#include <ed4_extern.hxx>
#include "ed4_awars.hxx"
#include "ed4_class.hxx"
#include "ed4_edit_string.hxx"
#include "ed4_nds.hxx"
#include "ed4_list.hxx"
#include "ed4_seq_colors.hxx"
#include "ed4_flags.hxx"
#include <iupac.h>
#include <consensus_config.h>
#include <item_sel_list.h>
#include <macros.hxx>
#include <awt.hxx>
#include <awt_config_manager.hxx>
#include <awt_misc.hxx>
#include <awt_sel_boxes.hxx>
#include <aw_awars.hxx>
#include <AW_helix.hxx>
#include <aw_msg.hxx>
#include <AW_rename.hxx>
#include <aw_root.hxx>
#include <ad_config.h>
#include <arb_defs.h>
#include <arb_global_defs.h>
#include <arb_progress.h>
#include <cctype>
#include <limits.h>
#include <vector>

Include dependency graph for ED4_no_class.cxx:

Classes
struct	group_folding

struct	cursorpos

struct	SpeciesMergeList

Macros
#define	SIGNIFICANT_FIELD_CHARS 30

Functions
static ARB_ERROR	update_group_folding (ED4_base base, group_folding folding)

static void	calculate_group_folding (group_folding &folding)

void	ED4_calc_terminal_extentions ()

static ARB_ERROR	update_extension_size (ED4_base *base)

void	ED4_resize_all_extensions ()

static ARB_ERROR	call_edit (ED4_base object, const ED4_work_info work_info)

static int	get_max_slider_xpos ()

static int	get_max_slider_ypos ()

static void	ed4_scroll (AW_window *aww, int xdiff, int ydiff, bool use_scroll_speed)

static void	scrollHalfPage (bool backwards, bool horizontal)

static void	executeKeystroke (AW_event *event, int repeatCount)

void	ED4_remote_event (AW_event *faked_event)

void	ED4_input_cb (AW_window *aww)

void	ED4_vertical_change_cb (AW_window *aww)

void	ED4_horizontal_change_cb (AW_window *aww)

void	ED4_scrollbar_change_cb (AW_window *aww)

void	ED4_motion_cb (AW_window *aww)

void	ED4_remote_set_cursor_cb (AW_root *awr)

void	ED4_jump_to_cursor_position (AW_window aww, const char awar_name, PositionType posType)

void	ED4_set_helixnr (AW_window aww, const char awar_name)

void	ED4_set_iupac (AW_window aww, const char awar_name)

void	ED4_exit ()

void	ED4_quit_editor (AW_window *aww)

static unsigned	ED4_timer (AW_root *)

void	ED4_trigger_instant_refresh ()

void	ED4_request_full_refresh ()

void	ED4_request_full_instant_refresh ()

void	ED4_request_relayout ()

static void	createGroupFromSelected (GB_CSTR group_name, GB_CSTR field_name, GB_CSTR field_content)

static void	group_species (bool use_field, AW_window *use_as_main_window)

static void	group_species_by_field_content (AW_window , AW_window use_as_main_window, AW_window *window_to_hide)

static AW_window *	create_group_species_by_field_window (AW_root aw_root, AW_window use_as_main_window)

void	group_species_cb (AW_window *aww, bool use_fields)

static GB_ERROR	ED4_load_new_config (char *name)

static ED4_EDITMODE	ED4_get_edit_mode (AW_root *root)

void	ed4_changesecurity (AW_root *root)

void	ed4_change_edit_mode (AW_root *root)

ARB_ERROR	rebuild_consensus (ED4_base *object)

void	ED4_new_editor_window (AW_window *aww)

static void	ED4_start_editor_on_configuration (AW_window *aww)

void	ED4_compression_changed_cb (AW_root *awr)

void	ED4_compression_toggle_changed_cb (AW_root *root, bool hideChanged)

AW_window *	ED4_create_editor_options_window (AW_root *root)

AW_window *	ED4_create_consensus_definition_window (AW_root *root)

static void	consensus_upper_lower_changed_cb (AW_root *awr, bool upper_changed)

void	ED4_create_consensus_awars (AW_root *aw_root)

void	ED4_reloadConfiguration (AW_window *aww)

AW_window *	ED4_create_loadConfiguration_window (AW_root *awr)

void	ED4_saveConfiguration (AW_window *aww, bool hide_aww)

AW_window *	ED4_create_saveConfigurationAs_window (AW_root *awr)

static char *	filter_loadable_SAIs (GBDATA *gb_sai)

AW_window *	ED4_create_loadSAI_window (AW_root *awr)

static GB_ERROR	createDataFromConsensus (GBDATA gb_species, ED4_group_manager group_man)

static ARB_ERROR	add_species_to_merge_list (ED4_base base, SpeciesMergeList smlp, GBDATA gb_species_data)

static int	SpeciesMergeListLength (SpeciesMergeList *sml)

static void	freeSpeciesMergeList (SpeciesMergeList *sml)

bool	nameIsUnique (const char short_name, GBDATA gb_species_data)

static void	create_new_species (AW_window *, SpeciesCreationMode creation_mode)

