#ifndef __INDEL_DEF_H
#define __INDEL_DEF_H


#include "indel_std.h"


#define  CodonSize     3
#define  NASize        4
#define  AASize       20

/*Options and parameters*/

typedef struct _options_block {
   long int   max_iter;   /* [burn-in period + data collection period] */
   int        num_throw;  /*length of burn-in period*/
   long int   max_idnum;  /*maximum number which can hold chain_ids*/
   short lmax, nmax, lmax0; /*maximun length, maximum number of insertions or deletions*/
	short select_num; /*the number of (c,t,p) to display in the output file*/
   int   seqtype; /*1:base, 2:aa*/
   Uint1Ptr orig_seq;    /*sequence of ancestor(origin) translated in "BASE"*/
   Uint1Ptr target_seq;   /*sequence and extant(target) translated in "BASE"*/
   int   orig_len, target_len; /*length of sequence*/
   int   model; /*model number(HKY85:4, TN93:5)*/
   int   num_t; /*the number of time periods. 
		Tmax is divided into num_t periods, 
		during each of which simulation is performed*/
	double branch_length; /*mean substitution number per site  per one time period */
   double *pi;  /*nucleotide composition*/
   double kappa;
   double *PMat; /*substitution matrix P(t)ij, that is, 
			the probability that i becomes j after t 
			based on the continuous time Markov model*/
	double lambda; /* [insertion+deletion] vs substitution ratio*/
   double *pID; /* length distribution of insertions and deletions */
	double x, y, z;
          /* x=zeta1:probability that insertion occurring at a non-MRC position becomes duplication.
            y=zeta2:extra-probability of duplication(insertion) at modulo rep center (MRC).
            z=zeta3:extra-probability of deletion at modulo rep center*/
   int    **MRC;
   int    filter;
} OptionsBlk, *OptionsBlkPtr;



/* Once accepted by MCMC, the information of each (c,t,p) is tranformed to the chain_id format
and stored in stock_id.   Therefore one chain_id corresponds to one (c,t,p).
 stock_id holds the information
 regarding the types and number of accepted (c,t,p)s and can be used for referring to the (c,t,p)s.
   */

typedef struct _chain_id {
   int    nind_index;      /* specifies (ni, nd) = (number of insertion, number of deletion)*/
   int    i_order, d_order; /* This number defines an array indicating the number of 
insertion/deletion of differnt lengths.
For example, (1,1,2,4) means two 1nt insertions, 
one 2nt insertion and one 4nt insertion occurring in this order. 
This 'ins_array'is transformed 
into a number using the function ArrayToID  in handle_cand.c  */

   int    order_index;
   int    t_index;
   short  *pos_vector;
	double lnL;
   int    num_visit;  /* indicates how many times the (c,t,p) was accepted by MCMC */

   double lnProbAS;
} ChainID, *ChainIDPtr;

typedef struct _stock_id {
   long int  max_idnum;
   long int  current_id;
   long int  total_accepted;
   short     select_num;
   short     select_id0;
   double    Ave_lnAS;
   ChainIDPtr PNTR chain_id_array;   
} StockID, *StockIDPtr;


/* The following struct is a look-up table for (c,t,p) candidates. This table enables
quick choosing of a candidate (i.e, MCMC propose) by random number. 
 However, due to the limitation of memomry, if the number of candidates exceed the 'max_stored',
the preparation of the table is given up 
and the candidate is nominated in an 'ab initio' manner.  */
 
typedef struct _pool {
	short lmax, nmax;
   int   target_d;
   int   num_t;
   int   orig_seqlen;
	short max_setnum; /*(nmax+1)*(nmax+1)*/
   double **rij; /*realtive possibily of set i->set j*/
	double   *num_cand;  /*log10(number of candidate of the set(ni, nd))*/
   double  *limit_nind; /*probability of each (ni,nd) set selected*/
   short max_stored;
  	int   **i_pool, **d_pool;
   double   *num_order;  /*log10(number of candidates of order)*/
   double   *num_t_cand; /*log10(number of candidates of t_vector)*/
} PoolStruct, *PoolStructPtr;

typedef struct _candidate {
	short  ni, nd;
   short  *ins_array, *del_array;
   short  *order;
   short  *id_array;
   short  *t_vector;
   short  *pos_vector;
	double lnL;
   short  chain_no; /*which element has been changed*/
   double  num_pos_cand;
} CandStruct, *CandStructPtr;



/* score_block is a struct that stores the estimated probability 
that the simulation results in a sequence identical to S (target sequence) */
typedef struct _score_block {
   int      target_seqlen;
   double   *lkl;
   int      *anc_no;
   int      count_per_cycle;
   double   *P; /*P=sum(ln(lkl[i]))*/
   int      current_cycle;
   int      max_cycle;
   double   MP, VP;/*mean and variance of P*/
}  ScoreBlk, *ScoreBlkPtr;

/*align struct Dec 22,2000     Several (c,t,p)s may correspond to an alignment model.
This struct organize the 'alignment' space.
*/
typedef struct _align_id {
   int    num_gap;
	short  *gap_length;
   short  *pos_vector;
	double lnL;
   int    num_visit;
   double lnProbAS;
} AlignID, *AlignIDPtr;

typedef struct _stock_align {
   long int  max_idnum;
   long int  current_id;
   long int  total_accepted;
   short     select_num;
   short     select_id0;
   double    Ave_lnAS;
   AlignIDPtr PNTR align_id_array;
} StockAlign, *StockAlignPtr;


/*  When (ni, nd) is going to be changed upon MCMC proposal, completely random drawing
from a new (ni, nd) group may cause too high a rate of MCMC rejection.  Hence, some
elements of (c,t,p) may well be conserved upon jumping from one (ni,nd) group to another.
Struct pool_cons provides a look-up table of 
the candidates (which have the conserved elements) of the new (ni, nd) group. */

typedef struct _pool_cons {
	int   *num_cons;  /*number of candidate of the set(ni, nd)*/
   int    max_stored;
  	int   *i_pool_cons, *d_pool_cons; /*only store the indel for new(ni,nd)*/
}PoolCons, *PoolConsPtr;


#endif