ARB: ED4_root Class Reference

ARB

#include <ed4_class.hxx>

Inheritance diagram for ED4_root:

Inheritance graph

Collaboration diagram for ED4_root:

Collaboration graph

Public Member Functions
GBDATA *	get_gb_main () const

const char *	get_alignment_name () const

const ConsensusBuildParams &	get_consensus_params ()

void	reset_consensus_params ()

void	loadable_SAIs_may_have_changed ()

void	announce_useraction_in (AW_window *aww)

ED4_window *	get_most_recently_used_window () const

ED4_device_manager *	get_device_manager ()

ED4_returncode	create_hierarchy (const char area_string_middle, const char area_string_top)

ARB_ERROR	init_alignment ()

void	recalc_font_group ()

AW_window *	create_first_window ()

ED4_returncode	generate_window (AW_device device, ED4_window new_window)

void	copy_window_struct (ED4_window source, ED4_window destination)

void	resize_all_requesting_childs ()

void	special_window_refresh (bool handle_updates)

ED4_returncode	refresh_all_windows (bool redraw)

void	request_refresh_for_all_terminals ()

void	request_refresh_for_specific_terminals (ED4_level lev)

void	request_refresh_for_consensus_terminals ()

void	request_refresh_for_sequence_terminals ()

void	announce_deletion (ED4_base *object)

ED4_returncode	add_to_highlighted (ED4_species_name_terminal *object)

void	remove_from_highlighted (ED4_species_name_terminal *object)

ED4_returncode	deselect_all ()

ED4_returncode	get_area_rectangle (AW_screen_area *rect, AW_pos x, AW_pos y)

ED4_index	pixel2pos (AW_pos click_x)

void	remove_all_callbacks ()

	ED4_root (GBDATA *gb_main_)

	~ED4_root ()

Public Attributes
char *	db_name

AW_root *	aw_root

AW_default	props_db

ED4_window *	first_window

ED4_main_manager *	main_manager

ED4_area_manager *	middle_area_man

ED4_area_manager *	top_area_man

ED4_root_group_manager *	root_group_man

ED4_highlighted_list *	highlighted_objects

ED4_scroll_links	scroll_links

bool	folding_action

ED4_reference_terminals	ref_terminals

ED4_species_mode	species_mode

ED4_scroll_picture	scroll_picture

BI_ecoli_ref *	ecoli_ref

GB_alignment_type	alignment_type

ED4_reference *	reference

ED4_seq_colors *	sequence_colors

AW_gc_manager *	gc_manager

ST_ML *	st_ml

AW_helix *	helix

int	helix_spacing

long	helix_add_spacing

long	terminal_add_spacing

char *	protstruct

long	protstruct_len

ed_key *	edk

bool	column_stat_activated

bool	column_stat_initialized

bool	visualizeSAI

bool	visualizeSAI_allSpecies

LoadableSaiState	loadable_SAIs

int	temp_gc

AW_font_group	font_group

Detailed Description

Definition at line 1408 of file ed4_class.hxx.

Constructor & Destructor Documentation

ED4_root::ED4_root ( GBDATA * gb_main_ )

Definition at line 1972 of file ED4_root.cxx.

ED4_root::~ED4_root ( )

Definition at line 2010 of file ED4_root.cxx.

References aw_root, db_name, ecoli_ref, edk, first_window, helix, highlighted_objects, main_manager, protstruct, reference, sequence_colors, st_ml, and STAT_destroy_ST_ML().

Member Function Documentation

GBDATA* ED4_root::get_gb_main ( ) const

inline

Definition at line 1422 of file ed4_class.hxx.

References gb_main.

