#include <iostream>
#include <sstream>
#include <stdio.h>
#include <fstream>
#include <string>
#include <cstdlib>
#include <ctime>
#include <cmath>
#include <iomanip>
#include <vector>
#include <stdlib.h>



using namespace std;

class Computer {

		public:


		void read(string address2){
			ifstream inFile;


           input=address2;

			int k1,k2,k3;
			bool f,f1,f2,f3,f4,f5,f6,f7,f8,f9;
			f=f1=f2=f3=f4=f5=f6=f7=f8=f9=false;

			string md1,p1,lm1,rm1,ming1,maxg1,t1,output,a,b,s1;



		output="output.txt";

		t1="30";
		p1="1";
		md1="1";
		g1="1";
		lm1="6";
		rm1="6";
		ming1="0";
		maxg1="0";
		s1="1";
		//getline(cin,input);
		input=input+' ';

		x=input.length();


		i=0;
		j=0;
		k1=k2=k3=0;
		for(i=0 ; i<=x ; i++){
			if((input[i]=='-')&&(input[i+1]=='h')){
				cout<<"Help commands:"<<"\n";
				cout<<"----------------------------------------------------------------------------------------------------"<<"\n";
				cout<<"-i input file"<<"\n";
				cout<<"-m left motif width (default 6)"<<"\n";
				cout<<"-M right motif width (default 6)"<<"\n";
				cout<<"-g min gap between two motif blocks (default 0)"<<"\n";
				cout<<"-G max gap between two motif blocks (default 0)"<<"\n";
				cout<<"-t number of times trying to repeat process to find best motif (default 30)"<<"\n";
				cout<<"-o output file (default output.txt)"<<"\n";
				cout<<"-f 1 for fasta file, or 2 for text file (no header) (default 1)"<<"\n";
				cout<<"-p 1 for the given strand, or 2 for both the given and reverse complement strands (default 1)"<<"\n";
				cout<<"-n 1 for PWM, or 2 for DWM (default 1)"<<"\n";
				cout<<"-s 1 for one occurrence motif site per sequence, or 2 for any number of repetitions (default 1)"<<"\n";
				cout<<"----------------------------------------------------------------------------------------------------"<<"\n";
			exit(0);
			}

			if((input[i]=='-')&&(input[i+1]=='i')){
				i=i+3;
				k3=i;
				address.clear();
				a=input[i];
				i++;
				while (input[i] != ' '){
			    a+=input[i];
			    k1++;
			    j++;
			    i++;}
			   //address=input.substr(k3,k1);
			   address=a;
			   }
			    k1=0;
			   j=0;
			   if((input[i]=='-')&&(input[i+1]=='o')){
				i=i+3;
				output.clear();
				k3=i;
				b=input[i];
				i++;
				while (input[i] != ' '){
			    b+=input[i];
			    k1++;
			    j++;
			    i++;
			   }
			   output=b;
		}
	}


		cout<<"\n";


		i=0;
		j=0;

	while(i <= x){
		if((input[i]=='-')&&(input[i+1]=='f')){
				j=0;
				i+=3;
				g1=input[i];
				i++;
				if(input[i] != ' '){
				g1=g1+input[i];
				i++;}
				//while (input[i] != ' ') {
				//lm1[j]=input[i];
				//j++;
				//i++;}
				}


			   else if((input[i]=='-')&&(input[i+1]=='n')){
				j=0;
				i+=3;
				md1=input[i];
				i++;
				if(input[i] != ' '){
				md1=md1+input[i];
				i++;}
				//while (input[i] != ' ') {
				//lm1[j]=input[i];
				//j++;
				//i++;}
				}



			   else if((input[i]=='-')&&(input[i+1]=='p')){
				j=0;
				i+=3;
				p1=input[i];
				i++;
				if(input[i] != ' '){
				p1=p1+input[i];
				i++;}
				//while (input[i] != ' ') {
				//lm1[j]=input[i];
				//j++;
				//i++;}
				}

				else if((input[i]=='-')&&(input[i+1]=='s')){
				j=0;
				i+=3;
				s1=input[i];
				i++;
				if(input[i] != ' '){
				s1=s1+input[i];
				i++;}
				//while (input[i] != ' ') {
				//lm1[j]=input[i];
				//j++;
				//i++;}
				}


			    else if((input[i]=='-')&&(input[i+1]=='m')){
				j=0;
				i+=3;
				lm1=input[i];
				i++;
				if(input[i] != ' '){
				lm1=lm1+input[i];
				i++;}
				//while (input[i] != ' ') {
				//lm1[j]=input[i];
				//j++;
				//i++;}
				}


			   else if((input[i]=='-')&&(input[i+1]=='M')){
				j=0;
				i+=3;
				rm1=input[i];
				i++;
				if(input[i] != ' '){
				rm1=rm1+input[i];
				i++;}
				//while (input[i] != ' ') {
				//rm1[j]=input[i];
				//j++;
				//i++;}
				}


			   else if((input[i]=='-')&&(input[i+1]=='g')){
				j=0;
				i+=3;
				ming1=input[i];
				i++;
				if(input[i] != ' '){
				ming1=ming1+input[i];
				i++;}
				//while (input[i] != ' ') {
				//ming1[j]=input[i];
				//j++;
				//i++;}
				}


			   else if((input[i]=='-')&&(input[i+1]=='G')){

				j=0;
				i+=3;
				maxg1=input[i];
				i++;
				if(input[i] != ' '){
				maxg1=maxg1+input[i];
				i++;}
				//while (input[i] != ' ') {
				//maxg1[j]=input[i];
				//j++;
				//i++;}
				}


			   else if((input[i]=='-')&&(input[i+1]=='t')){
				j=0;
				i+=3;
				t1=input[i];
				i++;
				if(input[i] != ' '){
				t1=t1+input[i];
				i++;}
				//while (input[i] != ' ') {
				//t1[j]=input[i];
				//j++;
				//i++;}
				}


				else
	       i++;

	}

	g=atoi(g1.c_str());
	p=atoi(p1.c_str());
	s=atoi(s1.c_str());
	md=atoi(md1.c_str());
	lml=atoi(lm1.c_str());
	rml=atoi(rm1.c_str());
	ming=atoi(ming1.c_str());
	maxg=atoi(maxg1.c_str());
	tf=atoi(t1.c_str());


	cout<<"\n";


		while(f==false){
		//cout<<"\n If you want choose Fasta file, please input 1 and Text file, please input 2:";
		//cin>>g;
		if(g==1 || g==2)
	      f=true;
	     else
	      {cout<<"\n Please input just number 1 (Text file) or 2 (Fasta file) for type of input file:";
		   cin>>g;}
	    }


		//cout<<"\n Please enter a your data file address:";
		//getline(cin,address3);

