# include <X11/Xlib.h>
# include <X11/Xutil.h>
# include <X11/Xos.h>
# include <X11/Xatom.h> 
# include <stdio.h>
# include <stdlib.h>
# include <sys/time.h>
# include <unistd.h>
# include <math.h>
# include <assert.h>


#include<string.h>
#include<iostream.h>
#include<fstream.h>

// This shows one dna molecule, s1 is from 5' to 3' side, offset is with respect to the s1's start and negative towards left and positive towards right. s2 will be from 3' to 5' side then.

#define maxlength 100
#define tracklength 100
#define max_free 1000

//-------------------------------------------------------------------------
Display *disp;
Colormap cm;
Window w;
GC gc;
int whiteColor,blackColor;
XColor greenColor,yellowColor,redColor,blueColor,purpleColor;

#define NIL (0)       // A name for the void pointer


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


struct molecule
{
  char* strand1; 
  int offset;
  char* strand2;
  
};
  int total_free=0;
int iscomplement(char* s1,int i1,int i2,char* s2,int j1,int j2,int direction) // s1 and s2 are in same direction for direction=1
{
  int iii,jjj;

  //  if(s1[i1]=='t' && s1[i1+1]=='e' && s1[i2]=='c' && s2[j1]=='a' && s2[j1+1]=='c' && s2[j2]=='g') cout<<"MIL GAYA";getchar();getchar();

  if(i1-i2==j1-j2)
    {
      if(direction==1)
	{
	  //	  int i,j=j1;
	  for(iii=i1,jjj=j1;iii<=i2;iii++,jjj++)
	    {
	      switch(s1[iii])
		{
		case 'a':if(s2[jjj]!='t' && s2[jjj]!='T') return 0;break;
		case 'c':if(s2[jjj]!='g' && s2[jjj]!='G') return 0;break;
		case 't':if(s2[jjj]!='a' && s2[jjj]!='A') return 0;break;
		case 'g':if(s2[jjj]!='c' && s2[jjj]!='C') return 0;break;
		case 'e':if(s2[jjj]!='f') return 0;break;
		case 'f':if(s2[jjj]!='e') return 0;break;
		case 'i':if(s2[jjj]!='j') return 0;break;
		case 'j':if(s2[jjj]!='i') return 0;break;
		case '1':if(s2[jjj]!='6') return 0;break;
		case '2':if(s2[jjj]!='7') return 0;break;
		case '3':if(s2[jjj]!='8') return 0;break;
		case '4':if(s2[jjj]!='9') return 0;break;
		case '5':if(s2[jjj]!='0') return 0;break;	
		case '6':if(s2[jjj]!='1') return 0;break;
		case '7':if(s2[jjj]!='2') return 0;break;
		case '8':if(s2[jjj]!='3') return 0;break;
		case '9':if(s2[jjj]!='4') return 0;break;
		case '0':if(s2[jjj]!='5') return 0;break;	
		case 'A':if(s2[jjj]!='T' && s2[jjj]!='t') return 0;break;
		case 'C':if(s2[jjj]!='G' && s2[jjj]!='g') return 0;break;
		case 'T':if(s2[jjj]!='A' && s2[jjj]!='a') return 0;break;
		case 'G':if(s2[jjj]!='C' && s2[jjj]!='c') return 0;break;
		 
		};
	      
	    }
	  return 1;
	}
      else
	{
	  //	  int i,j=j2;
	  for(iii=i1,jjj=j2;iii<=i2;iii++,jjj--)
	    {
	      switch(s1[iii])
		{
		case 'a':if(s2[jjj]!='t' && s2[jjj]!='T') return 0;break;
		case 'c':if(s2[jjj]!='g' && s2[jjj]!='G') return 0;break;
		case 't':if(s2[jjj]!='a' && s2[jjj]!='A') return 0;break;
		case 'g':if(s2[jjj]!='c' && s2[jjj]!='C') return 0;break;
		case 'e':if(s2[jjj]!='f') return 0;break;
		case 'f':if(s2[jjj]!='e') return 0;break;
		case 'i':if(s2[jjj]!='j') return 0;break;
		case 'j':if(s2[jjj]!='i') return 0;break;
		case '1':if(s2[jjj]!='6') return 0;break;
		case '2':if(s2[jjj]!='7') return 0;break;
		case '3':if(s2[jjj]!='8') return 0;break;
		case '4':if(s2[jjj]!='9') return 0;break;
		case '5':if(s2[jjj]!='0') return 0;break;
		case '6':if(s2[jjj]!='1') return 0;break;
		case '7':if(s2[jjj]!='2') return 0;break;
		case '8':if(s2[jjj]!='3') return 0;break;
		case '9':if(s2[jjj]!='4') return 0;break;
		case '0':if(s2[jjj]!='5') return 0;break;
		case 'A':if(s2[jjj]!='T' && s2[jjj]!='t') return 0;break;
		case 'C':if(s2[jjj]!='G' && s2[jjj]!='g') return 0;break;
		case 'T':if(s2[jjj]!='A' && s2[jjj]!='a') return 0;break;
		case 'G':if(s2[jjj]!='C' && s2[jjj]!='c') return 0;break;	     	     
		};
	    }
	  return 1;
	}
    }
  else return 0; 
}

struct join
{
molecule mm;
int jj;  // -1 for free, 0 for left, 1 for front, 2 for right.
};

//join headtrack[tracklength];
//int num_of_head=0;
join symboltrack[tracklength];
int num_of_symbol=0;

struct conc
{
  molecule mm;
  int cc;    // it shows the number of free molecules of this kind
};

conc free_molecule[max_free];
int num_of_free=0;


int dispcount=0;
void display()
{
  cout<<endl<<dispcount<<"===----------------------------------------------------------\n\n";
  dispcount++;

/*{
  for(int i=0;i<num_of_head;i++)
    cout<<headtrack[i].mm.strand1<<"\n"<<headtrack[i].mm.strand2<<"\n"<<headtrack[i].mm.offset<<"  "<<headtrack[i].jj<<endl;
*/
  cout<<"--------\n\n";
  
  for(int i=0;i<num_of_symbol;i++)
    {
      if(i==0) cout<<"I        ";
      else if(i%3==1) cout<<"A"<<i/3<<"       ";
      else if(i%3==2) cout<<"B"<<i/3<<"       ";
      else if(i%3==0) cout<<"C"<<i/3-1<<"       ";
      cout<<symboltrack[i].mm.strand1<<"\n         "<<symboltrack[i].mm.strand2<<"\n         "<<symboltrack[i].mm.offset<<"  "<<symboltrack[i].jj<<endl;
    }
  cout<<"-------------------\n\n";
  
  /*
 for(int i=0;i<num_of_free;i++)
    cout<<free_molecule[i].mm.strand1<<"\n"<<free_molecule[i].mm.offset<<"  "<<free_molecule[i].cc<<endl<<free_molecule[i].mm.strand2<<endl;
  */
  cout<<"-------------------------------------------------------------\n\n";
  //getchar();
}

char* strcatt(char* a, char* b)
{
  char* c= new char[maxlength];
  int l1=strlen(a);
  int l2=strlen(b);
  
  for(int ii=0;ii<l1;ii++)
    c[ii]=a[ii];
  for(int ii=0;ii<l2;ii++)
    c[l1+ii]=b[ii];
  c[l1+l2]=0;
  
  return c;
}

char* rev(char s[])
{
  char* s1=new char[100];
  int  k=  strlen(s);
  int i;
  for( i=0;i<k;i++)
    s1[i]=s[k-1-i];
  s1[i]=0;
  return s1;
}
molecule inv(molecule m)
{
  molecule m1;
int  l1=strlen(m.strand1);
  int l2=strlen(m.strand2);
  m1.strand1=rev(m.strand2);
  m1.strand2=rev(m.strand1);
  m1.offset=l2+m.offset-l1;
  return m1;
}