Referenced by calc_and_update_alignment_errors_cb(), ED4_terminal::changed_by_database(), create_group_species_by_field_window(), create_list_of_loaded_species(), create_new_species(), ED4_manager::deleted_from_database(), do_sth_with_species(), dot_missing_bases(), ED4_alignment_length_changed(), ed4_changesecurity(), ED4_compression_changed_cb(), ed4_create_all_awars(), ED4_create_consensus_awars(), ED4_create_loadConfiguration_window(), ED4_create_loadSAI_window(), ed4_create_mainDB_awars(), ED4_create_NDS_awars(), ED4_create_saveConfigurationAs_window(), ED4_create_search_awars(), ED4_CreateProteinViewer_window(), ED4_createVisualizeSAI_window(), ED4_exit(), ED4_expose_cb(), ED4_get_aligner_data_access(), ED4_get_and_jump_to_current(), ED4_get_and_jump_to_selected_SAI(), ED4_get_and_jump_to_species(), ED4_get_marked_from_menu(), ED4_getSaiColorString(), ED4_helix_jump_opposite(), ED4_horizontal_change_cb(), ED4_input_cb(), ED4_jump_to_current_species(), ED4_load_new_config(), ED4_mark_matching_species(), ED4_menu_highlight(), ED4_motion_cb(), ED4_pfold_select_SAI_and_update_option_menu(), ED4_popup_detect_bad_alignment_window(), ED4_popup_dot_missing_bases_window(), ED4_remove_faligner_entries(), ED4_resize_cb(), ED4_restore_curpos(), ED4_save_properties(), ED4_scrollbar_change_cb(), ED4_selected_SAI_changed_cb(), ED4_selected_species_changed_cb(), ED4_store_curpos(), ED4_timer(), ED4_undo_redo(), ED4_vertical_change_cb(), ED4_with_whole_block(), executeKeystroke(), EDB_root_bact::fill_data(), generate_window(), group_species(), ED4_manager::handle_move(), init_flag_awars(), insert_new_species_terminal(), modes_cb(), modsai_cb(), SpeciesFlag::prepare_itemfield(), PV_AddOrfTerminalsToLoadedSpecies(), PV_CallBackFunction(), PV_CreateAllTerminals(), PV_DisplayAminoAcidNames(), PV_ManageTerminals(), PV_PrintMissingDBentryInformation(), PV_SequenceUpdate_CB(), PV_WriteTranslatedSequenceToDB(), reload_ecoli_cb(), reload_helix_cb(), remove_from_consensus(), ED4_terminal::resolve_pointer_to_char_pntr(), saiChanged_callback(), EDB_root_bact::save_current_config(), SearchTree::SearchTree(), select_named_sequence_terminal(), ED4_cursor::set_to_terminal(), ED4_cursor::show_cursor_at(), trace_termChange_in_global_awar(), TranslateGeneToAminoAcidSequence(), ED4_manager::update_bases_and_rebuild_consensi(), and ED4_terminal::write_sequence().

const char* ED4_root::get_alignment_name ( ) const

inline

const ConsensusBuildParams & ED4_root::get_consensus_params ( )

Definition at line 25 of file ED4_consensus.cxx.

References aw_root.

Referenced by ED4_abstract_group_manager::build_consensus_string().

void ED4_root::reset_consensus_params ( )

Definition at line 30 of file ED4_consensus.cxx.

References NULp.

Referenced by ED4_consensus_definition_changed().

void ED4_root::loadable_SAIs_may_have_changed ( )

inline

Definition at line 1464 of file ed4_class.hxx.

References LSAI_OUTDATED, and LSAI_UPTODATE.

void ED4_root::announce_useraction_in ( AW_window * aww )

Definition at line 373 of file ED4_root.cxx.

References first_window, and win.

Referenced by ED4_postcbcb(), and generate_window().

ED4_window* ED4_root::get_most_recently_used_window ( ) const

inline

Definition at line 1470 of file ed4_class.hxx.

References e4_assert.

Referenced by ED4_MostRecentWinContext::ED4_MostRecentWinContext(), and PV_ManageTerminals().

ED4_device_manager * ED4_root::get_device_manager ( )

inline

Definition at line 2228 of file ed4_class.hxx.

References LEV_DEVICE, and ED4_manager::search_spec_child_rek().

Referenced by ED4_terminal::draw_drag_box(), ED4_terminal::event_sent_by_parent(), and EDB_root_bact::save_current_config().

ED4_returncode ED4_root::create_hierarchy	(	const char *	area_string_middle,
		const char *	area_string_top
	)

Definition at line 536 of file ED4_root.cxx.