AW_window *	ED4_create_new_seq_window (AW_root *root, SpeciesCreationMode creation_mode)

Variables
static bool	track_cursor = false

static long	tracked_cursorpos = -1

static int	timer_calls = 0

static int	timer_calls_triggered = 0

static AWT_config_mapping_def	editor_options_config_mapping []

static AWT_config_mapping_def	consensus_config_mapping []

static AWT_predefined_config	predefined_consensus_config []

Macro Definition Documentation

#define SIGNIFICANT_FIELD_CHARS 30

Definition at line 1019 of file ED4_no_class.cxx.

Referenced by createGroupFromSelected(), and group_species().

Function Documentation

static ARB_ERROR update_group_folding	(	ED4_base *	base,
		group_folding *	folding
	)

static

Definition at line 62 of file ED4_no_class.cxx.

References ED4_base::calc_group_depth(), ED4_base::has_property(), ED4_base::is_group_manager(), ED4_base::is_hidden(), max, group_folding::max_depth, group_folding::max_unfolded, group_folding::max_visible, NULp, and PROP_IS_FOLDED.

Referenced by calculate_group_folding().

static void calculate_group_folding ( group_folding & folding )

static

Definition at line 81 of file ED4_no_class.cxx.

References ED4_ROOT, ED4_root::main_manager, and update_group_folding().

Referenced by ED4_calc_terminal_extentions().

void ED4_calc_terminal_extentions ( )

Definition at line 87 of file ED4_no_class.cxx.

References AW_font_limits::ascent, ED4_root::aw_root, AW_root::awar(), BRACKET_WIDTH, calculate_group_folding(), SpeciesFlags::calculate_header_dimensions(), CHARACTEROFFSET, AW_font_limits::descent, ED4_AWAR_NDS_INFO_WIDTH, ED4_G_FLAG_INFO, ED4_G_SEQUENCES, ED4_G_STANDARD, ED4_get_NDS_width(), ED4_ROOT, ED4_root::first_window, FLAG_WIDTH, flags, folding, ED4_root::font_group, ED4_window::get_device(), AW_stylable::get_font_limits(), SpeciesFlags::get_header_length(), AW_font_limits::get_height(), AW_font_group::get_limits(), SpeciesFlags::get_pixel_width(), ED4_root::helix, ED4_root::helix_add_spacing, ED4_root::helix_spacing, INFO_TERM_TEXT_YOFFSET, AW_helix::is_enabled(), group_folding::max_unfolded, MAXINFO_WIDTH, MAXNAME_WIDTH, SpeciesFlags::mutable_instance(), ED4_root::protstruct, AW_awar::read_int(), ED4_root::recalc_font_group(), SEQ_TERM_TEXT_YOFFSET, ED4_root::terminal_add_spacing, TERMINAL_HEIGHT, and AW_font_limits::width.

Referenced by ED4_root::create_first_window(), and ED4_resize_all_extensions().

static ARB_ERROR update_extension_size ( ED4_base * base )

static

Definition at line 224 of file ED4_no_class.cxx.

References NULp, and ED4_base::resize_dynamic().

Referenced by ED4_resize_all_extensions().

void ED4_resize_all_extensions ( )

static ARB_ERROR call_edit	(	ED4_base *	object,
		const ED4_work_info *	work_info
	)

static

static int get_max_slider_xpos ( )

static

Definition at line 318 of file ED4_no_class.cxx.

References ED4_base::calc_world_coords(), current_device(), ED4_ROOT, ED4_base::extension, AW_device::get_area_size(), ED4_scroll_links::link_for_hor_slider, AW_screen_area::r, ED4_root::scroll_links, ED4_extension::size, WIDTH, and y.

Referenced by ED4_horizontal_change_cb(), ed4_scroll(), and ED4_scrollbar_change_cb().

static int get_max_slider_ypos ( )

static

Definition at line 332 of file ED4_no_class.cxx.

References AW_screen_area::b, ED4_base::calc_world_coords(), current_device(), ED4_ROOT, ED4_base::extension, AW_device::get_area_size(), HEIGHT, ED4_scroll_links::link_for_ver_slider, ED4_root::scroll_links, ED4_extension::size, and y.

Referenced by ed4_scroll(), ED4_scrollbar_change_cb(), and ED4_vertical_change_cb().

static void ed4_scroll	(	AW_window *	aww,
		int	xdiff,
		int	ydiff,
		bool	use_scroll_speed
	)

static

Definition at line 346 of file ED4_no_class.cxx.

