static SEXP make_fasta_index_data_frame(const IntAE *recno_buf,
const IntAE *fileno_buf,
const LLongAE *offset_buf,
const CharAEAE *desc_buf,
const IntAE *seqlength_buf)
{
SEXP df, colnames, tmp;
int i;
PROTECT(df = NEW_LIST(5));
PROTECT(colnames = NEW_CHARACTER(5));
PROTECT(tmp = mkChar("recno"));
SET_STRING_ELT(colnames, 0, tmp);
UNPROTECT(1);
PROTECT(tmp = mkChar("fileno"));
SET_STRING_ELT(colnames, 1, tmp);
UNPROTECT(1);
PROTECT(tmp = mkChar("offset"));
SET_STRING_ELT(colnames, 2, tmp);
UNPROTECT(1);
PROTECT(tmp = mkChar("desc"));
SET_STRING_ELT(colnames, 3, tmp);
UNPROTECT(1);
PROTECT(tmp = mkChar("seqlength"));
SET_STRING_ELT(colnames, 4, tmp);
UNPROTECT(1);
SET_NAMES(df, colnames);
UNPROTECT(1);
PROTECT(tmp = new_INTEGER_from_IntAE(recno_buf));
SET_ELEMENT(df, 0, tmp);
UNPROTECT(1);
PROTECT(tmp = new_INTEGER_from_IntAE(fileno_buf));
SET_ELEMENT(df, 1, tmp);
UNPROTECT(1);
PROTECT(tmp = NEW_NUMERIC(LLongAE_get_nelt(offset_buf)));
for (i = 0; i < LENGTH(tmp); i++)
REAL(tmp)[i] = (double) offset_buf->elts[i];
SET_ELEMENT(df, 2, tmp);
UNPROTECT(1);
PROTECT(tmp = new_CHARACTER_from_CharAEAE(desc_buf));
SET_ELEMENT(df, 3, tmp);
UNPROTECT(1);
PROTECT(tmp = new_INTEGER_from_IntAE(seqlength_buf));
SET_ELEMENT(df, 4, tmp);
UNPROTECT(1);
/* list_as_data_frame() performs IN-PLACE coercion */
list_as_data_frame(df, IntAE_get_nelt(recno_buf));
UNPROTECT(1);
return df;
}
/* --- .Call ENTRY POINT --- */
SEXP fasta_index(SEXP filexp_list,
SEXP nrec, SEXP skip, SEXP seek_first_rec, SEXP lkup)
{
int nrec0, skip0, seek_rec0, i, recno, old_nrec, new_nrec, k;
FASTAINDEX_loaderExt loader_ext;
FASTAloader loader;
IntAE *seqlength_buf, *fileno_buf;
SEXP filexp;
long long int offset, ninvalid;
const char *errmsg;
nrec0 = INTEGER(nrec)[0];
skip0 = INTEGER(skip)[0];
seek_rec0 = LOGICAL(seek_first_rec)[0];
loader_ext = new_FASTAINDEX_loaderExt();
loader = new_FASTAINDEX_loader(lkup, 1, &loader_ext);
seqlength_buf = loader_ext.seqlength_buf;
fileno_buf = new_IntAE(0, 0, 0);
for (i = recno = 0; i < LENGTH(filexp_list); i++) {
filexp = VECTOR_ELT(filexp_list, i);
offset = ninvalid = 0LL;
errmsg = parse_FASTA_file(filexp, nrec0, skip0, seek_rec0,
&loader, &recno, &offset, &ninvalid);
if (errmsg != NULL)
error("reading FASTA file %s: %s",
CHAR(STRING_ELT(GET_NAMES(filexp_list), i)),
errmsg_buf);
if (ninvalid != 0LL)
warning("reading FASTA file %s: ignored %lld "
"invalid one-letter sequence codes",
CHAR(STRING_ELT(GET_NAMES(filexp_list), i)),
ninvalid);
old_nrec = IntAE_get_nelt(fileno_buf);
new_nrec = IntAE_get_nelt(seqlength_buf);
for (k = old_nrec; k < new_nrec; k++)
IntAE_insert_at(fileno_buf, k, i + 1);
}
return make_fasta_index_data_frame(loader_ext.recno_buf,
fileno_buf,
loader_ext.offset_buf,
loader_ext.desc_buf,
seqlength_buf);
}
static void FASTAINDEX_load_empty_seq(FASTAloader *loader)
{
FASTAINDEX_loaderExt *loader_ext;
IntAE *seqlength_buf;
loader_ext = loader->ext;
seqlength_buf = loader_ext->seqlength_buf;
IntAE_insert_at(seqlength_buf, IntAE_get_nelt(seqlength_buf), 0);
return;
}
void _MatchBuf_report_match(MatchBuf *match_buf,
int PSpair_id, int start, int width)
{
IntAE *PSlink_ids, *count_buf, *start_buf, *width_buf;
PSlink_ids = match_buf->PSlink_ids;
count_buf = match_buf->match_counts;
if (count_buf->elts[PSpair_id]++ == 0)
IntAE_insert_at(PSlink_ids,
IntAE_get_nelt(PSlink_ids), PSpair_id);
if (match_buf->match_starts != NULL) {
start_buf = match_buf->match_starts->elts[PSpair_id];
IntAE_insert_at(start_buf, IntAE_get_nelt(start_buf), start);
}
if (match_buf->match_widths != NULL) {
width_buf = match_buf->match_widths->elts[PSpair_id];
IntAE_insert_at(width_buf, IntAE_get_nelt(width_buf), width);
}
return;
}
static void FASTAINDEX_load_seq_data(FASTAloader *loader,
const Chars_holder *seq_data)