References ED4_container::append_member(), aw_popup_ok(), ED4_window::aww, EDB_root_bact::calc_no_of_all(), ED4_manager::create_consensus(), arb_progress::done(), e4_assert, ecoli_ref, ED4_exit(), ED4_finish_and_show_notFoundMessage(), ED4_R_OK, ED4_request_relayout(), ED4_base::extension, first_window, font_group, force_group_update(), GB_pop_transaction(), GB_push_transaction(), GBS_global_string(), AW_font_group::get_max_height(), BI_ecoli_ref::init(), ED4_reference_terminals::init(), ED4_scroll_links::link_for_hor_slider, ED4_scroll_links::link_for_ver_slider, long, main_manager, ED4_remap::mark_compile_needed_force(), MAXINFO_WIDTH, MAXNAME_WIDTH, middle_area_man, ED4_window::next, NULp, BaseFrequencies::ok(), PROP_DYNA_RESIZE, ref_terminals, reference, ED4_root_group_manager::remap(), resize_all_requesting_childs(), root_group_man, EDB_root_bact::scan_string(), scroll_links, SEQUENCE_INFO_WIDTH, ED4_window::set_scrolled_rectangle(), SmartPtr< T, C >::setNull(), AW_window::show(), ED4_extension::size, ta, ED4_abstract_group_manager::table(), TERMINAL_HEIGHT, top_area_man, TREE_TERMINAL_WIDTH, ED4_root_group_manager::update_remap(), ED4_window::update_scrolled_rectangle(), ED4_window::update_window_coords(), WIDTH, and win.

Referenced by ARB_main(), and ED4_load_new_config().

ARB_ERROR ED4_root::init_alignment ( )

Definition at line 492 of file ED4_root.cxx.

References alignment_type, ED4_alignment_length_changed(), GB_add_callback(), GB_AT_UNKNOWN, GB_await_error(), GB_CB_CHANGED, GB_FIND, GB_read_int(), GB_search(), GBS_global_string(), GBT_get_alignment(), GBT_get_alignment_type(), GBT_get_startup_alignment(), MAXSEQUENCECHARACTERLENGTH, NULp, and ta.

Referenced by ARB_main().

void ED4_root::recalc_font_group ( )

Definition at line 515 of file ED4_root.cxx.

References ARRAY_ELEMS, current_device(), ED4_G_FLAG_INFO, ED4_G_SEQUENCES, ED4_G_STANDARD, font_group, AW_font_group::registerFont(), and AW_font_group::unregisterAll().

Referenced by ED4_calc_terminal_extentions().

AW_window * ED4_root::create_first_window ( )

Definition at line 1922 of file ED4_root.cxx.

References ED4_window::aww, DRAW, ED4_calc_terminal_extentions(), ED4_init_notFoundMessage(), generate_window(), max_seq_terminal_length, and NULp.

Referenced by ARB_main().

ED4_returncode ED4_root::generate_window	(	AW_device **	device,
		ED4_window **	new_window
	)

Definition at line 1329 of file ED4_root.cxx.

