GtXRFChecker* gt_xrf_checker_new(const char *file_path, GtError *err)
{
GtXRFChecker *xrc;
GtUword i;
gt_error_check(err);
gt_assert(file_path);
xrc = gt_calloc(1UL, sizeof (GtXRFChecker));
xrc->xpt = gt_xrf_abbr_parse_tree_new(file_path, err);
if (!xrc->xpt) {
gt_xrf_checker_delete(xrc);
return NULL;
}
xrc->abbrvs = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);
for (i = 0; i < gt_xrf_abbr_parse_tree_num_of_entries(xrc->xpt); i++) {
const GtXRFAbbrEntry *e = gt_xrf_abbr_parse_tree_get_entry(xrc->xpt, i);
const char *synonym;
gt_hashmap_add(xrc->abbrvs,
(void*) gt_xrf_abbr_entry_get_value(e, "abbreviation"),
(void*) e);
if ((synonym = gt_xrf_abbr_entry_get_value(e, "synonym"))) {
gt_hashmap_add(xrc->abbrvs, (void*) synonym, (void*) e);
}
}
xrc->splitter = gt_splitter_new();
return xrc;
}
static int gt_gff3validator_runner(int argc, const char **argv, int parsed_args,
void *tool_arguments, GtError *err)
{
GFF3ValidatorArguments *arguments = tool_arguments;
GtTypeChecker *type_checker = NULL;
GtXRFChecker *xrf_checker = NULL;
GtNodeStream *gff3_in_stream;
int had_err = 0;
gt_error_check(err);
gt_assert(arguments);
/* create a GFF3 input stream */
gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
argv + parsed_args);
gt_gff3_in_stream_check_id_attributes((GtGFF3InStream*) gff3_in_stream);
/* set different type checker if necessary */
if (gt_typecheck_info_option_used(arguments->tci)) {
type_checker = gt_typecheck_info_create_type_checker(arguments->tci, err);
if (!type_checker)
had_err = -1;
if (!had_err)
gt_gff3_in_stream_set_type_checker(gff3_in_stream, type_checker);
}
/* set XRF checker */
if (gt_xrfcheck_info_option_used(arguments->xci)) {
xrf_checker = gt_xrfcheck_info_create_xrf_checker(arguments->xci, err);
if (!xrf_checker)
had_err = -1;
if (!had_err)
gt_gff3_in_stream_set_xrf_checker(gff3_in_stream, xrf_checker);
}
/* enable strict mode (if necessary) */
if (!had_err && arguments->strict)
gt_gff3_in_stream_enable_strict_mode((GtGFF3InStream*) gff3_in_stream);
/* pull the features through the stream and free them afterwards */
if (!had_err)
had_err = gt_node_stream_pull(gff3_in_stream, err);
if (!had_err)
printf("input is valid GFF3\n");
/* free */
gt_node_stream_delete(gff3_in_stream);
gt_type_checker_delete(type_checker);
gt_xrf_checker_delete(xrf_checker);
return had_err;
}
static int gt_gff3_runner(int argc, const char **argv, int parsed_args,
void *tool_arguments, GtError *err)
{
GFF3Arguments *arguments = tool_arguments;
GtTypeChecker *type_checker = NULL;
GtXRFChecker *xrf_checker = NULL;
GtNodeStream *gff3_in_stream,
*sort_stream = NULL,
*load_stream = NULL,
*merge_feature_stream = NULL,
*add_introns_stream = NULL,
*set_source_stream = NULL,
*gff3_out_stream = NULL,
*last_stream;
int had_err = 0;
gt_error_check(err);
gt_assert(arguments);
/* create a gff3 input stream */
gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
argv + parsed_args);
if (arguments->verbose && arguments->outfp)
gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);
if (arguments->checkids)
gt_gff3_in_stream_check_id_attributes((GtGFF3InStream*) gff3_in_stream);
if (!arguments->addids)
gt_gff3_in_stream_disable_add_ids(gff3_in_stream);
last_stream = gff3_in_stream;
/* set different type checker if necessary */
if (gt_typecheck_info_option_used(arguments->tci)) {
type_checker = gt_typecheck_info_create_type_checker(arguments->tci, err);
if (!type_checker)
had_err = -1;
if (!had_err)
gt_gff3_in_stream_set_type_checker(gff3_in_stream, type_checker);
}
/* set XRF checker if necessary */
if (gt_xrfcheck_info_option_used(arguments->xci)) {
