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


#ifndef UTILITIES2_H
#define UTILITIES2_H
#include "listgen.h"
#include <time.h>
//-------------------------------------------------------------------
 

typedef Listgen<int> * tabtablist[4];
typedef struct 
             {
               char       pat[41];
	//		   char		  mat[5];
               int        len;
               int        den;
               int        sup;
			   int        tot;
               long double proba;
               long double  pvalue;
               char   listpos[20000];
               
             } elt ;

////////////////////////////
void  concat(char * tab, char c1, int nbpoints, char c2);
bool  matchpattern(char * s1, char * s2);
int max(int t1,int t2);
int  matching(char * tab,char * s1, char * s2);

int best(elt T[], int & nbelts,int taille,char *fich);
int besttot(elt T[], int & nbelts,int taille,char *fich);
int pospatt(char *fin,char *fpos,char *flog);
int prostat(double ppa,double ppc,double ppg,double ppt,char *fin, char *fpro, char *fstat);
int simrev(char *best,char *sim , char *rev);

long double fact(int x) ;


long double bino(int n, int k, long double q);
long double bino2(int n, int k, long double q);


long double binocum(int n, int k, long double q);


/////////////
char complem(char x) ;
bool testrev(char *dp, char *eq, int size);

char maj(char x) ;

//char *  concat(char c1, int nbpoints, char c2);

int revcomp(char *fich, int & lenseqs,int tseq []) ;

int create(tabtablist T) ;

//int join(Listgen<int> * A1,Listgen<int> * A2,int taille,char c1,char c2, Slist & L)

#endif