References AW_awar::add_callback(), alignment_type, announce_useraction_in(), ARB_strdup(), ARB_VERSION, AW_window::at(), AW_window::auto_space(), aw_clear_message_cb(), AW_GCM_DATA_AREA, AW_help_entry_pressed(), AW_init_color_group_defaults(), AW_insert_common_property_menu_entries(), AW_manage_GC(), aw_message(), AW_MIDDLE_AREA, AW_preset_window(), aw_root, aw_set_local_message(), AWAR_EDIT_MODE, AWAR_EDIT_RIGHTWARD, AWAR_EDIT_SECURITY_LEVEL, AWAR_EDIT_TITLE_MODE, AWAR_ERROR_MESSAGES, AWAR_INSERT_MODE, AW_root::awar_int(), AW_root::awar_string(), AWM_ALL, AWM_DISABLED, AWM_EXP, AWT_trigger_remote_action(), ED4_window::aww, AW_window::button_length(), AW_window::callback(), AW_window::close_sub_menu(), COPY_SPECIES, copy_window_struct(), AW_window::create_button(), CREATE_FROM_CONSENSUS, AW_window::create_input_field(), create_key_map_window(), AW_window::create_menu(), AW_window::create_mode(), create_naligner_window(), CREATE_NEW_SPECIES, AW_window::create_option_menu(), AW_window::create_text_field(), AW_window::create_text_toggle(), AW_window::create_toggle(), current_ed4w(), db_name, e4_assert, ED4_activate_col_stat(), ED4_ANY_PATTERN, ED4_AWAR_CONSENSUS_SHOW, ED4_AWAR_DIGITS_AS_REPEAT, ED4_AWAR_NDS_ECOLI_NAME, ED4_BO_COMPLEMENT, ED4_BO_LOWER_CASE, ED4_BO_REVERSE, ED4_BO_REVERSE_COMPLEMENT, ED4_BO_SHIFT_LEFT, ED4_BO_SHIFT_RIGHT, ED4_BO_UNALIGN_CENTER, ED4_BO_UNALIGN_LEFT, ED4_BO_UNALIGN_RIGHT, ED4_BO_UPPER_CASE, ED4_change_cursor(), ED4_clear_stored_curpos(), ED4_configure_species_flags(), ED4_create_consensus_definition_window(), ED4_create_editor_options_window(), ED4_create_faligner_window(), ED4_create_loadConfiguration_window(), ED4_create_loadSAI_window(), ED4_create_modsai_window(), ED4_create_nds_window(), ED4_create_new_seq_window(), ED4_create_replace_window(), ED4_create_saveConfigurationAs_window(), ED4_create_seq_colors_window(), ED4_create_viewDifferences_window(), ED4_CreateProteinViewer_window(), ED4_createVisualizeSAI_window(), ED4_disable_col_stat(), ED4_encodeSearchDescriptor(), ED4_G_DRAG, ED4_get_aligner_data_access(), ED4_get_and_jump_to_current(), ED4_get_marked_from_menu(), ED4_helix_jump_opposite(), ED4_jump_to_current_species(), ED4_jump_to_cursor_position(), ED4_menu_highlight(), ED4_menu_perform_block_operation(), ED4_MS_ALL, ED4_MS_DESELECT_MARKED, ED4_MS_INVERT, ED4_MS_INVERT_GROUP, ED4_MS_MARK_SELECTED, ED4_MS_NONE, ED4_MS_SELECT_MARKED, ED4_MS_TOGGLE_BLOCKTYPE, ED4_MS_UNMARK_ALL, ED4_MS_UNMARK_SELECTED, ED4_new_editor_window(), ED4_popup_detect_bad_alignment_window(), ED4_popup_dot_missing_bases_window(), ED4_popup_gc_window(), ED4_popup_helix_or_pfold_window(), ED4_popup_search_window(), ED4_POS_BASE, ED4_POS_ECOLI, ED4_POS_SEQUENCE, ED4_quit_editor(), ED4_R_BREAK, ED4_R_OK, ED4_reloadConfiguration(), ED4_remove_faligner_entries(), ED4_request_full_refresh(), ED4_restore_curpos(), ED4_save_properties(), ED4_saveConfiguration(), ED4_search_cb(), ED4_SearchPositionTypeId, ED4_set_col_stat_threshold(), ED4_set_helixnr(), ED4_set_iupac(), ED4_set_protection(), ED4_SM_INFO, ED4_SM_KILL, ED4_SM_MARK, ED4_SM_MOVE, ED4_start_plugin(), ED4_store_curpos(), ED4_toggle_detailed_column_stats(), ED4_undo_redo(), ED4_zoom_message_window(), FastAligner_create_variables(), FastAligner_set_reference_species(), first_window, GB_AT_AA, GB_AT_DNA, GB_AT_RNA, GB_give_buffer(), GB_path_in_arbprop(), GB_UNDO_REDO, GB_UNDO_UNDO, GBS_global_string(), GBS_global_string_copy(), gc_change_cb(), gc_manager, GDE_load_menu(), AW_window::get_at_position(), AW_window::get_at_xposition(), AW_window::get_device(), get_gb_main(), AW_window::get_root(), group_species_cb(), AW_window::help_text(), AW_window_menu_modes::init(), AW_window::insert_default_option(), AW_window::insert_help_topic(), insert_macro_menu_entry(), AW_window::insert_menu_topic(), AW_window::insert_option(), INSERT_SEARCH_FIELDS, AW_window::insert_sub_menu(), ED4_window::insert_window(), INTEGRATED_ALIGNERS_TITLE, ED4_window::is_hidden, AW_window::load_xfig(), AW_window::local_id(), macro_name, makeHelpCallback(), MAXWINDOWS, modes_cb(), ED4_window::next, ED4_window::no_of_windows, NULp, PROBE, propertyName(), props_db, reload_ecoli_cb(), reload_helix_cb(), s, SEARCH_PATTERNS, AW_window::sep______________(), sequence_colors, AW_window::set_bottom_area_height(), AW_window::shadow_width(), AW_window::show(), show_sina_window(), RootAsWindowCallback::simple(), sina_mask(), title_mode_changed(), toggle_helix_for_SAI(), type, AW_window::update_option_menu(), and y.

