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基因的双序列对比算法(needleman-wunsch)实现.cpp

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+#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  		//一次双序列比对后的结果
+{
+	public:
+		string str1;	//原始序列1
+		string str2;	//原始序列2
+		string res1;	//结果序列1
+		string res2;	//结果序列2
+		int score;		//序列总得分，反映两个序列的相似程度
+		int tag;		//禁止迭代多次
+};
+
+class SingleSeq  	//一个序列被整合后的样子
+{
+	public:
+		string str;		//一个序列的原始序列
+		string res;		//一个序列被整合后的样子
+};
+
+struct BacktrackingUnit {
+	int goUp;		//是否向上回溯
+	int goLeftUp;	//是否向左上回溯
+	int goLeft;		//是否向左回溯
+	int score;		//得分矩阵第(i, j)这个单元的分值
+};
+
+typedef struct BacktrackingUnit *unitLine;
+
+struct SequenceUnit {
+	string *str1;	//匹配序列1
+	string *str2;	//匹配序列2
+	int score;
+};
+
+/*
+比较三种路径之间谁最大
+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);
+}
+
+/*
+比较两个字符类型属于什么，match，dismatch，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)) {   // 到矩阵单元(0, 0)才算结束，这代表初始的两个字符串的每个字符都被比对到了
+			resUnit.str1 = str1;
+			resUnit.str2 = str2;
+			resUnit.res1 = res1;
+			resUnit.res2 = res2;
+			resUnit.tag = 1;
+			return resUnit;
+		}
+		if (temp->goUp) {    // 向上回溯一格
+			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) {    // 向左上回溯一格
+			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) {    // 向左回溯一格
+			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)
+{
+	//字符串str1,str2长度
+	const int m = str1.length();
+	const int n = str2.length();
+	int m1, m2, m3, mm;
+	unitLine **unit;
+
+	// 初始化
+	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;
+	}
+
+	// 动态规划算法计算得分矩阵每个单元的分值
+	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;
+			//判断路径来源
+			if (m1 == mm)
+				unit[i][j]->goUp = 1;
+			if (m2 == mm)
+				unit[i][j]->goLeftUp = 1;
+			if (m3 == mm)
+				unit[i][j]->goLeft = 1;
+		}
+	}
+
+	//开始回溯
+	ResUnit res;
+	res.tag = 0;
+	res = traceback(unit, m, n, str1, str2, "", "", 0, res);
+	res.score = unit[m][n]->score;
+
+	//释放内存
+	for (int i = 0; i <= m; i++) {
+		for (int j = 0; j <= n; j++) {
+			free(unit[i][j]);
+		}
+		free(unit[i]);
+	}
+	free(unit);
+	//返回值
+	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 << "请选择：\n1.输出到显示屏\n2.输出为文本\n";
+			cin >> choice;
+			if (choice != '1' && choice != '2') {
+				cout << "#请选择合法的选项！\n";
+				Sleep(1000);
+			} else
+				break;
+		}
+	}
+
+	while (true) {
+		cout << "请输入需要比对的基因序列：\n序列一:";
+		cin >> a;
+		if (legal_string(a))
+			break;
+		else {
+			cout << "#请输入合法的基因序列！\n";
+			Sleep(1000);
+		}
+	}
+
+	while (true) {
+		cout << "序列二:";
+		cin >> b;
+		if (legal_string(b))
+			break;
+		else {
+			cout << "#请输入合法的基因序列！\n";
+			Sleep(1000);
+		}
+	}
+
+	while (true) {
+		cout << "请选择比对规则:\n1.空缺优先（默认）\n2.错误优先\n3.没有优先\n";
+		cin >> c;
+		if (c != '1' && c != '2' && c != '3') {
+			cout << "#请选择合法的选项！\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 << "请选择：\n1.继续比对\n2.停止比对\n";
+		char c;
+		while (true) {
+			cin >> c;
+			if (c != '1' && c != '2') {
+				cout << "#请选择合法的选项！\n";
+				Sleep(1000);
+			} else
+				break;
+		}
+		if (c == '2')
+			break;
+	}
+	return 0;
+}
+
+/*
+"GGATCGA"
+"GAATTCAGTTA"
+*/