		//getline(cin,address);
	    while(f7==false){
		cout << "\n";
		myfile4.open(address.c_str() , ios::out | ios::app | ios::binary);
		 if(!myfile4.is_open()){
                cout << "\n ERROR Your Data is not correct.\n";
                cout<<"\n Please enter a your data file address:";
		        getline(cin,address);}
         else
           f7=true;
	   }



		while(f6==false){
		//cout<<"\n Please enter your method, for Mono-Nucleotide enter number 1 and Di-Nucleotide enter number 2:";
		//cin>>md;
		if(md==1 || md==2)
	      f6=true;
	     else
	      {cout<<"\n Please input just number 1 (Mono-Nucleotide) or 2 (Di-Nucleotide) for analysis method:";
	      cin>>md;}
	    }

		while(f5==false){
	  //  cout<<"\n Please choose read pattern (For just Positive direction input 1 and Positive and Negative direction input 2):";
	  //    cin>>p;
	     if(p==1 || p==2)
	      f5=true;
	     else
	      {cout<<"\n Please input just number 1 (Positive direction) or 2 (Positive and Negative direction) for pattern:";
	      cin>>p;}
	     }

	     while(f9==false){

	     if(s==1 || s==2 || s==3)
	      f9=true;
	     else
	      {cout<<"\n Please input just number 1 for one occurrence motif site per sequence, or 2 for any number of repetitions of motifs, or 3 for zero or one occurrence motif site per sequence:";
	      cin>>s;}
	     }

        while(f1==false){
		//cout<<"\n Please enter Length of left motif:";
        //    cin>>lml;
            if(lml>0 && lml<=25)
             f1=true;
            else
             {cout<<"\n Please enter length of left motif between 1 ~ 25:";
             cin>>lml;}
		 }

		while(f2==false){
       // cout<<"\n Please enter Length of right motif:";
       //     cin>>rml;
            if(rml>=0 && rml<=25)
             f2=true;
            else
            { cout<<"\n Please enter length of right motif between 0 ~ 24:";
             cin>>rml;}
		 }

		if(rml>0){
		while(f3==false){
       //  cout<<"\n Please enter minimum Length of Gap between two motif blocks:";
       //     cin>>ming;
           if(ming>=0 && ming<=25)
             f3=true;
            else
            { cout<<"\n Please enter minimum Length of Gap between 0 ~ 25:";
             cin>>ming;
             }
		 }
	 }
		while(f4==false){
       // cout<<"\n Please enter maximum Length of Gap between two motif blocks:";
       //     cin>>maxg;
           if(maxg>=0 && maxg<=25)
             f4=true;
            else
            {
             cout<<"\n Please enter maximum Length of Gap between 0 ~ 25:";
             cin>>maxg;

             }
		 }

		 while(f4==false){

           if(tf>=0 && tf<=100)
             f4=true;
            else
            {
		 cout<<"\n Please enter number of time trying to find motif(Maximum trying is 100):";
           cin>>tf;
		 }}



		 cout<<"\n\t\t\t Please waiting...\n";

		 //o="/home/mohammad/Documents/test1.txt";


		 	student=freopen(output.c_str(), "w",stdout);
			if( student == NULL)
          {
             printf("Can't reopen textfile1.txt\n");

           }
		}




		void output_information()
		{

			cout<<"\n-------------------------------------------------------------------------\n";
			//lml=22;
			//rml=0;
			lms=lml+rml;
			//md=2;
			if(md==1){
			nu=4;
			lm=lms;}
			else if (md==2){
			nu=16;
			lm=lms-1;}
			//max=3
            //tf=3;
			//p=2;
			x=1;
			a=0;
			l=0;
			l2=20;
			z=0;
			b=0;
			initial=1;
			r=0;
			ns=0;
			nmax=30;
			//g=2;
			//ming=0;
			//maxg=0;
			min=0;
			if(md==1){
			da[0]="A"; da[1]="C"; da[2]="G"; da[3]="T";
		    }
		    else if (md==2){
			da[0]="AA"; da[1]="AC"; da[2]="AG"; da[3]="AT"; da[4]="CA"; da[5]="CC"; da[6]="CG"; da[7]="CT";
			da[8]="GA"; da[9]="GC"; da[10]="GG"; da[11]="GT"; da[12]="TA"; da[13]="TC"; da[14]="TG"; da[15]="TT";
		    }


				}


		void textmining()
		{


                 if(!myfile4.is_open()){
                cout << "\n ERROR Your Dtat Is Not Correct.\n";
        }
        else
        {
			i1=0;
			i=0;
			j=0;
			flag=false;
                while((myfile4 >> noskipws >> ch ) && (!myfile4.eof())) {
				/*	if (k==0){
					cout<<">"<<i+1;
					cout<<'\n';
					k=1;
					}*/

					 if (ch!='\n'){
					 cout << ch ;
					 if(j<2000 and i<2000){
					 str4[i][j]=(ch);
                     j++;}
                    }
                     else{
						 if(g==2){
						lenstr2[i1]=j;
						cout<<'\t'<<lenstr2[i1];
						sum=sum+lenstr2[i1];
						i1++;
						}
						else if(g==1){

						lenstr2[i1]=j;
						if(flag==true)
						//cout<<'\t'<<lenstr2[i1];
						sum=sum+lenstr2[i1];
						i1++;


					}

					 str4[i][j]='\n';
                     flag= !flag;
                     j=0;
                     i++;
				     cout<<'\n';
				     k=0;

				      }

              }


              myfile4.close();
		  }
		  cout<<'\n';
		  max2=i;
		  max=i;
		  k=0;
		  y=0;
		  if(g==1){
		  i=1;
		  while(i<i1){
			  if(str4[i][0] != '>'){
			  		    for(j=0; j<lenstr2[i]; j++)
							{
								str4[i][j]=toupper(str4[i][j]);
								if(str4[i][j]=='A' || str4[i][j]=='C' || str4[i][j]=='G' || str4[i][j]=='T')
		                        //cout<<str4[i][j];
		                        str2[k][y]=str4[i][j];
		                        y++;
		                   }}
		       if ((str4[i][0] == '>')||(i+1==i1)){

		        lenstr2[k]=y;
		        k++;

		        y=0;
		      }
			   i++;
		   }
		   max=k;
		  }


		 // cout<<'\n'<<"Number of sequence:"<<max<<"  Number of line:"<<max<<'\n';


		  i1=0;
		  /*
		  if(g==1){
		  for(j=1 ; j<(max*2) ; j+=2){
			  flag=true;
			  x=0;
				 ns++;
		      for(k=0 ; k<lenstr2[i1] ; k++) {
		        str2[i1][k]=str4[j][k];

				 if (((str2[i1][k]=='A')||(str2[i1][k]=='C')||(str2[i1][k]=='G')||(str2[i1][k]=='T'))){
					 x++;
				 if(flag==true){
				 sigb[i1][0]=k;
				 flag=false;}
			 		 }
				 }
				 sigb[i1][1]=x;
		        i1++;
		       }
		       }
		       else */
		      if(g==2){
		       for(j=0 ; j<max ; j++){
			  flag=true;
			  x=0;
				 ns++;
		      for(k=0 ; k<lenstr2[i1] ; k++) {
				  str4[j][k]=toupper(str4[j][k]);
		        str2[i1][k]=str4[j][k];
				 if (((str2[i1][k]=='A')||(str2[i1][k]=='C')||(str2[i1][k]=='G')||(str2[i1][k]=='T'))){
					 x++;
				 if(flag==true){
				 sigb[i1][0]=k;
				 flag=false;}
			 		 }
				 }
				 sigb[i1][1]=x;
		        i1++;
		       }}


		for(i=0 ; i<ns ; i++){
		//cout<<">"<<i+1<< "\t"<<sigb[i][0]<<"\n";


	         for(k=0 ; k<lenstr2[i] ; k++)
	         {
				str2[i][k]=toupper(str2[i][k]);

	         //cout<<str2[i][k];

		 }
	      //   cout<<"\t"<<lenstr2[i]<<"\t"<<sigb[i][1]<<'\n';
	     //cout<<'\n';
		 }
		  sum=0;
		  g=0;
		  k=0;
          // printf("\n--------------------------------------------------------------------\n");
                for(i=0 ; i<(max2) ; i++)
                if(str4[i][0] =='>'){

                for(j=0 ; str4[i][j] !='\0' ; j++){
                str5[k][j]=str4[i][j];