Referenced by create_first_window(), and ED4_new_editor_window().

void ED4_root::copy_window_struct	(	ED4_window *	source,
		ED4_window *	destination
	)

Definition at line 799 of file ED4_root.cxx.

References ED4_window::coords, ED4_window::slider_pos_horizontal, and ED4_window::slider_pos_vertical.

Referenced by generate_window().

void ED4_root::resize_all_requesting_childs ( )

Definition at line 442 of file ED4_root.cxx.

References main_manager.

Referenced by create_hierarchy(), and ED4_resize_all_extensions().

void ED4_root::special_window_refresh ( bool handle_updates )

Definition at line 159 of file ED4_root.cxx.

References e4_assert, and ED4_WinContext::have_context().

Referenced by ED4_expose_cb().

ED4_returncode ED4_root::refresh_all_windows ( bool redraw )

Definition at line 169 of file ED4_root.cxx.

References ED4_R_OK, first_window, GB_touch(), GBT_get_SAI_data(), loadable_SAIs, LSAI_OUTDATED, LSAI_UPTODATE, main_manager, ED4_window::next, and ta.

Referenced by ED4_timer().

void ED4_root::request_refresh_for_all_terminals ( )

Definition at line 84 of file ED4_root.cxx.

References LEV_NONE, main_manager, and request_terminal_refresh().

void ED4_root::request_refresh_for_specific_terminals ( ED4_level lev )

Definition at line 88 of file ED4_root.cxx.

References main_manager, and request_terminal_refresh().

Referenced by diff_setting_changed_cb(), ED4_consensus_definition_changed(), ED4_set_col_stat_threshold(), refdata_changed_cb(), ED4_root_group_manager::resize_requested_children(), and set_diff_reference().

void ED4_root::request_refresh_for_consensus_terminals ( )

Definition at line 104 of file ED4_root.cxx.

References main_manager, and request_sequence_refresh().

Referenced by ED4_consensus_definition_changed().

void ED4_root::request_refresh_for_sequence_terminals ( )

Definition at line 107 of file ED4_root.cxx.

References main_manager, and request_sequence_refresh().

Referenced by colorDefChanged_callback(), colorDefTabNameChanged_callback(), refresh_display_cb(), saiChanged_callback(), searchParamsChanged(), seq_colors_changed_cb(), set_col_stat_activated_and_refresh(), setVisualizeSAI_cb(), and setVisualizeSAI_options_cb().

void ED4_root::announce_deletion ( ED4_base * object )

inline

Definition at line 1535 of file ed4_class.hxx.

References ED4_base::is_terminal(), and win.

Referenced by ED4_manager::delete_requested_children(), and ED4_terminal::delete_requested_children().

ED4_returncode ED4_root::add_to_highlighted ( ED4_species_name_terminal * object )

void ED4_root::remove_from_highlighted ( ED4_species_name_terminal * object )

ED4_returncode ED4_root::deselect_all ( )

Definition at line 317 of file ED4_root.cxx.

