ARB
Public Member Functions | Public Attributes | List of all members
ED4_root Class Reference

#include <ed4_class.hxx>

Inheritance diagram for ED4_root:
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Collaboration diagram for ED4_root:
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Public Member Functions

GBDATAget_gb_main () const
 
const ConsensusBuildParamsget_consensus_params ()
 
void reset_consensus_params ()
 
void loadable_SAIs_may_have_changed ()
 
void announce_useraction_in (AW_window *aww)
 
ED4_windowget_most_recently_used_window () const
 
ED4_device_managerget_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_windowcreate_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_selected (ED4_species_name_terminal *object)
 
void remove_from_selected (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

chardb_name
 
AW_rootaw_root
 
AW_default props_db
 
ED4_windowfirst_window
 
ED4_main_manager * main_manager
 
ED4_area_managermiddle_area_man
 
ED4_area_managertop_area_man
 
ED4_root_group_managerroot_group_man
 
ED4_selected_listselected_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_refecoli_ref
 
charalignment_name
 
GB_alignment_type alignment_type
 
ED4_referencereference
 
ED4_seq_colorssequence_colors
 
AW_gc_managergc_manager
 
ST_MLst_ml
 
AW_helixhelix
 
int helix_spacing
 
long helix_add_spacing
 
long terminal_add_spacing
 
charprotstruct
 
long protstruct_len
 
ed_keyedk
 
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 1407 of file ed4_class.hxx.

Constructor & Destructor Documentation

ED4_root::ED4_root ( GBDATA gb_main_)

Definition at line 1958 of file ED4_root.cxx.

ED4_root::~ED4_root ( )

Member Function Documentation

GBDATA* ED4_root::get_gb_main ( ) const
inline

Definition at line 1420 of file ed4_class.hxx.

References gb_main.

Referenced by ED4_terminal::changed_by_database(), create_group_species_by_field_window(), create_new_species(), createDataFromConsensus(), 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_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 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 1461 of file ed4_class.hxx.

References LSAI_OUTDATED, and LSAI_UPTODATE.

void ED4_root::announce_useraction_in ( AW_window aww)

Definition at line 372 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 1467 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
ED4_returncode ED4_root::create_hierarchy ( const char area_string_middle,
const char area_string_top 
)
ARB_ERROR ED4_root::init_alignment ( )
void ED4_root::recalc_font_group ( )
AW_window * ED4_root::create_first_window ( )
ED4_returncode ED4_root::generate_window ( AW_device **  device,
ED4_window **  new_window 
)

Definition at line 1319 of file ED4_root.cxx.

References AW_awar::add_callback(), alignment_name, 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, create_helix_props_window(), 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_pfold_create_props_window(), ED4_popup_dot_missing_bases_window(), ED4_popup_gc_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_request_relayout(), 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 
)
void ED4_root::resize_all_requesting_childs ( )

Definition at line 454 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 158 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)
void ED4_root::request_refresh_for_all_terminals ( )

Definition at line 83 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)
void ED4_root::request_refresh_for_consensus_terminals ( )

Definition at line 103 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 ( )
void ED4_root::announce_deletion ( ED4_base object)
inline
ED4_returncode ED4_root::add_to_selected ( ED4_species_name_terminal *  object)
void ED4_root::remove_from_selected ( ED4_species_name_terminal *  object)
ED4_returncode ED4_root::deselect_all ( )
ED4_returncode ED4_root::get_area_rectangle ( AW_screen_area rect,
AW_pos  x,
AW_pos  y 
)
ED4_index ED4_root::pixel2pos ( AW_pos  click_x)
void ED4_root::remove_all_callbacks ( )

Definition at line 1623 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 1422 of file ed4_class.hxx.

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

AW_root* ED4_root::aw_root

Definition at line 1423 of file ed4_class.hxx.

Referenced by add_to_selected(), 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(), init_alignment(), 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_selected(), 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 1424 of file ed4_class.hxx.

Referenced by ed4_create_all_awars(), and generate_window().

ED4_window* ED4_root::first_window
ED4_main_manager* ED4_root::main_manager
ED4_area_manager* ED4_root::middle_area_man
ED4_area_manager* ED4_root::top_area_man
ED4_root_group_manager* ED4_root::root_group_man
ED4_selected_list* ED4_root::selected_objects
ED4_scroll_links ED4_root::scroll_links
bool ED4_root::folding_action

Definition at line 1433 of file ed4_class.hxx.

ED4_reference_terminals ED4_root::ref_terminals
ED4_species_mode ED4_root::species_mode
ED4_scroll_picture ED4_root::scroll_picture

Definition at line 1436 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
char* ED4_root::alignment_name
GB_alignment_type ED4_root::alignment_type
ED4_reference* ED4_root::reference
ED4_seq_colors* ED4_root::sequence_colors
AW_gc_manager* ED4_root::gc_manager
ST_ML* ED4_root::st_ml
AW_helix* ED4_root::helix
int ED4_root::helix_spacing

Definition at line 1445 of file ed4_class.hxx.

Referenced by ED4_calc_terminal_extentions().

long ED4_root::helix_add_spacing

Definition at line 1446 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 1447 of file ed4_class.hxx.

Referenced by ED4_calc_terminal_extentions(), and ed4_create_all_awars().

char* ED4_root::protstruct
long ED4_root::protstruct_len
ed_key* ED4_root::edk

Definition at line 1450 of file ed4_class.hxx.

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

bool ED4_root::column_stat_activated
bool ED4_root::column_stat_initialized
bool ED4_root::visualizeSAI
bool ED4_root::visualizeSAI_allSpecies

Definition at line 1455 of file ed4_class.hxx.

Referenced by ED4_createVisualizeSAI_Awars(), and setVisualizeSAI_options_cb().

LoadableSaiState ED4_root::loadable_SAIs

Definition at line 1460 of file ed4_class.hxx.

Referenced by ED4_create_loadSAI_window(), and refresh_all_windows().

int ED4_root::temp_gc

Definition at line 1463 of file ed4_class.hxx.

Referenced by ED4_window::insert_window().

AW_font_group ED4_root::font_group

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