#include <ed4_class.hxx>

Inheritance diagram for ED4_manager:

Collaboration diagram for ED4_manager:

Public Member Functions
	E4B_AVOID_UNNEEDED_CASTS (manager)

	DECLARE_DUMP_FOR_BASECLASS (ED4_manager, ED4_base)

void	add_delete_callback (const ED4_managerCallback &cb)

void	remove_delete_callback (const ED4_managerCallback &cb)

int	refresh_flag_ok ()

void	changed_by_database () OVERRIDE

void	deleted_from_database () OVERRIDE

void	Show (bool refresh_all, bool is_cleared) OVERRIDE

bool	calc_bounding_box () FINAL_OVERRIDE

ED4_returncode	distribute_children ()

ED4_returncode	event_sent_by_parent (AW_event event, AW_window aww) FINAL_OVERRIDE

void	request_refresh (int clear=1) FINAL_OVERRIDE

ED4_returncode	clear_refresh ()

void	resize_requested_children () OVERRIDE

void	update_requested_children () OVERRIDE

void	delete_requested_children () OVERRIDE

void	Delete () FINAL_OVERRIDE

ED4_returncode	move_requested_by_parent (ED4_move_info *mi)

void	create_consensus (ED4_abstract_group_manager upper_group_manager, arb_progress progress)

ARB_ERROR	route_down_hierarchy (const ED4_route_cb &cb) FINAL_OVERRIDE

ED4_base *	find_first_that (ED4_level level, const ED4_basePredicate &fulfills_predicate)

ED4_returncode	move_requested_by_child (ED4_move_info *moveinfo)

void	resize_requested_by_child ()

ED4_returncode	refresh_requested_by_child ()

void	delete_requested_by_child ()

void	update_requested_by_child ()

ED4_base *	get_defined_level (ED4_level lev) const

void	update_consensus (ED4_manager old_parent, ED4_manager new_parent, ED4_base *sequence)

ED4_returncode	rebuild_consensi (ED4_base *start_species, ED4_update_flag update_flag)

ED4_returncode	check_in_bases (ED4_base *added_base)

ED4_returncode	check_out_bases (ED4_base *subbed_base)

ED4_returncode	update_bases (const ED4_base old_base, const ED4_base new_base, PosRange range=PosRange::whole())

ED4_returncode	update_bases (const char old_seq, int old_len, const char new_seq, int new_len, PosRange range=PosRange::whole())

ED4_returncode	update_bases (const char old_seq, int old_len, const ED4_base new_base, PosRange range=PosRange::whole())

ED4_returncode	update_bases (const BaseFrequencies old_table, const BaseFrequencies new_table, PosRange range=PosRange::whole())

ED4_returncode	update_bases_and_rebuild_consensi (const char old_seq, int old_len, ED4_base species, ED4_update_flag update_flag, PosRange range=PosRange::whole())

ED4_returncode	handle_move (ED4_move_info *moveinfo)

ED4_base *	get_competent_child (AW_pos x, AW_pos y, ED4_properties relevant_prop)

ED4_base *	get_competent_clicked_child (AW_pos x, AW_pos y, ED4_properties relevant_prop)

ED4_base *	search_spec_child_rek (ED4_level level)

ED4_base *	search_ID (const char *id) FINAL_OVERRIDE

void	remove_callbacks () OVERRIDE

ED4_terminal *	get_first_terminal (int start_index=0) const

ED4_terminal *	get_last_terminal (int start_index=-1) const

void	hide_children ()

void	unhide_children ()

bool	is_hidden () const FINAL_OVERRIDE

	ED4_manager (const ED4_objspec &spec_, const char id, AW_pos width, AW_pos height, ED4_manager parent)

	~ED4_manager () OVERRIDE

Public Member Functions inherited from ED4_base
void	draw_bb (int color)

	DECLARE_DUMP_FOR_ROOTCLASS (ED4_base)

GBDATA *	get_species_pointer () const

void	set_species_pointer (GBDATA *gbd)

bool	has_callback () const

int	adjust_clipping_rectangle ()

void	resize_dynamic ()