References ED4_multi_species_manager::deselect_all_species_and_SAI(), ED4_BT_NOBLOCK, ED4_R_OK, ED4_setBlocktype(), ED4_area_manager::get_multi_species_manager(), middle_area_man, and top_area_man.

Referenced by ED4_load_new_config(), and ED4_menu_highlight().

ED4_returncode ED4_root::get_area_rectangle	(	AW_screen_area *	rect,
		AW_pos	x,
		AW_pos	y
	)

Definition at line 754 of file ED4_root.cxx.

References AW_screen_area::b, current_device(), current_ed4w(), ED4_R_IMPOSSIBLE, ED4_R_OK, AW_device::get_area_size(), ED4_foldable::get_horizontal_folding(), ED4_folding_line::get_next(), AW_screen_area::l, AW_screen_area::r, and AW_screen_area::t.

Referenced by ED4_setColumnblockCorner().

ED4_index ED4_root::pixel2pos ( AW_pos click_x )

Definition at line 1941 of file ED4_root.cxx.

References CHARACTEROFFSET, ED4_G_SEQUENCES, font_group, ED4_remap::get_max_screen_pos(), AW_font_group::get_width(), ED4_root_group_manager::remap(), and root_group_man.

Referenced by ED4_setColumnblockCorner(), and ED4_cursor::show_clicked_cursor().

void ED4_root::remove_all_callbacks ( )

Definition at line 1606 of file ED4_manager.cxx.

References ED4_viewDifferences_disable(), first_window, and ED4_window::next.

Referenced by ED4_load_new_config().

Member Data Documentation

char* ED4_root::db_name

Definition at line 1424 of file ed4_class.hxx.

Referenced by generate_window(), and ~ED4_root().

AW_root* ED4_root::aw_root

Definition at line 1425 of file ed4_class.hxx.

Referenced by add_to_highlighted(), ARB_main(), ED4_cursor::changeType(), configureColumnStat(), create_new_species(), createDataFromConsensus(), ED4_window::delete_window(), ED4_calc_terminal_extentions(), ed4_changesecurity(), ed4_create_all_awars(), ED4_create_sequences_for_gde(), ED4_cursor::ED4_cursor(), ED4_exit(), ED4_input_cb(), ED4_pfold_calculate_secstruct_match(), ED4_pfold_create_props_window(), ED4_pfold_extend_nucleation_sites(), ED4_pfold_find_nucleation_sites(), ED4_pfold_find_turns(), ED4_pfold_resolve_overlaps(), ED4_pfold_select_SAI_and_update_option_menu(), ED4_pfold_set_SAI(), ED4_root_group_manager::ED4_root_group_manager(), ed4_scroll(), ED4_set_iupac(), ED4_show_protein_match_on_device(), ED4_trigger_instant_refresh(), ED4_viewDifferences_announceTerminalChange(), ED4_window::ED4_window(), ED4_Edit_String::edit(), ED4_terminal::event_sent_by_parent(), ED4_group_manager::fold(), generate_window(), get_consensus_params(), group_species(), group_species_cb(), highlight_and_update(), ED4_cursor::jump_screen_pos(), load_search_paras_from_file(), ED4_cursor::move_cursor(), PV_AddCorrespondingOrfTerminals(), PV_AddNewAAseqTerminals(), PV_AddOrfTerminalsToLoadedSpecies(), PV_SequenceUpdate_CB(), refresh_display_cb(), remove_from_highlighted(), replace_in_block(), ED4_window::reset_all_for_new_config(), resultsAreShown(), save_search_paras_to_file(), TranslateGeneToAminoAcidSequence(), SearchSettings::update(), ED4_terminal::write_sequence(), and ~ED4_root().

AW_default ED4_root::props_db

Definition at line 1426 of file ed4_class.hxx.

Referenced by ed4_create_all_awars(), and generate_window().

ED4_main_manager* ED4_root::main_manager

ED4_area_manager* ED4_root::middle_area_man

Definition at line 1430 of file ed4_class.hxx.

Referenced by create_hierarchy(), deselect_all(), ED4_create_sequences_for_gde(), ED4_load_new_config(), ED4_menu_highlight(), ED4_base::get_area_level(), and ED4_window::update_window_coords().

