int aln_pair_align(FILE *fp1, FILE *fp2, AlnParam *ap, int type, int misc_flag)
{
seq_t seq1, seq2;
int len1, len2, n;
char name1[MAX_NAME_LEN], name2[MAX_NAME_LEN];
path_t *pt, *pp;
AlnAln *aa;
INIT_SEQ(seq1); INIT_SEQ(seq2);
for (n = 0; ; ++n) {
len1 = read_fasta(fp1, &seq1, name1, 0);
len2 = read_fasta(fp2, &seq2, name2, 0);
if (len1 < 0 || len2 < 0) break;
aa = aln_align((char*)seq1.s, (char*)seq2.s, ap, type);
pp = aa->path; pt = aa->path + aa->path_len - 1;
printf(">%s\t%d\t%d\t%d\t%s\t%d\t%d\t%d\t%d\n", name1, len1, pt->i, pp->i,
name2, len2, pt->j, pp->j, aa->score);
if (aa->out1) printf("%s\n", aa->out1);
if (aa->outm) printf("%s\n", aa->outm);
if (aa->out2) printf("%s\n", aa->out2);
if (type != ALN_BOUND_ALIGN) printf("//\n");
fflush(stdout);
if (misc_flag)
aln_output_segment((char*)seq1.s, (char*)seq2.s, aa->path, aa->path_len, name1, name2);
aln_free_AlnAln(aa);
}
MYFREE(seq1.s); MYFREE(seq2.s);
return n;
}
/*
* Called from tcp_fsm.c / tcp_listen_state() (via _tcp_syn_hook) to
* append a new connection to the listen-queue of socket 'sock'.
*
* TCB on input ('orig') has received a SYN. Replace TCB on output
* with a cloned TCB that we append to the listen-queue and eventually
* is used by accept() to create a new socket.
*
* TCB on input ('orig') must still be listening for further connections
* on the same port as specified in call to _TCP_listen().
*/
int _sock_append (tcp_Socket **tcp)
{
tcp_Socket *clone;
tcp_Socket *orig = *tcp;
Socket *sock = NULL; /* associated socket for '*tcp' */
int i;
/* Lookup BSD-socket for Wattcp TCB
*/
if (!_tcp_find_hook || (sock = (*_tcp_find_hook)(orig)) == NULL)
{
SOCK_DEBUGF ((NULL, "\n sock_append: not found!?"));
return (0); /* i.e. could be a native Wattcp socket */
}
SOCK_DEBUGF ((sock, "\n sock_append:%d", sock->fd));
if (!(sock->so_options & SO_ACCEPTCONN))
{
SOCK_DEBUGF ((sock, ", not SO_ACCEPTCONN"));
return (-1); /* How could this happen? */
}
/* Find the first vacant slot for this clone
*/
for (i = 0; i < sock->backlog; i++)
if (!sock->listen_queue[i])
break;
if (i >= sock->backlog || i >= SOMAXCONN)
{
/* !!to-do: drop the oldest (or a random) slot in the listen-queue.
*/
SOCK_DEBUGF ((sock, ", queue full (idx %d)", i));
return (-1);
}
SOCK_DEBUGF ((sock, ", idx %d", i));
clone = SOCK_CALLOC (sizeof(*clone));
if (!clone)
{
SOCK_DEBUGF ((sock, ", ENOMEM"));
return (-1);
}
/* Link in the semi-connected socket (SYN received, ACK will be sent)
*/
sock->listen_queue[i] = clone;
sock->syn_timestamp[i] = set_timeout (0);
/* Copy the TCB (except Tx-buffer) to clone
*/
memcpy (clone, orig, sizeof(*clone) - sizeof(clone->data));
clone->safetytcp = SAFETYTCP;
/* Increase the TCP window (to 16kB)
*/
sock_setbuf ((sock_type*)clone, calloc(DEFAULT_RCV_WIN,1), DEFAULT_RCV_WIN);
/* Undo what tcp_handler() and tcp_listen_state() did to
* this listening socket.
*/
orig->hisport = 0;
orig->hisaddr = 0;
orig->myaddr = 0;
orig->seqnum = INIT_SEQ(); /* set new ISS */
orig->unhappy = FALSE;
CLR_PEER_MAC_ADDR (orig);
#if defined(USE_DEBUG) /* !!needs some work */
orig->last_acknum[0] = orig->last_acknum[1] = 0;
orig->last_seqnum[0] = orig->last_seqnum[1] = 0;
#endif
clone->next = _tcp_allsocs;
_tcp_allsocs = clone; /* prepend clone to TCB-list */
*tcp = clone; /* clone is now the new TCB */
return (0);
}