ED4_returncode	clear_background (int color=0)

void	set_links (ED4_base width_ref, ED4_base height_ref)

void	set_both_links (ED4_base *ref)

void	set_property (ED4_properties prop)

void	clr_property (ED4_properties prop)

bool	has_property (ED4_properties prop) const

void	calc_rel_coords (AW_pos x, AW_pos y)

void	calc_world_coords (AW_pos x, AW_pos y) const

const AW::Position &	calc_world_coords () const

void	update_world_coords_cache () const

AW::Rectangle	get_win_area (ED4_window *ed4w) const

void	request_resize ()

void	request_resize_of_linked ()

void	resize_requested_by_link (ED4_base *link)

void	set_update ()

int	calc_group_depth ()

void	check_all ()

short	in_border (AW_pos abs_x, AW_pos abs_y, ED4_movemode mode)

ED4_returncode	set_width ()

ED4_AREA_LEVEL	get_area_level (ED4_multi_species_manager **multi_species_manager=NULp) const

ED4_manager *	get_parent (ED4_level lev) const

void	unlink_from_parent ()

bool	has_parent (ED4_manager *Parent)

bool	is_child_of (ED4_manager *Parent)

virtual char *	resolve_pointer_to_string_copy (int *str_len=NULp) const

virtual const char *	resolve_pointer_to_char_pntr (int *str_len=NULp) const

ED4_group_manager *	is_in_folded_group () const

char *	get_name_of_species ()

ED4_terminal *	get_next_terminal ()

ED4_terminal *	get_prev_terminal ()

void	generate_configuration_string (GBS_strstruct &buffer)

const ED4_terminal *	get_consensus_relevant_terminal () const

	ED4_base (const ED4_objspec &spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)

virtual	~ED4_base ()

int	is_terminal () const

int	is_text_terminal () const

int	is_species_name_terminal () const

int	is_sequence_info_terminal () const

int	is_sequence_terminal () const

int	is_orf_terminal () const

int	is_pure_text_terminal () const

int	is_columnStat_terminal () const

int	is_bracket_terminal () const

int	is_spacer_terminal () const

int	is_line_terminal () const

int	is_flag_header_terminal () const

int	is_flag_terminal () const

int	is_manager () const

int	is_sequence_manager () const

int	is_multi_name_manager () const

int	is_name_manager () const

int	is_multi_species_manager () const

int	is_multi_sequence_manager () const

int	is_device_manager () const

int	is_group_manager () const

int	is_root_group_manager () const

int	is_abstract_group_manager () const

int	is_species_manager () const

int	is_area_manager () const

	E4B_DECL_CASTOP (area_manager)

	E4B_DECL_CASTOP (abstract_group_manager)

	E4B_DECL_CASTOP (bracket_terminal)

	E4B_DECL_CASTOP (columnStat_terminal)

	E4B_DECL_CASTOP (consensus_sequence_terminal)

	E4B_DECL_CASTOP (device_manager)

	E4B_DECL_CASTOP (group_manager)

	E4B_DECL_CASTOP (line_terminal)

	E4B_DECL_CASTOP (manager)

	E4B_DECL_CASTOP (multi_name_manager)

	E4B_DECL_CASTOP (multi_sequence_manager)

	E4B_DECL_CASTOP (multi_species_manager)

	E4B_DECL_CASTOP (name_manager)

	E4B_DECL_CASTOP (orf_terminal)

	E4B_DECL_CASTOP (pure_text_terminal)

	E4B_DECL_CASTOP (root_group_manager)

	E4B_DECL_CASTOP (sequence_info_terminal)

	E4B_DECL_CASTOP (sequence_manager)

	E4B_DECL_CASTOP (sequence_terminal)

	E4B_DECL_CASTOP (spacer_terminal)

	E4B_DECL_CASTOP (species_manager)

	E4B_DECL_CASTOP (species_name_terminal)

	E4B_DECL_CASTOP (terminal)

	E4B_DECL_CASTOP (text_terminal)

	E4B_DECL_CASTOP (flag_header_terminal)

	E4B_DECL_CASTOP (flag_terminal)

ED4_species_manager *	containing_species_manager () const

bool	is_consensus_manager () const

bool	is_SAI_manager () const

bool	is_species_seq_manager () const

ED4_species_type	get_species_type () const

bool	inside_consensus_manager () const

bool	inside_SAI_manager () const

bool	inside_species_seq_manager () const

bool	is_consensus_terminal () const

bool	is_SAI_terminal () const

bool	is_species_seq_terminal () const

bool	is_consensus_sequence_terminal () const

Public Member Functions inherited from ED4_container
ED4_manager *	owner ()

const ED4_manager *	owner () const

ED4_base *	member (ED4_index i) const

ED4_index	members () const

bool	empty () const

void	clear ()

void	insert_member (ED4_base *new_member)

void	append_member (ED4_base *new_member)

