/*--------------------------------------------------------------
main.c
P. Clote
--------------------------------------------------------------*/


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

//WARNING -- GLOBAL variables
MatrixType M;
TripletMatrixType S;


main(int argc, char *argv[]) {

  // variable declarations
  FILE *file;
  char  text[3*NN]; 
  char  paren[NN];

  short ExistBP[NN][NN];
  double n0;
  int s,b;
  char *nuclSeq;
  int i,n;   //i is loop control var, n is length of RNA sequence
  int k;
  char *flag, *rna, *secStr;
  short *a; //a points to array a[0],...,a[n]
            //where a[0]=n, and a[1],...,a[n] are RNA nucleotides
            //and where n <= NN-2

  /**** Error handling for input file ****/  
  if (argc != 3) {
    fprintf(stderr,"%s -s/-f string/finame\n",argv[0]);
    fprintf(stderr,"\t-s: enter RNA string \n");
    fprintf(stderr,"\t-f: enter file of RNA in FASTA format\n");
    exit(1);
    }

  flag = argv[1];
  rna  = argv[2];
  for (i=0;i<strlen(rna);i++) rna[i] = toupper(rna[i]);
  secStr = (char*) calloc(strlen(rna)+1,sizeof(char));
  a    = getRNA(flag,rna);
  n    = a[0];
  initializeExistBP(M,S,a,ExistBP);
  initialize(M,S,a,ExistBP);
  if (DEBUG){
    printf("\nInitialization\n");
    printMatrix(M,n);
    }
  printf("Num hairpins\tNum basepairs\n");
  for (k=1;k<=FF(1,n);k++){
    for (i=0;i<NN;i++) paren[i]='.'; //reset paren to empty
    backtrack(1,n,k,M,S,ExistBP,rna,paren);
    for (i=0;i<strlen(rna)+1;i++) secStr[i]=paren[i+1];
    secStr[strlen(rna)]='\0';
    printf("%d\t%d\t%s\n", k, BP(1,n,k),secStr);
    }
} 

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

Example: a.out -s ACGUACGUACGU

Num hairpins    Num basepairs
        1                       5
        2                       4
        3                       3
        4                       0


k=1 hairpin loop
ACGUACGUACGU
(((((..))))) 

k=2 hairpin loops
ACGUACGUACGU
(((..)))(..) 

k=3 hairpin loops
ACGUACGUACGU
(..)(..)(..)

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