References ED4_root::aw_root, AW_root::awar(), ED4_AWAR_SCROLL_SPEED_X, ED4_AWAR_SCROLL_SPEED_Y, ED4_horizontal_change_cb(), ED4_ROOT, ED4_vertical_change_cb(), get_max_slider_xpos(), get_max_slider_ypos(), AW_awar::read_int(), AW_window::set_horizontal_scrollbar_position(), AW_window::set_vertical_scrollbar_position(), AW_window::slider_pos_horizontal, and AW_window::slider_pos_vertical.

Referenced by ED4_input_cb(), ED4_motion_cb(), and scrollHalfPage().

static void scrollHalfPage	(	bool	backwards,
		bool	horizontal
	)

static

Definition at line 384 of file ED4_no_class.cxx.

References ED4_window::aww, current_ed4w(), ed4_scroll(), ED4_scrolled_rectangle::get_window_rect(), AW::Rectangle::height(), ED4_window::scrolled_rect, and AW::Rectangle::width().

Referenced by executeKeystroke().

static void executeKeystroke	(	AW_event *	event,
		int	repeatCount
	)

static

Definition at line 396 of file ED4_no_class.cxx.

References AD_NOWRITE, AW_KEY_DOWN, AW_KEY_END, AW_KEY_HOME, AW_KEY_NONE, AW_KEY_PGDN, AW_KEY_PGUP, AW_KEY_UP, AW_KEYMODE_ALT, AW_KEYMODE_CONTROL, aw_message(), awar_edit_mode, awar_edit_rightward, ED4_abstract_group_manager::build_consensus_string(), call_edit(), ED4_work_info::cannot_handle, ED4_work_info::char_position, current_cursor(), ED4_work_info::cursor_jump, e4_assert, ED4_JUMP_KEEP_VISIBLE, ED4_ROOT, ED4_U_UP_DOWN, ED4_Edit_String::edit(), error(), ED4_work_info::event, ED4_Edit_String::finish_edit(), ED4_base::flag, ED4_work_info::gb_data, GB_end_transaction_show_error(), gb_main, GB_push_transaction(), ED4_root::get_gb_main(), ED4_base::get_parent(), ED4_cursor::get_screen_pos(), ED4_cursor::get_sequence_pos(), ED4_base::get_species_pointer(), ED4_base::hidden, ED4_base::is_columnStat_terminal(), ED4_base::is_consensus_terminal(), ED4_base::is_pure_text_terminal(), ED4_work_info::is_sequence, ED4_base::is_sequence_terminal(), ED4_base::is_text_terminal(), ED4_cursor::jump_sequence_pos(), AW_event::keycode, AW_event::keymodifier, LEV_GROUP, ED4_work_info::mode, ED4_cursor::move_cursor(), NULp, ED4_work_info::out_seq_position, ED4_work_info::out_string, ED4_cursor::owner_of_cursor, ED4_manager::rebuild_consensi(), ED4_work_info::refresh_needed, ED4_work_info::repeat_count, ED4_terminal::request_refresh(), ED4_sequence_terminal::results(), ED4_work_info::rightward, ED4_root::root_group_man, ED4_manager::route_down_hierarchy(), scrollHalfPage(), ED4_SearchResults::searchAgain(), ED4_work_info::string, ta, ED4_consensus_sequence_terminal::temp_cons_seq, tracked_cursorpos, ED4_root_group_manager::update_remap(), and ED4_work_info::working_terminal.

Referenced by ED4_input_cb(), and ED4_remote_event().

void ED4_remote_event ( AW_event * faked_event )

Definition at line 534 of file ED4_no_class.cxx.

References executeKeystroke().

Referenced by ED4_host::forward_event().

void ED4_input_cb ( AW_window * aww )

Definition at line 539 of file ED4_no_class.cxx.

References AW_BUTTON_LEFT, AW_BUTTON_MIDDLE, AW_Keyboard_Press, AW_Keyboard_Release, AW_KEYMODE_ALT, AW_Mouse_Press, AW_Mouse_Release, ED4_root::aw_root, AW_WHEEL_DOWN, AW_WHEEL_UP, AW_event::button, AW_event::character, current_ed4w(), ED4_ROOT, ed4_scroll(), ED4_trigger_instant_refresh(), executeKeystroke(), ED4_root::font_group, AW_window::get_event(), ED4_root::get_gb_main(), AW_font_group::get_max_height(), AW_font_group::get_max_width(), KEY_PRESSED, KEY_RELEASED, AW_event::keycode, AW_event::keymodifier, ED4_root::main_manager, ED4_scroll_picture::old_x, ED4_scroll_picture::old_y, AW_root::peek_key_event(), ED4_scroll_picture::scroll, ED4_root::scroll_picture, ta, AW_event::type, ED4_foldable::win_to_world_coords(), AW_event::x, and AW_event::y.

Referenced by ED4_window::insert_window().

void ED4_vertical_change_cb ( AW_window * aww )

Definition at line 653 of file ED4_no_class.cxx.