                }
                k++;
                }




                	}
		//--------------------------------------------------------------
         void reverse(){
			 for(i=0 ; i<max ; i++){
				k=0;
				for(j=lenstr2[i]-1 ; j>=0 ; j--){
				 if(str2[i][j]=='A')
				 str3[i][k]='T';
				 else
				 if(str2[i][j]=='C')
				 str3[i][k]='G';
				 else
				 if(str2[i][j]=='G')
				 str3[i][k]='C';
				 else
				 if(str2[i][j]=='T')
				 str3[i][k]='A';

				 k++;
		}




	}
	 /*
	   cout<<"\n----------REVERSE------------------\n";
			for(i=0 ; i<max ; i++) {
				cout<<">"<<i+1<<'\n';
				for(j=0 ; j<lenstr2[i] ; j++){
					cout<<str3[i][j];}
					cout<<'\n';
				}
			 */
		 }
	    //--------------------------------------------------------------
	     void selectrandom()
	     {

			 srand((unsigned)time(NULL)*(r+x+1));

			   for(i=0 ; i<max ; i++)
			     rndnuml[i][r]=(rand() % (lenstr2[i]-maxg-lm-2));

			   for(i=0 ; i<max ; i++){
				   j=rndnuml[i][r]+maxg+lml;
				   k=rndnuml[i][r]+ming+lml;
			       rndnumr[i][r]=(rand() % (j-k+1))+k;


		  }

		 // for(i=0 ; i<max ; i++)
		  //  cout<<rndnuml[i][r]<<":"<<rndnumr[i][r]<<" "<<rndnumr[i][r]-rndnuml[i][r]-4<<"\n";




		 }

		 //-------------------------------------------------------------

		 void startlocation()
		  {

			//const int n1=lm , n2=max;
			//char ran1[n2][n1];



		     //char ran1[n2][n1];

			  for(j=0 ; j<max ; j++){
			  k=0;
			  rnd=rndnuml[j][r];
			  for(i=rnd ; i<rnd+lml ; i++){
				   ran1[j][k]=str2[j][i];
			    	  k++;
		        }

		        rnd=rndnumr[j][r];
			  for(i=rnd ; i<rnd+rml ; i++){
				   ran1[j][k]=str2[j][i];
			    	  k++;
		        }

		  }

				 count_nucleotide(ran1);

		  }


		 //-------------------------------------------------------------
		 void count_nucleotide(char test1[1000][50]){



			for(i=0 ; i<nu ; i++){
				for(j=0 ; j<(lm) ; j++)
				freq[i][j]=0;
				}

					for(j=0 ; j<lm ; j++){
						for(i=0 ; i<max ; i++){
						subnuc=test1[i][j];

						if (md==2)
						subnuc+=test1[i][j+1];

						for(k=0 ; k<nu ; k++)
				           if (da[k]==subnuc)
				          freq[k][j]=freq[k][j]+1;

				    }
			      }
			   }


	 //-----------------------------------------------------------------

	 void PPM(){

		// printf("\nTherefore the resulting Position Probability Matrix (PPM):\n");
		// printf("\n Column1  Column2  Column3  Column4  Column5\n");
		 sum=0;
		 for(i=0 ; i<lm ; i++){
		//	  cout<<da[i]<<"\t";
			    for(j=0 ; j<lm ; j++){
					freq1[i][j]=(float(freq[i][j])/(max+1));
					sum=sum+freq1[i][j];
			//		if(j<11)
			//       printf(" %.2f   ",freq1[i][j]);
			   }

		//cout<<'\n' ;
		 }
	//	 printf("\nThe Added total Table PPM:%.2f \n",sum);

	 }

	 //-----------------------------------------------------------------


		 void selectseq()
		 {




		 for(j=0 ; j<max ; j++){
			  k=0;
			  rnd=rndnuml[j][r];
			  for(i=rnd ; i<rnd+lml ; i++){
				   ran1[j][k]=str2[j][i];
			    	  k++;
		        }

		        rnd=rndnumr[j][r];
			  for(i=rnd ; i<rnd+rml ; i++){
				   ran1[j][k]=str2[j][i];
			    	  k++;
		        }

		  }


			 for(i=0 ; i<max ; i++){
				 for(j=0 ; j<lms ; j++)
					 if(selseq != i)
					 seq1[i][j]=ran1[i][j];
					 else
					 seq1[i][j]='*';
				 }
		//		 cout<<"\n------------------------------------------------------\n";
		if(p==2){

			for(j=0 ; j<max ; j++){
			  k=0;
			  rnd=rndnuml[j][r];
			  for(i=rnd ; i<rnd+lml ; i++){
				   ran1[j][k]=str3[j][i];
			    	  k++;
		        }

		        rnd=rndnumr[j][r];
			  for(i=rnd ; i<rnd+rml ; i++){
				   ran1[j][k]=str3[j][i];
			    	  k++;
		        }

		  }


			 for(i=0 ; i<max ; i++){
				 for(j=0 ; j<lms ; j++)
					 if(selseq != i)
					 seq5[i][j]=ran1[i][j];
					 else
					 seq5[i][j]='*';
				 }

		}


	}
		//--------------------------------------------------------------------------------
		void Background_count(){
		int sum=0;
		int sum2=0;


	    count_nucleotide(seq1);


			for(i=0 ; i<nu ; i++)
			   BG[i]=0;

			for(i=0 ; i<max ; i++){
			     if(i!=selseq)
			     for(j=0 ; j<lenstr2[i]-1 ; j++){
					 for(k=0 ; k<nu ; k++){
						 if(rml==0){
						 if (j<rndnuml[i][r]-1 || (j>(rndnuml[i][r]+rml-1))){
							subnuc=str2[i][j];

							  if(md==2)
						      subnuc+=str2[i][j+1];

			               if(subnuc==da[k])
			                  BG[k]++;}
			                 }
			                  else
			              	 {
						 if (j<rndnuml[i][r]-1 || ((j>(rndnuml[i][r]+lml-1)) && (j<rndnumr[i][r]-1)) || (j>(rndnumr[i][r]+rml-1))){
							subnuc=str2[i][j];

							if(md==2)
						    subnuc+=str2[i][j+1];

			               if(subnuc==da[k])
			                  BG[k]++;}
			            }
					}
			            }

			         }


	if(p==2){

			for(i=0 ; i<nu ; i++)
			   BG2[i]=0;

			for(i=0 ; i<max ; i++){
			     if(i!=selseq)
			     for(j=0 ; j<lenstr2[i]-1 ; j++){
					 for(k=0 ; k<nu ; k++){
						 if(rml==0){
						 if (j<rndnuml[i][r]-1 || (j>(rndnuml[i][r]+rml-1))){
							subnuc=str3[i][j];

							if(md==2)
						    subnuc+=str2[i][j+1];

			               if(subnuc==da[k])
			                  BG2[k]++;}
			                 }
			                  else
			              	 {
						 if (j<rndnuml[i][r]-1 || ((j>(rndnuml[i][r]+lml-1)) && (j<rndnumr[i][r]-1)) || (j>(rndnumr[i][r]+rml-1))){

							subnuc=str3[i][j];

							if(md==2)
						    subnuc+=str2[i][j+1];

			               if(subnuc==da[k])
			                  BG2[k]++;}
			            }
					}
			            }

			         }
			         //if(zm==84)
			         //for(i=0 ; i<nu ; i++)
			         //BG2[i]=1;

			         for(i=0 ; i<nu ; i++)
			         sum2=sum2+BG2[i];

