static int select_visitor_region_node(GtNodeVisitor *nv, GtRegionNode *rn,
GT_UNUSED GtError *err)
{
GtSelectVisitor *select_visitor;
gt_error_check(err);
select_visitor = select_visitor_cast(nv);
if (!gt_str_length(select_visitor->seqid) || /* no seqid was specified */
!gt_str_cmp(select_visitor->seqid, /* or seqids are equal */
gt_genome_node_get_seqid((GtGenomeNode*) rn))) {
if (select_visitor->contain_range.start != GT_UNDEF_ULONG) {
GtRange range = gt_genome_node_get_range((GtGenomeNode*) rn);
if (gt_range_overlap(&range, &select_visitor->contain_range)) {
/* an overlapping contain range was defined -> update range */
range.start = MAX(range.start, select_visitor->contain_range.start);
range.end = MIN(range.end, select_visitor->contain_range.end);
gt_genome_node_set_range((GtGenomeNode*) rn, &range);
gt_queue_add(select_visitor->node_buffer, rn);
}
else /* contain range does not overlap with <rn> range -> delete <rn> */
gt_genome_node_delete((GtGenomeNode*) rn);
}
else
gt_queue_add(select_visitor->node_buffer, rn);
}
else
gt_genome_node_delete((GtGenomeNode*) rn);
return 0;
}
static int gt_sort_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *err)
{
GtSortStream *sort_stream;
GtGenomeNode *node, *eofn;
int had_err = 0;
gt_error_check(err);
sort_stream = gt_sort_stream_cast(ns);
if (!sort_stream->sorted) {
while (!(had_err = gt_node_stream_next(sort_stream->in_stream, &node,
err)) && node) {
if ((eofn = gt_eof_node_try_cast(node)))
gt_genome_node_delete(eofn); /* get rid of EOF nodes */
else
gt_array_add(sort_stream->nodes, node);
}
if (!had_err) {
gt_genome_nodes_sort_stable(sort_stream->nodes);
sort_stream->sorted = true;
}
}
if (!had_err) {
gt_assert(sort_stream->sorted);
if (sort_stream->idx < gt_array_size(sort_stream->nodes)) {
*gn = *(GtGenomeNode**) gt_array_get(sort_stream->nodes,
sort_stream->idx);
sort_stream->idx++;
/* join region nodes with the same sequence ID */
if (gt_region_node_try_cast(*gn)) {
GtRange range_a, range_b;
while (sort_stream->idx < gt_array_size(sort_stream->nodes)) {
node = *(GtGenomeNode**) gt_array_get(sort_stream->nodes,
sort_stream->idx);
if (!gt_region_node_try_cast(node) ||
gt_str_cmp(gt_genome_node_get_seqid(*gn),
gt_genome_node_get_seqid(node))) {
/* the next node is not a region node with the same ID */
break;
}
range_a = gt_genome_node_get_range(*gn);
range_b = gt_genome_node_get_range(node);
range_a = gt_range_join(&range_a, &range_b);
gt_genome_node_set_range(*gn, &range_a);
gt_genome_node_delete(node);
sort_stream->idx++;
}
}
return 0;
}
}
if (!had_err) {
gt_array_reset(sort_stream->nodes);
*gn = NULL;
}
return had_err;
}
static void snp_annotator_stream_free(GtNodeStream *ns)
{
GtUword i;
GtSNPAnnotatorStream *sas;
if (!ns) return;
sas = gt_snp_annotator_stream_cast(ns);
gt_region_mapping_delete(sas->rmap);
while (gt_queue_size(sas->snps) > 0) {
gt_genome_node_delete((GtGenomeNode*) gt_queue_get(sas->snps));
}
while (gt_queue_size(sas->outqueue) > 0) {