ED4_area_manager* ED4_root::top_area_man

Definition at line 1431 of file ed4_class.hxx.

Referenced by create_hierarchy(), createGroupFromSelected(), deselect_all(), ED4_create_sequences_for_gde(), ED4_load_new_config(), ED4_base::get_area_level(), and ED4_window::update_window_coords().

ED4_root_group_manager* ED4_root::root_group_man

Definition at line 1432 of file ed4_class.hxx.

Referenced by create_hierarchy(), create_list_of_loaded_species(), ED4_alignment_length_changed(), ED4_compression_changed_cb(), ED4_consensus_display_changed(), ED4_find_MoreSequences_manager(), ED4_find_SAI_name_terminal(), ED4_find_species_name_terminal(), ED4_find_species_or_SAI_name_terminal(), ED4_jump_to_cursor_position(), ED4_mark_matching_species(), ED4_resize_all_extensions(), ED4_search_cb(), ED4_setColumnblockCorner(), ED4_show_helix_on_device(), ED4_show_protein_match_on_device(), ED4_with_all_loaded_species(), ED4_with_whole_block(), executeKeystroke(), ED4_cursor::get_sequence_pos(), ED4_cursor::jump_sequence_pos(), ED4_remap::mark_compile_needed_force(), pixel2pos(), PV_CreateAllTerminals(), PV_DisplayAminoAcidNames(), PV_HideAllTerminals(), PV_ManageTerminals(), PV_SaveData(), ED4_cursor::set_to_terminal(), and ED4_manager::update_bases().

ED4_highlighted_list* ED4_root::highlighted_objects

Definition at line 1433 of file ed4_class.hxx.

Referenced by add_to_highlighted(), ED4_block::autocorrect_type(), createGroupFromSelected(), ED4_load_new_config(), ED4_setColumnblockCorner(), ED4_with_whole_block(), get_first_selected_species(), get_selected_range(), group_species(), refresh_highlighted(), remove_from_highlighted(), and ~ED4_root().

ED4_scroll_links ED4_root::scroll_links

Definition at line 1434 of file ed4_class.hxx.

Referenced by create_hierarchy(), ED4_load_new_config(), ED4_new_editor_window(), get_max_slider_xpos(), get_max_slider_ypos(), EDB_root_bact::search_sequence_data_rek(), ED4_window::update_window_coords(), and ED4_base::~ED4_base().

bool ED4_root::folding_action

Definition at line 1435 of file ed4_class.hxx.

ED4_reference_terminals ED4_root::ref_terminals

Definition at line 1436 of file ed4_class.hxx.

Referenced by create_hierarchy(), createGroupFromSelected(), ED4_get_marked_from_menu(), ED4_load_new_config(), ED4_resize_all_extensions(), insert_new_species_terminal(), and toggle_detailed_column_stat().

ED4_species_mode ED4_root::species_mode

Definition at line 1437 of file ed4_class.hxx.

Referenced by ED4_no_dangerous_modes(), ED4_terminal::event_sent_by_parent(), and modes_cb().

ED4_scroll_picture ED4_root::scroll_picture

Definition at line 1438 of file ed4_class.hxx.

Referenced by ED4_input_cb(), ED4_load_new_config(), and ED4_motion_cb().

BI_ecoli_ref* ED4_root::ecoli_ref

Definition at line 1439 of file ed4_class.hxx.

Referenced by create_hierarchy(), ED4_alignment_length_changed(), ED4_jump_to_cursor_position(), ED4_load_new_config(), reload_ecoli_cb(), and ~ED4_root().

ED4_reference* ED4_root::reference

Definition at line 1441 of file ed4_class.hxx.

Referenced by create_hierarchy(), diff_type_changed_cb(), ED4_consensus_definition_changed(), ED4_create_viewDifferences_window(), ED4_toggle_viewDifferences(), ED4_viewDifferences_announceTerminalChange(), set_diff_reference(), update_reference_settings(), and ~ED4_root().

ED4_seq_colors* ED4_root::sequence_colors

Definition at line 1442 of file ed4_class.hxx.

Referenced by ARB_main(), ED4_CreateProteinViewer_window(), generate_window(), and ~ED4_root().