References ED4_window::coords, current_ed4w(), ED4_ROOT, ED4_root::get_gb_main(), get_max_slider_ypos(), ED4_window::scroll_rectangle(), AW_window::set_vertical_scrollbar_position(), AW_window::slider_pos_vertical, ED4_window::slider_pos_vertical, ta, ED4_window::update_window_coords(), win, ED4_coords::window_lower_clip_point, and ED4_coords::window_upper_clip_point.

Referenced by ed4_scroll(), and ED4_window::insert_window().

void ED4_horizontal_change_cb ( AW_window * aww )

void ED4_motion_cb ( AW_window * aww )

Definition at line 747 of file ED4_no_class.cxx.

References AW_BUTTON_LEFT, AW_BUTTON_MIDDLE, AW_Mouse_Drag, AW_event::button, current_ed4w(), ED4_ROOT, ed4_scroll(), AW_window::get_event(), ED4_root::get_gb_main(), ED4_root::main_manager, ED4_scroll_picture::old_x, ED4_scroll_picture::old_y, ED4_scroll_picture::scroll, ED4_root::scroll_picture, ta, AW_event::type, ED4_foldable::win_to_world_coords(), AW_event::x, and AW_event::y.

Referenced by ED4_window::insert_window().

void ED4_remote_set_cursor_cb ( AW_root * awr )

Definition at line 790 of file ED4_no_class.cxx.

References AW_root::awar(), AWAR_SET_CURSOR_POSITION, current_cursor(), ED4_JUMP_CENTERED, ED4_cursor::jump_sequence_pos(), AW_awar::read_int(), and AW_awar::write_int().

Referenced by ed4_bind_mainDB_awar_callbacks().

void ED4_jump_to_cursor_position	(	AW_window *	aww,
		const char *	awar_name,
		PositionType	posType
	)

void ED4_set_helixnr	(	AW_window *	aww,
		const char *	awar_name
	)

Definition at line 877 of file ED4_no_class.cxx.

References aw_message(), AW_root::awar(), current_cursor(), ED4_JUMP_CENTERED, ED4_ROOT, BI_helix::first_position(), GBS_global_string(), AW_window::get_root(), BI_helix::has_entries(), ED4_root::helix, ED4_cursor::jump_sequence_pos(), ED4_cursor::owner_of_cursor, and AW_awar::read_string().

Referenced by ED4_root::generate_window(), and jump_to_next_helix_cb().

void ED4_set_iupac	(	AW_window *	aww,
		const char *	awar_name
	)

Definition at line 903 of file ED4_no_class.cxx.

References ED4_root::alignment_type, aw_message(), ED4_root::aw_root, AW_root::awar(), current_cursor(), e4_assert, ED4_ROOT, iupac::encode(), ED4_cursor::get_sequence_pos(), ED4_cursor::in_consensus_terminal(), ED4_cursor::owner_of_cursor, AW_awar::read_string(), ED4_terminal::resolve_pointer_to_string_copy(), seq, and ED4_terminal::write_sequence().

Referenced by ED4_root::generate_window().

void ED4_exit ( )

Definition at line 933 of file ED4_no_class.cxx.

References ED4_root::aw_root, ED4_window::aww, ED4_window::cursor, ED4_window::delete_window(), ED4_ROOT, EXIT_SUCCESS, ED4_root::first_window, GB_close(), gb_main, ED4_root::get_gb_main(), AW_window::hide(), ED4_window::next, ED4_cursor::prepare_shutdown(), shutdown_macro_recording(), and AW_root::unlink_awars_from_DB().

Referenced by ARB_main(), ED4_root::create_hierarchy(), ED4_quit_editor(), and EDB_root_bact::fill_species().

void ED4_quit_editor ( AW_window * aww )

Definition at line 962 of file ED4_no_class.cxx.

References current_aww(), current_ed4w(), ED4_exit(), ED4_ROOT, ED4_root::first_window, AW_window::hide(), and ED4_window::is_hidden.

Referenced by ED4_root::generate_window().

static unsigned ED4_timer ( AW_root * )

static

Definition at line 976 of file ED4_no_class.cxx.

References ED4_ROOT, fflush(), GB_begin_transaction(), GB_commit_transaction(), gb_main, GB_tell_server_dont_wait(), ED4_root::get_gb_main(), and ED4_root::refresh_all_windows().

Referenced by ED4_trigger_instant_refresh().

void ED4_trigger_instant_refresh ( )

Definition at line 998 of file ED4_no_class.cxx.

References AW_root::add_timed_callback(), ED4_root::aw_root, ED4_ROOT, ED4_timer(), and fflush().

Referenced by ED4_get_aligner_data_access(), ED4_input_cb(), ED4_postcbcb(), ED4_request_full_instant_refresh(), ED4_request_relayout(), and ED4_terminal::event_sent_by_parent().

void ED4_request_full_refresh ( )

Definition at line 1005 of file ED4_no_class.cxx.

