/*-------------------------------------------------------------

Copyright (C) 2000 Stefan Schoenauer, Peter Clote. 
All Rights Reserved.

Permission to use, copy, modify, and distribute this
software and its documentation for NON-COMMERCIAL purposes
and without fee is hereby granted provided that this
copyright notice appears in all copies.


THE AUTHOR AND PUBLISHER MAKE NO REPRESENTATIONS OR
WARRANTIES ABOUT THE SUITABILITY OF THE SOFTWARE, EITHER
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
PARTICULAR PURPOSE, OR NON-INFRINGEMENT. THE AUTHORS
AND PUBLISHER SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED
BY LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING
THIS SOFTWARE OR ITS DERIVATIVES.

-------------------------------------------------------------*/


/*****************************************************************************
 * general.h:	general data structures and function definitions for the     *
 *		Project "Error optimized genetic code"                       *
 *                                                                           *
 * author:	S.Schoenauer                                                 *
 * creation:	3/17/1997                                                    *
 *****************************************************************************/

#ifndef bool
#define bool int
#endif

/* global definitions */
#define NUM_ACIDS 20      /* Number of amino acids */
#define NUM_ACIDS_SS 21   /* Number of amino acids plus start and stop codon */
#define STOP 20           /* STOP codon comes after 0..19 in list */
/* #define RAND_MAX 32767     maximum value returned by random() */
#define ALPHA 2           /* ALPHA,BETA,GAMMA using in monte_carlo() */
#define BETA  5
#define GAMMA 0


#define POS_INF       MAXFLOAT      /* positive and negative "infinity" */
#define NEG_INF       -MAXFLOAT      /* for finding min,max stats        */


/*****************************************************************

  Choice of constants:

Schoenauer's values : 2 min for run 5 500

#define kb 1.3807E-23      
       Boltzmans constant 
#define T_hi 1             
       starting high temperature; set for WAC matrix 
#define T_lo  1E-10        
       terminating low temperature; set for WAC matrix 

Clote's values : 6 min for run 5 500 

#define kb 1.0    
#define T_hi 10000.0 
#define T_lo  1E-40       

#define kb 1.0  
#define T_hi 100       
#define T_lo  1E-45       

The following values, I computed using EXCEL, assuming Delta E is
at most 1 initially (so T_hi yields 99% prob of change, while T_lo
yields less than 0.01 % prob of changing.

NOTE: get error (random value of above constants) if don't use decimal
or exp notation.

*****************************************************************/

#define kb 1.0     /* Boltzmans constant */
#define T_hi 10.0       /* starting high temperature; set for WAC matrix */
#define T_lo 1E-4       /* terminating low temperature; set for WAC matrix */

/* enumeration type of the nucleotide bases */
enum base {A, T, C, G};

/* A genetic code is represented by an array of the 64 codons.
   For each codon the array contains the number of the encoded amino acid. */
typedef unsigned int *gcode;

typedef unsigned int gcode_array[64];

typedef unsigned int gcode_triple[4][4][4];

typedef unsigned int *lincode;

/* This is the standard natural genetic code. */
extern gcode std_code;

/* This is a table to convert the numeric code into the one-letter code. */
extern unsigned char num2char[NUM_ACIDS_SS];

/* This is a table to convert the numeric code into the three-letter code. */
extern char *num2triple[NUM_ACIDS_SS];

/* smatrix contains the similarity matrix for amino acid substitutions */
extern float smatrix[NUM_ACIDS][NUM_ACIDS];

/* dmatrix contains the Mean Square Difference Matrix wrt polar requirement.*/
extern float dmatrix[NUM_ACIDS][NUM_ACIDS];

struct float4tuple
{
  float whole;
  float one;
  float two;
  float three;
};

typedef struct float4tuple Fourtuple;


/* prototypes for functins in general.c */

/* read_matrix() gets a filename and puts the scoring valus from the file into 
   smatrix. It does not check, whether the file really contains a scoring
   matrix or not. It expects that the scoring matrix is provided as an upper
   triangle matrix consisting of float values. */
int read_matrix(char *filename, float matrix[NUM_ACIDS][NUM_ACIDS]);

void print_matrix(float matrix[NUM_ACIDS][NUM_ACIDS]);


int rand_int(int n); /* random integer uniformly out of 0..(n-1) */
double rand_flt();   /* random flt uniformly out of [0..1[ */
void swap(unsigned int *i, unsigned int *j);


/* allows addressing of code entries by triple ijk */
#define get_code(code, i, j, k) code[i*16+j*4+k]