Nussinov78-0.1.0.0: C/nussinov.c

#include <stdlib.h>
#include <stdio.h>
#include <string.h>

int nussinov (int, char *);

int main () {
  char p[10000];
  int n;
  int e;
  while (1==scanf ("%9999s", &p)) { // only GNU C
    n = strlen(p);
    e = nussinov (n, p);
    printf ("%s %d\n", p, e);
    //free(p);
    //p=0;
  };
  return 0;
}

int nussinov (int n, char *p) {
  int l = n*n;
  int i;
  int j;
  int k;
  int at;
  int cur;
  int new;
  int *mat = calloc (l, sizeof(int));
//  printf (">>> %d\n", n);
  for (i = n-1; i>=0; i--) for (j=i; j<n; j++) {
    at = i * (n-1) + j;
    if (i==j) { //empty
      cur = 0;
    }
    if (i<j) { //left
      new = mat[(i+1)*(n-1) + j];
      if (cur < new) cur = new;
    };
    if (i<j) { //right
      new = mat[i*(n-1) + j-1];
      if (cur < new) cur = new;
    };
    if (i<j) { //pair
      new = i+1>=j ? 0 : mat[(i+1)*(n-1) +j-1];
      switch (p[i]) {
        case 'C': new += p[j]=='G' ? 1 : -999999; break;
        case 'G': new += p[j]=='C' || p[j]=='U' ? 1 : -999999; break;
        case 'A': new += p[j]=='U' ? 1 : -999999; break;
        case 'U': new += p[j]=='A' || p[j]=='G' ? 1 : -999999; break;
        default:  new = -999999;
      };
      if (cur < new) cur = new;
    };
    for (k = i+1; k<j; k++) { //split
      new = mat[i*(n-1) + k] + mat[(k+1)*(n-1) + j];
      if (cur < new) cur = new;
    };
    mat[at] = cur;
//    printf ("... i %d %c j %d %c : %d\n", i, p[i], j, p[j], cur);
  };
  free (mat);
  return cur;
}