// There should be a perfect match and the sticky ends should be of equal lengths.

int ligation(molecule &m, molecule m1, molecule m2)
{

  //char* temp;
  int  done=0;
  int l1=strlen(m1.strand1);
  int l2=strlen(m1.strand2);
  
  int  l3=strlen(m2.strand1);
  int l4=strlen(m2.strand2);

  if((l1==1 && l2==3)||(l1==3 && l2==1)||(l3==1 && l4==3)||(l3==3 && l4==1)) return 0;
  if( l1 > m1.offset + l2  &&  done==0)    //m1: upper strand has sticky end at right
    {
      if  (m2.offset <0 )   //M1 UP RIGHT M2 LOW LEFT 
	{
	  if(iscomplement(m1.strand1,m1.offset+l2,l1-1,m2.strand2,0,-m2.offset-1,1))
	    {
	      m.strand1=strcatt(m1.strand1,m2.strand1);
	      m.strand2=strcatt(m1.strand2,m2.strand2);
	      m.offset=m1.offset;
	      done=1;
	    }
	}	  
      if( l3-(m2.offset+l4) > 0 &&  done==0)    //M1 UP RIGHT M2 UP RIGHT
	{
	  if(iscomplement(m1.strand1,m1.offset+l2,l1-1,m2.strand1,m2.offset+l4,l3-1,-1))
	    {
	      m.strand1=strcatt(m1.strand1,rev(m2.strand2));
	      m.strand2=strcatt(m1.strand2,rev(m2.strand1));
	      m.offset=m1.offset;	     
	      done=1;
	    }
	}
    }
  if( m1.offset>0 &&  done==0) //in m1 upper strand has a sticky end to its left
    {
      if(m2.offset>0 &&  done==0) //M1 UP LEFT M2 UP LEFT
	{
	  if(iscomplement(m1.strand1,0,m1.offset-1,m2.strand1,0,m2.offset-1,-1))
	    {
	      m.strand1=strcatt(rev(m2.strand2),m1.strand1);
	      m.strand2=strcatt(rev(m2.strand1),m1.strand2);
	      m.offset=m2.offset+l4-l3;
	      done=1;
	    }
	}
      
      if( l4+m2.offset-l3 >0 && done==0)  //M1 UP LEFT M2 LOW RIGHT
	{
	  if(iscomplement(m1.strand1,0,m1.offset-1,m2.strand2,l3-m2.offset,l4-1,1))
	    {
	      m.strand1=strcatt(m2.strand1,m1.strand1);
	      m.strand2=strcatt(m2.strand2,m1.strand2);
	      m.offset=m2.offset;
	      done=1;
	    }
	}
    } 
  if ( l2+m1.offset-l1 >0 &&  done==0)   //m1: lower strand has a sticky end to its right
    {
      if(m2.offset>0 &&  done==0)  //M1 LOW RIGHT M2 UP LEFT
	{
	  if(iscomplement(m1.strand2,l1-m1.offset,l2-1,m2.strand1,0,m2.offset-1,1))
	    {
	      m.strand1=strcatt(m1.strand1,m2.strand1);
	      m.strand2=strcatt(m1.strand2,m2.strand2);
	      m.offset=m1.offset;
	      done=1;
	    }
	}
      
      if( l4+m2.offset-l3 >0 && done==0)  //M1 LOW RIGHT M2 LOW RIGHT 
	{
	  if(iscomplement(m1.strand2,l1-m1.offset,l2-1,m2.strand2,l3-m2.offset,l4-1,-1))
	    {
	      m.strand1=strcatt(m1.strand1,rev(m2.strand2));
	      m.strand2=strcatt(m1.strand2,rev(m2.strand1));
	      m.offset=m1.offset;
	      done=1;
	    }
	}
    }
  
  if(m1.offset<0 &&  done==0)  //in m1 lower strand has a sticky end to its left.
    {
      if  (m2.offset <0 )   //M1 LOW LEFT M2 LOW LEFT
	{
	  if(iscomplement(m1.strand2,0,-m1.offset-1,m2.strand2,0,-m2.offset-1,-1))
	    {
	      m.strand1=  strcatt(rev(m2.strand2),m1.strand1);
	      m.strand2=strcatt(rev(m2.strand1),m1.strand2);
	      m.offset=m2.offset+l4-l3;
	      done=1;
	    }
	}	  
      if( l3-(m2.offset+l4) > 0 &&  done==0)    //M1 LOW LEFT M2 UP RIGHT
	{
	  if(iscomplement(m1.strand2,0,-m1.offset-1,m2.strand1,m2.offset+l4,l3-1,1))
	    {
	      m.strand1=strcatt(m2.strand1,m1.strand1);
	      m.strand2=strcatt(m2.strand2,m1.strand2);
	      m.offset=m2.offset;
	      done=1;
	    }
	}
    }
  return done;
}

int search1(char s[], char p[])
{
 int l1= strlen(s);
for(int i=0;i<l1-5;i++)
  if((s[i]==p[0]|| s[i]==p[0]-32  ) && (s[i+1]==p[1] || s[i+1]==p[1]-32) && (s[i+2]==p[2]||s[i+2]==p[2]-32) && (s[i+3]==p[3] || s[i+3]==p[3]-32) && (s[i+4]==p[4] || s[i+4]==p[4]-32) && (s[i+5]==p[5] ||s[i+5]==p[5]-32 ) ) return i;

 return -1;
}
int search2(char s[],char p[])
{
  int l1=strlen(s);
  for(int i=0;i<l1-10;i++)
    if((s[i]==p[0]||s[i]==p[0]-32) && (s[i+1]==p[1]||s[i+1]==p[1]-32) && (s[i+9]==p[9]||s[i+9]==p[9]-32) && (s[i+10]==p[10]||s[i+10]==p[10]-32))
       return i;

  return -1;
}

int find(molecule m)
{
  for(int k=0;k<num_of_free;k++)
    {    
      if ( 
	  ( 
	   !strcmp(free_molecule[k].mm.strand1,m.strand1) && 
	   !strcmp(free_molecule[k].mm.strand1,m.strand1) && 
	   free_molecule[k].mm.offset==m.offset 
	   ) 
	  ||
	  ( 
	   !strcmp(free_molecule[k].mm.strand1,inv(m).strand1) && 
	   !strcmp(free_molecule[k].mm.strand1,inv(m).strand1) && 
	   free_molecule[k].mm.offset==inv(m).offset 
	   )
	  ) 
	return k;
    }
  return -1;
}

void copy(char*& s1,char* s2,int i,int j)
{  
  s1=new char[maxlength];
  int k1,k2;
 for(k2=i,k1=0;k2<=j;k1++,k2++)
   s1[k1]=s2[k2];
 s1[k1]=0; 
return;
}