{
FASTAINDEX_loaderExt *loader_ext;
IntAE *seqlength_buf;
loader_ext = loader->ext;
seqlength_buf = loader_ext->seqlength_buf;
seqlength_buf->elts[IntAE_get_nelt(seqlength_buf) - 1] +=
seq_data->length;
return;
}
void _MatchBuf_flush(MatchBuf *match_buf)
{
int nelt, i, PSlink_id;
nelt = IntAE_get_nelt(match_buf->PSlink_ids);
for (i = 0; i < nelt; i++) {
PSlink_id = match_buf->PSlink_ids->elts[i];
match_buf->match_counts->elts[PSlink_id] = 0;
if (match_buf->match_starts != NULL)
IntAE_set_nelt(match_buf->match_starts->elts[PSlink_id], 0);
if (match_buf->match_widths != NULL)
IntAE_set_nelt(match_buf->match_widths->elts[PSlink_id], 0);
}
IntAE_set_nelt(match_buf->PSlink_ids, 0);
return;
}
static void FASTAINDEX_load_desc_line(FASTAloader *loader,
int recno, long long int offset,
const Chars_holder *desc_line)
{
FASTAINDEX_loaderExt *loader_ext;
IntAE *recno_buf;
LLongAE *offset_buf;
CharAEAE *desc_buf;
loader_ext = loader->ext;
recno_buf = loader_ext->recno_buf;
IntAE_insert_at(recno_buf, IntAE_get_nelt(recno_buf), recno + 1);
offset_buf = loader_ext->offset_buf;
LLongAE_insert_at(offset_buf, LLongAE_get_nelt(offset_buf), offset);
desc_buf = loader_ext->desc_buf;
// This works only because desc_line->seq is nul-terminated!
append_string_to_CharAEAE(desc_buf, desc_line->ptr);
return;
}
static SEXP vwhich_XStringSet_XStringSet(SEXP pattern,
SEXP subject,
SEXP max_mismatch, SEXP min_mismatch,
SEXP with_indels, SEXP fixed,
SEXP algorithm)
{
XStringSet_holder P, S;
int P_length, S_length, i, j;
Chars_holder P_elt, S_elt;
const char *algo;
IntAEAE *ans_buf;
P = _hold_XStringSet(pattern);
P_length = _get_length_from_XStringSet_holder(&P);
S = _hold_XStringSet(subject);
S_length = _get_length_from_XStringSet_holder(&S);
algo = CHAR(STRING_ELT(algorithm, 0));
ans_buf = new_IntAEAE(S_length, S_length);
for (j = 0; j < S_length; j++)
IntAE_set_nelt(ans_buf->elts[j], 0);
_init_match_reporting("MATCHES_AS_COUNTS", 1);
for (i = 0; i < P_length; i++) {
P_elt = _get_elt_from_XStringSet_holder(&P, i);
for (j = 0; j < S_length; j++) {
S_elt = _get_elt_from_XStringSet_holder(&S, j);
_match_pattern_XString(&P_elt, &S_elt,
max_mismatch, min_mismatch, with_indels, fixed,
algo);
if (_get_match_count() != 0)
IntAE_insert_at(ans_buf->elts[j],
IntAE_get_nelt(ans_buf->elts[j]),
i + 1);
_drop_reported_matches();
}
}
return new_LIST_from_IntAEAE(ans_buf, 0);
}
void _MatchBuf_append_and_flush(MatchBuf *match_buf1,
MatchBuf *match_buf2, int view_offset)
{
int nelt, i, PSlink_id;
IntAE *start_buf1, *start_buf2, *width_buf1, *width_buf2;
if (match_buf1->ms_code == MATCHES_AS_NULL
|| match_buf2->ms_code == MATCHES_AS_NULL)
return;
if (IntAE_get_nelt(match_buf1->match_counts) !=
IntAE_get_nelt(match_buf2->match_counts)
|| match_buf1->ms_code != match_buf2->ms_code)
error("Biostrings internal error in "
"_MatchBuf_append_and_flush(): "
"buffers are incompatible");
nelt = IntAE_get_nelt(match_buf2->PSlink_ids);
for (i = 0; i < nelt; i++) {
PSlink_id = match_buf2->PSlink_ids->elts[i];
if (match_buf1->match_counts->elts[PSlink_id] == 0)
IntAE_insert_at(match_buf1->PSlink_ids,
IntAE_get_nelt(match_buf1->PSlink_ids),
PSlink_id);
match_buf1->match_counts->elts[PSlink_id] +=
match_buf2->match_counts->elts[PSlink_id];
if (match_buf1->match_starts != NULL) {
start_buf1 = match_buf1->match_starts->elts[PSlink_id];
start_buf2 = match_buf2->match_starts->elts[PSlink_id];
IntAE_append_shifted_vals(start_buf1,
start_buf2->elts, IntAE_get_nelt(start_buf2),
view_offset);
}
if (match_buf1->match_widths != NULL) {
width_buf1 = match_buf1->match_widths->elts[PSlink_id];
width_buf2 = match_buf2->match_widths->elts[PSlink_id];
IntAE_append(width_buf1,
width_buf2->elts, IntAE_get_nelt(width_buf2));
}
}
_MatchBuf_flush(match_buf2);
return;
}
