void gt_feature_info_delete(GtFeatureInfo *fi)
{
if (!fi) return;
gt_hashmap_delete(fi->id_to_genome_node);
gt_hashmap_delete(fi->id_to_pseudo_parent);
gt_free(fi);
}
static void gff3_visitor_free(GtNodeVisitor *nv)
{
GtGFF3Visitor *gff3_visitor = gff3_visitor_cast(nv);
gt_assert(gff3_visitor);
gt_string_distri_delete(gff3_visitor->id_counter);
gt_hashmap_delete(gff3_visitor->feature_node_to_id_array);
gt_hashmap_delete(gff3_visitor->feature_node_to_unique_id_str);
gt_cstr_table_delete(gff3_visitor->used_ids);
}
void gt_gtf_parser_delete(GtGTFParser *parser)
{
if (!parser) return;
gt_region_node_builder_delete(parser->region_node_builder);
gt_hashmap_delete(parser->gene_id_hash);
gt_hashmap_delete(parser->seqid_to_str_mapping);
gt_hashmap_delete(parser->source_to_str_mapping);
gt_hashmap_delete(parser->transcript_id_to_name_mapping);
gt_hashmap_delete(parser->gene_id_to_name_mapping);
gt_free(parser);
}
void gt_type_graph_delete(GtTypeGraph *type_graph)
{
unsigned long i;
if (!type_graph) return;
gt_bool_matrix_delete(type_graph->part_of_in_edges);
gt_bool_matrix_delete(type_graph->part_of_out_edges);
for (i = 0; i < gt_array_size(type_graph->nodes); i++)
gt_type_node_delete(*(GtTypeNode**) gt_array_get(type_graph->nodes, i));
gt_array_delete(type_graph->nodes);
gt_hashmap_delete(type_graph->nodemap);
gt_hashmap_delete(type_graph->name2id);
gt_free(type_graph);
}
void gt_layout_delete(GtLayout *layout)
{
if (!layout) return;
gt_rwlock_wrlock(layout->lock);
if (layout->twc && layout->own_twc)
gt_text_width_calculator_delete(layout->twc);
gt_hashmap_delete(layout->tracks);
gt_array_delete(layout->custom_tracks);
if (layout->blocks)
gt_hashmap_delete(layout->blocks);
gt_rwlock_unlock(layout->lock);
gt_rwlock_delete(layout->lock);
gt_free(layout);
}
void gt_xrf_abbr_entry_delete(GtXRFAbbrEntry *abbr_entry)
{
if (!abbr_entry) return;
gt_str_delete(abbr_entry->filename);
gt_hashmap_delete(abbr_entry->content);
gt_free(abbr_entry);
}
static void add_ids_visitor_free(GtNodeVisitor *nv)
{
GtAddIDsVisitor *add_ids_visitor = add_ids_visitor_cast(nv);
gt_hashmap_delete(add_ids_visitor->undefined_sequence_regions);
gt_cstr_table_delete(add_ids_visitor->defined_seqids);
gt_queue_delete(add_ids_visitor->node_buffer);
}
void gth_region_factory_save(GthRegionFactory *rf, GtArray *nodes,
GthInput *input)
{
GtHashmap *sequence_regions;
GtUword i, j;
GtStr *sequenceid;
GT_UNUSED int had_err;
gt_assert(rf && nodes && input);
gt_assert(!rf->factory_was_used);
rf->seqid_store = seqid_store_new(input);
sequence_regions = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);
sequenceid = gt_str_new();
for (i = 0; i < gth_input_num_of_gen_files(input); i++) {
gth_input_load_genomic_file(input, i, false);
for (j = 0; j < gth_input_num_of_gen_seqs(input, i); j++) {
gt_str_reset(sequenceid);
gth_input_save_gen_identifier(input, sequenceid, i, j);
make_sequence_region(sequence_regions, sequenceid, rf, input, i, j);
}
}
gt_str_delete(sequenceid);
had_err = gt_hashmap_foreach_in_key_order(sequence_regions,
save_sequence_region, nodes, NULL);
gt_assert(!had_err); /* should not happen */
gt_hashmap_delete(sequence_regions);
rf->factory_was_used = true;
}
void gt_diagram_delete(GtDiagram *diagram)
{
if (!diagram) return;
gt_rwlock_wrlock(diagram->lock);
gt_array_delete(diagram->features);
if (diagram->blocks)
gt_hashmap_delete(diagram->blocks);
gt_hashmap_delete(diagram->nodeinfo);
gt_hashmap_delete(diagram->collapsingtypes);
gt_hashmap_delete(diagram->groupedtypes);
gt_hashmap_delete(diagram->caption_display_status);
gt_array_delete(diagram->custom_tracks);
gt_rwlock_unlock(diagram->lock);
gt_rwlock_delete(diagram->lock);
gt_free(diagram);
}
void gt_seqid2seqnum_mapping_delete(GtSeqid2SeqnumMapping *mapping)
{
