#include <math.h>
#include <vector>
#include <algorithm>
#include <fstream>
#include <iostream>
#include <stdio.h>
#include <time.h>


#define Alignmentclassh Alignmentclassh
#define PSS4LineLength 8044 
//64722025
#define PSS4Val 4
#define LocalSimDomain 0.666666
#define GlobalSimDomain 0.83
#define AlignmentLen 28
#define ExtendStep 12


const int StartCount=8;
const int PalCount=4;

int conversL(char L);
int PDBIDHash(const char *PDBID);
int conversSeedVal(char *tmp,int step);


class AlignmentResult
{
public:
	int PDBPos;
	int TBegin;
	int TEnd;
	int PBegin;
	int PEnd;
	
	std::vector<int> TGapRecord;
	std::vector<int> PGapRecord;
	std::vector<char> AlignedT;
	std::vector<char> AlignedP;

	int TGapCount;
	int PGapCount;

	char *Text;
	char *Pattern;
	int PatternCount;
	int TextCount;

	float Similarity;
	float SimScore;
	double p_value;
	
	bool IsTbegin();
	bool IsTend();
	bool IsPbegin();
	bool IsPend();
	int Lextern();
	int Rextern();
	void gapinsert();


	void AssignOneResult(int PDBPos1,int TBegin1,int TEnd1,int PBegin1,int PEnd1,char *Text1,char *Pattern1,int PatternCount1,int TextCount1)
	{	
		
		PDBPos=PDBPos1;
		PBegin=PBegin1;
		PEnd=PEnd1;
		TBegin=TBegin1;
		TEnd=TEnd1;
	
		Text=Text1;
		Pattern=Pattern1;
		PatternCount=PatternCount1;
		TextCount=TextCount1;
		Similarity=1;
		SimScore=0;
			
	}

};

class AlignmentClass  
{
public:

	//int ShowMax(int a,int b,int c);
	//float S(char a,char b);// 罰分函數
	void MainAlignment(AlignmentResult &tmpAR);
	void ResultAsignMent(AlignmentResult& tmpA1,AlignmentResult& tmpA2);
	void test(AlignmentResult &tmpAR);
	float FinalAlign(AlignmentResult& tmpA,int tb,int te,int pb,int pe);
	//float s[4][4]={{1,0.1,0,0.1},{0.1,1,0.1,0},{0,0.1,1,0.1},{0.1,0,0.1,1}};
	//AligmentResult LExtend(AligmentResult tmpAS);
	//AligmentResult RExtend(AligmentResult tmpAS);
	//AligmentResult GlobalExtend(AligmentResult tmpAS);
	//AligmentResult FininalAlignment();
	//char P[PSS4LineLength],T[PSS4LineLength];
	/*
	char *Seed;
	char *Pattern;
	char *Text;
	int PatternCount;
	int TextCount;
	int Pbegin;
	int Pend;
	int Tbegin;
	int Tend;
	int PDBPos;*/

	//void Init(int PDBPos,char *Pattern,char *Text,int PatternCount,int TextCount,int Pbegin,int Pend,int Tbegin,int Tend);
	


};