EDB_root_bact Namespace Reference

Functions
void	calc_no_of_all (const char *string_to_scan, long *group, long *species)
ED4_returncode	fill_species (ED4_multi_species_manager *multi_species_manager, ED4_reference_terminals &refterms, const char *str, int *index, int group_depth, arb_progress *progress)
ED4_returncode	fill_data (ED4_multi_species_manager *multi_species_manager, ED4_reference_terminals &refterms, char *str, int group_depth, ED4_datamode datamode)
ED4_returncode	search_sequence_data_rek (ED4_multi_sequence_manager *multi_sequence_manager, ED4_reference_terminals &refterms, GBDATA *gb_ali_xxx, int count_too, ED4_index *max_sequence_terminal_length, bool isSAI)
void	scan_string (ED4_multi_species_manager *parent, ED4_reference_terminals &refterms, const char *str, int *index, arb_progress &progress)
void	save_current_config (char *confname)

Function Documentation

void EDB_root_bact::calc_no_of_all	(	const char *	string_to_scan,
		long *	group,
		long *	species
	)

Definition at line 20 of file EDB_root_bact.cxx.

Referenced by ED4_root::create_hierarchy().

ED4_returncode EDB_root_bact::fill_species	(	ED4_multi_species_manager *	multi_species_manager,
		ED4_reference_terminals &	refterms,
		const char *	str,
		int *	index,
		int	group_depth,
		arb_progress *	progress
	)

Definition at line 255 of file EDB_root_bact.cxx.

References arb_progress::aborted(), ARB_strndup(), aw_message(), e4_assert, ED4_counter, ED4_D_EXTENDED, ED4_D_SPECIES, ED4_exit(), ED4_R_ERROR, ED4_R_OK, ED4_R_WARNING, fill_data(), GBS_global_string_copy(), arb_progress::inc(), MAXNAMELEN, and message().

Referenced by ED4_get_marked_from_menu(), insert_new_species_terminal(), and scan_string().

ED4_returncode EDB_root_bact::fill_data	(	ED4_multi_species_manager *	multi_species_manager,
		ED4_reference_terminals &	refterms,
		char *	str,
		int	group_depth,
		ED4_datamode	datamode
	)

Definition at line 42 of file EDB_root_bact.cxx.

References ED4_container::append_member(), BRACKET_WIDTH, GBS_strstruct::cat(), e4_assert, ED4_counter, ED4_D_EXTENDED, ED4_D_SPECIES, ED4_R_BREAK, ED4_R_OK, ED4_ROOT, ED4_SP_SAI, ED4_SP_SPECIES, FLAG_WIDTH, GB_entry(), gb_main, GBT_find_SAI(), GBT_find_species(), ED4_root::get_alignment_name(), ED4_root::get_gb_main(), ED4_base::get_parent(), BaseFrequencies::ignore_me(), LEV_GROUP, LEV_ROOTGROUP, max_seq_terminal_length, MAX_SHOWN_MISSING_SPECIES, MAXNAME_WIDTH, NAME_BUFFERSIZE, not_found_counter, not_found_message, NULp, PROP_DRAGABLE, PROP_IS_HANDLE, PROP_MOVABLE, PROP_SELECTABLE, search_sequence_data_rek(), ED4_reference_terminals::sequence(), ED4_base::set_property(), ED4_abstract_group_manager::table(), and TERMINAL_HEIGHT.

Referenced by fill_species().

ED4_returncode EDB_root_bact::search_sequence_data_rek	(	ED4_multi_sequence_manager *	multi_sequence_manager,
		ED4_reference_terminals &	refterms,
		GBDATA *	gb_ali_xxx,
		int	count_too,
		ED4_index *	max_sequence_terminal_length,
		bool	isSAI
	)

Definition at line 137 of file EDB_root_bact.cxx.

References ED4_container::append_member(), e4_assert, ED4_counter, ED4_G_SEQUENCES, ED4_R_OK, ED4_ROOT, ED4_base::extension, ED4_root::first_window, GB_child(), GB_DB, GB_FLOATS, GB_get_grandfather(), GB_INTS, GB_nextChild(), GB_read_count(), GB_read_int(), GB_read_key(), GB_read_type(), GB_searchOrCreate_int(), ED4_base::get_consensus_relevant_terminal(), ED4_window::get_device(), ED4_base::get_name_of_species(), AW_stylable::get_string_size(), ED4_scroll_links::link_for_hor_slider, max, MAXSEQUENCECHARACTERLENGTH, NAME_BUFFERSIZE, NULp, PROP_ALIGNMENT_DATA, PROP_CONSENSUS_RELEVANT, PROP_CURSOR_ALLOWED, PROP_DRAGABLE, PROP_IS_HANDLE, PROP_MOVABLE, PROP_SELECTABLE, ED4_root::scroll_links, ED4_reference_terminals::sequence(), ED4_reference_terminals::sequence_info(), SEQUENCE_INFO_WIDTH, ED4_base::set_both_links(), ED4_base::set_property(), ED4_base::set_species_pointer(), ED4_extension::size, ED4_abstract_sequence_terminal::species_name, TERMINAL_HEIGHT, type, and WIDTH.

Referenced by fill_data().

void EDB_root_bact::scan_string	(	ED4_multi_species_manager *	parent,
		ED4_reference_terminals &	refterms,
		const char *	str,
		int *	index,
		arb_progress &	progress
	)

Definition at line 340 of file EDB_root_bact.cxx.

References ED4_build_group_manager_end(), ED4_build_group_manager_start(), ED4_counter, fill_species(), GB_GROUP_NAME_MAX, and ED4_manager::hide_children().

Referenced by ED4_root::create_hierarchy().

void EDB_root_bact::save_current_config

(

char *

confname

)

Definition at line 385 of file EDB_root_bact.cxx.

References aw_message_if(), ED4_ROOT, error(), gb_main, GBS_log_action_to(), ED4_base::generate_configuration_string(), GBT_config::get_comment(), ED4_root::get_device_manager(), ED4_root::get_gb_main(), ED4_base::is_area_manager(), ED4_container::member(), ED4_container::members(), NULp, GBS_strstruct::release(), GBT_config::save(), GBT_config::set_comment(), and GBT_config::set_definition().

Referenced by ED4_saveConfiguration().