBD>ѡ<EFBFBD>\n";
			Sleep(1000);
		} else
			break;
	}

	if (c == '2') {
		DIS_MATCH = -3;
		INDEL = -1;

	} else if (c == '3') {
		DIS_MATCH = INDEL = -1;
	}
}

int main()
{
	while (true) {
		string a, b;
		read(a, b);
		ResUnit s = NeedlemanWunch(a, b);
		if (choice == '2') {
			ofstream ofile{"ANS.txt", ios::out};
			ofile << s.res1 << endl;
			ofile << s.res2 << endl;
			ofile.close();
		} else {
			cout << s.res1 << endl;
			cout << s.res2 << endl;
		}
		Sleep(2000);
		cout << "<EFBFBD><EFBFBD>ѡ<EFBFBD><EFBFBD><EFBFBD><EFBFBD>\n1.<2E><><EFBFBD><EFBFBD><EFBFBD>ȶ<EFBFBD>\n2.ֹͣ<CDA3>ȶ<EFBFBD>\n";
		char c;
		while (true) {
			cin >> c;
			if (c != '1' && c != '2') {
				cout << "#<23><>ѡ<EFBFBD><D1A1><EFBFBD>Ϸ<EFBFBD><CFB7><EFBFBD>ѡ<EFBFBD>\n";
				Sleep(1000);
			} else
				break;
		}
		if (c == '2')
			break;
	}
	return 0;
}

/*
"GGATCGA"
"GAATTCAGTTA"
*/