ED4_returncode	remove_member (ED4_base *member)

ED4_index	search_member (ED4_extension *location, ED4_properties prop)

ED4_returncode	search_target_species (ED4_extension location, ED4_properties prop, ED4_base *found_member, ED4_level return_level)

ED4_returncode	move_member (ED4_index old_pos, ED4_index new_pos)

bool	members_ok () const

	ED4_container ()

virtual	~ED4_container ()

Additional Inherited Members
Static Public Member Functions inherited from ED4_base
static void	touch_world_cache ()

Public Attributes inherited from ED4_base
const ED4_objspec &	spec

ED4_manager *	parent

ED4_properties	dynamic_prop

char *	id

ED4_index	index

ED4_base *	width_link

ED4_base *	height_link

ED4_extension	extension

ED4_update_info	update_info

struct {
unsigned int hidden: 1

}	flag

Protected Member Functions inherited from ED4_container
bool	valid_index (ED4_index idx) const

bool	existing_index (ED4_index idx) const

Detailed Description

Definition at line 1190 of file ed4_class.hxx.

Constructor & Destructor Documentation

ED4_manager::ED4_manager	(	const ED4_objspec &	spec_,
		const char *	id,
		AW_pos	width,
		AW_pos	height,
		ED4_manager *	parent
	)

Definition at line 1213 of file ED4_manager.cxx.

ED4_manager::~ED4_manager ( )

Definition at line 1217 of file ED4_manager.cxx.

References ED4_container::clear().

Member Function Documentation

ED4_manager::E4B_AVOID_UNNEEDED_CASTS ( manager )

ED4_manager::DECLARE_DUMP_FOR_BASECLASS	(	ED4_manager	,
		ED4_base
	)

void ED4_manager::add_delete_callback ( const ED4_managerCallback & cb )

inline

Definition at line 1197 of file ed4_class.hxx.

References ED4_cb_list< BASE, BASECB >::add_cb().

Referenced by ED4_reference::define().

void ED4_manager::remove_delete_callback ( const ED4_managerCallback & cb )

inline

Definition at line 1198 of file ed4_class.hxx.

References ED4_cb_list< BASE, BASECB >::remove_cb().

Referenced by ED4_reference::clear().

int ED4_manager::refresh_flag_ok ( )

Definition at line 677 of file ED4_manager.cxx.

References fflush(), ED4_base::id, ED4_base::is_manager(), ED4_container::member(), ED4_container::members(), ED4_update_info::refresh, and ED4_base::update_info.

Referenced by refresh_requested_by_child(), and Show().

void ED4_manager::changed_by_database ( )

virtual

Reimplemented from ED4_base.

Definition at line 34 of file ED4_base.cxx.

References request_refresh().

void ED4_manager::deleted_from_database ( )

virtual

Reimplemented from ED4_base.

Definition at line 126 of file ED4_base.cxx.

References e4_assert, ED4_ROOT, ED4_U_UP, ED4_root::get_gb_main(), ED4_base::is_species_manager(), NULp, ED4_base::parent, rebuild_consensi(), ED4_container::remove_member(), ED4_base::request_resize(), ta, and update_consensus().

void ED4_manager::Show	(	bool	refresh_all,
		bool	is_cleared
	)

virtual

Implements ED4_base.

Reimplemented in FINAL_TYPE< SEQTYPE >, ED4_root_group_manager, and FINAL_TYPE< SEQTYPE >.

Definition at line 941 of file ED4_manager.cxx.

References ED4_base::adjust_clipping_rectangle(), AW_screen_area::b, ED4_base::calc_world_coords(), ED4_update_info::clear_at_refresh, ED4_base::clear_background(), current_device(), current_ed4w(), e4_assert, ED4_container::existing_index(), ED4_base::extension, ED4_base::flag, AW_clipable::get_cliprect(), HEIGHT, ED4_base::hidden, AW_screen_area::l, ED4_container::member(), ED4_container::members(), AW::nearlyEqual(), AW_device::pop_clip_scale(), PROP_HORIZONTAL, PROP_VERTICAL, AW_device::push_clip_scale(), AW_screen_area::r, ED4_update_info::refresh, refresh_flag_ok(), ED4_base::Show(), ED4_extension::size, ED4_base::spec, ED4_objspec::static_prop, AW_screen_area::t, ED4_base::update_info, WIDTH, ED4_foldable::win_to_world_coords(), and y.