			}

			        //if(zm==84)
			         //for(i=0 ; i<nu ; i++)
			         //BG[i]=1;
		//	cout<<"\nprint nucleotide count of random select PFM:\n";
		//		   printf("   Backgrand   \n");
				  for(i=0 ; i<nu ; i++){
		//            cout<<da[i]<<"\t"<<BG[i]<<"\t";
		            sum=sum+BG[i];

		            //sum2=sum2+BG2[i];
		//		      for(j=0 ; j<(lm-1) ; j++)
		//		          printf("%d  ",freq[i][j]);
		//	      cout<<"\n";
				}

		//		cout<<"\nprint LIKELIHOOD: ((MatrixPFM[i]+0.25 )/ (total number of colum+1))\n";
				for(i=0 ; i<nu ; i++){
		//			  cout<<da[i]<<" ";
		          if(md==1){
					  BG[i]=(BG[i]+0.25)/sum;
					  if(p==2)
					  BG2[i]=(BG2[i]+0.25)/sum2;
				  }
				  else if(md==2){
					  BG[i]=(BG[i]+0.0625)/sum;
					  if(p==2)
					  BG2[i]=(BG2[i]+0.0625)/sum2;
				  }
		//			 printf("%.3f ", BG[i]);
				      for(j=0 ; j<(lm) ; j++){
						if(md==1)
			               freq1[i][j]=(float((freq[i][j])+0.25)/max);
			             else if(md==2)
			               freq1[i][j]=(float((freq[i][j])+0.0625)/max);

		//		          printf("%.2f  ",freq1[i][j]);
					  }}

					  if(p==2){
					  count_nucleotide(seq5);
					  for(i=0 ; i<nu ; i++)
					    for(j=0 ; j<(lm) ; j++){
						   if(md==1)
			                  freq2[i][j]=(float((freq[i][j])+0.25)/max);
			               else if(md==2)
			                  freq2[i][j]=(float((freq[i][j])+0.0625)/max);
		//		      cout<<"\n";
				  }
			  }
		}

	//--------------------------------------------------------------
	void choosemethod(){



	}

	//--------------------------------------------------------------
		  void subseqlength3(){

		//  cout<<"\n"<<"--------------------subsequence--------------------------\n";

		  a=0;

		    for(i=ming ; i<=maxg; i++){
			    for(l=0 ; l<(lenstr2[z]-lms-i-2) ; l++){
					k=0;
					for(j=0 ; j<lms ; j++)
					 {
						 if(j<lml)
						 {
					      seq2[a][j]  =str2[z][l+j];

					     }
				          else
				         {
					     seq2[a][j]  =str2[z][l+j+i];

				     }
				     }
				     positionl[a][0]=l;
				     positionr[a][0]=l+lml+i;

			         a++;
			        }
				}

				/*
			 	 for(i=a ; i<9000 ; i++)
			 	   for(j=0 ; j<lms ; j++)
			 	     seq2[i][j]='\0';


			 	 for (l=0 ; l<a ; l++){
					 cout<<l<<":";
			 	 for (j=0 ; j<lm ; j++)
			 	 cout<<seq2[l][j];

			 	 cout<<"\t"<<" "<<positionl[l]<<","<<positionr[l];
			// 	if (l%3==0)
			 	 cout<<"\n";

			 	 }*/
			 }

		//--------------------------------------------------------------

		void score(){

		//	cout<<"\n-----------------calculate score for seq"<<selseq<<"----------------\n";
		//	cout<<" \n-----------------------------------------\nselect sequance "<<selseq<< "\n";

			 sum=0;


			 for(i=0 ; i<a ; i++){
				 score1[i]=0;
				 div=0;
			    for(j=0 ; j<(lm) ; j++){
					subnuc=seq2[i][j];

					if(md==2)
					subnuc+=seq2[i][j+1];

					for(k=0 ; k<nu ; k++)

					if (subnuc==da[k]){
			//		   printf("Log%.2f ",freq1[k][j]);
					    div=div+log(BG[k]);
					    score1[i]=score1[i]+log(freq1[k][j]);
					   }
				/*
					   if(j<(lm-1))
					   cout<<"+";
					   else
					  printf("/%.6f",div);   */

					}
					score1[i]=score1[i]/div;
		//			cout<<"="<<score1[i]<<" number:"<<i<<"\n";
					//sum=sum+score1[i];

					}
				if(zm != 84){
				maxscor[0]=score1[0];
				for(i=min ; i<a ; i++){
				 if(maxscor[0]>score1[i]){
				     maxscor[0]=score1[i];
				     k=i;
				 }

			 }
	//			cout<<"\nMaximume Value Number:"<<score1[k]<<"\n";

				rndnuml[z][r]=positionl[k][0];
				rndnumr[z][r]=positionr[k][0];
				state[z][r]='P';
		}
		/*else{
			cout<<"\n---------test score1--------\n";
			for(i=0; i<a; i++)
			cout<<score1[i]<<"\n";
			cout<<"\n---------test Freq1--------\n";
			for(j=0 ; j<(nu) ; j++){
				for(k=0 ; k<lm ; k++)
				cout<<freq1[j][k]<<"\t";
				cout<<"\n";}
			cout<<"\n---------test BG--------\n";
			for(i=0; i<nu; i++)
			cout<<BG[i]<<"\n";
			}*/



//	cout<<"\n-------------------Random Number between 0.000 until 1.000--------------------\n";
			 }

			 //--------------------------------------------------------------
		 void selectreverseseq()
		 {



		a=0;

		   for(i=ming ; i<=maxg; i++){
			    for(l=0 ; l<(lenstr2[z]-lms-i-2) ; l++){
					k=0;
					for(j=0 ; j<lms ; j++)

						 if(j<lml)
						 {
					      seq4[a][j]  =str3[z][l+j];
					 }
				          else
				         {
					     seq4[a][j]  =str3[z][l+j+i];

				     }

				     positionl[a][1]=l;
				     positionr[a][1]=l+lml+i;

			         a++;

				}
			 }
			 	/*
			 	//if(z==6) {
			 	 for(i=a ; i<9000 ; i++)
			 	   for(j=0 ; j<lms ; j++)
			 	     seq4[i][j]='\0';


			 	 for (l=0 ; l<a ; l++){
					 cout<<l<<":";
			 	 for (j=0 ; j<lm ; j++)
			 	 cout<<seq4[l][j];

		  cout<<"\t"<<" "<<positionl[l][1]<<","<<positionr[l][1]<<" : "<<positionr[l][0]-positionl[l][0]-lml;
		//	 	if (l%3==0)
			 	 cout<<"\n";
			 }
			 	 }	*/
	       }

		//--------------------------------------------------------------

			 //---------------------------------------------------------
			 void score2twoway(){

		//	cout<<"\n-----------------calculate score for seq"<<selseq<<"----------------\n";
		//	cout<<" \n-----------------------------------------\nselect sequance "<<selseq<< "\n";

			// sum2[0]=0;
			// sum2[1]=0;


			 for(i=min ; i<a ; i++){
				 score2[i][0]=0;
				 score2[i][1]=0;
				 div1[0]=0;
				 div1[1]=0;
			    for(j=0 ; j<lm ; j++){
					subnuc=seq2[i][j];
					subnuc1=seq4[i][j];

					if(md==2){
					subnuc+=seq2[i][j+1];
					subnuc1+=seq4[i][j+1];}

					for(k=0 ; k<nu ; k++){

					if (subnuc==da[k]){
					 // printf("Log%.2f ",freq1[k][j]);
					    div1[0]=div1[0]+log(BG[k]);
					    score2[i][0]=score2[i][0]+log(freq1[k][j]);
					   }
				   if (subnuc1==da[k]){
				//	   printf("Log%.2f ",freq1[k][j]);
					    div1[1]=div1[1]+log(BG2[k]);
					    score2[i][1]=score2[i][1]+log(freq2[k][j]);
					   }


