// --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
// 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 "utilities2.h";
  

//// function MAIN /////////////////////////////////////////////////////
int main(int vnbre, char *arg[])
//int main()
{
  int nombre=0; int i,vtaille;
  elt  * tab; 
  FILE * outrec, *outrep,*inproba;
  double pa,pc,pg,pt;
   time_t start;
 try
 {      if (vnbre > 2) 
        {printf("\nError: Invalid number of parameters\n");
		 printf("\nSYNTAX: Bestpatterns [number_of_patterns] defaults=20\n"); 
         return 0;
		}
        else
			if (vnbre==2)
			{
				vtaille = atoi(arg[1]);
				if (vtaille < 10 || vtaille > 2000)
				{
				printf("\nError: Min=10 and Max=2000\n");
				return 0;
				};
			} 
			else vtaille=40;
			tab= new elt[vtaille];
			inproba = fopen("fproba.txt","r") ;
        		if (inproba==NULL) {printf("Error in reading used probabilities");return 0;};
			if ( feof(inproba) ){printf("Error : proba file is empty");return 0;};
			fscanf(inproba,"%lf %lf %lf %lf",&pa,&pc,&pg,&pt);
			//printf("%lf %lf %lf %lf",pa,pc,pg,pt);
                        fclose(inproba);
			outrec= fopen("bestzstot.txt","w");
			outrep= fopen("runreport.txt","a");


////////////////
time(&start);
printf("\n*** Selecting the best %i patterns for the z-zcore of the total number of occurences on %s:...\n",vtaille,ctime(&start));
   fprintf(outrep,"\n*** Selecting the best %i patterns for the z-zcore of the total number of occurences on %s:...\n",vtaille,ctime(&start));
  
	
	// printf ("\nStatus:");
	printf ("\nFrom family A: %i",besttot(tab,nombre,vtaille,"resA.txt"));
	printf ("\nFrom family C: %i",besttot(tab,nombre,vtaille,"resC.txt"));
        printf ("\nFrom family G: %i",besttot(tab,nombre,vtaille,"resG.txt"));
	printf ("\nFrom family T: %i",besttot(tab,nombre,vtaille,"resT.txt"));
		 
        fprintf(outrec,"Pattern\t") ;
      //  fprintf(outrec,"Max\t") ;
        fprintf(outrec,"Length\t") ;
        fprintf(outrec,"Density\t") ;
 		fprintf(outrec,"Support\t") ;
        fprintf(outrec,"Total\t") ;
		fprintf(outrec,"Zs-supp\t") ;
        fprintf(outrec,"Zs-tot\t") ;
        fprintf(outrec,"Sequences_and_Positions\n") ;

        for (i=0;i<nombre;i++)
        { 
			fprintf(outrec,"%s\t",tab[i].pat) ;
		//	fprintf(outrec,"%s\t",tab[i].mat) ;
			fprintf(outrec,"%i\t",tab[i].len) ;
			fprintf(outrec,"%i\t",tab[i].den) ;
			fprintf(outrec,"%i\t",tab[i].sup) ;
			fprintf(outrec,"%i\t",tab[i].tot) ;
			fprintf(outrec,"%Le\t",tab[i].proba) ;
			fprintf(outrec,"%Le\t",tab[i].pvalue) ;
			fprintf(outrec,"%s\n",tab[i].listpos) ;
 
        }; 
        fclose(outrec);


printf("\n--> see file: bestzstot.txt\n");
fprintf(outrep,"\n--> see file: bestzstot.txt\n");


printf("\n*** Sites extraction with their positions.......\n");
fprintf(outrep,"\n*** Sites extraction with their positions.......\n");
//
pospatt("bestzstot.txt","sites-positions-tot.txt","sites-for-logo-tot.txt");

printf("\n--> see files: sites-positions-tot.txt & sites-for-logo-tot.txt\n");
fprintf(outrep,"\n--> see files: sites-positions-tot.txt & sites-for-logo-tot.txt\n");


printf("\n*** Profiles,Consensus and mean information content.......\n");
fprintf(outrep,"\n*** Profiles,Consensus and mean information content.......\n");
//
prostat(pa,pc,pg,pt,"sites-for-logo-tot.txt","patt-profiles-tot.txt","patt-cons-mic-tot.txt");

printf("\n--> see files: patt-profiles-tot.txt & patt-cons-mic-tot.txt\n");
fprintf(outrep,"\n--> see files: patt-profiles-tot.txt & patt-cons-mic-tot.txt\n");

printf("\n*** Information about pattern similarity and reverse complements.......\n");
fprintf(outrep,"\n*** Information about pattern similarity and reverse complements.......\n" );

simrev("bestzstot.txt","patt-similarity-tot.txt","patt-rev-com-tot.txt");

printf("\n--> see files: patt-similarity-tot.txt & patt-rev-com-tot.txt\n");
fprintf(outrep,"\n--> see files: patt-similarity-tot.txt & patt-rev-com-tot.txt\n");

printf("\nDone ! \n");
fprintf(outrep,"\nDone ! \n");
fclose(outrep);
///////////////
        
}
catch (exception &e)
{ printf("exception: %s\n",e.what()) ; }
return 0;
}