int restriction1(molecule &m1,molecule &m2, molecule m)
{
int  k=search1(m.strand1,"cagcag");
 int l1=strlen(m.strand1);
 int l2=strlen(m.strand2);
 // molecule m1,m2;
  if(k!=-1 && k>=m.offset && k+6+28<=l1 && k+6+28<=m.offset+l2 && m.strand1[k+6+24]!='A' && m.strand1[k+6+24]!='C' && m.strand1[k+6+24]!='T' && m.strand1[k+6+24]!='G' && m.strand1[k+6+24]!='+' && m.strand2[k+6+27]!='A' && m.strand2[k+6+27]!='C' && m.strand2[k+6+27]!='T' && m.strand2[k+6+27]!='G' && m.strand2[k+6+27]!='+' )
    {
      // k+6+25;
      copy(m1.strand1,m.strand1,0,k+6+24);
      copy(m2.strand1,m.strand1,k+6+25,l1-1);
      copy(m1.strand2,m.strand2,0,k+6+26);
      copy(m2.strand2,m.strand2,k+6+27,l2-1);
      m1.offset=m.offset;
      m2.offset=2;
      return 1;
    }  
  else
    { 
      k=search1(m.strand2,"gacgac");
      if(k!=-1 && k+6+m.offset<=l1 && k+6<=l2 && k>=28 && k+m.offset >=28 && m.strand2[k-25]!='A' && m.strand2[k-25]!='C' && m.strand2[k-25]!='T' && m.strand2[k-25]!='G' && m.strand2[k-25]!='+' && m.strand1[k-28]!='A' && m.strand1[k-28]!='C' && m.strand1[k-28]!='T' && m.strand1[k-28]!='G' && m.strand1[k-28]!='+' )
	{

	  copy(m1.strand1,m.strand1,0,k-28);
	  copy(m2.strand1,m.strand1,k-27,l1-1);
	  copy(m1.strand2,m.strand2,0,k-26);
	  copy(m2.strand2,m.strand2,k-25,l2-1);
	  m1.offset=m.offset;
	  m2.offset=2;
	  return 1;
	}
    }
   return 0;
}

/*
  int restriction2(molecule &m1, molecule &m2, molecule m)
  {
  int  k=search1(m.strand1,"ctggag");
  int l1=strlen(m.strand1);
  int l2=strlen(m.strand2);//molecule m1,m2;
  if(k!=-1 && k>=m.offset && k+6+17<=l1 && k+6+17<=m.offset+l2)
  {
  // k+6+25;
  copy(m1.strand1,m.strand1,0,k+6+15);
  copy(m2.strand1,m.strand1,k+6+16,l1-1);
  copy(m1.strand2,m.strand2,0,k+6+13);
  copy(m2.strand2,m.strand2,k+6+14,l2-1);
  m1.offset=m.offset;
  m2.offset=-2;
  return 1;
  }  
  else
  { 
  k=search1(m.strand2,"gaggtc");
  if(k!=-1 &&  k+6+m.offset<=l1 && k+6<=l2 && k>=17 && k+m.offset >=17)
  {
  
  copy(m1.strand1,m.strand1,0,k-15);
  copy(m2.strand1,m.strand1,k-14,l1-1);
  copy(m1.strand2,m.strand2,0,k-17);
  copy(m2.strand2,m.strand2,k-16,l2-1);
  m1.offset=m.offset;
  m2.offset=-2;
  return 1;
  }
  }
  return 0;
  }
*/


int restriction3(molecule &m1, molecule &m2, molecule m)
{
  int k=search2(m.strand1,"gc*******gc");
  int l1=strlen(m.strand1);
  int l2=strlen(m.strand2);//molecule m1,m2;
  if(k!=-1 && k>=m.offset && k+11<=l1 && k+11<=m.offset+l2 && m.strand1[k+6]!='A' && m.strand1[k+6]!='C' && m.strand1[k+6]!='T' && m.strand1[k+6]!='G' && m.strand1[k+6]!='+' && m.strand2[k+4]!='A' && m.strand2[k+4]!='C' && m.strand2[k+4]!='T' && m.strand2[k+4]!='G' && m.strand2[k+4]!='+'  ) //return 0;
    {
      copy(m1.strand1,m.strand1,0,k+6);
      copy(m2.strand1,m.strand1,k+7,l1-1);
      copy(m1.strand2,m.strand2,0,k+3);
      copy(m2.strand2,m.strand2,k+4,l2-1);
      m1.offset=m.offset;
      m2.offset=-3;
      
      return 1;
    }
  return 0;
}

int restriction4(molecule &m1, molecule &m2, molecule m)
{
  int k=search2(m.strand1,"cc*******gg");
  int l1=strlen(m.strand1);
  int l2=strlen(m.strand2);
  //molecule m1,m2;
  if(k!=-1  && k>=m.offset && k+11<=l1 && k+11<=m.offset+l2 && m.strand1[k+6]!='A' && m.strand1[k+6]!='C' && m.strand1[k+6]!='T' && m.strand1[k+6]!='G' && m.strand1[k+6]!='+' && m.strand2[k+4]!='A' && m.strand2[k+4]!='C' && m.strand2[k+4]!='T' && m.strand2[k+4]!='G' && m.strand2[k+4]!='+' ) //return 0;
    {
      copy(m1.strand1,m.strand1,0,k+6);
      copy(m2.strand1,m.strand1,k+7,l1-1);
      copy(m1.strand2,m.strand2,0,k+3);
      copy(m2.strand2,m.strand2,k+4,l2-1);
      m1.offset=m.offset;
      m2.offset=-3;
      
      return 1;
    }
  return 0;
}









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


void graphic_disp()
{
  int distance=40;
  int sticky_length=10;
  int width=3;
  int Hx1=20,Hy1=20,Hx2=360,Hy2=20;
  int Sx1=20,Sy1=160,Sx2=360,Sy2=160;
  //int h_length=60;
  int s_length=60;
  //  track_head();
  //track_symbol();
  XClearWindow(disp,w);
   XSetForeground(disp,gc,blackColor);

   //  XDrawLine(disp,w,gc,Hx1,Hy1,Hx2,Hy2);
   // XDrawString(disp,w,gc,Hx2+5,Hy2,"Heads",5);
  XDrawLine(disp,w,gc,Sx1,Sy1,Sx2,Sy2);
  XDrawString(disp,w,gc,Sx2+5,Sy2,"Symbols",7);


  /*  for(int i=0;i<num_of_head;i++)
      if(headtrack[i].jj==-1)
      {
	int lll=strlen(headtrack[i].mm.strand2);
	if(headtrack[i].mm.strand2[lll-2]=='a' && headtrack[i].mm.strand2[lll-1]=='a' && strlen(headtrack[i].mm.strand1)==lll-2 )
	  {
	    XDrawString(disp,w,gc,Hx1+distance*(i+1)+width,Hy1+h_length-width,"*",1);
	    //	   tag= "A";
	  }
	else if(
		(i%3==0 &&   headtrack[i].mm.strand2[lll-2]=='a' && headtrack[i].mm.strand2[lll-1]=='c' && strlen(headtrack[i].mm.strand1)==lll-2 )
		||
		(i%3==1 &&     headtrack[i].mm.strand2[lll-2]=='c' && headtrack[i].mm.strand2[lll-1]=='t'  && strlen(headtrack[i].mm.strand1)==lll-2 )
		||
		(i%3==2 &&   headtrack[i].mm.strand2[lll-2]=='t' && headtrack[i].mm.strand2[lll-1]=='a'   && strlen(headtrack[i].mm.strand1)==lll-2 )
		)
	  {
	    //  tag=" ";
	    //    XDrawString(disp,w,gc,Hx1+distance*(i+1)+width,Hy1+h_length-width,"A",1);	  
	  }
	else
	  {
	    //	    tag= "g";
	    //	    XDrawString(disp,w,gc,Hx1+distance*(i+1)+width,Hy1+h_length-width,"g",1);
	  }
	int hhh=strlen(headtrack[i].mm.strand2)*h_length/35;
	
	if(hhh<=h_length)
	  {
	    XDrawLine(disp,w,gc,Hx1+distance*(i+1),Hy1,Hx1+distance*(i+1),Hy1+hhh);
	    XDrawLine(disp,w,gc,Hx1+distance*(i+1)-width,Hy1,Hx1+distance*(i+1)-width,Hy1+hhh);
	    
