// Search all sequence runs for matches according to the context against the
// spectra. Updates score_stats and the number of candidate spectra found.
void
spectrum::search_runs(const search_context &context, score_stats &stats) {
const int no_runs = context.sequence_runs.size();
for (int i=0; i<no_runs; i++) {
search_run(context, context.sequence_runs[i], stats);
if (CP.show_progress)
std::cerr << i+1 << " of " << no_runs << " sequences, "
<< stats.candidate_spectrum_count << " candidates\r"
<< std::flush;
}
if (CP.show_progress)
std::cerr << std::endl;
}
int batch_decoder_run(batch_decoder_t *bd)
{
int32 ctloffset, ctlcount, ctlincr;
lineiter_t *li, *ali = NULL;
search_run(bd->fwdtree);
search_run(bd->fwdflat);
ctloffset = cmd_ln_int32_r(bd->config, "-ctloffset");
ctlcount = cmd_ln_int32_r(bd->config, "-ctlcount");
ctlincr = cmd_ln_int32_r(bd->config, "-ctlincr");
if (bd->alignfh)
ali = lineiter_start(bd->alignfh);
for (li = lineiter_start(bd->ctlfh); li; li = lineiter_next(li)) {
alignment_t *al = NULL;
char *wptr[4];
int32 nf, sf, ef;
if (li->lineno < ctloffset) {
if (ali)
ali = lineiter_next(ali);
continue;
}
if ((li->lineno - ctloffset) % ctlincr != 0) {
if (ali)
ali = lineiter_next(ali);
continue;
}
if (ctlcount != -1 && li->lineno >= ctloffset + ctlcount)
break;
if (ali)
al = parse_alignment(ali->buf, search_factory_d2p(bd->sf));
sf = 0;
ef = -1;
nf = str2words(li->buf, wptr, 4);
if (nf == 0) {
/* Do nothing. */
}
else if (nf < 0) {
E_ERROR("Unexpected extra data in control file at line %d\n", li->lineno);
}
else
{
char *file, *uttid;
file = wptr[0];
uttid = NULL;
if (nf > 1)
sf = atoi(wptr[1]);
if (nf > 2)
ef = atoi(wptr[2]);
if (nf > 3)
uttid = wptr[3];
/* Do actual decoding. */
batch_decoder_decode(bd, file, uttid, sf, ef, al);
}
alignment_free(al);
if (ali) ali = lineiter_next(ali);
}
featbuf_producer_shutdown(search_factory_featbuf(bd->sf));
return 0;
}