				   }
				/*	   if(j<lm-1)
					   cout<<"+";
					   else
					  printf("/%.6f",div[1]);
					  */
					}
					score2[i][0]=score2[i][0]/div1[0];
					score2[i][1]=score2[i][1]/div1[1];
					//cout<<"="<<score2[i][0]<<" number1:"<<i<<"\n";
					//cout<<"="<<score2[i][1]<<" number2:"<<i<<"\n";

				//	sum2[0]=sum2[0]+score1[i][0];
				//	sum2[1]=sum2[1]+score1[i][1];

					}

				maxscor[0]=score2[0][0];
				for(i=0 ; i<a ; i++){
				 if(maxscor[0]>score2[i][0]){
				     maxscor[0]=score2[i][0];
				     k1=i;
				 }}


				 maxscor[1]=score2[0][1];
				for(i=0 ; i<a ; i++){
				 if(maxscor[1]>score2[i][1]){
				     maxscor[1]=score2[i][1];
				     k2=i;
				 }}


			//	cout<<"\nMaximume Value Number:"<<score1[k1][0]<<"\t"<<score1[k2][1]<<"\n";
		                rndnuml[z][r]=positionl[k1][0];
				rndnumr[z][r]=positionr[k1][0];
				state[z][r]='P';

			//	cout<<"\nMaximume Value Number:"<<score1[k1][0]<<"\t"<<score1[k2][1]<<"\n";
		  if (maxscor[0]>maxscor[1])
		  {
				rndnuml[z][r]=positionl[k2][1];
				rndnumr[z][r]=positionr[k2][1];
				state[z][r]='N';
			}
			//for(i=0; i<max; i++)
		    //cout<<i<<"*"<<rndnuml[i][r]<<"\t"<<rndnumr[i][r]<<"\n";

		}

			 //---------------------------------------------------------

			 void randomgenerate(){

				int RND_MAX=1000;
				srand((unsigned)time(NULL)*(sum+r));
				sum=(rand() % (RND_MAX));
			    rndsel=sum/RND_MAX;
			 }




		//--------------------------------------------------------------

		void PFM(){


	//		cout<<"\n-----------------------------------------------------";
	//		 printf("\nAfter Calculate 64 step , We have 64 SubSequnce:\n");

			 for(j=0 ; j<max ; j++){

			 k=0;

			 for(i=rndnuml[j][r] ; i<rndnuml[j][r]+lml ; i++){
				 if(state[j][r]=='P')
				 seq1[j][k]=str2[j][i];
				 else if(state[j][r]=='N')
				 seq1[j][k]=str3[j][i];
		      	     k++;
		        	     }
		       for(i=rndnumr[j][r] ; i<rndnumr[j][r]+rml ; i++){
				if(state[j][r]=='P')
				 seq1[j][k]=str2[j][i];
				 else if(state[j][r]=='N')
				 seq1[j][k]=str3[j][i];
		      	     k++;
		        	     }
		        	        }




		/*
			for(i=0 ; i<max ; i++){
				cout<<">"<<i+1;
				cout<<"\n";
			   for(j=0 ; j<12 ; j++)
			        printf("%c",seq1[i][j]);
			        cout<<"\n";
		} */

		count_nucleotide(seq1);



	/*	cout<<"\nprint nucleotide count of random select PFM:\n";
			   printf("  \n");
				  for(i=0 ; i<=15 ; i++){
		            cout<<da[i]<<"  ";
				      for(j=0 ; j<11; j++)
				          printf("%d  ",freq[i][j]);
				      cout<<"\n";
				}  */

		//		cout<<"\nprint LIKELIHOOD: ((MatrixPFM[i]+0.0625 )/ (total number of colum+1))\n";
				for(i=0 ; i<nu ; i++){
		//			  cout<<da[i]<<"\t";
					     for(j=0 ; j<(lm) ; j++){
							 if(md==1)
			                   freq1[i][j]=(float((freq[i][j])+0.25)/(max+1));
			                 else if (md==2)
			                   freq1[i][j]=(float((freq[i][j])+0.0625)/(max+1));
		//		          printf("%.2f ",freq1[i][j]);
					  }
		//		      cout<<"\n";
				      }



		//		cout<<"\nEntropy for each colum: -[i(1..n) Px*log(Px)]:\n";
				for(i=0 ; i<(lm) ; i++){
					entropy[i]=0;
				   for(j=0 ; j<nu ; j++){

				      entropy[i]=entropy[i]+(freq1[j][i]*log2(freq1[j][i]));}

				      entropy[i]=entropy[i]*(-1);
	//		      printf("%.4f  ", entropy[i]);

			   }

			   entropytotal[r][0]=0;
			   for(i=0 ; i<(lm) ; i++){
				entropytotal[r][0]=entropytotal[r][0]+entropy[i];
			}
				//cout<<"\nTotal Added all Colums is:"<<entropytotal[r][0];




		}
		//--------------------------------------------------------------
			void step1(){
	//	cout<<"\n\n------Step1 By New Sequence Computional (Seq1 , Seq3)-------\n";

		selseq=z;
		//max=lenstr2[z];
		selectseq();
		Background_count();
		subseqlength3();

		if(p==1){
		score();
	    }
	    else if (p==2)	{
	    selectreverseseq();
	    score2twoway();
        }
		//randomgenerate();
		initial=z;
		//randomly();


		}

		//--------------------------------------------------------------
		void step2(){
		z=0;
		while(z<max){

			step1();
			z++;

		}


	//	cout<<"\n";
		PFM();



		}
		//--------------------------------------------------------------


		void step11(){
			//cout<<"\n********************************************************************************";
			float f1,f2,f0;
			f2=0;

			int x2=0;
			//float check[200];
			temp_e[0]=0;
			temp_e[1]=0;


			while((bb==false)&&(temp_e[1]<30)){

			step2();
			f1=entropytotal[r][0];
			f0=abs(f1-f2);
			if ((f0 < 0.00000001)){
				bb=true;
				//entropytotal[r][0]=f2;
				testi[r]=f1;
				//cout<<"\nentropytotal[0]:"<<f2<<"\tentropytotal[1]:"<<f1;
				//cout<<"\nNumber Total Step Repeat is:"<<temp_e[1];

				x2++;
				//check[x2]=f1;


			}
			else
			{

				x2=temp_e[1];

				//check[x2]=f1;
				temp_e[1]++;

				f2=f1;
			}
		}
		if(temp_e[1]>=10){
			testi[r]=f1;
			bb=true;
			//cout<<"\nentropytotal[0]:"<<f2<<"\tentropytotal[1]:"<<f1;
			//	cout<<"\nNumber Total Step Repeat is:"<<temp_e[1];
		}

		//cout<<"\n";


			//for(i=0 ; i<x2 ; i++)
			//cout<<check[i]<<"\n";

    		x=0;
		}
		//--------------------------------------------------------------
		void step21(){
			 k=lml+rml+maxg;

	         for(i=0; i<max; i++){
             if(k>(lenstr2[i]-2)){

			cout<<"ERROR: Length of the site "<<i+1<<" is less than your input parameters(Left Motif + Right Motif + Gap).\n";

			 exit (EXIT_FAILURE);
			 }}

			for(i1=0 ; i1<tf ; i1++){
		//cout<<"\n----------------------------------------------------------------------\n";

		bb=false;

	    step11();