	    XDrawLine(disp,w,gc,Hx1+distance*(i+1),Hy1+hhh,Hx1+distance*(i+1)+sticky_length,Hy1+hhh);
	  }
	else
	  {
	    hhh=h_length;
	    XDrawLine(disp,w,gc,Hx1+distance*(i+1),Hy1,Hx1+distance*(i+1)-2*width,Hy1+hhh);
	    XDrawLine(disp,w,gc,Hx1+distance*(i+1)-width,Hy1,Hx1+distance*(i+1)-3*width,Hy1+hhh);
	    
	    XDrawLine(disp,w,gc,Hx1+distance*(i+1)-2*width,Hy1+hhh,Hx1+distance*(i+1)-2*width+sticky_length,Hy1+hhh);

	  }
	
      }
    else if(headtrack[i].jj==0)
      {
	//ignore
      }
    else if(headtrack[i].jj==1)
      {
	XDrawLine(disp,w,gc,Hx1+(i+1)*distance-width,Hy1,Hx1+distance*(i+1)-width,Hy1+h_length+s_length+20);
	XDrawLine(disp,w,gc,Hx1+(i+1)*distance,Hy1,Hx1+distance*(i+1),Hy1+h_length+s_length+20);
      }
    else 
      {
	XDrawLine(disp,w,gc,Hx1+(i+1)*distance-width,Hy1,Hx1+distance*(i+1)-width,Hy1+h_length);
	XDrawLine(disp,w,gc,Hx1+(i+1)*distance,Hy1,Hx1+distance*(i+1),Hy1+h_length-width);
	XDrawLine(disp,w,gc,Hx1+(i+1)*distance,Hy1+h_length-width,Hx1+distance*(i+2)-width,Hy1+h_length-width);		
	XDrawLine(disp,w,gc,Hx1+(i+1)*distance-width,Hy1+h_length,Hx1+distance*(i+2),Hy1+h_length);
	XDrawLine(disp,w,gc,Hx1+(i+2)*distance-width,Hy1,Hx1+distance*(i+2)-width,Hy1+h_length-width);
	XDrawLine(disp,w,gc,Hx1+(i+2)*distance,Hy1,Hx1+distance*(i+2),Hy1+h_length);
   }  
  */

  for(int i=0;i<num_of_symbol;i++)    
    {
      
      
      
      XSetForeground(disp,gc,blackColor);

      if(i==0)
	XDrawString(disp,w,gc,Sx1+distance*(i+1)-10,Sy1-s_length-25,"I",1);
      else if(i%3==1)
	XDrawString(disp,w,gc,Sx1+distance*(i+1)-10,Sy1-s_length-25,"A",1);
      else if(i%3==2)
	XDrawString(disp,w,gc,Sx1+distance*(i+1)-10,Sy1-s_length-25,"B",1);
      else if(i%3==0)
	XDrawString(disp,w,gc,Sx1+distance*(i+1)-10,Sy1-s_length-25,"C",1);
      
      if(symboltrack[i].jj==-1)
	{
	  if(i==0 && strlen(symboltrack[i].mm.strand1)==31  && strlen(symboltrack[i].mm.strand2)==33 && symboltrack[i].mm.strand2[31]=='a' && symboltrack[i].mm.strand2[32]=='t'  ) 
	     //&& symboltrack[i].mm.strand1[28]=='g' && symboltrack[i].mm.strand1[29]=='t' && symboltrack[i].mm.strand1[30]=='c' && symboltrack[i].mm.strand2[28]=='c' && symboltrack[i].mm.strand2[29]=='a' && symboltrack[i].mm.strand2[30]=='g' && symboltrack[i].mm.strand2[31]=='a' && symboltrack[i].mm.strand2[32]=='t' )
	    { 
	      
	      //XDrawLine(disp,w,gc,Sx1+(i+1)*distance,Sy1,Sx1+distance*(i+1),Sy1-s_length);
	      XSetForeground(disp,gc,yellowColor.pixel);
	    }  
	  else if(i%3==1 && strlen(symboltrack[i].mm.strand1)==15  && symboltrack[i].mm.strand1[14]=='1' && strlen(symboltrack[i].mm.strand2)==17)
	    // && symboltrack[i].mm.strand1[29]=='c' && symboltrack[i].mm.strand1[30]=='c' && symboltrack[i].mm.strand2[29]=='g' && symboltrack[i].mm.strand2[30]=='g' && symboltrack[i].mm.strand2[31]=='a' && symboltrack[i].mm.strand2[32]=='t')
	    { 
	      XSetForeground(disp,gc,yellowColor.pixel);
	    }
	  else if(i%3==2 && strlen(symboltrack[i].mm.strand1)==15  && symboltrack[i].mm.strand1[14]=='2' && strlen(symboltrack[i].mm.strand2)==17)
	    // && symboltrack[i].mm.strand1[29]=='c' && symboltrack[i].mm.strand1[30]=='c' && symboltrack[i].mm.strand2[29]=='g' && symboltrack[i].mm.strand2[30]=='g' && symboltrack[i].mm.strand2[31]=='g' && symboltrack[i].mm.strand2[32]=='c')
	    {
	      XSetForeground(disp,gc,yellowColor.pixel);
	    }

	  else if(i%3==0 && strlen(symboltrack[i].mm.strand1)==15  && symboltrack[i].mm.strand1[14]=='3' && strlen(symboltrack[i].mm.strand2)==17)
	    // && symboltrack[i].mm.strand1[29]=='c' && symboltrack[i].mm.strand1[30]=='c' && symboltrack[i].mm.strand2[29]=='g' && symboltrack[i].mm.strand2[30]=='g' && symboltrack[i].mm.strand2[31]=='t' && symboltrack[i].mm.strand2[32]=='a')
	    { 
	      XSetForeground(disp,gc,yellowColor.pixel);
	    }
	  else if( i%3==1 && strlen(symboltrack[i].mm.strand1)==14 && strlen(symboltrack[i].mm.strand2)==16)
	    // && symboltrack[i].mm.strand1[28]=='c' && symboltrack[i].mm.strand1[29]=='c' && symboltrack[i].mm.strand2[28]=='g' && symboltrack[i].mm.strand2[29]=='g' && symboltrack[i].mm.strand2[31]=='a' && symboltrack[i].mm.strand2[32]=='t' )
	    {
	        
	   XSetForeground(disp,gc,blackColor);
	    }
	  else if( i%3==2 && strlen(symboltrack[i].mm.strand1)==14 && strlen(symboltrack[i].mm.strand2)==16)
	    // && symboltrack[i].mm.strand1[28]=='c' && symboltrack[i].mm.strand1[29]=='c' && symboltrack[i].mm.strand2[28]=='g' && symboltrack[i].mm.strand2[29]=='g' && symboltrack[i].mm.strand2[31]=='g' && symboltrack[i].mm.strand2[32]=='c' )
	    {
	        
	   XSetForeground(disp,gc,blackColor);
	    }
	  else if( i%3==0 && strlen(symboltrack[i].mm.strand1)==14 && strlen(symboltrack[i].mm.strand2)==16)
	    // && symboltrack[i].mm.strand1[28]=='c' && symboltrack[i].mm.strand1[29]=='c' && symboltrack[i].mm.strand2[28]=='g' && symboltrack[i].mm.strand2[29]=='g' && symboltrack[i].mm.strand2[31]=='t' && symboltrack[i].mm.strand2[32]=='a'   )
	    {
	       