Referenced by ED4_root_group_manager::Show().

bool ED4_manager::calc_bounding_box ( )

virtual

Implements ED4_base.

Definition at line 715 of file ED4_manager.cxx.

References ED4_container::existing_index(), ED4_base::extension, ED4_base::flag, HEIGHT, ED4_base::hidden, ED4_container::member(), ED4_extension::position, PROP_HORIZONTAL, PROP_VERTICAL, ED4_base::request_resize_of_linked(), ED4_extension::set_size_does_change(), ED4_extension::size, ED4_base::spec, ED4_objspec::static_prop, ED4_base::touch_world_cache(), WIDTH, X_POS, and Y_POS.

Referenced by resize_requested_children().

ED4_returncode ED4_manager::distribute_children ( )

Definition at line 760 of file ED4_manager.cxx.

References ED4_R_OK, ED4_container::existing_index(), ED4_base::extension, HEIGHT, max, ED4_container::member(), ED4_extension::position, PROP_HORIZONTAL, PROP_VERTICAL, refresh_requested_by_child(), ED4_extension::size, ED4_base::spec, ED4_objspec::static_prop, ED4_base::touch_world_cache(), WIDTH, X_POS, and Y_POS.

Referenced by resize_requested_children().

ED4_returncode ED4_manager::event_sent_by_parent	(	AW_event *	event,
		AW_window *	aww
	)

virtual

Implements ED4_base.

Definition at line 644 of file ED4_manager.cxx.

References ED4_base::calc_rel_coords(), ED4_R_BREAK, ED4_R_IMPOSSIBLE, ED4_base::event_sent_by_parent(), ED4_container::existing_index(), ED4_container::member(), ED4_extension::position, ED4_container::search_member(), ED4_base::spec, ED4_objspec::static_prop, X_POS, and Y_POS.

void ED4_manager::request_refresh ( int clear = 1 )

virtual

Implements ED4_base.

Definition at line 1187 of file ED4_manager.cxx.

References ED4_container::existing_index(), ED4_container::member(), ED4_base::parent, refresh_requested_by_child(), ED4_base::request_refresh(), ED4_update_info::set_clear_at_refresh(), ED4_update_info::set_refresh(), and ED4_base::update_info.

Referenced by changed_by_database().

ED4_returncode ED4_manager::clear_refresh ( )

Definition at line 1068 of file ED4_manager.cxx.

References e4_assert, ED4_R_OK, ED4_base::is_manager(), ED4_container::member(), ED4_container::members(), ED4_update_info::refresh, ED4_update_info::set_clear_at_refresh(), ED4_update_info::set_refresh(), and ED4_base::update_info.

void ED4_manager::resize_requested_children ( )

virtual

Implements ED4_base.

Reimplemented in ED4_root_group_manager, and FINAL_TYPE< SEQTYPE >.

Definition at line 808 of file ED4_manager.cxx.

References calc_bounding_box(), distribute_children(), ED4_container::existing_index(), ED4_container::member(), ED4_base::request_resize(), ED4_update_info::resize, ED4_base::resize_requested_children(), ED4_update_info::set_resize(), and ED4_base::update_info.

Referenced by ED4_root_group_manager::resize_requested_children().

void ED4_manager::update_requested_children ( )

virtual

Implements ED4_base.

Reimplemented in ED4_multi_species_manager.

Definition at line 1113 of file ED4_manager.cxx.

References e4_assert, ED4_container::member(), ED4_container::members(), ED4_base::update_info, ED4_update_info::update_requested, and ED4_base::update_requested_children().

Referenced by ED4_multi_species_manager::update_requested_children().

void ED4_manager::delete_requested_children ( )

virtual

Implements ED4_base.

Reimplemented in ED4_multi_species_manager.

Definition at line 1144 of file ED4_manager.cxx.

References ED4_root::announce_deletion(), ED4_update_info::delete_requested, ED4_base::delete_requested_children(), e4_assert, ED4_ROOT, ED4_container::member(), ED4_container::members(), ED4_base::unlink_from_parent(), and ED4_base::update_info.

Referenced by ED4_multi_species_manager::delete_requested_children().

void ED4_manager::Delete ( )

virtual

Implements ED4_base.

