// helpers
//
static void imap_session_reset(ImapSession *session)
{
ClientState_T current;
TRACE(TRACE_DEBUG,"[%p]", session);
memset(session->tag, 0, sizeof(session->tag));
memset(session->command, 0, sizeof(session->command));
session->use_uid = 0;
session->command_type = 0;
session->command_state = FALSE;
session->parser_state = FALSE;
dbmail_imap_session_args_free(session, FALSE);
PLOCK(session->lock);
current = session->state;
PUNLOCK(session->lock);
if (current == CLIENTSTATE_AUTHENTICATED)
session->ci->timeout.tv_sec = server_conf->timeout;
else
session->ci->timeout.tv_sec = server_conf->login_timeout;
ci_uncork(session->ci);
return;
}
void clone_link(WorkPtr work) {
int r, s;
int i, j, rootI, rootJ, *index;
index = work->index;
#ifndef NOAUXINFO
for(r=work->i_beg; r<work->i_end; r++) {
i = (index == NULL) ? r : index[r];
if (IGNORE_SEQ(i)) continue;
if (seqInfo[i].len<window_len) continue;
for(s=MAX(r+1,work->j_beg); s<work->j_end; s++) {
j = (index == NULL) ? s : index[s];
rootI = mini_find_parent(i);
rootJ = mini_find_parent(j);
if ((rootI != rootJ) && !(IS_FLAG(FIX,rootI)&&IS_FLAG(FIX,rootJ) ))
if ((strlen(seqID[i].clone)>0) &&
(strlen(seqID[j].clone)>0) &&
(strcmp(seqID[i].clone,seqID[j].clone)==0)) {
make_uniond2(rootI,rootJ,0);
}
}
}
PLOCK(&find_parent_mutex);
for(i=0; i<num_seqs; i++)
tree[i].cluster = find_parent(i);
PUNLOCK(&find_parent_mutex);
#endif
}
void imap_cb_read(void *arg)
{
ImapSession *session = (ImapSession *) arg;
ci_read_cb(session->ci);
uint64_t have = p_string_len(session->ci->read_buffer);
uint64_t need = session->ci->rbuff_size;
int enough = (need>0?(have >= need):(have >= 0));
int state;
PLOCK(session->ci->lock);
state = session->ci->client_state;
PUNLOCK(session->ci->lock);
TRACE(TRACE_DEBUG,"state [%d] enough %d: %" PRIu64 "/%" PRIu64 "", state, enough, have, need);
if (state & CLIENT_ERR) {
imap_session_bailout(session);
} else if (state & CLIENT_EOF) {
ci_cork(session->ci);
if (enough)
imap_handle_input(session);
else
imap_session_bailout(session);
} else if (have > 0)
imap_handle_input(session);
}
void socket_write_cb(int UNUSED fd, short UNUSED what, void *arg)
#endif
{
ImapSession *session = (ImapSession *)arg;
ClientState_T state;
PLOCK(session->lock);
state = session->state;
PUNLOCK(session->lock);
#ifdef DEBUG
TRACE(TRACE_DEBUG,"[%p] on [%d] state [%d] event:%s%s%s%s", session,
(int) fd, state,
(what&EV_TIMEOUT) ? " timeout": "",
(what&EV_READ) ? " read": "",
(what&EV_WRITE) ? " write": "",
(what&EV_SIGNAL) ? " signal": ""
);
#endif
switch(state) {
case CLIENTSTATE_QUIT_QUEUED:
break; // ignore
case CLIENTSTATE_LOGOUT:
imap_session_bailout(session);
break;
case CLIENTSTATE_ERROR:
imap_handle_abort(session);
break;
default:
ci_write_cb(session->ci);
break;
}
dm_queue_drain();
}
void merge_pair(WorkPtr work, int rootI, int i, int rootJ, int j,
int dir) {
PLOCK(&invert_mutex);
short invert;
invert = (int) (tree[i].orient != tree[j].orient) ^ dir;
PUNLOCK(&invert_mutex);
if (dump_file != NULL) {
PLOCK(&dump_mutex);
fprintf(dump_file,"%d %d %d\n",i,j,dir);
fflush(dump_file);
PUNLOCK(&dump_mutex);
}
make_uniond2(rootI,rootJ,invert);
total_matches++;
tree[i].match = j;
if (tree[j].match==-1) {
tree[j].match = i;
}
}
void MergeSlaveClusterTable(int32_t *buffer, int rlen) {
// Get the slave's cluster table and add to ours
int i, id, rep, rep_root, last;
int q;
assert(rlen%MPIBUFRECSZ==0);
assert(rlen<MPIBUFRECSZ*num_seqs);
last = -1;
for(i=0; i<rlen; ) {
id = buffer[i];
i++;
rep= buffer[i];
i++;
#ifdef MPIORIENT
int witness, orient;
witness = buffer[i];
i++;
orient = buffer[i];
i++;
#endif
PLOCK(&write_union_mutex);
PLOCK(&find_parent_mutex);
if (last != rep) {
last = rep;
rep_root = find_parent(rep);
}
id = find_parent(id);
if (id == rep_root) {
PUNLOCK(&find_parent_mutex);
PUNLOCK(&write_union_mutex);
continue;
}
// if (orient) invert_orientation(j);