References ED4_ROOT, and ED4_root::main_manager.

Referenced by ED4_menu_highlight(), ED4_request_full_instant_refresh(), ED4_root::generate_window(), reload_ecoli_cb(), and reload_helix_cb().

void ED4_request_full_instant_refresh ( )

Definition at line 1008 of file ED4_no_class.cxx.

References ED4_request_full_refresh(), and ED4_trigger_instant_refresh().

Referenced by ED4_compression_changed_cb(), and gc_change_cb().

void ED4_request_relayout ( )

Definition at line 1013 of file ED4_no_class.cxx.

References ED4_resize_all_extensions(), ED4_ROOT, ED4_trigger_instant_refresh(), and ED4_root::main_manager.

Referenced by ED4_root::create_hierarchy(), ed4_create_all_awars(), ED4_popup_helix_or_pfold_window(), ED4_group_manager::fold(), ED4_manager::handle_move(), header_changed_cb(), NDS_changed(), and ED4_group_manager::unfold().

static void createGroupFromSelected	(	GB_CSTR	group_name,
		GB_CSTR	field_name,
		GB_CSTR	field_content
	)

static

Definition at line 1021 of file ED4_no_class.cxx.

References ED4_container::append_member(), ED4_manager::create_consensus(), e4_assert, ED4_build_group_manager_end(), ED4_build_group_manager_start(), ED4_counter, ED4_ROOT, ED4_list_elem< T >::elem(), ED4_group_manager::fold(), GB_FIND, GB_read_as_string(), GB_search(), ED4_area_manager::get_multi_species_manager(), ED4_base::get_parent(), ED4_list< T >::head(), ED4_root::highlighted_objects, ED4_multi_species_manager::invalidate_species_counters(), ED4_base::is_consensus_manager(), ED4_base::is_multi_species_manager(), ED4_base::is_species_manager(), LEV_GROUP, LEV_MULTI_SPECIES, LEV_SPECIES, ED4_list_elem< T >::next(), NULp, ED4_root::ref_terminals, ED4_manager::resize_requested_by_child(), ED4_base::set_width(), SIGNIFICANT_FIELD_CHARS, ED4_root::top_area_man, ED4_base::touch_world_cache(), and ED4_manager::update_requested_by_child().

Referenced by group_species().

static void group_species	(	bool	use_field,
		AW_window *	use_as_main_window
	)

static

static void group_species_by_field_content	(	AW_window *	,
		AW_window *	use_as_main_window,
		AW_window *	window_to_hide
	)

static

Definition at line 1187 of file ED4_no_class.cxx.

References group_species(), and AW_window::hide().

Referenced by create_group_species_by_field_window().

static AW_window* create_group_species_by_field_window	(	AW_root *	aw_root,
		AW_window *	use_as_main_window
	)

static

Definition at line 1192 of file ED4_no_class.cxx.

References AW_window::auto_space(), AW_POPDOWN(), AWAR_FIELD_CHOSEN, create_itemfield_selection_button(), ED4_ROOT, FIELD_FILTER_STRING_READABLE, ED4_root::get_gb_main(), group_species_by_field_content(), makeHelpCallback(), NULp, and SPECIES_get_selector().

Referenced by group_species_cb().

void group_species_cb	(	AW_window *	aww,
		bool	use_fields
	)

Definition at line 1218 of file ED4_no_class.cxx.

References AW_window::activate(), ED4_root::aw_root, create_group_species_by_field_window(), ED4_ROOT, and group_species().

Referenced by ED4_root::generate_window().

static GB_ERROR ED4_load_new_config ( char * name )

static

Definition at line 1230 of file ED4_no_class.cxx.

References ED4_reference_terminals::clear(), ED4_root::create_hierarchy(), ED4_root::deselect_all(), ED4_root::ecoli_ref, ED4_init_notFoundMessage(), ED4_ROOT, error(), ED4_root::first_window, ED4_root::get_gb_main(), ED4_root::highlighted_objects, ED4_scroll_links::link_for_hor_slider, ED4_scroll_links::link_for_ver_slider, ED4_root::main_manager, max_seq_terminal_length, GBT_config::MIDDLE_AREA, ED4_root::middle_area_man, ED4_window::next, NULp, ED4_scroll_picture::old_x, ED4_scroll_picture::old_y, ED4_root::ref_terminals, ED4_root::remove_all_callbacks(), ED4_window::reset_all_for_new_config(), ED4_scroll_picture::scroll, ED4_root::scroll_links, ED4_root::scroll_picture, ED4_list< T >::size(), GBT_config::TOP_AREA, and ED4_root::top_area_man.

Referenced by ED4_start_editor_on_configuration().

static ED4_EDITMODE ED4_get_edit_mode ( AW_root * root )

static

Definition at line 1274 of file ED4_no_class.cxx.