AW_gc_manager* ED4_root::gc_manager

Definition at line 1443 of file ed4_class.hxx.

Referenced by create_editColorTranslationTable_window(), ED4_CreateProteinViewer_window(), and generate_window().

ST_ML* ED4_root::st_ml

Definition at line 1444 of file ed4_class.hxx.

Referenced by ARB_main(), configureColumnStat(), ED4_toggle_detailed_column_stats(), and ~ED4_root().

AW_helix* ED4_root::helix

Definition at line 1445 of file ed4_class.hxx.

Referenced by add_area_for_gde(), ARB_main(), calc_and_update_alignment_errors_cb(), ED4_alignment_length_changed(), ED4_calc_terminal_extentions(), ED4_helix_jump_opposite(), ED4_popup_helix_or_pfold_window(), ED4_set_helixnr(), ED4_host::get_helix(), reload_helix_cb(), and ~ED4_root().

int ED4_root::helix_spacing

Definition at line 1446 of file ed4_class.hxx.

Referenced by ED4_calc_terminal_extentions().

long ED4_root::helix_add_spacing

Definition at line 1447 of file ed4_class.hxx.

Referenced by ED4_calc_terminal_extentions(), and ed4_create_all_awars().

long ED4_root::terminal_add_spacing

Definition at line 1448 of file ed4_class.hxx.

Referenced by ED4_calc_terminal_extentions(), and ed4_create_all_awars().

char* ED4_root::protstruct

Definition at line 1449 of file ed4_class.hxx.

Referenced by ARB_main(), ED4_alignment_length_changed(), ED4_calc_terminal_extentions(), ED4_pfold_select_SAI_and_update_option_menu(), ED4_manager::update_bases_and_rebuild_consensi(), and ~ED4_root().

long ED4_root::protstruct_len

Definition at line 1450 of file ed4_class.hxx.

Referenced by ARB_main(), ED4_alignment_length_changed(), ED4_pfold_select_SAI_and_update_option_menu(), and ED4_manager::update_bases_and_rebuild_consensi().

ed_key* ED4_root::edk

Definition at line 1451 of file ed4_class.hxx.

Referenced by ARB_main(), ED4_Edit_String::edit(), and ~ED4_root().

bool ED4_root::column_stat_activated

Definition at line 1453 of file ed4_class.hxx.

Referenced by ED4_activate_col_stat(), ED4_disable_col_stat(), and set_col_stat_activated_and_refresh().

bool ED4_root::column_stat_initialized

Definition at line 1454 of file ed4_class.hxx.

Referenced by col_stat_activated(), ED4_activate_col_stat(), ED4_disable_col_stat(), ED4_toggle_detailed_column_stats(), and show_detailed_column_stats_activated().

bool ED4_root::visualizeSAI

Definition at line 1455 of file ed4_class.hxx.

Referenced by ED4_createVisualizeSAI_Awars(), ED4_host::SAIs_visualized(), and setVisualizeSAI_cb().

bool ED4_root::visualizeSAI_allSpecies

Definition at line 1456 of file ed4_class.hxx.

Referenced by ED4_createVisualizeSAI_Awars(), and setVisualizeSAI_options_cb().

LoadableSaiState ED4_root::loadable_SAIs

Definition at line 1463 of file ed4_class.hxx.

Referenced by ED4_create_loadSAI_window(), and refresh_all_windows().

int ED4_root::temp_gc

Definition at line 1466 of file ed4_class.hxx.

Referenced by ED4_window::insert_window().

AW_font_group ED4_root::font_group

Definition at line 1467 of file ed4_class.hxx.

Referenced by create_hierarchy(), ED4_text_terminal::draw(), ED4_calc_terminal_extentions(), ED4_input_cb(), ED4_resize_all_extensions(), ED4_cursor::jump_screen_pos(), move_and_update_rectangle(), pixel2pos(), recalc_font_group(), ED4_cursor::set_abs_x(), ED4_cursor::set_screen_relative_pos(), ED4_cursor::show_cursor_at(), and toggle_detailed_column_stat().

The documentation for this class was generated from the following files: