#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"
*/