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第二学期大作业 序列比对.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 choice1, choice2;
+
+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;
+};
+
+int max3(int a, int b, int c)
+{
+	return max(max(a, b), c);
+}
+
+int Compare(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)
+{
+	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)
+		exit(1);
+	for (int i = 0; i <= m; i++)
+	{
+		if ((unit[i] = (unitLine *)malloc(sizeof(unitLine) * (n + 1))) == NULL)
+			exit(1);
+		for (int j = 0; j <= n; j++)
+		{
+			if ((unit[i][j] = (unitLine)malloc(sizeof(struct BacktrackingUnit))) == NULL)
+				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;
+	}
+
+	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 + Compare(str1[i - 1], str2[j - 1]);
+			m3 = unit[i][j - 1]->score + INDEL;
+			mm = max3(m1, m2, m3);
+			unit[i][j]->score = mm;
+
+			if (m1 == mm)
+				unit[i][j]->goUp = 1;
+			if (m2 == mm)
+				unit[i][j]->goLeftUp = 1;
+			if (m3 == mm)
+				unit[i][j]->goLeft = 1;
+		}
+	}
+
+	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);
+	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)
+{
+	if (!choice1 && !choice2)
+	{
+		while (true)
+		{
+			cout << "请选择：\n1.键盘读入\n2.文本读入\n";
+			cin >> choice1;
+			if (choice1 != '1' && choice1 != '2')
+			{
+				cout << "#请选择合法的选项！\n";
+				Sleep(1000);
+			}
+			else
+				break;
+		}
+		while (true)
+		{
+			cout << "请选择：\n1.输出到显示屏\n2.输出为文本\n";
+			cin >> choice2;
+			if (choice2 != '1' && choice2 != '2')
+			{
+				cout << "#请选择合法的选项！\n";
+				Sleep(1000);
+			}
+			else
+				break;
+		}
+	}
+
+	if (choice1 == '1')
+	{
+		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);
+			}
+		}
+	}
+	else
+	{
+		while (true)
+		{
+			char x;
+			cout << "文本输入完成请输入 1\n";
+			while (true)
+			{
+				cin >> x;
+				if (x == '1')
+					break;
+			}
+			ifstream ifile("TEST.txt");
+			if (!ifile)
+			{
+				cerr << "没有找到文件！请将输入放入 TEST.txt 中。\n";
+				continue;
+			}
+			string a, b;
+			ifile >> a >> b;
+			ifile.close();
+			if (!legal_string(a) || !legal_string(b))
+			{
+				cout << "#请输入合法的基因序列！\n";
+				Sleep(1000);
+			}
+			else
+				break;
+		}
+	}
+	char c;
+	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 (choice2 == '1')
+		{
+			cout << s.res1 << endl;
+			cout << s.res2 << endl;
+		}
+		else
+		{
+			ofstream ofile{"ANS.txt", ios::out};
+			ofile << s.res1 << endl;
+			ofile << s.res2 << endl;
+			ofile.close();
+		}
+		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"
+*/