	   XSetForeground(disp,gc,blackColor);
	    }	  

	  else
	    {
	      XSetForeground(disp,gc,redColor.pixel);
	    }
	  
	  XDrawLine(disp,w,gc,Sx1+(i+1)*distance,Sy1,Sx1+distance*(i+1),Sy1-s_length);
	  XDrawLine(disp,w,gc,Sx1+(i+1)*distance-width,Sy1,Sx1+distance*(i+1)-width,Sy1-s_length);
	  
	  XDrawLine(disp,w,gc,Sx1+(i+1)*distance-width,Sy1-s_length,Sx1+distance*(i+1)-sticky_length-width,Sy1-s_length);
	}
      else if(symboltrack[i].jj==0)
	{
	  //ignore
	}
      else if(symboltrack[i].jj==1)
	{
	  //ignore
	}
      else 
	{
	    XSetForeground(disp,gc,redColor.pixel);
	    XDrawLine(disp,w,gc,Sx1+(i+1)*distance,Sy1,Sx1+distance*(i+1),Sy1-s_length);
	    XDrawLine(disp,w,gc,Sx1+(i+1)*distance,Sy1-s_length,Sx1+distance*(i+2),Sy1-s_length);
	    XDrawLine(disp,w,gc,Sx1+(i+2)*distance,Sy1,Sx1+distance*(i+2),Sy1-s_length);	
	}





      if(i==0)
	{
	  XSetForeground(disp,gc,yellowColor.pixel);
	  XDrawRectangle(disp,w,gc,Sx1+(i+1)*distance-5,Sy1+50,10,10);
	}
      else if(i%3==1 && strlen(symboltrack[i].mm.strand1)>=15 && symboltrack[i].mm.strand1[14]=='1' )
	{
	  XSetForeground(disp,gc,yellowColor.pixel);
	  XDrawRectangle(disp,w,gc,Sx1+(i+1)*distance-5,Sy1+50,10,10);
	}
      else if(i%3==2 && strlen(symboltrack[i].mm.strand1)>=15 && symboltrack[i].mm.strand1[14]=='2' )
	{
	  XSetForeground(disp,gc,yellowColor.pixel);
	  XDrawRectangle(disp,w,gc,Sx1+(i+1)*distance-5,Sy1+50,10,10);
	}
      else if(i%3==0 && strlen(symboltrack[i].mm.strand1)>=15 && symboltrack[i].mm.strand1[14]=='3' )
	{
	  XSetForeground(disp,gc,yellowColor.pixel);
	  XDrawRectangle(disp,w,gc,Sx1+(i+1)*distance-5,Sy1+50,10,10);
	}
      else if(i%3==1)
	{
	  XSetForeground(disp,gc,blackColor);
	  XDrawRectangle(disp,w,gc,Sx1+(i+1)*distance-5,Sy1+50,10,10);
	  XFillRectangle(disp,w,gc,Sx1+(i+1)*distance-5,Sy1+50,10,10);
	  
	}
      else if(i%3==2)
	{
	  XSetForeground(disp,gc,blackColor);
	  XDrawRectangle(disp,w,gc,Sx1+(i+1)*distance-5,Sy1+50,10,10);
	  XFillRectangle(disp,w,gc,Sx1+(i+1)*distance-5,Sy1+50,10,10);
	  
	}
      else if(i%3==0)
	{
	  XSetForeground(disp,gc,blackColor);
	  XDrawRectangle(disp,w,gc,Sx1+(i+1)*distance-5,Sy1+50,10,10);
	  XFillRectangle(disp,w,gc,Sx1+(i+1)*distance-5,Sy1+50,10,10);
	  
	}
      
    
      
      
    }     
  XFlush(disp);
  //sleep(0);
  
}



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


void run()
{
  molecule result,result1,result2;
  int kk,kk1,kk2;
  /*for(int i=0;i<num_of_head;i++)
    {    
      
      if(i<num_of_symbol && (rand()+0.0)/RAND_MAX <0.25 )
	
	if(ligation(result,headtrack[i].mm,symboltrack[i].mm))
	  {
	    headtrack[i].jj=1;
	    symboltrack[i].jj=1;
	    headtrack[i].mm=result;
	    symboltrack[i].mm=inv(result);
	    cout<<"\nLIGATION"<<"   head "<<i<<"  symbol "<<i<<"\n";graphic_disp();
	    sleep(0);
	    getchar();
	  }
	

      if(i>0 && (rand()+0.0)/RAND_MAX <0.25)

		if(ligation(result,headtrack[i].mm,headtrack[i-1].mm))
	  {
	    headtrack[i].jj=0;
	    headtrack[i-1].jj=2;
	    headtrack[i].mm=result;
	    headtrack[i-1].mm=inv(result);
	    cout<<"\nLIGATION"<<"   head "<<i<<"  head "<<i-1<<"\n";graphic_disp();sleep(0);getchar();
	  }
	

      if(i<num_of_head-1   && (rand()+0.0)/RAND_MAX <0.25) 

		if(ligation(result,headtrack[i].mm,headtrack[i+1].mm))
	  {
	    headtrack[i].jj=2;
	    headtrack[i+1].jj=0;
	    headtrack[i].mm=result;
	    headtrack[i+1].mm=inv(result);
	    cout<<"\nLIGATION"<<"   head "<<i<<"  head "<<i+1<<"\n";graphic_disp();sleep(0);getchar();
	  }
	

      for(int j=0;j<num_of_free;j++)

		if(free_molecule[j].cc>0  && (rand()+0.0)/RAND_MAX < free_molecule[j].cc/25.0 ) if(ligation(result,headtrack[i].mm,free_molecule[j].mm))
	  {
	    free_molecule[j].cc--;
	    headtrack[i].mm=result;
	    total_free--;
	    cout<<"\nLIGATION"<<"  head "<<i<<"  with free"<<"\n";graphic_disp();sleep(0);getchar();
	  }
	


    }
  */


  for(int i=0;i<num_of_symbol;i++)
    {
      if(i>0   && (rand()+0.0)/RAND_MAX <0.25) 
	if(ligation(result,symboltrack[i].mm,symboltrack[i-1].mm))
	  {
	    symboltrack[i].jj=0;
	    symboltrack[i-1].jj=2;
	    symboltrack[i].mm=result;
	    symboltrack[i-1].mm=inv(result);
	    
	    if(i-1==0)
	      cout<<"\nLIGATION"<<"   symbol "<<"A"<<"0"<<"    symbol "<<"I"<<"\n";
	    else if(i%3==2)
	      cout<<"\nLIGATION"<<"   symbol "<<"B"<<i/3<<"  symbol "<<"A"<<i/3<<"\n";
	    else if(i%3==0)
	      cout<<"\nLIGATION"<<"   symbol "<<"C"<<i/3-1<<"  symbol "<<"B"<<i/3-1<<"\n";
	    else if(i%3==1)
	      cout<<"\nLIGATION"<<"   symbol "<<"A"<<i/3<<"  symbol "<<"C"<<i/3-1<<"\n";
	     
	    graphic_disp();
	    sleep(0);getchar();	  
}
      if(i<num_of_symbol-1   && (rand()+0.0)/RAND_MAX <0.25) 
	if(ligation(result,symboltrack[i].mm,symboltrack[i+1].mm))
	  {
	    symboltrack[i].jj=2;
	    symboltrack[i+1].jj=0;
	    symboltrack[i].mm=result;
	    symboltrack[i+1].mm=inv(result);