	       // cout<<"\n##########NEW Genrate for Calculate to find motif of Step: "<<r+2<<"  ############\n" ;


	        r++;
	        b=1;
	    	selectrandom();


              }


             cout<<"\n-----------------------------------------\n";



		sum=testi[0];
		l=0;
		cout<<"\nEntropy is :\n";
		for(i=0 ; i<tf ; i++){
			 printf("%4f \t",testi[i]);
		     if(testi[i]<sum){
		  sum=testi[i];
		  l=i;
		  }
		  cout<<"\n";
		}
          cout<<"minentropy["<<l<<"]: "<<sum<<"\n";

		  if(s==1)
		  cout<<"\n-------------------One Occurrence Per Sequence (oops) of Motifs-----------------\n";
		  else if(s==2)
		  cout<<"\n-------------------Any Number of Repetitions (anr) of Motifs-----------------\n";
		  else if(s==3)
		  cout<<"\n-------------------Zero or One Occurrence per Sequence (zoops) of Motifs-----------------\n";



		cout<<"\n"<<"Start position of left motif:"<<"\t"<<"Start position of right motif:"<<"\n";


			for(i=0 ; i<max ; i++){
			  initialmotif[i][0]=rndnuml[i][l];
			  initialmotif[i][1]=rndnumr[i][l];
			  if(s != 3)
			  cout<<initialmotif[i][0]<<" \t\t\t\t "<<initialmotif[i][1];
			  state[i][0]=state[i][l];
			  if(s != 3)
			  cout<<"\n";
		  }
		   cout<<"\n";


		  for(i=0 ; i<max ; i++){
			k=0;
		     for(j=initialmotif[i][0] ; j<initialmotif[i][0]+lml ; j++){
		          if(state[i][0]=='P')
		          finalmotif[i][k]=str2[i][j];
		          else if(state[i][0]=='N')
		          finalmotif[i][k]=str3[i][j];
		          k++;
			  }
			  for(j=initialmotif[i][1] ; j<initialmotif[i][1]+rml ; j++){
		         if(state[i][0]=='P')
		          finalmotif[i][k]=str2[i][j];
		          else if(state[i][0]=='N')
		          finalmotif[i][k]=str3[i][j];
		          k++;
			  }
		  }

		  if(s==3){
			  zeromotif();

			    }

		  else if (s==1){
		  for(i=0 ; i<max ; i++){
			  if(g1=="1"){
				  for(j=0 ; str5[i][j] !='\n' ; j++)
				  cout<<str5[i][j];
			  }
			  else {
				cout<<">"<<i+1;
				}

				cout<<"\t"<<"Direction: "<<state[i][0];
				cout<<"\n";

			   for(j=0 ; j<lms ; j++){
			        printf("%c",finalmotif[i][j]);}
			        cout<<"\n";
		} }


		//  for(i=0 ; i<max ; i++)
		  //cout<<rndnuml[i][l]<<"\t"<<rndnumr[i][l]<<"\n";


		 cout<<"\n***********************************************\n";


				if(s==1 || s==2)
				count_nucleotide(finalmotif);
				else
				count_nucleotide(finalmotifz);


				cout<<"\n Nucleotide count of select Position Frequency Matrix(PFM):\n\n  ";
				for(i=0 ; i<lm ; i++){
				 if (i<=9)
				   cout<<"     ("<<i+1<<")";
				 else
				   cout<<"    ("<<i+1<<")";}

				cout<<"\n";

				  for(i=0 ; i<nu ; i++){
					  cout<<da[i]<<"\t";
				      for(j=0 ; j<(lm) ; j++)
				          cout<<freq[i][j]<<"\t";
				      cout<<"\n";
				}

		if(s==2){
		secondmotif();
		}




	}
	//-------------------------------ZOOPS---------------------------------------
	void zeromotif(){
	zm=84;
	r=0;
	z=0;
	sum=0;
	sum2=0;
	sum3=0;

	//double sumscore[1000],BG4[16];

	int BG3[16];

	float landa=0.99;
	long double sumbg3=1, scorez[2000], div, sumQ[2000], score1[2000], sumscore[2000],BG4[16],y1=0;

	if(md==2)
	landa=0.999;

	while(z<max){

	for(i=0 ; i<max ; i++){
	    rndnuml[i][r]=initialmotif[i][0];
		rndnumr[i][r]=initialmotif[i][1];
	}
		selseq=z;
		//max=lenstr2[z];
		selectseq();

		Background_count();
		for(k1=0 ; k1<nu ; k1++){
			BG4[k1]=BG[k1];
			//cout<<BG4[k1]<<"\t";
			}
		subseqlength3();

		sum=0;


			 for(i=0 ; i<a ; i++){
				if(i<2000){
				 score1[i]=1;
				 div=1;
			    for(j=0 ; j<(lm) ; j++){
					subnuc=seq2[i][j];

					if(md==2)
					subnuc+=seq2[i][j+1];

					for(k=0 ; k<nu ; k++)

					if ((subnuc==da[k])){
					    score1[i]=score1[i]*(freq1[k][j]);
					   }
				}


					for(k1=0; k1<lenstr2[z]-1; k1++){
						if(k1<2000){
						if(rml==0){
					     if((k1<positionl[i][0] || k1>positionl[i][0]+lml))
					       for(k=0 ; k<nu ; k++){
					        subnuc=str2[z][k1];
					        if(md==2)
					        subnuc+=str2[z][k1+1];
					        if(subnuc == da[k])
					        div=((div)*(BG[k]));
				            }}
				         else if(rml>0){
						  if((((k1<positionl[i][0]) || (k1>positionl[i][0]+lml && k1<positionr[i][0]) || (k1>positionr[i][0]))))
					        for(k=0 ; k<nu ; k++){
					        subnuc=str2[z][k1];
					        if(md==2)
					        subnuc+=str2[z][k1+1];
					        if(subnuc == da[k])
					        div=((div)*(BG[k]));
				          }
					     }
				        }
					}

				      //div=1;
					score1[i]=score1[i]*(div);

					y1=(landa)/(float)(lenstr2[z]-lm+1);

	                y1=1-y1;

				}
					}

	    sumscore[z]=0;

	    for(i=0 ; i<a ; i++){
			if(i<2000)
				sumscore[z]+=score1[i];
				}

				//cout<<"sumscore:"<<sumscore[z]<<"\n";

				for(i1=0; i1<nu ; i1++){
					BG3[i1]=0;}



					for(k1=0; k1<lenstr2[z]-1; k1++){
						if(k1<2000){
						subnuc1=str2[z][k1];
						if(md==2)
					    subnuc1+=str2[z][k1+1];

						for(k=0 ; k<nu ; k++){
						   if(subnuc1 == da[k])
						     BG3[k]++;
					    }
					}
					}


				sumbg3=1;
				for(i1=0; i1<nu ; i1++){
					//sumbg3=sumbg3 * (BG4[i1]*BG3[i1]);
					sumbg3=sumbg3 * pow(BG4[i1], BG3[i1]);
					//cout<<BG4[i1]<<"\t"<<BG3[i1]<<"\n";
					}
					//cout<<"\nsumBG:"<<sumbg3<<"\n";



		//cout<<"\n--------Sum SCORE-----\n"<<z<<"  "<<sumscore[z];

		sum=0;
		sumQ[z]=0;
    for(i1=0 ; i1<a ; i1++){
		if(i1<2000){
		scorez[i1]=score1[i1]/(sumbg3*y1+sumscore[z]);
		sumQ[z]+=scorez[i1];}
		}
    //cout<<"sumQ:"<<sumQ[z]<<"\n";

	    initial=z;
	    z++;

