#include "ed4_class.hxx"
#include "ed4_awars.hxx"
#include "ed4_tools.hxx"
#include "ed4_block.hxx"
#include "ed4_dots.hxx"
#include "ed4_detect_bad_ali.hxx"
#include "ed4_nds.hxx"
#include "ed4_list.hxx"
#include "ed4_plugins.hxx"
#include "ed4_visualizeSAI.hxx"
#include "ed4_naligner.hxx"
#include "ed4_ProteinViewer.hxx"
#include "ed4_protein_2nd_structure.hxx"
#include "graph_aligner_gui.hxx"
#include "ed4_colStat.hxx"
#include "ed4_seq_colors.hxx"
#include "ed4_flags.hxx"
#include <ed4_extern.hxx>
#include <fast_aligner.hxx>
#include <AW_helix.hxx>
#include <gde.hxx>
#include <awt.hxx>
#include <awt_map_key.hxx>
#include <aw_awars.hxx>
#include <aw_preset.hxx>
#include <aw_msg.hxx>
#include <arb_progress.h>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <aw_advice.hxx>
#include <rootAsWin.h>
#include "../WINDOW/aw_status.hxx"
#include <arb_version.h>
#include <arb_file.h>
#include <arb_defs.h>
#include <arbdbt.h>
#include <ad_cb.h>
#include <macros.hxx>
#include <st_window.hxx>
#include <cctype>
#include <map>

Include dependency graph for ED4_root.cxx:

Macros
#define	INSERT_SEARCH_FIELDS(Short, label_prefix, prefix)

Enumerations
enum	MenuHighlightType { ED4_MS_NONE, ED4_MS_ALL, ED4_MS_INVERT, ED4_MS_INVERT_GROUP, ED4_MS_UNMARK_ALL, ED4_MS_MARK_SELECTED, ED4_MS_UNMARK_SELECTED, ED4_MS_SELECT_MARKED, ED4_MS_DESELECT_MARKED, ED4_MS_TOGGLE_BLOCKTYPE }

Functions
static ARB_ERROR	request_terminal_refresh (ED4_base *base, ED4_level lev)

static ARB_ERROR	request_sequence_refresh (ED4_base *base, bool consensi)

static ARB_ERROR	change_char_table_length (ED4_base *base, int new_length)

void	ED4_alignment_length_changed (GBDATA *gb_alignment_len, GB_CB_TYPE gbtype)

static ARB_ERROR	force_group_update (ED4_base *base)

static void	reload_helix_cb ()

static void	reload_ecoli_cb ()

	DECLARE_CBTYPE_FVV_AND_BUILDERS (ED4_Species_Callback, ARB_ERROR, GBDATA *)

static ARB_ERROR	do_sth_with_species (ED4_base base, const ED4_Species_Callback cb)

static ARB_ERROR	ED4_with_all_loaded_species (const ED4_Species_Callback &cb)

static bool	is_named (ED4_base base, const char wanted_name)

static bool	is_species_named (ED4_base base, const char species_name)

static bool	is_SAI_named (ED4_base base, const char sai_name)

ED4_species_name_terminal *	ED4_find_species_or_SAI_name_terminal (const char *species_name)

ED4_species_name_terminal *	ED4_find_species_name_terminal (const char *species_name)

ED4_species_name_terminal *	ED4_find_SAI_name_terminal (const char *sai_name)

static char *	get_group_consensus (const char *species_name, PosRange range)

static bool	get_selected_range (PosRange &range)

static GBDATA *	get_next_selected_species ()

static GBDATA *	get_first_selected_species (int *total_no_of_selected_species)

static ARB_ERROR	ED4_delete_temp_entries (GBDATA *species, GB_CSTR alignment_name)

static void	ED4_remove_faligner_entries ()

static void	toggle_helix_for_SAI (AW_window *aww)

static void	title_mode_changed (AW_root aw_root, AW_window aww)

static void	ED4_undo_redo (AW_window *aww, GB_UNDO_TYPE undo_type)

static AW_window *	ED4_zoom_message_window (AW_root *root)