References AD_ALIGN, AD_INSERT, AD_REPLACE, AW_root::awar(), AWAR_EDIT_MODE, AWAR_INSERT_MODE, and AW_awar::read_int().

Referenced by ed4_change_edit_mode(), and ed4_changesecurity().

void ed4_changesecurity ( AW_root * root )

Definition at line 1279 of file ED4_no_class.cxx.

References AD_ALIGN, ED4_root::aw_root, AW_root::awar(), AWAR_EDIT_SECURITY_LEVEL, AWAR_EDIT_SECURITY_LEVEL_ALIGN, AWAR_EDIT_SECURITY_LEVEL_CHANGE, ED4_get_edit_mode(), ED4_ROOT, GB_change_my_security(), ED4_root::get_gb_main(), AW_awar::map(), NULp, and AW_awar::read_int().

Referenced by ed4_change_edit_mode(), and ed4_create_all_awars().

void ed4_change_edit_mode ( AW_root * root )

Definition at line 1297 of file ED4_no_class.cxx.

References awar_edit_mode, ed4_changesecurity(), and ED4_get_edit_mode().

Referenced by ed4_create_all_awars().

ARB_ERROR rebuild_consensus ( ED4_base * object )

Definition at line 1302 of file ED4_no_class.cxx.

References ED4_base::is_consensus_manager(), LEV_SEQUENCE_STRING, NULp, and ED4_base::request_refresh().

Referenced by ED4_manager::rebuild_consensi().

void ED4_new_editor_window ( AW_window * aww )

Definition at line 1313 of file ED4_no_class.cxx.

References ED4_window::aww, ED4_R_BREAK, ED4_ROOT, ED4_root::generate_window(), ED4_scroll_links::link_for_hor_slider, ED4_scroll_links::link_for_ver_slider, NULp, ED4_root::scroll_links, ED4_window::set_scrolled_rectangle(), AW_window::show(), and ED4_window::update_scrolled_rectangle().

Referenced by ED4_root::generate_window().

static void ED4_start_editor_on_configuration ( AW_window * aww )

static

Definition at line 1334 of file ED4_no_class.cxx.

References aw_message(), AW_root::awar(), AWAR_EDIT_CONFIGURATION, ED4_load_new_config(), error(), AW_window::get_root(), AW_window::hide(), AW_awar::read_string(), and AW_window::show().

Referenced by ED4_create_loadConfiguration_window(), and ED4_reloadConfiguration().

void ED4_compression_changed_cb ( AW_root * awr )

void ED4_compression_toggle_changed_cb	(	AW_root *	root,
		bool	hideChanged
	)

Definition at line 1392 of file ED4_no_class.cxx.

References AW_root::awar(), e4_assert, ED4_AWAR_COMPRESS_SEQUENCE_GAPS, ED4_AWAR_COMPRESS_SEQUENCE_HIDE, ED4_AWAR_COMPRESS_SEQUENCE_TYPE, ED4_RM_DYNAMIC_GAPS, ED4_RM_MAX_ALIGN, ED4_RM_NONE, ED4_RM_SHOW_ABOVE, AW_awar::read_int(), and AW_awar::write_int().

Referenced by ed4_create_all_awars().

AW_window* ED4_create_editor_options_window ( AW_root * root )

AW_window* ED4_create_consensus_definition_window ( AW_root * root )

Definition at line 1541 of file ED4_no_class.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AW_SCALER_LINEAR, AWT_create_IUPAC_info_window(), AWT_insert_config_manager(), CONSENSUS_CONFIG_ID, ED4_AWAR_CONSENSUS_CONSIDBOUND, ED4_AWAR_CONSENSUS_COUNTGAPS, ED4_AWAR_CONSENSUS_GAPBOUND, ED4_AWAR_CONSENSUS_GROUP, ED4_AWAR_CONSENSUS_LOWER, ED4_AWAR_CONSENSUS_SHOW, ED4_AWAR_CONSENSUS_UPPER, makeHelpCallback(), and NULp.

Referenced by ED4_popup_dot_missing_bases_window(), and ED4_root::generate_window().

static void consensus_upper_lower_changed_cb	(	AW_root *	awr,
		bool	upper_changed
	)

static

Definition at line 1609 of file ED4_no_class.cxx.

References AW_root::awar(), ED4_AWAR_CONSENSUS_LOWER, ED4_AWAR_CONSENSUS_UPPER, ED4_consensus_definition_changed(), AW_awar::read_int(), and AW_awar::write_int().

Referenced by ED4_create_consensus_awars().

void ED4_create_consensus_awars ( AW_root * aw_root )

void ED4_reloadConfiguration ( AW_window * aww )

Definition at line 1639 of file ED4_no_class.cxx.

References ED4_start_editor_on_configuration().

Referenced by ED4_root::generate_window().

