static int gt_fasta_reader_rec_run(GtFastaReader *fasta_reader,
GtFastaReaderProcDescription
proc_description,
GtFastaReaderProcSequencePart
proc_sequence_part,
GtFastaReaderProcSequenceLength
proc_sequence_length, void *data,
GtError *err)
{
GtFastaReaderRec *fr = gt_fasta_reader_rec_cast(fasta_reader);
GtStr *description, *sequence;
int had_err = 0;
gt_error_check(err);
/* at least one function has to be defined */
gt_assert(proc_description || proc_sequence_part || proc_sequence_length);
/* init */
description = gt_str_new();
sequence = gt_str_new();
/* make sure file is not empty */
if (!gt_io_has_char(fr->seqio)) {
gt_error_set(err, "sequence file \"%s\" is empty",
gt_io_get_filename(fr->seqio));
had_err = -1;
}
/* parse file */
while (!had_err && gt_io_has_char(fr->seqio)) {
/* reset */
gt_str_reset(description);
gt_str_reset(sequence);
/* parse entry */
had_err = parse_fasta_entry(description, sequence, fr->seqio, err);
/* process entry */
if (!had_err && proc_description) {
had_err = proc_description(gt_str_get(description),
gt_str_length(description), data, err);
}
if (!had_err && proc_sequence_part) {
had_err = proc_sequence_part(gt_str_get(sequence),
gt_str_length(sequence), data, err);
}
if (!had_err && proc_sequence_length)
had_err = proc_sequence_length(gt_str_length(sequence), data, err);
}
/* free */
gt_str_delete(description);
gt_str_delete(sequence);
return had_err;
}
static int parse_bed_file(GtBEDParser *bed_parser, GtIO *bed_file, GtError *err)
{
int had_err = 0;
gt_error_check(err);
gt_assert(bed_file);
while (!had_err && gt_io_has_char(bed_file)) {
switch (gt_io_peek(bed_file)) {
case BLANK_CHAR:
had_err = bed_parser_blank_line(bed_file, err);
break;
case COMMENT_CHAR:
had_err = bed_parser_comment_line(bed_file, err);
break;
case GT_CARRIAGE_RETURN:
gt_io_next(bed_file);
if (gt_io_peek(bed_file) == GT_END_OF_LINE)
gt_io_next(bed_file);
break;
case GT_END_OF_LINE:
gt_io_next(bed_file);
break;
default:
had_err = bed_line(bed_parser, bed_file, err);
}
}
if (!had_err)
had_err = gt_io_expect(bed_file, GT_END_OF_FILE, err);
return had_err;
}
static int parse_obo_file(GtOBOParseTree *obo_parse_tree,
GtIO *obo_file, GtError *err)
{
int had_err = 0;
gt_error_check(err);
gt_assert(obo_parse_tree && obo_file);
while (!had_err && ignored_char(obo_file)) {
had_err = ignored_line(obo_file, err);
}
if (!had_err)
had_err = header(obo_parse_tree, obo_file, err);
while (!had_err && gt_io_has_char(obo_file)) {
switch (gt_io_peek(obo_file)) {
case OBO_BLANK_CHAR:
had_err = blank_line(obo_file, err);
break;
case OBO_COMMENT_CHAR:
had_err = comment_line(obo_file, err);
break;
case GT_CARRIAGE_RETURN:
gt_io_next(obo_file);
if (gt_io_peek(obo_file) == GT_END_OF_LINE)
gt_io_next(obo_file);
break;
case GT_END_OF_LINE:
gt_io_next(obo_file);
break;
default:
had_err = stanza(obo_parse_tree, obo_file, err);
}
}
if (!had_err)
had_err = gt_io_expect(obo_file, GT_END_OF_FILE, err);
if (!had_err)
had_err = gt_obo_parse_tree_validate_stanzas(obo_parse_tree, err);
return had_err;
}
static int parse_xrf_abbr_file(GtXRFAbbrParseTree *xrf_abbr_parse_tree,
GtIO *xrf_abbr_file, GtError *err)
{
int had_err = 0;
gt_error_check(err);
gt_assert(xrf_abbr_parse_tree && xrf_abbr_file);
while (!had_err && gt_xrf_abbr_parse_tree_ignored_char(xrf_abbr_file)) {
had_err = gt_xrf_abbr_parse_tree_ignored_line(xrf_abbr_file, err);
}
while (!had_err && gt_io_has_char(xrf_abbr_file)) {
switch (gt_io_peek(xrf_abbr_file)) {
case XRF_BLANK_CHAR:
had_err = gt_xrf_abbr_parse_tree_blank_line(xrf_abbr_file, err);
break;
case XRF_COMMENT_CHAR:
had_err = gt_xrf_abbr_parse_tree_comment_line(xrf_abbr_file, err);
break;
case GT_CARRIAGE_RETURN:
gt_io_next(xrf_abbr_file);
if (gt_io_peek(xrf_abbr_file) == GT_END_OF_LINE)
gt_io_next(xrf_abbr_file);
break;
case GT_END_OF_LINE:
gt_io_next(xrf_abbr_file);
break;
default:
had_err = gt_xrf_abbr_parse_tree_entry(xrf_abbr_parse_tree,
xrf_abbr_file, err);
}
}
if (!had_err)
had_err = gt_io_expect(xrf_abbr_file, GT_END_OF_FILE, err);
if (!had_err)
had_err = gt_xrf_abbr_parse_tree_validate_entries(xrf_abbr_parse_tree,
err);
return had_err;
}