    }

    //cout<<"\n------------------------------------------\nLanda"<<landa<<"\n";
    /* cout<<"MIN"<<j<<":"<<min1;

    for(i=0; i<max; i++){
		sum3=abs(sumscore[i]-sum);
		sum3=pow(sum3,2);
		sum2+=sum3;
	}
	cout<<"\n"<<sum2<<"\n";
	sum2=sum2/(max-1);
		sum2=sqrt(sum2);
    cout<<sum2<<"\n----------\n";
	sum2*=1;
	cout<<"\n------Sum2----\n";
	//cout<<sum2;

	if(md==1)
	sum2=sum/10;
	else if(md==2)
	sum2=sum/10000000;
	*/
	//cout<<sum2<<"\n-------------------------------\n";
	int TP,TN,FN,FP;
	TP=TN=FN=FP=0;
	//(sumscore[i]<=(sum+sum2)) &&
	for(i=0; i<max; i++){
		if(i<323 && sumQ[i]>=(landa))
		TP++;
		if(i<323 && sumQ[i]<(landa))
		FN++;
		if(i>322 && sumQ[i]>=(landa))
		FP++;
		if(i>322 && sumQ[i]<(landa))
		TN++;
		}

		//cout<<"\n---------TP--------\n";
		//cout<<"TP:"<<TP<<"\n"<<"FN:"<<FN<<"\n"<<"FP:"<<FP<<"\n"<<"TN:"<<TN<<"\n";
	for(i=0 ; i<max ; i++){
						  if(sumQ[i]<(landa))
					      cout<<"N/A \t\t\t\t N/A\n";
					      else{
			             cout<<initialmotif[i][0]<<" \t\t\t\t "<<initialmotif[i][1];
			             cout<<"\n";}

		                cout<<"\n";}


                for (i=0; i<max; i++)
                {
					if(g1=="1"){
				     for(j=0 ; str5[i][j] !='\n' ; j++){
				       cout<<str5[i][j];}
				       cout<<"\tQ_Score:"<<sumQ[i];
			          }
			         else if(g1=="2"){
				      cout<<">"<<i+1<<"\tQ_Score:"<<sumQ[i];
				     }
				    cout<<"\t"<<"Direction: "<<state[i][0];
				    cout<<"\n";
			         if(sumQ[i]<(landa))
					      cout<<" N/A";
					      else
                    for (j = 0; j < lms; j++)
                        {
						cout<<finalmotif[i][j];
					   }

                         cout<<"\n";}
                         x=0;
                         for(i=0 ; i<max; i++){
							 if(sumQ[i]>=(landa))
                              for(j=0 ; j<(lm) ; j++)
							    finalmotifz[i][j]=finalmotif[i][j];
							 else
							   for(j=0 ; j<(lm) ; j++)
							     finalmotifz[i][j]=' ';

							 }


	cout<<"\n-------------------------------------------------------------\n";
	cout<<"\n-------------------------------------------------------------\n";
	cout<<"\n-------------------------------------------------------------\n";
    }
	//----------------------------------------------------------------------------------------
	void zeromotif1(){
	float score11[2000];
	float z8,z9;
	zm=84;
	count_nucleotide(finalmotif);

	sum=0;
	sum2=0;
	sum3=0;
	a=max;

	for(i=0 ; i<max ; i++){
		if(i!=selseq)
		for(j=0 ; j<lenstr2[i]-1 ; j++){
					 for(k=0 ; k<nu ; k++){
						 if(rml==0){
						 if (j<initialmotif[i][0]-1 || (j>(initialmotif[i][0]+rml-1))){
							subnuc=str2[i][j];

							  if(md==2)
						      subnuc+=str2[i][j+1];

			               if(subnuc==da[k])
			                  BG[k]++;}
			                 }
			                  else
			              	 {
						 if (j<initialmotif[i][0]-1 || ((j>(initialmotif[i][0]+lml-1)) && (j<initialmotif[i][1]-1)) || (j>(initialmotif[i][1]+rml-1))){
							subnuc=str2[i][j];

							if(md==2)
						    subnuc+=str2[i][j+1];

			               if(subnuc==da[k])
			                  BG[k]++;}
			            }
					}
			            }

			            for(i=0 ; i<nu ; i++){
			            sum=sum+BG[i];

				}
			}

				for(i=0 ; i<nu ; i++){

		          if(md==1){
					  BG[i]=(BG[i]+0.25)/sum;
					  if(p==2)
					  BG2[i]=(BG2[i]+0.25)/sum2;
				  }
				  else if(md==2){
					  BG[i]=(BG[i]+0.0625)/sum;
					  if(p==2)
					  BG2[i]=(BG2[i]+0.0625)/sum2;
				  }

				      for(j=0 ; j<(lm) ; j++){
						if(md==1)
			               freq1[i][j]=(float((freq[i][j])+0.25)/max);
			             else if(md==2)
			               freq1[i][j]=(float((freq[i][j])+0.0625)/max);


					  }}


				 score1[i]=0;
				 div=0;
			    for(j=0 ; j<(lm) ; j++){
					subnuc=finalmotif[i][j];

					if(md==2)
					subnuc+=finalmotif[i][j+1];

					for(k=0 ; k<nu ; k++)

					if (subnuc==da[k]){
					   //printf("Log%.2f ",freq1[k][j]);
					    div=div+log(BG[k]);
					    score1[i]=score1[i]+(freq1[k][j]);
					   }





					score1[i]=-1 * score1[i]/div;
					//cout<<"="<<score1[i]<<" number:"<<i<<"\n";
					//sum=sum+score1[i];

					}

	cout<<"\n-------------------Score------------------\n";
	for(i=0; i<max; i++){
	//cout<<i+1<<"-"<<score1[i]<<"\n";
	sum+=score1[i];
	score11[i]=score1[i];
    position[i]=i+1;
    }

    for(i=(max-1); i>=0; i--)
	for(j=0; j<i ; j++)
		if(score11[j]>score11[j+1]){
			z9=score11[j];
			z8=position[j];
			score11[j]=score11[j+1];
			position[j]=position[j+1];
			score11[j+1]=z9;
			position[j+1]=z8;}

			i=(max)/2;
			sum=sum/max;
			//cout<<"\n------Middle----\n"<<sum<<"\n----------\n";

	for(i=0; i<max; i++){
		sum3=abs(score1[i]-sum);
		//sum3=pow(sum3,2);
		sum2+=sum3;
	}
	//cout<<sum2<<"\n";
	sum2=sum2/(max-1);
		sum2=sqrt(sum2);
    //cout<<sum2<<"\n----------\n";
	sum2*=1;
	cout<<sum2<<"\n----------\n";
	cout<<"\n-------------------Score------------------\n";
	int TP,TN,FN,FP;
	TP=TN=FN=FP=0;
	for(i=0; i<max; i++){
		if(i<323 && score1[i]>sum2)
		TP++;
		if(i<323 && score1[i]<sum2)
		FN++;
		if(i>322 && score1[i]>sum2)
		FP++;
		if(i>322 && score1[i]<sum2)
		TN++;
		}

		cout<<"\n---------TP--------\n";
		cout<<"TP:"<<TP<<"\n"<<"FN:"<<FN<<"\n"<<"FP:"<<FP<<"\n"<<"TN:"<<TN<<"\n";
	//cout<<i+1<<"   "<<position[i]<<"-"<<score11[i]<<"\n";




	        for(i=0 ; i<max ; i++){
						  if(sum2 > score1[i])
					      cout<<"N/A \t\t\t\t N/A\n";
					      else{
			             cout<<initialmotif[i][0]<<" \t\t\t\t "<<initialmotif[i][1];
			             cout<<"\n";}

		                cout<<"\n";}


                for (i=0; i<max; i++)
                {
					if(g1=="1"){
				     for(j=0 ; str5[i][j] !='\n' ; j++)
				       cout<<str5[i][j];
			          }
			         else {
				      cout<<">"<<i+1;
				     }
				    cout<<"\t"<<"Direction: "<<state[i][0];
				    cout<<"\n";
			         if(sum2 > score1[i])
					      cout<<" N/A";
					      else
                    for (j = 0; j < lms; j++)
                        {
						cout<<finalmotif[i][j];
					   }

