GtOrphanage* gt_orphanage_new(void)
{
GtOrphanage *o = gt_malloc(sizeof *o);
o->orphans = gt_queue_new();
o->missing_parents = gt_cstr_table_new();
o->orphan_ids = gt_cstr_table_new();
return o;
}
GthRegionFactory* gth_region_factory_new(bool use_desc_ranges)
{
GthRegionFactory *srf = gt_calloc(1, sizeof *srf);
srf->used_seqids = gt_cstr_table_new();
srf->use_desc_ranges = use_desc_ranges;
return srf;
}
GtNodeVisitor* gt_stat_visitor_new(bool gene_length_distri,
bool gene_score_distri,
bool exon_length_distri,
bool exon_number_distri,
bool intron_length_distri,
bool cds_length_distri,
bool used_sources)
{
GtNodeVisitor *nv = gt_node_visitor_create(gt_stat_visitor_class());
GtStatVisitor *sv = stat_visitor_cast(nv);
if (gene_length_distri)
sv->gene_length_distribution = gt_disc_distri_new();
if (gene_score_distri)
sv->gene_score_distribution = gt_disc_distri_new();
if (exon_length_distri)
sv->exon_length_distribution = gt_disc_distri_new();
if (exon_number_distri)
sv->exon_number_distribution = gt_disc_distri_new();
if (intron_length_distri)
sv->intron_length_distribution = gt_disc_distri_new();
if (cds_length_distri)
sv->cds_length_distribution = gt_disc_distri_new();
if (used_sources)
sv->used_sources = gt_cstr_table_new();
return nv;
}
static int gt_seqids_runner(GT_UNUSED int argc, const char **argv,
int parsed_args,
GT_UNUSED void *tool_arguments, GtError *err)
{
GtNodeStream *in_stream, *v_stream;
GtCstrTable *cst;
int had_err = 0;
gt_error_check(err);
cst = gt_cstr_table_new();
in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
argv + parsed_args);
v_stream = gt_visitor_stream_new(in_stream, gt_collect_ids_visitor_new(cst));
had_err = gt_node_stream_pull(v_stream, err);
if (!had_err) {
GtStrArray *seqids;
GtUword i;
seqids = gt_cstr_table_get_all(cst);
for (i = 0; i < gt_str_array_size(seqids); i++) {
printf("%s\n", gt_str_array_get(seqids, i));
}
gt_str_array_delete(seqids);
}
gt_node_stream_delete(v_stream);
gt_node_stream_delete(in_stream);
gt_cstr_table_delete(cst);
return had_err;
}
void gt_symbol_init(void)
{
if (!symbols)
symbols = gt_cstr_table_new();
if (!symbol_mutex)
symbol_mutex = gt_mutex_new();
}
static GtCstrTable* gt_rdb_mysql_get_indexes(GtRDB *rdb, GtError *err)
{
GT_UNUSED GtRDBMySQL *rdbm;
GtRDBStmt *stmt;
GtCstrTable *tab;
int rval = 0;
gt_assert(rdb);
gt_error_check(err);
rdbm = gt_rdb_mysql_cast(rdb);
/* TODO: implement a way to do this in MySQL 4 */
if ((stmt = gt_rdb_prepare(rdb, "SELECT DISTINCT INDEX_NAME "
"FROM INFORMATION_SCHEMA.STATISTICS ",
0,
err)) == NULL)
return NULL;
tab = gt_cstr_table_new();
while (!rval) {
GtStr *key;
rval = gt_rdb_stmt_exec(stmt, err);
if (rval) break;
key = gt_str_new();
gt_rdb_stmt_get_string(stmt, 0, key, err);
gt_cstr_table_add(tab, gt_str_get(key));
gt_str_delete(key);
}
if (rval < 0) {
gt_cstr_table_delete(tab);
gt_rdb_stmt_delete(stmt);
return NULL;
}
gt_rdb_stmt_delete(stmt);
return tab;
}
static GtCstrTable* gt_rdb_mysql_get_tables(GtRDB *rdb, GtError *err)
{
GtRDBMySQL *rdbm;
MYSQL_RES *res;
MYSQL_ROW row;
GtCstrTable *tab;
gt_assert(rdb);
gt_error_check(err);
rdbm = gt_rdb_mysql_cast(rdb);
gt_assert(&rdbm->conn);
res = mysql_list_tables(&rdbm->conn, NULL); /* NULL means 'all tables' */
if (!res) {
gt_error_set(err, "error trying to list tables: %s",
mysql_error(&rdbm->conn));
return NULL;
}
tab = gt_cstr_table_new();
while ((row = mysql_fetch_row(res))) {
char buf[BUFSIZ];
GtUword *lengths;
memset(buf, 0, BUFSIZ);