gt_genome_node_delete((GtGenomeNode*) gt_queue_get(sas->outqueue));
}
for (i = 0; i < gt_array_size(sas->instreams); i++) {
gt_node_stream_delete(*(GtNodeStream**) gt_array_get(sas->instreams, i));
}
for (i = 0; i < gt_array_size(sas->cur_gene_set); i++) {
gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(sas->cur_gene_set, i));
}
gt_array_delete(sas->cur_gene_set);
gt_node_stream_delete(sas->merge_stream);
gt_array_delete(sas->instreams);
gt_queue_delete(sas->snps);
gt_queue_delete(sas->outqueue);
}
static void gv_test_calc_integrity(AgnUnitTest *test)
{
const char *filename = "data/gff3/gaeval-stream-unit-test-2.gff3";
GtNodeStream *align_in = gt_gff3_in_stream_new_unsorted(1, &filename);
AgnGaevalParams params = { 0.6, 0.3, 0.05, 0.05, 400, 200, 100 };
GtNodeVisitor *nv = agn_gaeval_visitor_new(align_in, params);
AgnGaevalVisitor *gv = gaeval_visitor_cast(nv);
gt_node_stream_delete(align_in);
GtNodeStream *gff3in = gt_gff3_in_stream_new_unsorted(1, &filename);
GtHashmap *typestokeep = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);
gt_hashmap_add(typestokeep, "mRNA", "mRNA");
GtNodeStream *filtstream = agn_filter_stream_new(gff3in, typestokeep);
GtLogger *logger = gt_logger_new(true, "", stderr);
GtNodeStream *ics = agn_infer_cds_stream_new(filtstream, NULL, logger);
GtNodeStream *ies = agn_infer_exons_stream_new(ics, NULL, logger);
GtError *error = gt_error_new();
GtArray *feats = gt_array_new( sizeof(GtFeatureNode *) );
GtNodeStream *featstream = gt_array_out_stream_new(ies, feats, error);
int result = gt_node_stream_pull(featstream, error);
if(result == -1)
{
fprintf(stderr, "[AgnGaevalVisitor::gv_test_calc_integrity] error "
"processing GFF3: %s\n", gt_error_get(error));
return;
}
gt_node_stream_delete(gff3in);
gt_node_stream_delete(filtstream);
gt_node_stream_delete(featstream);
gt_node_stream_delete(ics);
gt_node_stream_delete(ies);
gt_logger_delete(logger);
gt_hashmap_delete(typestokeep);
agn_assert(gt_array_size(feats) == 2);
GtFeatureNode *g1 = *(GtFeatureNode **)gt_array_get(feats, 0);
GtFeatureNode *g2 = *(GtFeatureNode **)gt_array_get(feats, 1);
double cov1 = gaeval_visitor_calculate_coverage(gv, g1, error);
double cov2 = gaeval_visitor_calculate_coverage(gv, g2, error);
double int1 = gaeval_visitor_calculate_integrity(gv, g1, cov1, NULL, error);
double int2 = gaeval_visitor_calculate_integrity(gv, g2, cov2, NULL, error);
bool test1 = fabs(cov1 - 1.000) < 0.001 &&
fabs(cov2 - 0.997) < 0.001 &&
fabs(int1 - 0.850) < 0.001 &&
fabs(int2 - 0.863) < 0.001;
agn_unit_test_result(test, "calculate integrity", test1);
gt_error_delete(error);
gt_array_delete(feats);
gt_genome_node_delete((GtGenomeNode *)g1);
gt_genome_node_delete((GtGenomeNode *)g2);
gt_node_visitor_delete(nv);
}
static void automatic_sequence_region_delete(AutomaticSequenceRegion *auto_sr)
{
GtUword i;
if (!auto_sr) return;
gt_genome_node_delete(auto_sr->sequence_region);
for (i = 0; i < gt_array_size(auto_sr->feature_nodes); i++) {