q = tree[rep_root].last;
tree[q].next = id;
tree[rep_root].last = tree[id].last;
tree[id].cluster = rep_root;
if (IS_FLAG(FIX,id)) SET_FLAG(FIX,rep_root);
assert(tree[tree[rep_root].last].next<0);
PUNLOCK(&write_union_mutex);
PUNLOCK(&find_parent_mutex);
}
}
void complete_pairwise_cluster(WorkPtr work, int i, int * candidates, int num_cands) {
int s, limit;
int j, rootI, rootJ;
int num_mat_pos, num_mat_rc;
if (clonelink) clone_link(work);
if (IGNORE_SEQ(i)) return;
if (seqInfo[i].len<window_len) return;
set_up_word_table(work, i);
for(s=0; s<num_cands; s++) {
j = candidates[s];
//printf(" Candidated %d\n",j);
rootI = mini_find_parent(i);
rootJ = mini_find_parent(j);
assert(i<num_seqs);
if ((rootI != rootJ) && !(IS_FLAG(FIX,rootI)&&IS_FLAG(FIX,rootJ) )) {
// only try to cluster if not already clustered
// and both are not fixed lcusters
NUM_num_matches++;
limit = seqInfo[j].len/BASESPERELT-1;
check_heuristics(i,j,limit,&num_mat_pos,&num_mat_rc);
if( (num_mat_pos >= NM_threshold) &&
(!IGNORE_SEQ(j)) &&
(d2(work,i,j,0)<=theta)) {
merge_pair(work,rootI,i,rootJ,j,0);
};
if ( rc_check &&
(num_mat_rc >= NM_threshold)&&
(!IGNORE_SEQ(j)) &&
(d2(work,i,j,1)<=theta)){
merge_pair(work,rootI,i,rootJ,j,1);
}
}
}
clear_word_table(work,i);
PLOCK(&find_parent_mutex);
for(s=0; s<num_cands; s++)
tree[candidates[s]].cluster = find_parent(candidates[s]);
PUNLOCK(&find_parent_mutex);
}
void do_pairwise_cluster(WorkPtr work) {
int r, s, limit;
int i, j, rootI, rootJ, *index,k;
uint16_t w0;
int num_mat_pos, num_mat_rc,invert, samp_pos, samp_rc;
index = work->index;
if (clonelink) clone_link(work);
//printf("Slave %d-t%d here ib=%d ie=%d; jb=%d je=%d,\n",
// myid,work->thread_num,work->i_beg,work->i_end,work->j_beg,work->j_end);
for(r=work->i_beg; r<work->i_end; r++) {
i = (index == NULL) ? r : index[r];
//printf("%d %ld %ld %d\n",i,data,seq[i].seq,seq[i].len);
if (IGNORE_SEQ(i)) continue;
if (seqInfo[i].len<window_len) continue;
set_up_word_table(work, i);
for(s=MAX(r+1,work->j_beg); s<work->j_end; s++) {
j = (index == NULL) ? s : index[s];
rootI = mini_find_parent(i);
rootJ = mini_find_parent(j);
if ((rootI != rootJ) && !(IS_FLAG(FIX,rootI)&&IS_FLAG(FIX,rootJ) )) {
// only try to cluster if not already clustered
// and both are not fixed lcusters
num_mat_pos=num_mat_rc=samp_pos=samp_rc=0;
NUM_num_matches++;
limit = seqInfo[j].len/BASESPERELT-1;
for(k=1; k < limit ;k=k+2) {
if (work->tableP[seq[j][k]]) samp_pos ++;
if (work->tableR[seq[j][k]]) samp_rc ++;
}
if ((samp_pos<=2) && (samp_rc<= 2) )
samp_pos=samp_rc=0;
else
for(k=0; k < limit;k=k+2) {
w0 = seq[j][k];
if (work->tableP[w0]) samp_pos++;
if (work->tableR[w0]) samp_rc++;
}
if (samp_pos >sample_thresh)
num_mat_pos = tv_heuristic_pos(work,i,j);
if (samp_rc > sample_thresh)
num_mat_rc = tv_heuristic_rc(work,i,j);
if( (num_mat_pos >= NM_threshold) &&
(!IGNORE_SEQ(j)) &&
(dist(work,i,j,0)<=theta)) {
PLOCK(&invert_mutex);
invert = (int) (tree[i].orient != tree[j].orient);
PUNLOCK(&invert_mutex);
if (dump_file != NULL) {
PLOCK(&dump_mutex);
fprintf(dump_file,"%d: %d %d %d\n",
work->thread_num,i,j,1);
fflush(dump_file);
PUNLOCK(&dump_mutex);
}
make_uniond2(rootI,rootJ,invert);
total_matches++;
tree[i].match = j;
if (tree[j].match==-1) {
tree[j].match = i;
}
};
if ( rc_check &&
(num_mat_rc >= NM_threshold)&&
(!IGNORE_SEQ(j)) &&
(dist(work,i,j,1)<=theta)){
PLOCK(&invert_mutex);
invert = (tree[i].orient==tree[j].orient);
PUNLOCK(&invert_mutex);
if (dump_file != NULL) {
PLOCK(&dump_mutex);
fprintf(dump_file,"%d: %d %d %d\n",
work->thread_num,i,j,-1);
fflush(dump_file);
PUNLOCK(&dump_mutex);
}
make_uniond2(rootI,rootJ,invert);
total_matches++;
tree[i].match = j;
if (tree[j].match==-1) {
tree[j].match = i;
}
}
}
}
clear_word_table(work,i);
}
PLOCK(&find_parent_mutex);
for(i=0; i<num_seqs; i++)
tree[i].cluster = find_parent(i);
PUNLOCK(&find_parent_mutex);
}