lengths = mysql_fetch_lengths(res);
(void) snprintf(buf, MIN(BUFSIZ, lengths[0])*sizeof (char), "%s",
(char*) row[0] ? (char*) row[0] : "NULL");
gt_cstr_table_add(tab, buf);
}
mysql_free_result(res);
return tab;
}
GtNodeVisitor* gt_add_ids_visitor_new(bool ensure_sorting)
{
GtNodeVisitor *nv = gt_node_visitor_create(gt_add_ids_visitor_class());
GtAddIDsVisitor *add_ids_visitor = add_ids_visitor_cast(nv);
add_ids_visitor->node_buffer = gt_queue_new();
add_ids_visitor->defined_seqids = gt_cstr_table_new();
add_ids_visitor->undefined_sequence_regions =
gt_hashmap_new(GT_HASH_STRING, NULL,
(GtFree) automatic_sequence_region_delete);
add_ids_visitor->ensure_sorting = ensure_sorting;
return nv;
}
static void gt_gff3_visitor_init(GtGFF3Visitor *gff3_visitor)
{
gff3_visitor->version_string_shown = false;
gff3_visitor->fasta_directive_shown = false;
gff3_visitor->id_counter = gt_string_distri_new();
gff3_visitor->feature_node_to_id_array =
gt_hashmap_new(GT_HASH_DIRECT, NULL, (GtFree) gt_array_delete);
gff3_visitor->feature_node_to_unique_id_str =
gt_hashmap_new(GT_HASH_DIRECT, NULL, (GtFree) gt_str_delete);
gff3_visitor->fasta_width = 0;
gff3_visitor->used_ids = gt_cstr_table_new();
/* XXX */
gff3_visitor->retain_ids = getenv("GT_RETAINIDS") ? true : false;
gff3_visitor->allow_nonunique_ids = false;
}
GtNodeStream* gt_sequence_node_add_stream_new(GtNodeStream *in_stream,
GtRegionMapping *rm,
GT_UNUSED GtError *err)
{
GtNodeStream *ns = gt_node_stream_create(gt_sequence_node_add_stream_class(),
gt_node_stream_is_sorted(in_stream));
GtSequenceNodeAddStream *s = gt_sequence_node_add_stream_cast(ns);
gt_assert(in_stream);
s->rm = rm;
s->in_stream = gt_node_stream_ref(in_stream);
s->seqid_table = gt_cstr_table_new();
s->seqids = NULL;
s->cur_seqid = 0;
s->collect_vis = gt_collect_ids_visitor_new(s->seqid_table);
return ns;
}
GtNodeVisitor* gt_gff3_visitor_new(GtFile *outfp)
{
GtNodeVisitor *nv = gt_node_visitor_create(gt_gff3_visitor_class());
GtGFF3Visitor *gff3_visitor = gff3_visitor_cast(nv);
gff3_visitor->version_string_shown = false;
gff3_visitor->fasta_directive_shown = false;
gff3_visitor->id_counter = gt_string_distri_new();
gff3_visitor->feature_node_to_id_array =
gt_hashmap_new(GT_HASH_DIRECT, NULL, (GtFree) gt_array_delete);
gff3_visitor->feature_node_to_unique_id_str =
gt_hashmap_new(GT_HASH_DIRECT, NULL, (GtFree) gt_str_delete);
gff3_visitor->fasta_width = 0;
gff3_visitor->outfp = outfp;
gff3_visitor->used_ids = gt_cstr_table_new();
gff3_visitor->retain_ids = false;
return nv;
}
/* takes ownership of <files> */
static GtNodeStream* gff3_in_stream_plain_new(GtStrArray *files,
bool ensure_sorting)
{
GtNodeStream *ns = gt_node_stream_create(gt_gff3_in_stream_plain_class(),
ensure_sorting);
GtGFF3InStreamPlain *gff3_in_stream_plain = gff3_in_stream_plain_cast(ns);
gff3_in_stream_plain->next_file = 0;
gff3_in_stream_plain->files = files;
gff3_in_stream_plain->stdinstr = gt_str_new_cstr("stdin");
gff3_in_stream_plain->ensure_sorting = ensure_sorting;
gff3_in_stream_plain->stdin_argument = false;
gff3_in_stream_plain->file_is_open = false;
gff3_in_stream_plain->fpin = NULL;
gff3_in_stream_plain->line_number = 0;
gff3_in_stream_plain->genome_node_buffer = gt_queue_new();
gff3_in_stream_plain->checkids = false;
gff3_in_stream_plain->checkregions = false;
gff3_in_stream_plain->gff3_parser = gt_gff3_parser_new(NULL);
gff3_in_stream_plain->used_types = gt_cstr_table_new();
gff3_in_stream_plain->progress_bar = false;
return ns;
}