	    //	    cout<<"\nLIGATION"<<"  symbol "<<i<<"  symbol "<<i+1<<"\n";
	     if(i==0)
	       cout<<"\nLIGATION"<<"   symbol "<<"I"<<"  symbol "<<"A"<<"0"<<"\n";
	    else if(i%3==1)
	      cout<<"\nLIGATION"<<"   symbol "<<"A"<<i/3<<"  symbol "<<"B"<<i/3<<"\n";
	    else if(i%3==2)
	      cout<<"\nLIGATION"<<"   symbol "<<"B"<<i/3<<"  symbol "<<"C"<<i/3<<"\n";
	    else if(i%3==0)
	      cout<<"\nLIGATION"<<"   symbol "<<"C"<<i/3-1<<"  symbol "<<"A"<<i/3<<"\n";
	     

	    graphic_disp();sleep(0);getchar();	 

 }
      for(int j=0;j<num_of_free;j++)
	if(free_molecule[j].cc>0  && (rand()+0.0)/RAND_MAX < free_molecule[j].cc/25.0) if(ligation(result,symboltrack[i].mm,free_molecule[j].mm))
	  {
	    free_molecule[j].cc--;
	    symboltrack[i].mm=result;
	    total_free--;


	    if(i==0)
	      cout<<"\nLIGATION"<<"   symbol "<<"I"<<"  with free"<<"\n";
	    else if(i%3==1)
	      cout<<"\nLIGATION"<<"   symbol "<<"A"<<i/3<<"  with free"<<"\n";
	    else if(i%3==2)
	      cout<<"\nLIGATION"<<"   symbol "<<"B"<<i/3<<"  with free"<<"\n";
	    else if(i%3==0)
	      cout<<"\nLIGATION"<<"   symbol "<<"C"<<i/3-1<<"  with free"<<"\n";



	    graphic_disp();sleep(0);getchar();	  
	  }
    }
  
  for(int i=0;i<num_of_free;i++)
    for(int j=i+1;j<num_of_free;j++)
      {
	if(free_molecule[i].cc>0 && free_molecule[j].cc>0 && (rand()+0.0)/RAND_MAX < 0 )	if(ligation(result,free_molecule[i].mm,free_molecule[j].mm))
	  {
	    free_molecule[i].cc--;
	    free_molecule[j].cc--;
	    
	    kk=find(result);
	    if(kk!=-1)
	      free_molecule[kk].cc++;
	    else
	      {	    
		free_molecule[num_of_free].mm=result;
		free_molecule[num_of_free].cc++;
		num_of_free++;
	      }
	    total_free--;
	    cout<<"\nLIGATION"<<"   free with free\n";graphic_disp();sleep(0);getchar();
	  }
      }
  
  display();  

/*
  for(int i=0;i<num_of_head;i++)
    { 
      if( (rand()+0.0)/RAND_MAX < 0.25)   if(restriction1(result1, result2, headtrack[i].mm))
	{
	  if(headtrack[i].jj==-1)
	    {
	      headtrack[i].mm=result1;
	      kk2=find(result2);
	      if(kk2!=-1)
		free_molecule[kk2].cc++;
	      else
		{
		  free_molecule[num_of_free].mm=result2;
		  free_molecule[num_of_free].cc++;
		  num_of_free++;
		}
	      total_free++;
	    }
	  else if(headtrack[i].jj==0)
	    {
	      headtrack[i].mm=result1;
	      headtrack[i-1].mm=inv(result2);
	      headtrack[i].jj=-1;
	      headtrack[i-1].jj=-1;
	    }
	  else if(headtrack[i].jj==1)
	    {
	      headtrack[i].mm=result1;
	      symboltrack[i].mm=inv(result2);
	      headtrack[i].jj=-1;
	      symboltrack[i].jj=-1;
	    }
	  else
	    {
	      headtrack[i].mm=result1;
	      headtrack[i+1].mm=inv(result2);
	      headtrack[i].jj=-1;
	      headtrack[i+1].jj=-1;
	    } 
	  cout<<"\nRestriction1"<<"   head "<<i;graphic_disp();sleep(0);getchar();

	}

      
      if( (rand()+0.0)/RAND_MAX < 0.25)   if(restriction2(result1, result2,headtrack[i].mm))
      	{
	 
	  if(headtrack[i].jj==-1)
	    {
	      headtrack[i].mm=result1;
	      kk2=find(result2);
	      if(kk2!=-1)
		free_molecule[kk2].cc++;
	      else
		{
		  
		  free_molecule[num_of_free].mm=result2;
		  free_molecule[num_of_free].cc++;
		  num_of_free++;
		}
	      total_free++;
	    }
	  else if(headtrack[i].jj==0)
	    {
	      headtrack[i].mm=result1;
	      headtrack[i-1].mm=inv(result2);
	      headtrack[i].jj=-1;
	      headtrack[i-1].jj=-1;
	    }
	  else if(headtrack[i].jj==1)
	    {
	      headtrack[i].mm=result1;
	      symboltrack[i].mm=inv(result2);
	      headtrack[i].jj=-1;
	      symboltrack[i].jj=-1;
	    }
	  else
	    {
	      headtrack[i].mm=result1;
	      headtrack[i+1].mm=inv(result2);
	      headtrack[i].jj=-1;
	      headtrack[i+1].jj=-1;
	    }
	  cout<<"\nRestriction2"<<"   head "<<i;graphic_disp();sleep(0);getchar(); 
	}
      if( (rand()+0.0)/RAND_MAX < 0.25) 	if(restriction3(result1, result2,headtrack[i].mm))
      	{

	  if(headtrack[i].jj==-1)
	    {
	      headtrack[i].mm=result1;
	     kk2=find(result2);
	      if(kk2!=-1)
		free_molecule[kk2].cc++;
	      else
		{
		  free_molecule[num_of_free].mm=result2;
		  free_molecule[num_of_free].cc++;
		  num_of_free++;
		}
	      total_free++;
	    }
	  else if(headtrack[i].jj==0)
	    {
	      headtrack[i].mm=result1;
	      headtrack[i-1].mm=inv(result2);
	      headtrack[i].jj=-1;
	      headtrack[i-1].jj=-1;
	    }
	  else if(headtrack[i].jj==1)
	    {
	      headtrack[i].mm=result1;
	      symboltrack[i].mm=inv(result2);
	      headtrack[i].jj=-1;
	      symboltrack[i].jj=-1;
	    }
	  else
	    {
	      headtrack[i].mm=result1;
	      headtrack[i+1].mm=inv(result2);
	      headtrack[i].jj=-1;
	      headtrack[i+1].jj=-1;
	    } 
	  cout<<"\nRestriction3"<<"   head "<<i;graphic_disp();sleep(0);getchar();
	}
      if( (rand()+0.0)/RAND_MAX < 0.25) 	if(restriction4(result1, result2,headtrack[i].mm))
	{

	  if(headtrack[i].jj==-1)
	    {
	      headtrack[i].mm=result1;
	      kk2=find(result2);
	      if(kk2!=-1)
		free_molecule[kk2].cc++;
	      else
		{
		  free_molecule[num_of_free].mm=result2;
		  free_molecule[num_of_free].cc++;
		  num_of_free++;
		}
	      total_free++;
	    }
	  else if(headtrack[i].jj==0)
	    {
	      headtrack[i].mm=result1;
	      headtrack[i-1].mm=inv(result2);
	      headtrack[i].jj=-1;
	      headtrack[i-1].jj=-1;
	    }
	  else if(headtrack[i].jj==1)
	    {
	      headtrack[i].mm=result1;
	      symboltrack[i].mm=inv(result2);
	      headtrack[i].jj=-1;
	      symboltrack[i].jj=-1;
	    }
	  else
	    {
	      headtrack[i].mm=result1;
	      headtrack[i+1].mm=inv(result2);
	      headtrack[i].jj=-1;
	      headtrack[i+1].jj=-1;
	    }
	  cout<<"\nRestriction4"<<"   head "<<i;graphic_disp();sleep(0);getchar(); 
	}
    }

