// --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
// Copyright (C) 2007 Author: Fathi Elloumi.

// This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version.

// This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

// You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
// ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------


#include "slist.h"
#include <time.h>
int best(long double T[], int & nbelts,int taille,char *fich)
{
FILE *infresult;
char s1[20],s2[20],s3[20],s4[20],s5[20],s6[20],s7[20],s8[25];
char epat[41],elistpos[20000];
int i,j,pos;
int elen,eden,esup,etot;
long double eproba,epvalue;
infresult= fopen(fich,"r") ;
if (infresult==NULL) {printf("Error in reading file : %s",fich);return 0;};
if ( feof(infresult) ){printf("Error : input file %s is empty",fich);return 0;};
fscanf(infresult,"%s %s %s %s %s %s %s %s",s1,s2,s3,s4,s5,s6,s7,s8);
//printf("%s %s %s %s %s %s %s %s %s\n",s1,s2,s3,s4,s5,s6,s7,s8,s9);
     while ( !feof( infresult) )
    	{
				fscanf(infresult,"%s %i %i %i %i %Le %Le %s",epat,&elen,&eden,&esup,&etot,&eproba,&epvalue,elistpos);
			//	printf("%s %s %i %i %i %i %Le %Le %s",epat,emat,&elen,&eden,&esup,&etot,&eproba,&epvalue,elistpos);
				if   ( feof(infresult) )  break;
                if (nbelts==0)//if1
				{ nbelts=1;
			      T[0]=eproba;
				}
				else //if1
				if (eproba <= T[nbelts-1] )//if2
				{ 
					if (nbelts < taille) //if3
				    { 
				    T[nbelts]=eproba;
				    nbelts++;
				    };//if3
				} 
				else //if2
				{
					i=0;
					while (eproba <=T[i]) i++;
					if (nbelts==taille) pos=taille-1; else { pos=nbelts; nbelts++; };
					for (j=pos;j>i;j--) T[j]=T[j-1];
					T[i]=eproba;
				};
		}; // while
		fclose(infresult);
////////////
 return 1;
 }

//// function MAIN /////////////////////////////////////////////////////
 
int main(int nbre, char *arg[])

 {
 char nucleotide[4]={'A','C','G','T'};
long double tabproba[4]={0.328008,0.167476,0.193845,0.310671}; // bacillus subtilis nucleotides frequencies

// long double tabproba[4]={0.328008,0.167476,0.193845,0.310671};
 char fich[4][9]={"resA.txt","resC.txt","resG.txt","resT.txt"};
 long double pa,pc,pg,pt,totpatt,tab[2000];//------------------------/// maj
 char reponse;
 char chtotbd[7];
 FILE * in1, *in2,*outrec;
 int i,j,nbretotal,k,vsup,vlen,TOTBD,taille_seqs,indice,nombre,voutput;
 int tabtailles[100];
 tabtablist super;
 Slist matrice_lst_patterns[4][4];
 Slist L;
 bool finish,stop;
 time_t start,end;
 double dif;
 char namefile[20],buffer[33];
try
{

//----------------------- parameters -----------------------------

if ((nbre!=5) && (nbre!=7)&& (nbre!=10) && (nbre!=12))
{ printf("Error: Invalid number of parameters\n");
printf("\nSYNTAX: search_best_random_scores minsupport <min_support_value> maxlength <max_length_pattern_value> [stats <prA> <prC> <prG> <prT> ][output <number_of_patterns>] \n"); 
printf("\nDEFAULTS PARAMETERS: [stats with nucleotides Bacillus Subtilis probs] [output=40]");
  return 0;
};
stop=false;
 

 if ((nbre>=5) && ((strcmp(arg[1],"minsupport")!=0) || (strcmp(arg[3],"maxlength")!=0)))
 {printf("Error: Invalid key words: should be -minsupport- or -maxlength-\n"); return 0;}; ////39

 if ( (nbre==7)   && (strcmp(arg[5],"output")!=0))
 {printf("Error: Invalid key word: should be -output-\n"); return 0;};

 if ( (nbre>=10)  && (strcmp(arg[5],"stats")!=0))
 {printf("Error: Invalid key word: should be -stats-\n"); return 0;};

 if ( (nbre==12)   && (strcmp(arg[10],"output")!=0))
 {printf("Error: Invalid key word: should be -output-\n"); return 0;};

 vsup=atoi(arg[2]);vlen=atoi(arg[4]);
 if (vsup==0) vsup=2; if (vlen==0) vlen=12;
 if (vsup<2) 
{printf ("Error: Invalid value for minsupport\n");stop=true;};
if ((vlen<2) || (vlen>40))
{printf ("Error: maxlength value must be between 2 and 40\n");stop=true;};
if (stop) return 0;

voutput=40;
if (nbre==7) 
    {
         voutput=atoi(arg[6]) ;
	if ((voutput<10) || (voutput>2000))
	{printf ("Error: output must be between 10 and 2000\n");return 0;};
         