Definition at line 1178 of file ED4_manager.cxx.

References ED4_cb_list< BASE, BASECB >::call(), ED4_cb_list< BASE, BASECB >::clear(), ED4_base::Delete(), ED4_container::member(), and ED4_container::members().

Referenced by ED4_text_terminal::deleted_from_database(), ED4_sequence_terminal::deleted_from_database(), ED4_terminal::kill_object(), and toggle_detailed_column_stat().

ED4_returncode ED4_manager::move_requested_by_parent ( ED4_move_info * mi )

Definition at line 587 of file ED4_manager.cxx.

References ED4_R_IMPOSSIBLE, ED4_move_info::end_x, ED4_move_info::end_y, handle_move(), ED4_base::in_border(), and ED4_move_info::mode.

Referenced by handle_move().

void ED4_manager::create_consensus	(	ED4_abstract_group_manager *	upper_group_manager,
		arb_progress *	progress
	)

ARB_ERROR ED4_manager::route_down_hierarchy ( const ED4_route_cb & cb )

virtual

Reimplemented from ED4_base.

Definition at line 392 of file ED4_base.cxx.

References cb, error(), ED4_container::member(), ED4_container::members(), and ED4_base::route_down_hierarchy().

Referenced by create_list_of_loaded_species(), create_new_species(), dot_missing_bases(), ED4_consensus_display_changed(), ED4_with_all_loaded_species(), executeKeystroke(), and rebuild_consensi().

ED4_base * ED4_manager::find_first_that	(	ED4_level	level,
		const ED4_basePredicate &	fulfills_predicate
	)

Definition at line 402 of file ED4_base.cxx.

References ED4_base::is_manager(), ED4_objspec::level, ED4_container::member(), ED4_container::members(), NULp, and ED4_base::spec.

Referenced by ED4_find_MoreSequences_manager(), ED4_find_SAI_name_terminal(), ED4_find_species_name_terminal(), and ED4_find_species_or_SAI_name_terminal().

ED4_returncode ED4_manager::move_requested_by_child ( ED4_move_info * moveinfo )

void ED4_manager::resize_requested_by_child ( )

inline

Definition at line 2192 of file ed4_class.hxx.

References ED4_base::request_resize(), ED4_update_info::resize, and ED4_base::update_info.

Referenced by createGroupFromSelected(), ED4_remap::mark_compile_needed_force(), ED4_base::request_resize(), and toggle_detailed_column_stat().

ED4_returncode ED4_manager::refresh_requested_by_child ( )

Definition at line 664 of file ED4_manager.cxx.

References e4_assert, ED4_R_OK, ED4_base::parent, ED4_update_info::refresh, refresh_flag_ok(), refresh_requested_by_child(), ED4_update_info::set_refresh(), and ED4_base::update_info.

Referenced by distribute_children(), refresh_requested_by_child(), request_refresh(), and ED4_terminal::request_refresh().

void ED4_manager::delete_requested_by_child ( )

Definition at line 1097 of file ED4_manager.cxx.

References ED4_update_info::delete_requested, delete_requested_by_child(), ED4_base::parent, and ED4_base::update_info.

Referenced by ED4_terminal::Delete(), and delete_requested_by_child().

void ED4_manager::update_requested_by_child ( )

Definition at line 1091 of file ED4_manager.cxx.

References ED4_base::parent, ED4_base::update_info, ED4_update_info::update_requested, and update_requested_by_child().

Referenced by createGroupFromSelected(), ED4_multi_species_manager::invalidate_species_counters(), ED4_base::set_update(), and update_requested_by_child().

ED4_base * ED4_manager::get_defined_level ( ED4_level lev ) const

Definition at line 696 of file ED4_base.cxx.

References e4_assert, ED4_base::is_group_manager(), ED4_base::is_manager(), ED4_base::is_multi_species_manager(), ED4_objspec::level, ED4_container::member(), ED4_container::members(), NULp, and ED4_base::spec.

Referenced by ED4_group_manager::fold(), ED4_area_manager::get_multi_species_manager(), ED4_abstract_group_manager::get_multi_species_manager(), ED4_base::set_width(), and toggle_consensus_display().

void ED4_manager::update_consensus	(	ED4_manager *	old_parent,
		ED4_manager *	new_parent,
		ED4_base *	sequence
	)

Definition at line 395 of file ED4_manager.cxx.

