#ifndef __SUBS_DEF_H
#define __SUBS_DEF_H



#include "indel_std.h"

#define    MinRange   0
#define    Step       1
#define    NumStep    15


/*  To shorten the computation time for simulation of substitution,
we do not apply the substitution matrix (P_mat_ij) in a site-by-site manner.
Instead, we count A,G,C,T nucleotides beforehand 
and calculate, based on binominal distribution,the probabilities that, 
for example, one, two, three.... 'A' s undergo 
substitution.  subs_hist stores this distribution for one base type, 
while subs_matrix stores the distributions for four base types.*/

typedef struct _subs_hist {
	short index;
   int   min_len;
   int   len_range;
   double **hist;
   double *PMatEach;
} SubsHist, *SubsHistPtr;


typedef struct  _subs_matrix {
	int num_step;
   SubsHistPtr PNTR subs_hist_array;
} SubsMatrix, *SubsMatrixPtr;


/* simul_struct records intermediate and the final sequences 
that appear during simulation runs. */
typedef struct _simul_struct {
   int      seqlen;
	Uint1Ptr simul_seq;
   int      *num_base;
   short    **pos_base;
   short    *pos_record;
} SimulStruct, *SimulStructPtr;


#endif