	 
    }
 else 
 {
    if (nbre>=10)
    {
	pa=atof(arg[6]);pc=atof(arg[7]);pg=atof(arg[8]);pt=atof(arg[9]);
        if (((pa <=0.0) || (pa >=1.0)) ||((pc <=0.0) || (pc >=1.0)) ||((pg <=0.0) || (pg >=1.0)) ||((pt <=0.0) || (pt >=1.0)))
        {printf("Error: Invalid probablity values\n"); return 0;}
        printf ("Stats with probability values: %Lf & %Lf & %Lf & %Lf\n",pa,pc,pg,pt);
	tabproba[0]=pa;tabproba[1]=pc;tabproba[2]=pg;tabproba[3]=pt;
          if (nbre==12)
            {
              voutput=atoi(arg[11]) ;
	     if ((voutput<10) || (voutput>2000))
	     {printf ("Error: output must be between 10 and 2000\n");return 0;};
            };

    };
 
 };

system("cls");
printf("PARAMETERS:\n");
printf("input_promo_file: 1000 samples");
printf ("min_support: %i max_lenght:%i\n",vsup,vlen); 
printf ("Stats with probability values: %Lf & %Lf & %Lf & %Lf\n",tabproba[0],tabproba[1],tabproba[2],tabproba[3]); 
printf ("Output number: %i \n",voutput); 
//
printf("\nCONTINUE ? (if yes type Y):");scanf("%c",&reponse);
if (reponse!='Y') {printf("\n BYE !"); return 0;};

//----------------------------------------------------------------
outrec= fopen("random-scores.txt","w"); //---------------------------------- maj
fprintf(outrec,"Totpatt\tTime");for (i=1;i<=voutput;i++) fprintf(outrec,"\tzs%i ",i);fprintf(outrec,"\n");
 
//for (indice=1;indice<=1000;indice++)
for (indice=1;indice<=1000;indice++)
{ 
   strcpy(namefile,"sample");
   itoa (indice,buffer,10);
   strcat(namefile,buffer);strcat(namefile,".txt");
   printf("\n%s",namefile);  

/// START ......................................................................../////  
	time (&start);

  j= revcomp(namefile,taille_seqs,tabtailles); // reverse complement
   if (j==0)
  { printf("Error in input file: %s\n",namefile); return 0; };
   if (j==1)
   { printf("Error: number of sequences must be greater than 1\n"); return 0; };

   if (vsup>j)
  { printf("Error: min_support must be less or equal than the number of sequences:%i\n",j); return 0; };

  //printf("number of sequences:%i\n",j);
   int l,c;
 // for (l=0;l<j;l++)printf("\n %i ",tabtailles[l]);
//////////------------------------------ PROCESSSING -------------------------------///  
  super[0] = new Listgen<int>[2*j];      // for nucleotide A
  super[1] = new Listgen<int>[2*j];      // for nucleotide C
  super[2] = new Listgen<int>[2*j];      // for nucleotide G
  super[3] = new Listgen<int>[2*j];      // for nucleotide T
 
   k= create(super); // creation of 4 nucleotides arrays of positions

  if (k==0) {printf("Error in processing file that contains sequences and their reverses"); return 0;};

    totpatt=0.0;
   for (l=0;l<4;l++)
      { printf("Processing family: %c ...\n",nucleotide[l]);
      for (c=0;c<4;c++) 
        {
          matrice_lst_patterns[l][c].join(super[l],super[c],2*j,nucleotide[l],nucleotide[c],vsup,vlen-2);
    //      matrice_lst_patterns[l][c].affich();
         };
        matrice_lst_patterns[l][0].append_v2( matrice_lst_patterns[l][1]);
        matrice_lst_patterns[l][0].append_v2( matrice_lst_patterns[l][2]);
        matrice_lst_patterns[l][0].append_v2( matrice_lst_patterns[l][3]);
        //printf("Liste des patterns -----------------------\n");
       // matrice_lst_patterns[l][0].affich();
        matrice_lst_patterns[l][0].morespecific_v2(vsup,vlen-2);
		//	printf("Statistics:...\n");
          totpatt=totpatt + matrice_lst_patterns[l][0].affichjmp2(fich[l],tabtailles,j,tabproba);



	    

					

   matrice_lst_patterns[l][0].delete_list_pattern();

 

    };
  //printf("\nTotal patterns for 4  families= %12.0Lf\n",totpatt) ;       

  time (&end);
  dif = difftime (end,start);
  //printf ("\nRunTime = %.2lf seconds.\n", dif );
//////////////////////////////
        
        fprintf(outrec,"%12.0Lf\t",totpatt);
		fprintf(outrec,"%.2lf",dif) ;
        nombre=0;
	    printf ("\nStatus:");
		printf ("\nFamily A: %i",best(tab,nombre,voutput,"resA.txt"));
		printf ("\nFamily C: %i",best(tab,nombre,voutput,"resC.txt"));
        printf ("\nFamily G: %i",best(tab,nombre,voutput,"resG.txt"));
		printf ("\nFamily T: %i",best(tab,nombre,voutput,"resT.txt"));

        for (i=0;i<nombre;i++)
        { 
			fprintf(outrec,"\t%Le",tab[i]) ;

 
        }; 
	    fprintf(outrec,"\n") ;


//////////////////////////////
}; // indice
 fclose(outrec);
}
catch (exception &e)
{ printf("exception: %s\n",e.what()) ; }
return 0;
}