if (!mapping) return;
gt_hashmap_delete(mapping->map);
gt_free(mapping->filename);
gt_free(mapping);
}
static void gt_hmmer_parse_status_delete(GtHMMERParseStatus *s)
{
if (!s) return;
gt_str_delete(s->cur_model);
gt_hashmap_delete(s->models);
gt_free(s);
}
static void filter_stream_free(GtNodeStream *ns)
{
AgnFilterStream *stream = filter_stream_cast(ns);
gt_node_stream_delete(stream->in_stream);
gt_queue_delete(stream->cache);
gt_hashmap_delete(stream->typestokeep);
}
void gt_line_breaker_captions_delete(GtLineBreaker *lb)
{
GtLineBreakerCaptions *lbcap;
if (!lb) return;
lbcap = gt_line_breaker_captions_cast(lb);
gt_hashmap_delete(lbcap->linepositions);
}
void gt_line_breaker_bases_delete(GtLineBreaker *lb)
{
GtLineBreakerBases *lbb;
if (!lb) return;
lbb = gt_line_breaker_bases_cast(lb);
gt_hashmap_delete(lbb->itrees);
}
void gt_diagram_reset_track_selector_func(GtDiagram *diagram)
{
gt_assert(diagram);
gt_rwlock_wrlock(diagram->lock);
diagram->select_func = default_track_selector;
gt_hashmap_delete(diagram->blocks);
diagram->blocks = NULL;
gt_rwlock_unlock(diagram->lock);
}
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);
}
void gt_type_node_delete(GtTypeNode *type_node)
{
if (!type_node) return;
gt_hashmap_delete(type_node->cache);
gt_array_delete(type_node->is_a_out_edges);
gt_array_delete(type_node->part_of_list);
gt_array_delete(type_node->is_a_list);
gt_free(type_node);
}
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);
}
void gtr_register_components(GtR *gtr)
{
gt_assert(gtr);
/* add tools */
gt_toolbox_delete(gtr->tools);
gtr->tools = gtt_tools();
/* add unit tests */
gt_hashmap_delete(gtr->unit_tests);
gtr->unit_tests = gtt_unit_tests();
}
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);
}
void gt_ma_clean(void)
{
gt_assert(ma);
gt_mutex_lock(bookkeeping_lock);
ma->bookkeeping = false;
gt_hashmap_delete(ma->allocated_pointer);
gt_mutex_unlock(bookkeeping_lock);
gt_mutex_delete(bookkeeping_lock);
free(ma);
ma = NULL;
}
void gt_xrf_checker_delete(GtXRFChecker *xrc)
{
if (!xrc) return;
if (xrc->reference_count) {
xrc->reference_count--;
return;
}
gt_xrf_abbr_parse_tree_delete(xrc->xpt);
gt_hashmap_delete(xrc->abbrvs);
gt_splitter_delete(xrc->splitter);
gt_free(xrc);
}
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);
}
void gt_ltrfileout_stream_free(GtNodeStream *ns)
{
GtLTRdigestFileOutStream *ls = gt_ltrdigest_file_out_stream_cast(ns);
if (ls->tabout_file != NULL)
gt_file_delete(ls->tabout_file);
if (ls->pbsout_file != NULL)
gt_file_delete(ls->pbsout_file);
if (ls->pptout_file != NULL)
gt_file_delete(ls->pptout_file);
if (ls->ltr5out_file != NULL)
gt_file_delete(ls->ltr5out_file);
if (ls->ltr3out_file != NULL)
gt_file_delete(ls->ltr3out_file);
if (ls->elemout_file != NULL)
gt_file_delete(ls->elemout_file);
gt_hashmap_delete(ls->pdomout_files);
gt_hashmap_delete(ls->pdomali_files);
gt_hashmap_delete(ls->pdomaa_files);
gt_node_visitor_delete((GtNodeVisitor*) ls->lv);
gt_node_stream_delete(ls->in_stream);
}
int main(int argc, char **argv)
{
if(argc != 2)
{
fputs("usage: vang schema.file\n", stderr);
return 1;
}
gt_lib_init();
char *schemafile = argv[1];
FILE *schema = fopen(schemafile, "r");
if(schema == NULL)
{
fprintf(stderr, "error: unable to open schema file '%s'\n", schemafile);
return 1;
}
GtArray *entry_datatypes = gt_array_new( sizeof(char *) );
GtHashmap *entries = gt_hashmap_new( GT_HASH_STRING, NULL,
(GtFree)vang_schema_entry_delete );
VangSchemaEntry *entry;
while( (entry = vang_schema_entry_next(schema)) != NULL )
{
char *datatype = (char *)vang_schema_entry_get_datatype(entry);
VangSchemaEntry *testentry = gt_hashmap_get(entries, datatype);
if(testentry != NULL)
{
fprintf( stderr, "warning: already have an entry for data type '%s'; "
"replacing\n", datatype );
vang_schema_entry_delete(testentry);
}
gt_hashmap_add(entries, datatype, entry);
gt_array_add(entry_datatypes, datatype);
}
unsigned long i;
for(i = 0; i < gt_array_size(entry_datatypes); i++)
{
const char *type = *(const char **)gt_array_get(entry_datatypes, i);
VangSchemaEntry *entry = gt_hashmap_get(entries, type);
vang_schema_entry_to_string(entry, stdout);
puts("");
}
gt_array_delete(entry_datatypes);
gt_hashmap_delete(entries);
gt_lib_clean();
return 0;
}
void gt_diagram_set_track_selector_func(GtDiagram *diagram,
GtTrackSelectorFunc bsfunc,
void *ptr)
{
gt_assert(diagram);
gt_rwlock_wrlock(diagram->lock);
/* register selector function and attached pointer */
diagram->select_func = bsfunc;
diagram->ptr = ptr;
/* this could change track assignment -> discard current blocks and requeue */
gt_hashmap_delete(diagram->blocks);
diagram->blocks = NULL;
gt_rwlock_unlock(diagram->lock);
}
void gt_bed_parser_delete(GtBEDParser *bed_parser)
{
if (!bed_parser) return;
gt_free(bed_parser->block_type);
gt_free(bed_parser->thick_feature_type);
gt_free(bed_parser->feature_type);
gt_str_delete(bed_parser->another_word);
gt_str_delete(bed_parser->word);
gt_hashmap_delete(bed_parser->seqid_to_str_mapping);
while (gt_queue_size(bed_parser->feature_nodes))
gt_genome_node_delete(gt_queue_get(bed_parser->feature_nodes));
gt_queue_delete(bed_parser->feature_nodes);
gt_region_node_builder_delete(bed_parser->region_node_builder);
gt_free(bed_parser);
}
static int check_cds_phases_if_necessary(GtFeatureNode *fn,
GtCDSCheckVisitor *v,
bool second_pass, GtError *err)
{
GtFeatureNodeIterator *fni;
GtFeatureNode *node;
GtArray *cds_features = NULL;
GtHashmap *multi_features = NULL;
int had_err = 0;
gt_error_check(err);
gt_assert(fn);
fni = gt_feature_node_iterator_new_direct(fn);
while ((node = gt_feature_node_iterator_next(fni))) {
if (gt_feature_node_has_type(node, gt_ft_CDS)) {
if (gt_feature_node_is_multi(node)) {
GtArray *features;
if (!multi_features)
multi_features = gt_hashmap_new(GT_HASH_DIRECT, NULL,
(GtFree) gt_array_delete);
if ((features =
gt_hashmap_get(multi_features,
gt_feature_node_get_multi_representative(node)))) {
gt_array_add(features, node);
}
else {
GtFeatureNode *representative;
features = gt_array_new(sizeof (GtFeatureNode*));
representative = gt_feature_node_get_multi_representative(node);
gt_array_add(features, representative);
gt_hashmap_add(multi_features, representative, features);
}
}
else {
if (!cds_features)
cds_features = gt_array_new(sizeof (GtFeatureNode*));
gt_array_add(cds_features, node);
}
}
}
if (cds_features)
had_err = check_cds_phases(cds_features, v, false, second_pass, err);
if (!had_err && multi_features)
had_err = gt_hashmap_foreach(multi_features, check_cds_phases_hm, v, err);
gt_array_delete(cds_features);
gt_hashmap_delete(multi_features);
gt_feature_node_iterator_delete(fni);
return had_err;
}
void gtr_delete(GtR *gtr)
{
if (!gtr) return;
gt_fa_fclose(gtr->logfp);
gt_str_delete(gtr->testspacepeak);
gt_str_delete(gtr->debugfp);
gt_str_delete(gtr->test_only);
gt_str_delete(gtr->manoutdir);
gt_toolbox_delete(gtr->tools);
gt_hashmap_delete(gtr->unit_tests);
if (gtr->L) lua_close(gtr->L);
#ifndef WITHOUT_CAIRO
gt_style_delete_without_state(gtr->style);
#endif
gt_free(gtr);
}
void gt_md5_tab_delete(GtMD5Tab *md5_tab)
{
GtUword i;
if (!md5_tab) return;
if (md5_tab->reference_count) {
md5_tab->reference_count--;
return;
}
gt_fa_xmunmap(md5_tab->fingerprints);
gt_fa_unlock(md5_tab->fingerprints_file);
gt_fa_xfclose(md5_tab->fingerprints_file);
gt_hashmap_delete(md5_tab->md5map);
if (md5_tab->owns_md5s) {
for (i = 0; i < md5_tab->num_of_md5s; i++)
gt_free(md5_tab->md5_fingerprints[i]);
gt_free(md5_tab->md5_fingerprints);
}
gt_free(md5_tab);
}