                         cout<<"\n";}}
	//----------------------------------------------------------------------------------------------
		void secondmotif(){

			//int k5,j3,i3,a1,l3=0;
               //int scoremotif1[max];
                char match[100];
               //int scoremotif2[1000][200];
                //string secmotif[1000][2000];


                cout<<"\n---------------------------New motifs discovery position------------------------------\n";
                md=1;
                nu=4;
                lm=lms;
                da[0]="A"; da[1]="C"; da[2]="G"; da[3]="T";
               count_nucleotide(finalmotif);



                for (i = 0; i < lms; i++)
                {

                    k = 0;
                    l = 0;
                    for (j = 0; j < nu; j++)
                    {
                        if (freq[j][i] > k)
                        {
                            k = freq[j][i];
                            l = j;

                        }

                    }
                    fsum=fsum+k;

                    if (l == 0)
                    {
                        match[i] = 'A';
                    }
                    else if (l == 1)
                    {
                        match[i] = 'C';
                    }
                    else if (l == 2)
                    {
                        match[i] = 'G';
                    }
                    else if (l == 3)
                    {
                        match[i] = 'T';
                    }

                }

                cout<<"The best match of sequences for motif detection:\n\t";
                for (i = 0; i <lms; i++)
                    cout<<match[i]<<"\t";
                cout<<"\n";


                for(i=0; i<max; i++)
                {
					temp_e[i]=0;
                    for(j=0; j<lm; j++)
                    {
						subnuc="";
                        for(k=0; k<nu; k++)
                        {
							subnuc=finalmotif[i][j];
							if(md==2)
							subnuc=subnuc+finalmotif[i][j];

                            if (subnuc== da[k])
                            {
                                temp_e[i] += freq[k][j];

                            }
                        }
                    }
                    if (i == 0)
                    {
                        l2 = 0;
                        min = temp_e[0];
                    }

                    if(min > temp_e[i])
                    {
                        min = temp_e[i];
                        l2 = i;
                    }

                    //cout<< i << ":" << temp_e[i] << "\n";
                }
                //cout<< "\n Minimum:" << min<<"\n";
               //cout<< "Min:" << l2 << "-" << temp_e[l2];
                //cout<< "\n";
                    subnuc="";

                for (i=0; i<max; i++)
                {

                                a = 0;

                                for (i1 = ming; i1 <= maxg; i1++)
                                {

                                    for (l = 0; l < (lenstr2[i] - lms - i1); l++)
                                    {
                                        score2[i][l] = 0;
                                        k = 0;
                                       if ( l > (initialmotif[i][1] + rml) || l< (initialmotif[i][0]-lms-i1))
                                        {
											subnuc="";
                                             for (j = 0; j < lms; j++)
                                            {

                                                if (j < lml)
                                                {
                                                    seq2[a][j] = str2[i][l + j];
                                                    for (k2 = 0; k2 < nu; k2++)
                                                    {
								                      subnuc=seq2[a][j];
								                      if(md==2)
							                          subnuc=subnuc+seq2[a][j];

                                                        if (subnuc == da[k2])
                                                        {
                                                            score2[i][l] += freq[k2][j];
                                                        }
                                                    }
                                                }
                                                else
                                                {
                                                    seq2[a][j] = str2[i][l + j + i1];
                                                    for (k2 = 0; k2 < nu; k2++)
                                                    {
								                   subnuc=seq2[a][j];
								                   if(md==2)
							                       subnuc=subnuc+seq2[a][j];

                                                        if (subnuc == da[k2])
                                                        {
                                                            score2[i][l] += freq[k2][j];
                                                        }
                                                    }
                                                }

                                               //cout<< seq2[a][j];
                                               //secmotif[i][a1] += seq2[a][j];
                                               //subnuc1 = subnuc1+seq2[a][j];
                                            }
                                            subnuc1 =seq2[a];

                                            //cout<< " - " << scoremotif2[i][l] << "\n";
                                            //cout<< " - " << subnuc << "\n";

                                            if (min <= score2[i][l])
                                            {
							                x=l+1+i1+lml;
							                if(g1=="1")
				                             for(A=0 ; str5[i][A] !='\n' ; A++)
				                               cout<<str5[i][A];
				                                    else
                                                      cout<<"Site:" << (i) ;

                                                cout<< "\tLeft Position:" << (l)<<", Right Position:"<<(x) << " - " << subnuc1 << "\n";

                                                subnuc1="";
                                            }

                                           a++;
                                        }
                                    }

                        }
                    }


			//exit:

		}


                //std::vector<int> lenstr2;

		        char ch,str2[1000][1000],str3[1000][1000],str4[2000][1000],str5[1000][1000],state[1000][100];
	            int i , i1,j,k1,k2,k,l,l2,md,nu,lms,tf,p,rnd,rnd1,rnd2,rnd3,nmax,min,max,max2,ming,maxg,x,y,A,B,C,D,a,b,r,ns,g,z,lml,rml,lm,s,zm;
	            int selseq,initial,lenstr2[1000],freq[16][50],rndnuml[1000][100],rndnumr[1000][100],rndnuml2[1000][100],rndnumr2[1000][100],initialmotif[1000][2],sigb[1000][2];
	            int temp_e[1000],positionl[9000][2],positionr[9000][2], position[2000];
	            float freq1[16][50],freq2[4][50],score1[9000],score2[9000][2];
	            float BG[16],BG2[16],entropytotal[100][2],entropy[50],minentropy[100],testi[100];
	            float fsum,rndsel,sum,sum2,sum3,t,div,div1[2],maxscor[2];
	            string subnuc,subnuc1;
	            bool flag,bb;
                char line,finalmotif[1000][50],finalmotifz[1000][50],strmotif[1000][50],seq1[1000][50],seq5[1000][50],seq2[9000][50],seq4[9000][50],ran1[1000][50];
                string da[16];
                string g1,seq,temp,temp2,temp3,address,input;
                ifstream myfile1,myfile2,myfile3,myfile4;
                FILE *student;
                ostringstream buff;
};

int main(int argc, char *argv[])
{


	//Some stuff to interact with the class will go here
	Computer computer_one;

	 string input2;
	 input2=argv[1];
	 input2+=" ";
	 int i=2;
	 while(i < argc)
	 {
	 input2+=argv[i];
	 input2+=" ";
	 i++;
	 }


	computer_one.read(input2);
	computer_one.output_information();

	computer_one.textmining();

	computer_one.reverse();
	//computer_one.subseqlength3();
	computer_one.selectrandom();
	//computer_one.randomgenerate();
	computer_one.startlocation();
	computer_one.PPM();
	//computer_one.count_nucleotide();
	//computer_one.PFM();
	//computer_one.selectseq();
	//computer_one.test();
	//computer_one.score();


	//computer_one.step1();
	//computer_one.step2();


	//computer_one.step11();

	computer_one.step21();


	//computer_one.secondmotif();





	fclose(stdout);


	return 0;
}