gt_genome_node_delete(*(GtGenomeNode**)
gt_array_get(auto_sr->feature_nodes, i));
}
gt_array_delete(auto_sr->feature_nodes);
gt_free(auto_sr);
}
static void gv_test_introns_confirmed(AgnUnitTest *test)
{
GtGenomeNode *intron, *gap;
GtStr *seqid = gt_str_new_cstr("chr");
GtArray *introns = gt_array_new( sizeof(GtGenomeNode *) );
intron = gt_feature_node_new(seqid, "intron", 1000, 1170, GT_STRAND_REVERSE);
gt_array_add(introns, intron);
intron = gt_feature_node_new(seqid, "intron", 1225, 1305, GT_STRAND_REVERSE);
gt_array_add(introns, intron);
intron = gt_feature_node_new(seqid, "intron", 1950, 2110, GT_STRAND_REVERSE);
gt_array_add(introns, intron);
intron = gt_feature_node_new(seqid, "intron", 2545, 2655, GT_STRAND_REVERSE);
gt_array_add(introns, intron);
intron = gt_feature_node_new(seqid, "intron", 2800, 2950, GT_STRAND_REVERSE);
gt_array_add(introns, intron);
GtArray *gaps = gt_array_new( sizeof(GtGenomeNode *) );
double intcon = gaeval_visitor_introns_confirmed(introns, gaps);
bool test1 = fabs(intcon - 0.0) < 0.0001;
agn_unit_test_result(test, "introns confirmed (no gaps)", test1);
gap = gt_feature_node_new(seqid, "match_gap", 1000, 1170, GT_STRAND_REVERSE);
gt_array_add(gaps, gap);
gap = gt_feature_node_new(seqid, "match_gap", 1225, 1302, GT_STRAND_REVERSE);
gt_array_add(gaps, gap);
gap = gt_feature_node_new(seqid, "match_gap", 1950, 2110, GT_STRAND_REVERSE);
gt_array_add(gaps, gap);
gap = gt_feature_node_new(seqid, "match_gap", 2575, 2655, GT_STRAND_REVERSE);
gt_array_add(gaps, gap);
gap = gt_feature_node_new(seqid, "match_gap", 2800, 2950, GT_STRAND_REVERSE);
gt_array_add(gaps, gap);
intcon = gaeval_visitor_introns_confirmed(introns, gaps);
bool test2 = fabs(intcon - 0.6) < 0.0001;
agn_unit_test_result(test, "introns confirmed (gaps)", test2);
while(gt_array_size(introns) > 0)
{
intron = *(GtGenomeNode **)gt_array_pop(introns);
gt_genome_node_delete(intron);
}
gt_array_delete(introns);
while(gt_array_size(gaps) > 0)
{
gap = *(GtGenomeNode **)gt_array_pop(gaps);
gt_genome_node_delete(gap);
}
gt_array_delete(gaps);
gt_str_delete(seqid);
}
static int select_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)
{
GtSelectStream *fs;
int had_err;
gt_error_check(err);
fs = gt_select_stream_cast(ns);
/* we still have nodes in the buffer */
if (gt_select_visitor_node_buffer_size(fs->select_visitor)) {
/* return one of them */
*gn = gt_select_visitor_get_node(fs->select_visitor);
return 0;
}
/* no nodes in the buffer -> get new nodes */
while (!(had_err = gt_node_stream_next(fs->in_stream, gn, err)) && *gn) {
gt_assert(*gn && !had_err);
had_err = gt_genome_node_accept(*gn, fs->select_visitor, err);
if (had_err) {
/* we own the node -> delete it */
gt_genome_node_delete(*gn);
*gn = NULL;
break;
}
if (gt_select_visitor_node_buffer_size(fs->select_visitor)) {
*gn = gt_select_visitor_get_node(fs->select_visitor);
return 0;
}
}
/* either we have an error or no new node */
gt_assert(had_err || !*gn);
return had_err;
}
int gt_feature_index_add_gff3file(GtFeatureIndex *feature_index,
const char *gff3file, GtError *err)
{
GtNodeStream *gff3_in_stream;
GtGenomeNode *gn;
GtArray *tmp;
int had_err = 0;
GtUword i;
gt_error_check(err);
gt_assert(feature_index && gff3file);
tmp = gt_array_new(sizeof (GtGenomeNode*));
gff3_in_stream = gt_gff3_in_stream_new_unsorted(1, &gff3file);
while (!(had_err = gt_node_stream_next(gff3_in_stream, &gn, err)) && gn)
gt_array_add(tmp, gn);
if (!had_err) {
GtNodeVisitor *feature_visitor = gt_feature_visitor_new(feature_index);
for (i=0;i<gt_array_size(tmp);i++) {
gn = *(GtGenomeNode**) gt_array_get(tmp, i);
/* no need to lock, add_*_node() is synchronized */
had_err = gt_genome_node_accept(gn, feature_visitor, NULL);
gt_assert(!had_err); /* cannot happen */
}
gt_node_visitor_delete(feature_visitor);
}
gt_node_stream_delete(gff3_in_stream);
for (i=0;i<gt_array_size(tmp);i++)
gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(tmp, i));
gt_array_delete(tmp);
return had_err;
}
void gt_feature_node_iterator_delete(GtFeatureNodeIterator *fni)
{
if (!fni) return;
gt_genome_node_delete((GtGenomeNode*) fni->fn);
gt_array_delete(fni->feature_stack);
gt_free(fni);
}
int gt_diagram_unit_test(GtError *err)
{
int had_err = 0;
GtGenomeNode *gn;
GtDiagramTestShared sh;
GtRange testrng = {100, 10000};
gt_error_check(err);
gn = gt_feature_node_new_standard_gene();
sh.fi = gt_feature_index_memory_new();
sh.sty = gt_style_new(err);
sh.err = err;
sh.errstatus = 0;
gt_feature_index_add_feature_node(sh.fi, gt_feature_node_cast(gn), err);
gt_genome_node_delete(gn);
sh.d = gt_diagram_new(sh.fi, "ctg123", &testrng, sh.sty, err);
/* removed the multithreading test for now until it is fixed */
gt_diagram_unit_test_sketch_func(&sh);
gt_ensure(sh.errstatus == 0);
gt_style_delete(sh.sty);
gt_diagram_delete(sh.d);
gt_feature_index_delete(sh.fi);
return had_err;
}
static int genome_node_lua_delete(lua_State *L)
{
GtGenomeNode **gn;
gn = check_genome_node(L, 1);
gt_genome_node_delete(*gn);
return 0;
}
static void split_cds_feature(GtFeatureNode *cds_feature, GtFeatureNode *fn)
{
GtArray *parents;
unsigned long i;
gt_assert(cds_feature && fn);
/* find parents */
parents = find_cds_parents(cds_feature, fn);
/* remove CDS feature */
gt_feature_node_remove_leaf(fn, cds_feature);
/* add CDS feature to all parents */
for (i = 0; i < gt_array_size(parents); i++) {
GtFeatureNode *parent = *(GtFeatureNode**) gt_array_get(parents, i);
const char *id = gt_feature_node_get_attribute(parent, GT_GFF_ID);
if (!i) {
gt_feature_node_set_attribute(cds_feature, GT_GFF_PARENT, id);
gt_feature_node_add_child(parent, cds_feature);
}
else {
GtFeatureNode *new_cds = gt_feature_node_clone(cds_feature);
gt_feature_node_set_attribute(new_cds, GT_GFF_PARENT, id);
gt_feature_node_add_child(parent, new_cds);
gt_genome_node_delete((GtGenomeNode*) cds_feature);
}
}
gt_array_delete(parents);
}
static int snp_annotator_stream_process_current_gene(GtSNPAnnotatorStream *sas,
GtError *err)
{
int had_err = 0;
GtUword i;
GtUword nof_genes = gt_array_size(sas->cur_gene_set);
gt_error_check(err);
if (gt_queue_size(sas->snps) > 0) {
/* we need to process SNPs for a gene cluster*/
gt_assert(gt_queue_size(sas->outqueue) == 0);
for (i = 0; !had_err && i < nof_genes; i++) {
GtNodeVisitor *sav;
GtFeatureNode *gene;
gene = *(GtFeatureNode**) gt_array_get(sas->cur_gene_set, i);
sav = gt_snp_annotator_visitor_new(gene, sas->tt, sas->rmap, err);
if (!sav)
had_err = -1;
if (!had_err) {
if (i < nof_genes-1) {
had_err = gt_queue_iterate(sas->snps,
snp_annotator_stream_process_snp,
sav, err);
} else {
while (!had_err && gt_queue_size(sas->snps) > 0) {
GtFeatureNode *snp = (GtFeatureNode*) gt_queue_get(sas->snps);
had_err = gt_genome_node_accept((GtGenomeNode*) snp, sav, err);
gt_queue_add(sas->outqueue, snp);
gt_genome_node_delete((GtGenomeNode*) snp);
}
}
gt_node_visitor_delete(sav);
}
gt_genome_node_delete((GtGenomeNode*) gene);
}
} else {
/* no SNPs for this gene cluster, delete it */
for (i = 0; !had_err && i < nof_genes; i++) {
gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(sas->cur_gene_set,
i));
}
}
gt_assert(gt_queue_size(sas->snps) == 0);
gt_array_reset(sas->cur_gene_set);
return had_err;
}
static void remove_elem(GtDlistelem *elem, GtDlist *trees,
GtHashmap *target_to_elem, GtStr *key)
{
GtGenomeNode *node = gt_dlistelem_get_data(elem);
gt_genome_node_delete(node);
gt_dlist_remove(trees, elem);
gt_hashmap_remove(target_to_elem, gt_str_get(key));
}
void gt_orphanage_reset(GtOrphanage *o)
{
gt_assert(o);
while (gt_queue_size(o->orphans))
gt_genome_node_delete(gt_queue_get(o->orphans));
gt_cstr_table_reset(o->missing_parents);
gt_cstr_table_reset(o->orphan_ids);
}
static void buffer_stream_free(GtNodeStream *ns)
{
GtBufferStream *bs = buffer_stream_cast(ns);
while (gt_queue_size(bs->node_buffer))
gt_genome_node_delete(gt_queue_get(bs->node_buffer));
gt_queue_delete(bs->node_buffer);
gt_node_stream_delete(bs->in_stream);
}
static void targetbest_filter_stream_free(GtNodeStream *gs)
{
GtTargetbestFilterStream *tfs = targetbest_filter_stream_cast(gs);
for (; tfs->next != NULL; tfs->next = gt_dlistelem_next(tfs->next))
gt_genome_node_delete(gt_dlistelem_get_data(tfs->next));
gt_dlist_delete(tfs->trees);
gt_hashmap_delete(tfs->target_to_elem);
gt_node_stream_delete(tfs->in_stream);
}
static void gtf_in_stream_free(GtNodeStream *ns)
{
GtGTFInStream *gtf_in_stream = gtf_in_stream_cast(ns);
gt_free(gtf_in_stream->filename);
gt_type_checker_delete(gtf_in_stream->type_checker);
while (gt_queue_size(gtf_in_stream->genome_node_buffer))
gt_genome_node_delete(gt_queue_get(gtf_in_stream->genome_node_buffer));
gt_queue_delete(gtf_in_stream->genome_node_buffer);
}
void gt_orphanage_delete(GtOrphanage *o)
{
if (!o) return;
gt_cstr_table_delete(o->orphan_ids);
gt_cstr_table_delete(o->missing_parents);
while (gt_queue_size(o->orphans))
gt_genome_node_delete(gt_queue_get(o->orphans));
gt_queue_delete(o->orphans);
gt_free(o);
}
void gt_rec_map_delete(GtRecMap *rm)
{
if (!rm) return;
if (rm->reference_count) {
rm->reference_count--;
return;
}
gt_genome_node_delete((GtGenomeNode*) rm->fn);
gt_free(rm);
}
static int filter_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *error)
{
AgnFilterStream *stream;
GtFeatureNode *fn;
int had_err;
gt_error_check(error);
stream = filter_stream_cast(ns);
if(gt_queue_size(stream->cache) > 0)
{
*gn = gt_queue_get(stream->cache);
return 0;
}
while(1)
{
had_err = gt_node_stream_next(stream->in_stream, gn, error);
if(had_err)
return had_err;
if(!*gn)
return 0;
fn = gt_feature_node_try_cast(*gn);
if(!fn)
return 0;
GtFeatureNode *current;
GtFeatureNodeIterator *iter = gt_feature_node_iterator_new(fn);
for(current = gt_feature_node_iterator_next(iter);
current != NULL;
current = gt_feature_node_iterator_next(iter))
{
const char *type = gt_feature_node_get_type(current);
bool keepfeature = false;
if(gt_hashmap_get(stream->typestokeep, type) != NULL)
keepfeature = true;
if(keepfeature)
{
gt_genome_node_ref((GtGenomeNode *)current);
gt_queue_add(stream->cache, current);
}
}
gt_feature_node_iterator_delete(iter);
gt_genome_node_delete((GtGenomeNode *)fn);
if(gt_queue_size(stream->cache) > 0)
{
*gn = gt_queue_get(stream->cache);
return 0;
}
}
return 0;
}
static void gt_load_stream_free(GtNodeStream *ns)
{
unsigned long i;
GtLoadStream *load_stream = gt_load_stream_cast(ns);
for (i = load_stream->idx; i < gt_array_size(load_stream->nodes); i++) {
gt_genome_node_delete(*(GtGenomeNode**)
gt_array_get(load_stream->nodes, i));
}
gt_array_delete(load_stream->nodes);
gt_node_stream_delete(load_stream->in_stream);
}
static int gt_ltr_cluster_stream_next(GtNodeStream *ns,
GtGenomeNode **gn,
GtError *err)
{
GtLTRClusterStream *lcs;
GtGenomeNode *ref_gn;
int had_err = 0;
unsigned long i = 0;
gt_error_check(err);
lcs = gt_ltr_cluster_stream_cast(ns);
if (lcs->first_next) {
while (!(had_err = gt_node_stream_next(lcs->in_stream, gn, err)) && *gn) {
gt_assert(*gn && !had_err);
ref_gn = gt_genome_node_ref(*gn);
gt_array_add(lcs->nodes, ref_gn);
had_err = gt_genome_node_accept(*gn, (GtNodeVisitor*) lcs->lcv, err);
if (had_err) {
gt_genome_node_delete(*gn);
*gn = NULL;
break;
}
}
lcs->feat_to_encseq =
gt_ltr_cluster_prepare_seq_visitor_get_encseqs(lcs->lcv);
lcs->feat_to_encseq_keys =
gt_ltr_cluster_prepare_seq_visitor_get_features(lcs->lcv);
if (!had_err) {
for (i = 0; i < gt_str_array_size(lcs->feat_to_encseq_keys); i++) {
had_err = process_feature(lcs,
gt_str_array_get(lcs->feat_to_encseq_keys, i),
err);
if (had_err)
break;
}
}
if (!had_err) {
*gn = *(GtGenomeNode**) gt_array_get(lcs->nodes, lcs->next_index);
lcs->next_index++;
lcs->first_next = false;
return 0;
}
} else {
if (lcs->next_index >= gt_array_size(lcs->nodes))
*gn = NULL;
else {
*gn = *(GtGenomeNode**) gt_array_get(lcs->nodes, lcs->next_index);
lcs->next_index++;
}
return 0;
}
return had_err;
}
static void snp_annotator_visitor_free(GtNodeVisitor *nv)
{
GtSNPAnnotatorVisitor *sav;
if (!nv) return;
sav = snp_annotator_visitor_cast(nv);
gt_genome_node_delete((GtGenomeNode*) sav->gene);
if (sav->own_tt)
gt_trans_table_delete(sav->tt);
gt_region_mapping_delete(sav->rmap);
gt_hashmap_delete(sav->rnaseqs);
}
static void feature_in_stream_free(GtNodeStream *ns)
{
GtFeatureInStream *stream = feature_in_stream_cast(ns);
gt_str_array_delete(stream->seqids);
while (gt_queue_size(stream->regioncache) > 0)
{
GtGenomeNode *gn = gt_queue_get(stream->regioncache);
gt_genome_node_delete(gn);
}
gt_queue_delete(stream->regioncache);
}
static void gt_ltr_cluster_stream_free(GtNodeStream *ns)
{
unsigned long i;
GtLTRClusterStream *lcs = gt_ltr_cluster_stream_cast(ns);
gt_node_visitor_delete((GtNodeVisitor*) lcs->lcv);
gt_hashmap_delete(lcs->feat_to_encseq);
gt_str_array_delete(lcs->feat_to_encseq_keys);
for (i = 0; i < gt_array_size(lcs->nodes); i++)
gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(lcs->nodes, i));
gt_array_delete(lcs->nodes);
gt_node_stream_delete(lcs->in_stream);
}
static void gff3_in_stream_plain_free(GtNodeStream *ns)
{
GtGFF3InStreamPlain *gff3_in_stream_plain = gff3_in_stream_plain_cast(ns);
gt_str_array_delete(gff3_in_stream_plain->files);
gt_str_delete(gff3_in_stream_plain->stdinstr);
while (gt_queue_size(gff3_in_stream_plain->genome_node_buffer)) {
gt_genome_node_delete(gt_queue_get(gff3_in_stream_plain
->genome_node_buffer));
}
gt_queue_delete(gff3_in_stream_plain->genome_node_buffer);
gt_gff3_parser_delete(gff3_in_stream_plain->gff3_parser);
gt_cstr_table_delete(gff3_in_stream_plain->used_types);
gt_file_delete(gff3_in_stream_plain->fpin);
}
static int feature_node_lua_remove_leaf(lua_State *L)
{
GtGenomeNode **parent, **leaf;
GtFeatureNode *pf, *lf;
parent = check_genome_node(L, 1);
leaf = check_genome_node(L, 2);
pf = gt_feature_node_try_cast(*parent);
luaL_argcheck(L, pf, 1, "not a feature node");
lf = gt_feature_node_try_cast(*leaf);
luaL_argcheck(L, lf, 2, "not a feature node");
gt_feature_node_remove_leaf(pf, lf);
gt_genome_node_delete((GtGenomeNode*) lf);
return 0;
}
static int delete_mRNAs(GT_UNUSED void *key, void *value,
GT_UNUSED void *data, GT_UNUSED GtError *err)
{
GtArray *gt_genome_node_array = (GtArray*) value;
GtUword i;
gt_assert(key && value);
for (i = 0; i < gt_array_size(gt_genome_node_array); i++) {
GtGenomeNode *gn = *(GtGenomeNode**) gt_array_get(gt_genome_node_array, i);
gt_genome_node_delete(gn);
}
return 0;
}
static void chseqids_stream_free(GtNodeStream *gs)
{
GtChseqidsStream *cs;
unsigned long i;
cs = chseqids_stream_cast(gs);
gt_mapping_delete(cs->chseqids_mapping);
for (i = cs->buffer_index; i < gt_array_size(cs->gt_genome_node_buffer);
i++) {
gt_genome_node_delete(*(GtGenomeNode**)
gt_array_get(cs->gt_genome_node_buffer, i));
}
gt_array_delete(cs->gt_genome_node_buffer);
gt_node_stream_delete(cs->in_stream);
}
