#include "ed4_class.hxx"
#include "ed4_awars.hxx"
#include "ed4_edit_string.hxx"
#include "ed4_nds.hxx"
#include "ed4_visualizeSAI.hxx"
#include "ed4_ProteinViewer.hxx"
#include "ed4_protein_2nd_structure.hxx"
#include "ed4_dots.hxx"
#include "ed4_detect_bad_ali.hxx"
#include "ed4_naligner.hxx"
#include "ed4_seq_colors.hxx"
#include "graph_aligner_gui.hxx"
#include <ed4_extern.hxx>
#include <st_window.hxx>
#include <gde.hxx>
#include <AW_helix.hxx>
#include <AP_pro_a_nucs.hxx>
#include <ad_config.h>
#include <awt_map_key.hxx>
#include <awt.hxx>
#include <aw_preset.hxx>
#include <aw_awars.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <aw_advice.hxx>
#include <arbdbt.h>
#include <arb_defs.h>
#include <arb_global_defs.h>
#include <macros.hxx>
#include <aw_question.hxx>

Include dependency graph for ED4_main.cxx:

Functions
void	replaceChars (char *s, char o, char n)

void	set_and_realloc_gde_array (uchar &the_names, uchar &the_sequences, long &allocated, long &numberspecies, long &maxalign, const char name, int name_len, const char seq, int seq_len)

static char *	add_area_for_gde (ED4_area_manager area_man, uchar &the_names, uchar *&the_sequences, long &allocated, long &numberspecies, long &maxalign, int show_sequence, int show_SAI, int show_helix, int show_consensus, int show_remark)

static char *	ED4_create_sequences_for_gde (GBDATA &the_species, uchar &the_names, uchar **&the_sequences, long &numberspecies, long &maxalign)

void	ED4_setup_gaps_and_alitype (const char *gap_chars, GB_alignment_type alitype)

static void	ED4_gap_chars_changed (AW_root *root)

void	ED4_with_all_edit_windows (void(cb)(ED4_window ))

static void	redraw_cursor (ED4_window *win)

static void	ED4_edit_direction_changed (AW_root *)

static void	ed4_bind_mainDB_awar_callbacks (AW_root *root)

static void	ed4_create_mainDB_awars (AW_root *root)

static void	ed4_create_all_awars (AW_root root, const char config_name)

static void	ED4_postcbcb (AW_window *aww)

static void	seq_colors_changed_cb ()

int	ARB_main (int argc, char *argv[])

Function Documentation

void replaceChars	(	char *	s,
		char	o,
		char	n
	)

inline

Definition at line 71 of file ED4_main.cxx.

Referenced by add_area_for_gde(), and set_and_realloc_gde_array().

void set_and_realloc_gde_array	(	uchar **&	the_names,
		uchar **&	the_sequences,
		long &	allocated,
		long &	numberspecies,
		long &	maxalign,
		const char *	name,
		int	name_len,
		const char *	seq,
		int	seq_len
	)

inline

Definition at line 83 of file ED4_main.cxx.

References ARB_recalloc(), ARB_strndup(), and replaceChars().

Referenced by add_area_for_gde().

static char* add_area_for_gde	(	ED4_area_manager *	area_man,
		uchar **&	the_names,
		uchar **&	the_sequences,
		long &	allocated,
		long &	numberspecies,
		long &	maxalign,
		int	show_sequence,
		int	show_SAI,
		int	show_helix,
		int	show_consensus,
		int	show_remark
	)

static

static char* ED4_create_sequences_for_gde	(	GBDATA **&	the_species,
		uchar **&	the_names,
		uchar **&	the_sequences,
		long &	numberspecies,
		long &	maxalign
	)

static

Definition at line 219 of file ED4_main.cxx.

References add_area_for_gde(), ARB_calloc(), ARB_recalloc(), ED4_root::aw_root, AW_root::awar(), ED4_root::middle_area_man, NULp, AW_awar::read_int(), and ED4_root::top_area_man.

Referenced by ed4_create_all_awars().

void ED4_setup_gaps_and_alitype	(	const char *	gap_chars,
		GB_alignment_type	alitype
	)

Definition at line 253 of file ED4_main.cxx.

References BaseFrequencies::setup().

Referenced by ED4_gap_chars_changed().

static void ED4_gap_chars_changed ( AW_root * root )

static

Definition at line 257 of file ED4_main.cxx.

References ED4_root::alignment_type, AW_root::awar_string(), ED4_AWAR_GAP_CHARS, ED4_setup_gaps_and_alitype(), and AW_awar::read_string().

Referenced by ed4_create_all_awars().

void ED4_with_all_edit_windows ( void(*)(ED4_window *) cb )

Definition at line 263 of file ED4_main.cxx.

References cb, ED4_root::first_window, and win.

Referenced by ED4_edit_direction_changed().

static void redraw_cursor ( ED4_window * win )

static

Definition at line 270 of file ED4_main.cxx.

References ED4_window::cursor, and ED4_cursor::redraw().

Referenced by ED4_edit_direction_changed().

static void ED4_edit_direction_changed ( AW_root * )

static

Definition at line 271 of file ED4_main.cxx.

References ED4_with_all_edit_windows(), and redraw_cursor().

Referenced by ed4_create_all_awars().

static void ed4_bind_mainDB_awar_callbacks ( AW_root * root )

static

Definition at line 275 of file ED4_main.cxx.

References AW_awar::add_callback(), AW_root::awar(), AWAR_SAI_NAME, AWAR_SET_CURSOR_POSITION, AWAR_SPECIES_NAME, ED4_remote_set_cursor_cb(), ED4_selected_SAI_changed_cb(), and ED4_selected_species_changed_cb().

Referenced by ARB_main().

static void ed4_create_mainDB_awars ( AW_root * root )

static

Definition at line 284 of file ED4_main.cxx.

References AWAR_CURSOR_POSITION, AWAR_CURSOR_POSITION_LOCAL, AWAR_FIELD_CHOSEN, AW_root::awar_int(), AWAR_RANGE, AWAR_SAI_GLOBAL, AWAR_SAI_NAME, AWAR_SET_CURSOR_POSITION, AWAR_SPECIES_NAME, AW_root::awar_string(), gb_main, ED4_root::get_gb_main(), info2bio(), and NO_FIELD_SELECTED.

Referenced by ed4_create_all_awars().

static void ed4_create_all_awars	(	AW_root *	root,
		const char *	config_name
	)

static

Definition at line 301 of file ED4_main.cxx.

References AD_ALIGN, AW_awar::add_callback(), AW_awar::add_target_var(), ED4_root::alignment_type, GAP::anyGapChars(), ARB_init_global_awars(), aw_message(), ED4_root::aw_root, AW_ROOT_DEFAULT, AWAR_EDIT_CONFIGURATION, AWAR_EDIT_HELIX_SPACING, awar_edit_mode, AWAR_EDIT_MODE, awar_edit_rightward, AWAR_EDIT_RIGHTWARD, AWAR_EDIT_SECURITY_LEVEL, AWAR_EDIT_SECURITY_LEVEL_ALIGN, AWAR_EDIT_SECURITY_LEVEL_CHANGE, AWAR_EDIT_TERMINAL_SPACING, AWAR_EDIT_TITLE_MODE, AWAR_INSERT_MODE, AW_root::awar_int(), AW_root::awar_string(), create_naligner_variables(), create_sina_variables(), e4_assert, ED4_AWAR_ANNOUNCE_CHECKSUM_CHANGES, ED4_AWAR_COMPRESS_SEQUENCE_GAPS, ED4_AWAR_COMPRESS_SEQUENCE_HIDE, ED4_AWAR_COMPRESS_SEQUENCE_PERCENT, ED4_AWAR_COMPRESS_SEQUENCE_TYPE, 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_CURSOR_TYPE, ED4_AWAR_DIGITS_AS_REPEAT, ED4_AWAR_FAST_CURSOR_JUMP, ED4_AWAR_GAP_CHARS, ED4_AWAR_REP_REPLACE_PATTERN, ED4_AWAR_REP_SEARCH_PATTERN, ED4_AWAR_SCROLL_MARGIN, ED4_AWAR_SCROLL_SPEED_X, ED4_AWAR_SCROLL_SPEED_Y, ED4_AWAR_SPECIES_TO_CREATE, ed4_change_edit_mode(), ed4_changesecurity(), ED4_compression_changed_cb(), ED4_compression_toggle_changed_cb(), ED4_create_consensus_awars(), ED4_create_detect_bad_alignment_awars(), ED4_create_dot_missing_bases_awars(), ed4_create_mainDB_awars(), ED4_create_NDS_awars(), ED4_create_search_awars(), ED4_create_sequences_for_gde(), ED4_createVisualizeSAI_Awars(), ED4_edit_direction_changed(), ED4_gap_chars_changed(), ED4_request_relayout(), ED4_RIGHT_ORIENTED_CURSOR, error(), GB_AT_AA, GB_AT_DNA, gb_main, GBK_terminatef(), GDE_init(), GDE_WINDOWTYPE_EDIT4, ED4_root::get_gb_main(), ED4_root::helix_add_spacing, name_value_pair::name, NULp, PFOLD_AWAR_ENABLE, PFOLD_AWAR_MATCH_METHOD, PFOLD_AWAR_PAIR_TEMPLATE, PFOLD_AWAR_SAI_FILTER, PFOLD_AWAR_SELECTED_SAI, PFOLD_AWAR_SYMBOL_TEMPLATE, PFOLD_AWAR_SYMBOL_TEMPLATE_2, pfold_match_type_awars, pfold_pair_chars, PFOLD_PAIR_CHARS_2, pfold_pairs, PFOLD_PAIRS, ED4_root::props_db, PV_CreateAwars(), SECSTRUCT_SEQUENCE, AW_awar::set_minmax(), ED4_root::terminal_add_spacing, and name_value_pair::value.

Referenced by ARB_main().

static void ED4_postcbcb ( AW_window * aww )

static

Definition at line 407 of file ED4_main.cxx.

References ED4_root::announce_useraction_in(), and ED4_trigger_instant_refresh().

Referenced by ARB_main().

static void seq_colors_changed_cb ( )

static

Definition at line 411 of file ED4_main.cxx.

References ED4_root::request_refresh_for_sequence_terminals().

Referenced by ARB_main().

int ARB_main	(	int	argc,
		char *	argv[]
	)

Definition at line 415 of file ED4_main.cxx.

References ED4_root::alignment_type, ARB_strdup(), aw_initstatus(), aw_message(), aw_popup_ok(), ED4_root::aw_root, AWT_install_cb_guards(), AWT_install_postcb_cb(), configure_macro_recording(), ed_key::create_awars(), ED4_root::create_first_window(), ED4_root::create_hierarchy(), DEFAULT_CONFIGURATION, ARB_ERROR::deliver(), e4_assert, ed4_bind_mainDB_awar_callbacks(), ed4_create_all_awars(), ED4_exit(), ED4_G_SEQUENCES, ED4_pfold_set_SAI(), ED4_postcbcb(), ED4_root::edk, error(), GBT_config::exists(), EXIT_SUCCESS, ED4_root::first_window, GB_AT_AA, GB_AT_DNA, GB_AT_RNA, GB_await_error(), GB_close(), gb_main, GB_open(), GBS_global_string(), ED4_root::get_alignment_name(), GBT_config::get_definition(), ED4_WinContext::have_context(), ED4_root::helix, BI_helix::init(), ED4_root::init_alignment(), ED4_objspec::init_object_specs(), AW_root::main_loop(), GBT_config::MIDDLE_AREA, NULp, ED4_root::protstruct, ED4_root::protstruct_len, PV_CallBackFunction(), seq_colors_changed_cb(), ED4_root::sequence_colors, shutdown_macro_recording(), ED4_root::st_ml, STAT_create_ST_ML(), ta, GBT_config::TOP_AREA, and warning().

Variable Documentation

AW_HEADER_MAIN ED4_root* ED4_ROOT = NULp

Definition at line 49 of file ED4_main.cxx.

Referenced by ED4_host::announce_current_species(), ED4_block::autocorrect_type(), ED4_abstract_group_manager::build_consensus_string(), calc_and_update_alignment_errors_cb(), calculate_group_folding(), ED4_terminal::changed_by_database(), ED4_cursor::changeType(), clear_and_update_rectangle(), col_stat_activated(), colorDefChanged_callback(), colorDefTabNameChanged_callback(), configureColumnStat(), create_editColorTranslationTable_window(), create_group_species_by_field_window(), create_list_of_loaded_species(), create_new_species(), createDataFromConsensus(), createGroupFromSelected(), ED4_manager::delete_requested_children(), ED4_terminal::delete_requested_children(), ED4_window::delete_window(), ED4_manager::deleted_from_database(), ED4_multi_species_manager::deselect_all_species_and_SAI(), diff_setting_changed_cb(), diff_type_changed_cb(), do_sth_with_species(), dot_missing_bases(), ED4_text_terminal::draw(), ED4_terminal::draw_drag_box(), ED4_activate_col_stat(), ED4_alignment_length_changed(), ED4_calc_terminal_extentions(), ed4_changesecurity(), ED4_compression_changed_cb(), ED4_consensus_definition_changed(), ED4_consensus_display_changed(), ED4_create_consensus_awars(), ED4_create_loadConfiguration_window(), ED4_create_loadSAI_window(), ED4_create_NDS_awars(), ED4_create_saveConfigurationAs_window(), ED4_create_search_awars(), ED4_create_viewDifferences_window(), ED4_CreateProteinViewer_window(), ED4_createVisualizeSAI_Awars(), ED4_createVisualizeSAI_window(), ED4_cursor::ED4_cursor(), ED4_disable_col_stat(), ED4_exit(), ED4_expose_cb(), ED4_find_MoreSequences_manager(), ED4_find_SAI_name_terminal(), ED4_find_species_name_terminal(), ED4_find_species_or_SAI_name_terminal(), 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_jump_to_cursor_position(), ED4_load_new_config(), ED4_mark_matching_species(), ED4_menu_highlight(), ED4_MostRecentWinContext::ED4_MostRecentWinContext(), ED4_motion_cb(), ED4_new_editor_window(), ED4_no_dangerous_modes(), ED4_perform_block_operation(), 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_popup_detect_bad_alignment_window(), ED4_popup_dot_missing_bases_window(), ED4_popup_helix_or_pfold_window(), ED4_quit_editor(), ED4_remove_faligner_entries(), ED4_request_full_refresh(), ED4_request_relayout(), ED4_resize_all_extensions(), ED4_resize_cb(), ED4_restore_curpos(), ED4_root_group_manager::ED4_root_group_manager(), ED4_save_properties(), ed4_scroll(), ED4_scrollbar_change_cb(), ED4_search_cb(), ED4_selected_SAI_changed_cb(), ED4_selected_species_changed_cb(), ED4_set_col_stat_threshold(), ED4_set_helixnr(), ED4_set_iupac(), ED4_setColumnblockCorner(), ED4_show_helix_on_device(), ED4_show_protein_match_on_device(), ED4_store_curpos(), ED4_timer(), ED4_toggle_detailed_column_stats(), ED4_toggle_viewDifferences(), ED4_trigger_instant_refresh(), ED4_undo_redo(), ED4_vertical_change_cb(), ED4_viewDifferences_announceTerminalChange(), ED4_WinContext::ED4_WinContext(), ED4_window::ED4_window(), ED4_with_all_loaded_species(), ED4_with_whole_block(), ED4_Edit_String::edit(), ED4_terminal::event_sent_by_parent(), executeKeystroke(), EDB_root_bact::fill_data(), filter_loadable_SAIs(), ED4_group_manager::fold(), ED4_base::get_area_level(), get_first_selected_species(), ED4_host::get_helix(), ED4_window::get_matching_ed4w(), get_max_slider_xpos(), get_max_slider_ypos(), get_selected_range(), ED4_cursor::get_sequence_pos(), ED4_sequence_terminal::GetAliType(), group_species(), group_species_cb(), ED4_manager::handle_move(), highlight_and_update(), init_flag_awars(), insert_new_species_terminal(), ED4_window::insert_window(), ED4_multi_species_manager::invert_selection_of_all_species(), ED4_cursor::jump_screen_pos(), ED4_cursor::jump_sequence_pos(), load_search_paras_from_file(), ED4_remap::mark_compile_needed_force(), ED4_multi_species_manager::marked_species_select(), modes_cb(), modsai_cb(), move_and_update_rectangle(), ED4_cursor::move_cursor(), SpeciesFlag::prepare_itemfield(), propertyName(), PV_AddCorrespondingOrfTerminals(), PV_AddNewAAseqTerminals(), PV_AddOrfTerminalsToLoadedSpecies(), PV_CallBackFunction(), PV_ComplementarySequence(), PV_CreateAllTerminals(), PV_DisplayAminoAcidNames(), PV_HideAllTerminals(), PV_ManageTerminals(), PV_PrintMissingDBentryInformation(), PV_SaveData(), PV_SequenceUpdate_CB(), PV_WriteTranslatedSequenceToDB(), refdata_changed_cb(), refresh_display_cb(), refresh_highlighted(), reload_ecoli_cb(), reload_helix_cb(), remove_from_consensus(), replace_in_block(), ED4_window::reset_all_for_new_config(), ED4_root_group_manager::resize_requested_children(), ED4_terminal::resolve_pointer_to_char_pntr(), resultsAreShown(), saiChanged_callback(), ED4_host::SAIs_visualized(), EDB_root_bact::save_current_config(), save_search_paras_to_file(), EDB_root_bact::search_sequence_data_rek(), searchParamsChanged(), SearchTree::SearchTree(), ED4_multi_species_manager::select_all(), select_named_sequence_terminal(), ED4_cursor::set_abs_x(), set_col_stat_activated_and_refresh(), set_diff_reference(), ED4_cursor::set_screen_relative_pos(), ED4_cursor::set_to_terminal(), setVisualizeSAI_cb(), setVisualizeSAI_options_cb(), ED4_cursor::show_clicked_cursor(), ED4_cursor::show_cursor_at(), show_detailed_column_stats_activated(), toggle_detailed_column_stat(), trace_termChange_in_global_awar(), TranslateGeneToAminoAcidSequence(), SearchSettings::update(), ED4_manager::update_bases(), ED4_manager::update_bases_and_rebuild_consensi(), update_reference_settings(), ED4_window::update_window_coords(), ED4_terminal::write_sequence(), ED4_base::~ED4_base(), and ED4_terminal::~ED4_terminal().

int TERMINAL_HEIGHT

Definition at line 51 of file ED4_main.cxx.

Referenced by ED4_root::create_hierarchy(), ED4_build_group_manager_start(), ED4_calc_terminal_extentions(), ED4_resize_all_extensions(), EDB_root_bact::fill_data(), PV_AddNewAAseqTerminals(), and EDB_root_bact::search_sequence_data_rek().

int INFO_TERM_TEXT_YOFFSET

Definition at line 53 of file ED4_main.cxx.

Referenced by ED4_text_terminal::draw(), ED4_terminal::draw_drag_box(), and ED4_calc_terminal_extentions().

int SEQ_TERM_TEXT_YOFFSET

Definition at line 54 of file ED4_main.cxx.

Referenced by ED4_calc_terminal_extentions().

int MAXSEQUENCECHARACTERLENGTH

Definition at line 56 of file ED4_main.cxx.

Referenced by ED4_terminal::changed_by_database(), ED4_remap::compile(), ED4_manager::create_consensus(), ED4_alignment_length_changed(), ED4_jump_to_cursor_position(), ED4_remap::ED4_remap(), ED4_resize_all_extensions(), ED4_setColumnblockCorner(), ED4_root::init_alignment(), and EDB_root_bact::search_sequence_data_rek().

int MAXNAME_WIDTH

Definition at line 57 of file ED4_main.cxx.

Referenced by ED4_root::create_hierarchy(), ED4_build_group_manager_start(), ED4_calc_terminal_extentions(), EDB_root_bact::fill_data(), and ED4_base::set_width().

int MAXINFO_WIDTH

Definition at line 58 of file ED4_main.cxx.

Referenced by ED4_root::create_hierarchy(), ED4_calc_terminal_extentions(), and ED4_resize_all_extensions().

int FLAG_WIDTH

Definition at line 59 of file ED4_main.cxx.

Referenced by ED4_calc_terminal_extentions(), and EDB_root_bact::fill_data().

long ED4_counter = 0

Definition at line 61 of file ED4_main.cxx.

Referenced by createGroupFromSelected(), ED4_build_group_manager_end(), ED4_build_group_manager_start(), EDB_root_bact::fill_data(), EDB_root_bact::fill_species(), PV_AddNewAAseqTerminals(), EDB_root_bact::scan_string(), EDB_root_bact::search_sequence_data_rek(), and toggle_detailed_column_stat().

size_t not_found_counter

Definition at line 63 of file ED4_main.cxx.

Referenced by ED4_finish_and_show_notFoundMessage(), ED4_init_notFoundMessage(), and EDB_root_bact::fill_data().

GBS_strstruct* not_found_message

Definition at line 64 of file ED4_main.cxx.

Referenced by ED4_finish_and_show_notFoundMessage(), ED4_init_notFoundMessage(), and EDB_root_bact::fill_data().

long max_seq_terminal_length

Definition at line 66 of file ED4_main.cxx.

Referenced by ED4_root::create_first_window(), ED4_load_new_config(), EDB_root_bact::fill_data(), and toggle_detailed_column_stat().

ED4_EDITMODE awar_edit_mode

Definition at line 67 of file ED4_main.cxx.

Referenced by ed4_change_edit_mode(), ed4_create_all_awars(), and executeKeystroke().

long awar_edit_rightward

Definition at line 68 of file ED4_main.cxx.

Referenced by ed4_create_all_awars(), and executeKeystroke().

bool DRAW

Definition at line 69 of file ED4_main.cxx.

Referenced by ED4_root::create_first_window(), and ED4_cursor::show_cursor_at().

Variables
AW_HEADER_MAIN ED4_root *	ED4_ROOT = NULp

int	TERMINAL_HEIGHT

int	INFO_TERM_TEXT_YOFFSET

int	SEQ_TERM_TEXT_YOFFSET

int	MAXSEQUENCECHARACTERLENGTH

int	MAXNAME_WIDTH

int	MAXINFO_WIDTH

int	FLAG_WIDTH

long	ED4_counter = 0

size_t	not_found_counter

GBS_strstruct *	not_found_message

long	max_seq_terminal_length

ED4_EDITMODE	awar_edit_mode

long	awar_edit_rightward

bool	DRAW

Functions

Variables

Function Documentation

Variable Documentation