*/

  for(int i=0;i<num_of_symbol;i++)
    {
     
      
      /*
	if( (rand()+0.0)/RAND_MAX < 0.35)       if(restriction2(result1, result2,symboltrack[i].mm))
      	{
	
	if(symboltrack[i].jj==-1)
	{
	symboltrack[i].mm=result1;
	
	
	
	kk2=find(result2);
	if(kk2==-1)
	{	    
	free_molecule[num_of_free].mm=result2;
	free_molecule[num_of_free].cc++;
	num_of_free++;
	}
	else
	{
	free_molecule[kk2].cc++;
	}
	total_free++;
	
	}
	else if(symboltrack[i].jj==0)
	{
	symboltrack[i].mm=result1;
	symboltrack[i-1].mm=inv(result2);
	symboltrack[i].jj=-1;
	symboltrack[i-1].jj=-1;
	}
	
	else if(symboltrack[i].jj==1)
	{
	symboltrack[i].mm=result1;
	headtrack[i].mm=inv(result2);
	symboltrack[i].jj=-1;
	headtrack[i].jj=-1;
	}
	
	else
	{
	symboltrack[i].mm=result1;
	symboltrack[i+1].mm=inv(result2);
	symboltrack[i].jj=-1;
	symboltrack[i+1].jj=-1;
	} 
	
	cout<<"\nRestriction2"<<"   symbol "<<i;graphic_disp();sleep(0);getchar();
	}
      */
      //      if( (rand()+0.0)/RAND_MAX < 0.50)
	{
	  if(restriction3(result1, result2,symboltrack[i].mm))
	    {
	      
	      if(symboltrack[i].jj==-1)
		{
		  symboltrack[i].mm=result1;
		  
		  kk2=find(result2);
		  if(kk2==-1)
		    {	    
		      free_molecule[num_of_free].mm=result2;
		      free_molecule[num_of_free].cc++;
		      num_of_free++;
		    }
		  else
		    {
		      free_molecule[kk2].cc++;
		    }
		  total_free++;
		}
	      else if(symboltrack[i].jj==0)
		{
		  symboltrack[i].mm=result1;
		  symboltrack[i-1].mm=inv(result2);
		  symboltrack[i].jj=-1;
		  symboltrack[i-1].jj=-1;
		}
	      
	      /*
		else if(symboltrack[i].jj==1)
		{
		symboltrack[i].mm=result1;
		headtrack[i].mm=inv(result2);
		symboltrack[i].jj=-1;
		headtrack[i].jj=-1;
		}
	      */
	      
	      else
		{
		  symboltrack[i].mm=result1;
		  symboltrack[i+1].mm=inv(result2);
		  symboltrack[i].jj=-1;
		  symboltrack[i+1].jj=-1;
		} 
	      
	      if(i==0)
		cout<<"\nRestriction3"<<"   symbol "<<"I";
	      else if(i%3==1)
		cout<<"\nRestriction3"<<"   symbol "<<"A"<<i/3;
	      else if(i%3==2)
		cout<<"\nRestriction3"<<"   symbol "<<"B"<<i/3;
	      else if(i%3==0)
		cout<<"\nRestriction3"<<"   symbol "<<"C"<<i/3-1;
	      
	      graphic_disp();sleep(0);getchar();
	      
	    }
	  //	  if( (rand()+0.0)/RAND_MAX < 0.50) 	
	  if(restriction4(result1, result2,symboltrack[i].mm))
	    {
	      
	      if(symboltrack[i].jj==-1)
		{
		  symboltrack[i].mm=result1;
		  
		  kk2=find(result2);
		  if(kk2==-1)
		    {	    
		      free_molecule[num_of_free].mm=result2;
		      free_molecule[num_of_free].cc++;
		      num_of_free++;
		    }
		  else
		    {
		      free_molecule[kk2].cc++;
		    }
		  total_free++;
		}
	      else if(symboltrack[i].jj==0)
		{
		  symboltrack[i].mm=result1;
		  symboltrack[i-1].mm=inv(result2);
		  symboltrack[i].jj=-1;
		  symboltrack[i-1].jj=-1;
		}
	      
	      
	      /*	  else if(symboltrack[i].jj==1)
			  {
			  symboltrack[i].mm=result1;
			  headtrack[i].mm=inv(result2);
			  symboltrack[i].jj=-1;
			  headtrack[i].jj=-1;
			  }
	      */
	      
	      
	      else
		{
		  symboltrack[i].mm=result1;
		  symboltrack[i+1].mm=inv(result2);
		  symboltrack[i].jj=-1;
		  symboltrack[i+1].jj=-1;
		} 

	      if(i==0)
		cout<<"\nRestriction4"<<"   symbol "<<"I";
	      else if(i%3==1)
		cout<<"\nRestriction4"<<"   symbol "<<"A"<<i/3;
	      else if(i%3==2)
		cout<<"\nRestriction4"<<"   symbol "<<"B"<<i/3;
	      else if(i%3==0)
		cout<<"\nRestriction4"<<"   symbol "<<"C"<<i/3-1;
	      
	      //	     	      cout<<"\nRestriction4"<<"   symbol "<<i;
	      graphic_disp();sleep(0);getchar();
	      
	    }
	  
	  // if( (rand()+0.0)/RAND_MAX < 0.50)   
	  if(restriction1(result1, result2,symboltrack[i].mm))
	    {
	      
	      if(symboltrack[i].jj==-1)
		{
		  symboltrack[i].mm=result1;
		  
		  kk2=find(result2);
		  if(kk2==-1)
		    {	    
		      free_molecule[num_of_free].mm=result2;
		      free_molecule[num_of_free].cc++;
		      num_of_free++;
		    }
		  else
		    {
		      free_molecule[kk2].cc++;
		    }
		  total_free++;
		}
	      else if(symboltrack[i].jj==0)
		{
		  symboltrack[i].mm=result1;
		  symboltrack[i-1].mm=inv(result2);
		  symboltrack[i].jj=-1;
		  symboltrack[i-1].jj=-1;
		}
	      /*
		else if(symboltrack[i].jj==1)
		{
		symboltrack[i].mm=result1;
		headtrack[i].mm=inv(result2);
		symboltrack[i].jj=-1;
		headtrack[i].jj=-1;
		}
	      */
	      else
		{
		  symboltrack[i].mm=result1;
		  symboltrack[i+1].mm=inv(result2);
		  symboltrack[i].jj=-1;
		  symboltrack[i+1].jj=-1;
		} 


	      if(i==0)
		cout<<"\nRestriction1"<<"   symbol "<<"I";
	      else if(i%3==1)
		cout<<"\nRestriction1"<<"   symbol "<<"A"<<i/3;
	      else if(i%3==2)
		cout<<"\nRestriction1"<<"   symbol "<<"B"<<i/3;
	      else if(i%3==0)
		cout<<"\nRestriction1"<<"   symbol "<<"C"<<i/3-1;
	      