xrf_checker = gt_xrfcheck_info_create_xrf_checker(arguments->xci, err);
if (!xrf_checker)
had_err = -1;
if (!had_err)
gt_gff3_in_stream_set_xrf_checker(gff3_in_stream, xrf_checker);
}
/* set offset (if necessary) */
if (!had_err && arguments->offset != GT_UNDEF_WORD)
gt_gff3_in_stream_set_offset(gff3_in_stream, arguments->offset);
/* set offsetfile (if necessary) */
if (!had_err && gt_str_length(arguments->offsetfile)) {
had_err = gt_gff3_in_stream_set_offsetfile(gff3_in_stream,
arguments->offsetfile, err);
}
/* enable strict mode (if necessary) */
if (!had_err && arguments->strict)
gt_gff3_in_stream_enable_strict_mode((GtGFF3InStream*) gff3_in_stream);
/* enable tidy mode (if necessary) */
if (!had_err && arguments->tidy)
gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream*) gff3_in_stream);
if (!had_err && arguments->fixboundaries)
gt_gff3_in_stream_fix_region_boundaries((GtGFF3InStream*) gff3_in_stream);
/* create load stream (if necessary) */
if (!had_err && arguments->load) {
load_stream = gt_load_stream_new(last_stream);
last_stream = load_stream;
}
/* create sort stream (if necessary) */
if (!had_err && (arguments->sort || arguments->sortlines ||
arguments->sortnum)) {
sort_stream = gt_sort_stream_new(last_stream);
last_stream = sort_stream;
}
/* create merge feature stream (if necessary) */
if (!had_err && arguments->mergefeat) {
gt_assert(sort_stream);
merge_feature_stream = gt_merge_feature_stream_new(sort_stream);
last_stream = merge_feature_stream;
}
/* create addintrons stream (if necessary) */
if (!had_err && arguments->addintrons) {
gt_assert(last_stream);
add_introns_stream = gt_add_introns_stream_new(last_stream);
last_stream = add_introns_stream;
}
/* create setsource stream (if necessary) */
if (!had_err && gt_str_length(arguments->newsource) > 0) {
gt_assert(last_stream);
GtNodeVisitor *ssv = gt_set_source_visitor_new(arguments->newsource);
set_source_stream = gt_visitor_stream_new(last_stream, ssv);
last_stream = set_source_stream;
}
/* create gff3 output stream */
if (!had_err && arguments->show) {
if (arguments->sortlines) {
gff3_out_stream = gt_gff3_linesorted_out_stream_new(last_stream,
arguments->outfp);
gt_gff3_linesorted_out_stream_set_fasta_width(
(GtGFF3LinesortedOutStream*) gff3_out_stream,
arguments->width);
if (arguments->retainids)
gt_gff3_linesorted_out_stream_retain_id_attributes(
(GtGFF3LinesortedOutStream*) gff3_out_stream);
} else if (arguments->sortnum) {
gff3_out_stream = gt_gff3_numsorted_out_stream_new(last_stream,
arguments->outfp);
gt_gff3_numsorted_out_stream_set_fasta_width(
(GtGFF3NumsortedOutStream*) gff3_out_stream,
arguments->width);
if (arguments->retainids)
gt_gff3_numsorted_out_stream_retain_id_attributes(
(GtGFF3NumsortedOutStream*) gff3_out_stream);
} else {
gff3_out_stream = gt_gff3_out_stream_new(last_stream, arguments->outfp);
gt_gff3_out_stream_set_fasta_width((GtGFF3OutStream*) gff3_out_stream,
arguments->width);
if (arguments->retainids)
gt_gff3_out_stream_retain_id_attributes((GtGFF3OutStream*)
gff3_out_stream);
}
gt_assert(gff3_out_stream);
last_stream = gff3_out_stream;
}
/* pull the features through the stream and free them afterwards */
if (!had_err)
had_err = gt_node_stream_pull(last_stream, err);
/* free */
gt_node_stream_delete(gff3_out_stream);
gt_node_stream_delete(sort_stream);
gt_node_stream_delete(load_stream);
gt_node_stream_delete(merge_feature_stream);
gt_node_stream_delete(add_introns_stream);
gt_node_stream_delete(set_source_stream);
gt_node_stream_delete(gff3_in_stream);
gt_type_checker_delete(type_checker);
gt_xrf_checker_delete(xrf_checker);
return had_err;
}