AW_window* ED4_create_loadConfiguration_window ( AW_root * awr )

Definition at line 1643 of file ED4_no_class.cxx.

References AW_POPDOWN(), AWAR_EDIT_CONFIGURATION, awt_create_CONFIG_selection_list(), ED4_ROOT, ED4_start_editor_on_configuration(), ED4_root::get_gb_main(), makeHelpCallback(), and NULp.

Referenced by ED4_root::generate_window().

void ED4_saveConfiguration	(	AW_window *	aww,
		bool	hide_aww
	)

Definition at line 1670 of file ED4_no_class.cxx.

References AW_root::awar(), AWAR_EDIT_CONFIGURATION, AW_window::get_root(), AW_window::hide(), AW_awar::read_string(), and EDB_root_bact::save_current_config().

Referenced by ED4_create_saveConfigurationAs_window(), and ED4_root::generate_window().

AW_window* ED4_create_saveConfigurationAs_window ( AW_root * awr )

Definition at line 1678 of file ED4_no_class.cxx.

References AW_POPDOWN(), AWAR_EDIT_CONFIGURATION, awt_create_CONFIG_selection_list(), ED4_ROOT, ED4_saveConfiguration(), ED4_root::get_gb_main(), makeHelpCallback(), and NULp.

Referenced by ED4_root::generate_window().

static char* filter_loadable_SAIs ( GBDATA * gb_sai )

static

Definition at line 1706 of file ED4_no_class.cxx.

References ARB_strdup(), ED4_find_SAI_name_terminal(), ED4_ROOT, GB_FIND, GB_search(), GBT_get_name(), ED4_root::get_alignment_name(), and NULp.

Referenced by ED4_create_loadSAI_window().

AW_window* ED4_create_loadSAI_window ( AW_root * awr )

Definition at line 1720 of file ED4_no_class.cxx.

References AW_POPDOWN(), AWAR_SAI_NAME, awt_create_SAI_selection_list(), ED4_get_and_jump_to_selected_SAI(), ED4_ROOT, filter_loadable_SAIs(), ED4_root::get_gb_main(), ED4_root::loadable_SAIs, LSAI_UPTODATE, makeHelpCallback(), and NULp.

Referenced by ED4_root::generate_window().

static GB_ERROR createDataFromConsensus	(	GBDATA *	gb_species,
		ED4_group_manager *	group_man
	)

static

static ARB_ERROR add_species_to_merge_list	(	ED4_base *	base,
		SpeciesMergeList **	smlp,
		GBDATA *	gb_species_data
	)

static

Definition at line 1802 of file ED4_no_class.cxx.

References ARB_strdup(), error(), GB_append_exportedError(), GBS_global_string(), GBT_find_species_rel_species_data(), ED4_base::is_species_name_terminal(), SpeciesMergeList::next, NULp, ED4_base::resolve_pointer_to_string_copy(), SpeciesMergeList::species, and SpeciesMergeList::species_name.

Referenced by create_new_species().

static int SpeciesMergeListLength ( SpeciesMergeList * sml )

static

Definition at line 1829 of file ED4_no_class.cxx.

References length, and SpeciesMergeList::next.

Referenced by create_new_species().

static void freeSpeciesMergeList ( SpeciesMergeList * sml )

static

Definition at line 1839 of file ED4_no_class.cxx.

References SpeciesMergeList::next, and SpeciesMergeList::species_name.

Referenced by create_new_species().

bool nameIsUnique	(	const char *	short_name,
		GBDATA *	gb_species_data
	)

inline

Definition at line 1848 of file ED4_no_class.cxx.

References GBT_find_species_rel_species_data().

Referenced by create_new_species().

static void create_new_species	(	AW_window *	,
		SpeciesCreationMode	creation_mode
	)

static

Definition at line 1853 of file ED4_no_class.cxx.

References add(), add_species_to_merge_list(), ARB_strdup(), AW_get_nameserver_addid(), aw_message(), aw_message_if(), ED4_root::aw_root, AW_root::awar(), AWTC_generate_one_name(), AWTC_generate_random_name(), AWTC_makeUniqueShortName(), COPY_SPECIES, CREATE_FROM_CONSENSUS, CREATE_NEW_SPECIES, createDataFromConsensus(), current_cursor(), ARB_ERROR::deliver(), e4_assert, ED4_AWAR_CREATE_FROM_CONS_DATA_SOURCE, ED4_AWAR_SPECIES_TO_CREATE, ED4_get_and_jump_to_species(), ED4_ROOT, error(), freeSpeciesMergeList(), GB_abort_transaction(), GB_await_error(), GB_begin_transaction(), GB_copy_dropProtectMarksAndTempstate(), GB_create_container(), GB_DB, GB_end_transaction(), GB_FIND, GB_get_subfields(), gb_main, GB_read_as_string(), GB_read_string(), GB_read_type(), GB_search(), gb_species_data, GB_STRING, GBS_global_string(), GBT_find_or_create_species(), GBT_find_species_rel_species_data(), GBT_get_species_data(), GBT_write_string(), ED4_root::get_alignment_name(), ED4_root::get_gb_main(), ED4_base::get_parent(), arb_progress::inc_and_check_user_abort(), ED4_base::is_consensus_terminal(), LEV_GROUP, nameIsUnique(), SpeciesMergeList::next, NOWHERE, NULp, ED4_cursor::owner_of_cursor, AW_awar::read_int(), AW_awar::read_string(), ED4_terminal::resolve_pointer_to_char_pntr(), ED4_manager::route_down_hierarchy(), SpeciesMergeList::species, SpeciesMergeList::species_name, SpeciesMergeListLength(), and type.

