/*--------------------------------------------
  Constants
--------------------------------------------*/

#define __SPECTRUM_H__
#include <assert.h>

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>      // character handling


#define DEBUG 0
#define NN 1000
#define KK  201

#define THETA 3
  //NN is upper bound for sequence length of RNA
  //Nucleotide sequence a1,...,an is stored by
  //array with values (n,a1,a2,...,an); ie length is a[0] in array

#define INF INT_MAX/2
#define MIN(x,y) ((x)<=(y) ? (x) : (y) )
#define MAX(x,y) ((x)>(y)  ? (x) : (y) )
#define FF(i,j) (((j)-(i)+1)/(THETA+2))

/*--------------------------------------------
          Type definitions 
--------------------------------------------*/
typedef int MatrixType[NN][NN][KK];
typedef int Triplet[3];
typedef Triplet TripletMatrixType[NN][NN][KK];

/*--------------------------------------------
  Functional macros
--------------------------------------------*/

#define BP(i,j,k)              M[i][j][k]
#define SS(i,j,k)              S[i][j][k]

/*--------------------------------------------
NOTE:
  1) For 1<=i<=j<=n, and 0<=k<(j-i+1)/(THETA+2), 
     M[i][j][k] is maximum number of basepairs in secondary str on
     a_i,...,a_j with k hairpin loops, each of threshold at least
     THETA
--------------------------------------------*/





/*--------------------------------------------
          Prototypes
--------------------------------------------*/
//Functions from misc.c
void error(char *);
short *getRNA(char *flag, char *rna);
int guPair(char, char);
int auPair(char, char);
int cgPair(char, char);
int bondEnergy(int, int, char *);
int basePair(char, char);
int watsonCrick(char, char);
void printMatrix(MatrixType,int);

//Functions from energy.c
void initializeParen(short [NN/2][NN],int);
void initialize(MatrixType, TripletMatrixType, short*,short[NN][NN]);  
void initializeExistBP(MatrixType, TripletMatrixType, short*,short[NN][NN]);  
int backtrack(int,int,int,MatrixType,TripletMatrixType,short[NN][NN],char*,char[NN]);

//Functions from backtrack.c
void createLevelSecStr(short [NN/2][NN],int ,short *,MatrixType);