References check_in_bases(), and check_out_bases().

Referenced by deleted_from_database(), handle_move(), and remove_from_consensus().

ED4_returncode ED4_manager::rebuild_consensi	(	ED4_base *	start_species,
		ED4_update_flag	update_flag
	)

Definition at line 117 of file ED4_manager.cxx.

References ED4_R_OK, ED4_U_UP, ED4_U_UP_DOWN, ARB_ERROR::expect_no_error(), ED4_base::is_consensus_manager(), ED4_base::is_group_manager(), ED4_container::member(), ED4_container::members(), NULp, ED4_base::parent, rebuild_consensus(), and route_down_hierarchy().

Referenced by deleted_from_database(), ED4_sequence_terminal::deleted_from_database(), executeKeystroke(), handle_move(), and update_bases_and_rebuild_consensi().

ED4_returncode ED4_manager::check_in_bases ( ED4_base * added_base )

Definition at line 153 of file ED4_manager.cxx.

References e4_assert, ED4_R_OK, ED4_base::get_consensus_relevant_terminal(), ED4_base::is_group_manager(), ED4_base::is_root_group_manager(), ED4_base::is_species_manager(), NULp, ED4_terminal::resolve_pointer_to_string_copy(), seq, and update_bases().

Referenced by update_consensus().

ED4_returncode ED4_manager::check_out_bases ( ED4_base * subbed_base )

Definition at line 177 of file ED4_manager.cxx.

References e4_assert, ED4_R_OK, ED4_base::get_consensus_relevant_terminal(), ED4_base::is_group_manager(), ED4_base::is_root_group_manager(), ED4_base::is_species_manager(), NULp, ED4_terminal::resolve_pointer_to_string_copy(), seq, and update_bases().

Referenced by update_consensus().

ED4_returncode ED4_manager::update_bases	(	const ED4_base *	old_base,
		const ED4_base *	new_base,
		PosRange	range = `PosRange::whole()`
	)

Definition at line 267 of file ED4_manager.cxx.

References e4_assert, ED4_R_OK, ED4_base::get_consensus_relevant_terminal(), ED4_base::is_group_manager(), ED4_base::is_root_group_manager(), ED4_base::is_species_manager(), and ED4_terminal::resolve_pointer_to_string_copy().

Referenced by check_in_bases(), check_out_bases(), ED4_sequence_terminal::deleted_from_database(), insert_new_species_terminal(), update_bases(), and update_bases_and_rebuild_consensi().

ED4_returncode ED4_manager::update_bases	(	const char *	old_seq,
		int	old_len,
		const char *	new_seq,
		int	new_len,
		PosRange	range = `PosRange::whole()`
	)

Definition at line 317 of file ED4_manager.cxx.

References add(), BaseFrequencies::changed_range(), e4_assert, ED4_R_OK, ED4_ROOT, PosRange::is_whole(), ED4_remap::mark_compile_needed(), min, ED4_root_group_manager::remap(), ED4_root::root_group_man, and WITH_ALL_ABOVE_GROUP_MANAGER_TABLES.

ED4_returncode ED4_manager::update_bases	(	const char *	old_seq,
		int	old_len,
		const ED4_base *	new_base,
		PosRange	range = `PosRange::whole()`
	)

Definition at line 200 of file ED4_manager.cxx.

References BaseFrequencies::changed_range(), e4_assert, ED4_base::get_consensus_relevant_terminal(), ED4_base::is_species_manager(), PosRange::is_whole(), min, NULp, ED4_terminal::resolve_pointer_to_string_copy(), and update_bases().

ED4_returncode ED4_manager::update_bases	(	const BaseFrequencies *	old_table,
		const BaseFrequencies *	new_table,
		PosRange	range = `PosRange::whole()`
	)

Definition at line 354 of file ED4_manager.cxx.

References add(), BaseFrequencies::changed_range(), e4_assert, ED4_R_OK, ED4_ROOT, PosRange::is_whole(), ED4_remap::mark_compile_needed(), ED4_root_group_manager::remap(), ED4_root::root_group_man, and WITH_ALL_ABOVE_GROUP_MANAGER_TABLES.

ED4_returncode ED4_manager::update_bases_and_rebuild_consensi	(	const char *	old_seq,
		int	old_len,
		ED4_base *	species,
		ED4_update_flag	update_flag,
		PosRange	range = `PosRange::whole()`
	)