/* I/O support routines. */

/* Sys V/BSD difference. */
#ifdef CUBE
#include	<fcntl.h>
#else
#include	<sys/file.h>
#endif

#include <stdio.h>
#include "gotoh_ds.h"

extern int	open();
extern int	read();

/* Read target sequence. */
int get_target(target_file, target_buf)
     char	*target_file;
     char	*target_buf;
{
  int	t_fd;
  int	t_length;

  t_fd = open(target_file, O_RDONLY);
  if (t_fd < 0) {
    fprintf(stderr, "%s (%d): cannot read target file %s.\n",
	    __FILE__, __LINE__, target_file);
    lexit(1);
  }
  t_length = read(t_fd, target_buf, MAX_LENGTH);
  close(t_fd);
  return t_length;
}

/* Functions to manage a database file.

   This code is more complicated than you might expect. In order
   to reduce the number of i/o operations, the file format
   is such that one read gets one sequence and the length of
   the next sequence:

   [id0 len1][id len_next_seq seq]*[idn 0 seqn]

   The id and length fields constitue the header.  Note that
   the first sequence is a null sequence. It's header provides
   the length of the first real sequence. The user supplied
   buffer must be big enough to hold seq data and the header.*/

static int	db_fd;
static int	len_next_seq;

extern int	atoi();

int open_db(db_file)
     char	*db_file;
{
  char	header[HEADER_LENGTH+1];

  header[HEADER_LENGTH] = 0;
  /* Open database file. */
  db_fd = open(db_file, O_RDONLY);
  if (db_fd < 0) {
    fprintf(stderr, "%s (%d): cannot read data base file %s.\n",
	    __FILE__, __LINE__, db_file);
    lexit(1);
  }

  /* Read header of initial null sequence.
     Something's wrong if a whole header cannot be read. */
  if (read(db_fd, header, HEADER_LENGTH) < HEADER_LENGTH) {
    fprintf(stderr, "%s (%d): corrupt header.\n", __FILE__, __LINE__);
    lexit(1);
  }
  len_next_seq = atoi(header + LENGTH_OFFSET);
}

int close_db()
{
  close(db_fd);
}

int get_seq(buf)
     char	*buf;
{
  int		seq_len;

  if (!len_next_seq) return 0;

  /* Read sequence. */
  seq_len = len_next_seq;
  len_next_seq += HEADER_LENGTH;
  if (len_next_seq != read(db_fd, buf, len_next_seq)) {
    fprintf(stderr, "%s (%d): corrupt sequence.\n", __FILE__, __LINE__);
    lexit(1);
  }
  len_next_seq = atoi(buf + LENGTH_OFFSET);

  return seq_len;
}