# ifndef _ENTROPY_H_
# define _ENTROPY_H_

# include "util.h"
# include "Seq.h"
# include "limits.h"
typedef double ** nrMatrixPtr ;
typedef double  * nrVectorPtr ;

typedef struct {
  int Nsites, Naa ;
  nrMatrixPtr Table ;
  nrVectorPtr SumAA,SumSite ;
  char ** aaName ;
  char ** SiteName ;
  int  *  aaInt ;
  int  *  SiteInt ;
} Profile ;

Profile * ConstructAAProfile(int Nsites, int * siteInt, char ** siteName)  ;
void PrintProfile(Profile *p)  ;
int Lookup(int i, int *table) ;
void ComputeProfile(Sequences * S, Profile * p) ;
nrVectorPtr ConstructComputeEntropy(Profile *p) ;
void PrintProfileWEntropy(Profile *p, nrVectorPtr Entropy)  ;

/** Summation Convention :
 **   s over Sequences 
 **   r over Residue sites
 **   t over amino acid Types
 */


# endif