Referenced by ED4_create_new_seq_window().

AW_window* ED4_create_new_seq_window	(	AW_root *	root,
		SpeciesCreationMode	creation_mode
	)

Definition at line 2203 of file ED4_no_class.cxx.

References AW_POPDOWN(), COPY_SPECIES, CREATE_FROM_CONSENSUS, create_new_species(), CREATE_NEW_SPECIES, e4_assert, ED4_AWAR_CREATE_FROM_CONS_ALL_UPPER, ED4_AWAR_CREATE_FROM_CONS_CREATE_POINTS, ED4_AWAR_CREATE_FROM_CONS_DATA_SOURCE, ED4_AWAR_CREATE_FROM_CONS_REPL_EQUAL, ED4_AWAR_CREATE_FROM_CONS_REPL_POINT, ED4_AWAR_SPECIES_TO_CREATE, NULp, and valid().

Referenced by ED4_root::generate_window().

Variable Documentation

bool track_cursor = false

static

Definition at line 255 of file ED4_no_class.cxx.

long tracked_cursorpos = -1

static

Definition at line 256 of file ED4_no_class.cxx.

Referenced by executeKeystroke().

int timer_calls = 0

static

Definition at line 973 of file ED4_no_class.cxx.

int timer_calls_triggered = 0

static

Definition at line 974 of file ED4_no_class.cxx.

AWT_config_mapping_def editor_options_config_mapping[]

static

Initial value:

= {
    { ED4_AWAR_COMPRESS_SEQUENCE_GAPS,    "compressgaps" },
    { ED4_AWAR_COMPRESS_SEQUENCE_HIDE,    "hidenucs" },
    { ED4_AWAR_COMPRESS_SEQUENCE_PERCENT, "hidepercent" },
    { AWAR_EDIT_HELIX_SPACING,            "helixspacing" },
    { AWAR_EDIT_TERMINAL_SPACING,         "terminalspacing" },
    { ED4_AWAR_SCROLL_SPEED_X,            "scrollspeedx" },
    { ED4_AWAR_SCROLL_SPEED_Y,            "scrollspeedy" },
    { ED4_AWAR_SCROLL_MARGIN,             "scrollmargin" },
    { ED4_AWAR_GAP_CHARS,                 "gapchars" },
    { ED4_AWAR_DIGITS_AS_REPEAT,          "digitsasrepeat" },
    { ED4_AWAR_FAST_CURSOR_JUMP,          "fastcursorjump" },
    { ED4_AWAR_ANNOUNCE_CHECKSUM_CHANGES, "announcechecksumchanges" },
    { NULp, NULp }
}

Definition at line 1431 of file ED4_no_class.cxx.

AWT_config_mapping_def consensus_config_mapping[]

static

Initial value:

= {
    { ED4_AWAR_CONSENSUS_COUNTGAPS,   CONSENSUS_CONFIG_COUNTGAPS },
    { ED4_AWAR_CONSENSUS_GAPBOUND,    CONSENSUS_CONFIG_GAPBOUND },
    { ED4_AWAR_CONSENSUS_GROUP,       CONSENSUS_CONFIG_GROUP },
    { ED4_AWAR_CONSENSUS_CONSIDBOUND, CONSENSUS_CONFIG_CONSIDBOUND },
    { ED4_AWAR_CONSENSUS_UPPER,       CONSENSUS_CONFIG_UPPER },
    { ED4_AWAR_CONSENSUS_LOWER,       CONSENSUS_CONFIG_LOWER },
    { NULp, NULp }
}

Definition at line 1525 of file ED4_no_class.cxx.

AWT_predefined_config predefined_consensus_config[]

static

Initial value:

= {
    { "*create_species_from_consensus", "Consensus settings to create a new species \nfrom group consensus using\n\"Create/Create new species from consensus\"", "considbound='30';countgaps='0';gapbound='60';group='0';lower='0';upper='0'" },
    { NULp, NULp, NULp }
}

Definition at line 1536 of file ED4_no_class.cxx.

Classes

Macros

Functions

Variables

Macro Definition Documentation

Function Documentation

Variable Documentation