	     
	      //	      cout<<"\nRestriction1"<<"   symbol "<<i;
	      graphic_disp();sleep(0);getchar();
	    }
	}
    }


  for(int i=0;i<num_of_free;i++)
    {
      if(free_molecule[i].cc>0 && (rand()+0.0)/RAND_MAX < 0 )
	//free_molecule[i].cc/400.0)
	if(restriction1(result1, result2,free_molecule[i].mm))
	  {
	
	    free_molecule[i].cc--;
	    kk1=find(result1);
	    kk2=find(result2);
	    if(kk1==-1)
	      {
		free_molecule[num_of_free].mm=result1;
		free_molecule[num_of_free].cc++;
		num_of_free++;
	      }
	    else
	      {
		free_molecule[kk1].cc++;
	      }
	    
	    if(kk2==-1)
	      {
		free_molecule[num_of_free].mm=result2;
		free_molecule[num_of_free].cc++;
		num_of_free++;
	      }
	    else
	      {
		free_molecule[kk2].cc++;
	      }    
	    total_free++;
	    cout<<"\nRestriction1"<<"   free molecule";graphic_disp();sleep(0);getchar();
	  }
      
      if(free_molecule[i].cc>0  && (rand()+0.0)/RAND_MAX < 0)
	//free_molecule[i].cc/400.0)
	
	/*if(restriction2(result1, result2,free_molecule[i].mm))
	  {

	    free_molecule[i].cc--;
	    kk1=find(result1);
	    kk2=find(result2);
	    if(kk1==-1)
	      {
		free_molecule[num_of_free].mm=result1;
		free_molecule[num_of_free].cc++;
		num_of_free++;
	      }
	    else
	      {
		free_molecule[kk1].cc++;
	      }
	    
	    if(kk2==-1)
	      {
		free_molecule[num_of_free].mm=result2;
		free_molecule[num_of_free].cc++;
		num_of_free++;
	      }
	    else
	      {
		free_molecule[kk2].cc++;
	      }
	    total_free++;
	    cout<<"\nRestriction2"<<"   free molecule";graphic_disp();sleep(0);getchar();
	  }
	*/

      if(free_molecule[i].cc>0  && (rand()+0.0)/RAND_MAX < 0)
	//free_molecule[i].cc/400.0) 
	if(restriction3(result1, result2,free_molecule[i].mm))
	  {

	    free_molecule[i].cc--;
	    kk1=find(result1);
	    kk2=find(result2);
	    if(kk1==-1)
	      {
		free_molecule[num_of_free].mm=result1;
		free_molecule[num_of_free].cc++;
		num_of_free++;
	      }
	    else
	      {
		free_molecule[kk1].cc++;
	      }
	    
	    if(kk2==-1)
	      {
		free_molecule[num_of_free].mm=result2;
		free_molecule[num_of_free].cc++;
		num_of_free++;
	      }
	    else
	      {
		free_molecule[kk2].cc++;
	      }
	    total_free++;	    
	    cout<<"\nRestriction3"<<"   free molecule";graphic_disp();sleep(0);getchar();
	  }
      
      if(free_molecule[i].cc>0  && (rand()+0.0)/RAND_MAX < 0)
	//free_molecule[i].cc/400.0)  
	if(restriction4(result1, result2,free_molecule[i].mm))
	  {

	    free_molecule[i].cc--;
	    kk1=find(result1);
	    kk2=find(result2);
	    if(kk1==-1)
	      {
		free_molecule[num_of_free].mm=result1;
		free_molecule[num_of_free].cc++;
		num_of_free++;
	      }
	    else
	      {
		free_molecule[kk1].cc++;
	      }
	    
	    if(kk2==-1)
	      {
		free_molecule[num_of_free].mm=result2;
		free_molecule[num_of_free].cc++;
		num_of_free++;
	      }
	    else
	      {
		free_molecule[kk2].cc++;
	      }
	    total_free++;
	    cout<<"\nRestriction4"<<"   free molecule";graphic_disp();sleep(0);getchar();
	  }
    }
}




 

int main(int argc, char* argv[])
{
  ifstream fin;
  if(argc==1) 
    {
      cout<<"Please enter the input file name\n";
      return 0;
    } 
  else 
    fin.open(argv[1]);
  //  ifstream fin=

  
  /*
  fin>>num_of_head;
  for(int i=0;i<num_of_head;i++)
    {
      headtrack[i].mm.strand1=new char[maxlength];
      headtrack[i].mm.strand2=new char[maxlength];
      fin>>headtrack[i].mm.strand1>>headtrack[i].mm.strand2>>headtrack[i].mm.offset>>headtrack[i].jj;
    }
  */

  fin>>num_of_symbol;
  for(int i=0;i<num_of_symbol;i++)
    {
      symboltrack[i].mm.strand1=new char[maxlength];
      symboltrack[i].mm.strand2=new char[maxlength];
      fin>>symboltrack[i].mm.strand1>>symboltrack[i].mm.strand2>>symboltrack[i].mm.offset>>symboltrack[i].jj;
    }

  fin>>num_of_free;

  for(int i=0;i<num_of_free;i++)
    
    {
      free_molecule[i].mm.strand1=new char[maxlength];
      free_molecule[i].mm.strand2=new char[maxlength];
      
      fin>>free_molecule[i].mm.strand1>>free_molecule[i].mm.strand2>>free_molecule[i].mm.offset>>free_molecule[i].cc;

      total_free+=free_molecule[i].cc;
    }
  //int steps=1;


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

      disp = XOpenDisplay(NIL);
      assert(disp);

      // Get some colors

      blackColor = BlackPixel(disp, DefaultScreen(disp));
      whiteColor = WhitePixel(disp, DefaultScreen(disp));

      cm=DefaultColormap(disp,DefaultScreen(disp));

      greenColor.red=0;
      greenColor.green=65000 ;
      greenColor.blue=0;
      greenColor.flags=DoRed | DoGreen | DoBlue;
      XAllocColor(disp,cm,&greenColor);
      
      yellowColor.red=32000;
      yellowColor.green=32000 ;
      yellowColor.blue=0;
      yellowColor.flags=DoRed | DoGreen | DoBlue;
      XAllocColor(disp,cm,&yellowColor);
      redColor.red=65000;
      redColor.green= 0;
      redColor.blue=0;
      redColor.flags=DoRed | DoGreen | DoBlue;
      XAllocColor(disp,cm,&redColor);
      blueColor.red=0;
      blueColor.green=0 ;
      blueColor.blue=65000;
      blueColor.flags=DoRed | DoGreen | DoBlue;
      XAllocColor(disp,cm,&blueColor);
      purpleColor.red=32000;
      purpleColor.green=0 ;
      purpleColor.blue=32000;
      purpleColor.flags=DoRed | DoGreen | DoBlue;
      XAllocColor(disp,cm,&purpleColor);
      

      // Create the window

      w = XCreateSimpleWindow(disp, DefaultRootWindow(disp), 0, 0, 
				     450, 300, 0, whiteColor, whiteColor);

      // We want to get MapNotify events

      XSelectInput(disp, w, StructureNotifyMask);

      // "Map" the window (that is, make it appear on the screen)

      XMapWindow(disp, w);

      // Create a "Graphics Context"

      gc = XCreateGC(disp, w, 0, NIL);

      // Tell the GC we draw using the white color

      XSetForeground(disp, gc, blackColor);

      // Wait for the MapNotify event

      for(;;) {
	    XEvent e;
	    XNextEvent(disp, &e);
	    if (e.type == MapNotify)
		  break;
      }

      // Draw the line
      
      //XDrawLine(disp, w, gc, 10, 10, 380, 10);
      
      //      XDrawLine(disp, w, gc, 10, 190, 110, 190);



      

      // Send the "DrawLine" request to the server


      graphic_disp();

      XFlush(disp);
      sleep(0);//getchar();
      // Wait for 10 seconds


      //      sleep(2);


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

      getchar();

  int steps=8000;
  display();
  for(int k=0;k<steps;k++)
    {
      run();
      display();
      getchar();  
    }
  getchar();
  return 0;
}