static char *	cat (char toBuf, const char s1, const char *s2)

static void	insert_search_fields (AW_window_menu_modes awmm, const char label_prefix, const char macro_prefix, const char pattern_awar_name, const char show_awar_name, int short_form, ED4_SearchPositionType type, ED4_window ed4w)

static void	ED4_set_protection (AW_window *aww, int wanted_protection)

static void	ED4_menu_highlight (AW_window *aww, MenuHighlightType hilight)

static void	ED4_menu_perform_block_operation (AW_window *, ED4_blockoperation_type type)

static void	modes_cb (AW_window *, ED4_species_mode smode)

void	ED4_no_dangerous_modes ()

static char *	get_helix_string (GBDATA gb_main, const char alignment_name)

const AlignDataAccess *	ED4_get_aligner_data_access ()

static AW_window *	ED4_create_faligner_window (AW_root awr, const AlignDataAccess data_access)

static const char *	propertyName (GBDATA *gb_main, int mode)

static void	ED4_save_properties (AW_window *aw, int mode)

void	ED4_popup_gc_window (AW_window awp, AW_gc_manager gcman)

static void	gc_change_cb (GcChange whatChanged)

static void	ED4_popup_helix_or_pfold_window (AW_window *aw_parent, GB_alignment_type aliType)

char *	detectProperties (GBDATA *gb_main)

Variables
static ED4_highlighted_elem *	curr_aligner_elem = NULp

Macro Definition Documentation

#define INSERT_SEARCH_FIELDS	(	Short,
		label_prefix,
		prefix
	)

Value:

insert_search_fields(awmm,                                  \
                         #label_prefix,                         \
                         #prefix,                               \
                         ED4_AWAR_##prefix##_SEARCH_PATTERN,    \
                         ED4_AWAR_##prefix##_SEARCH_SHOW,       \
                         Short,                                 \
                         ED4_##prefix##_PATTERN,                \
                         current_ed4w()                         \
        )

Referenced by ED4_root::generate_window().

Enumeration Type Documentation

enum MenuHighlightType

Enumerator
ED4_MS_NONE
ED4_MS_ALL
ED4_MS_INVERT
ED4_MS_INVERT_GROUP
ED4_MS_UNMARK_ALL
ED4_MS_MARK_SELECTED
ED4_MS_UNMARK_SELECTED
ED4_MS_SELECT_MARKED
ED4_MS_DESELECT_MARKED
ED4_MS_TOGGLE_BLOCKTYPE

Definition at line 1087 of file ED4_root.cxx.

Function Documentation

static ARB_ERROR request_terminal_refresh	(	ED4_base *	base,
		ED4_level	lev
	)

static

Definition at line 77 of file ED4_root.cxx.

References ED4_base::is_terminal(), LEV_NONE, ED4_objspec::level, NULp, ED4_base::request_refresh(), and ED4_base::spec.

Referenced by ED4_root::request_refresh_for_all_terminals(), ED4_root::request_refresh_for_specific_terminals(), and request_sequence_refresh().

static ARB_ERROR request_sequence_refresh	(	ED4_base *	base,
		bool	consensi
	)

static

Definition at line 93 of file ED4_root.cxx.

References error(), ED4_base::is_consensus_manager(), LEV_SEQUENCE_STRING, LEV_SPECIES, ED4_objspec::level, request_terminal_refresh(), ED4_base::route_down_hierarchy(), and ED4_base::spec.

Referenced by ED4_root::request_refresh_for_consensus_terminals(), and ED4_root::request_refresh_for_sequence_terminals().

static ARB_ERROR change_char_table_length	(	ED4_base *	base,
		int	new_length
	)

static

Definition at line 448 of file ED4_root.cxx.

References BaseFrequencies::change_table_length(), ED4_base::is_abstract_group_manager(), NULp, and ED4_abstract_group_manager::table().

Referenced by ED4_alignment_length_changed().

void ED4_alignment_length_changed	(	GBDATA *	gb_alignment_len,
		GB_CB_TYPE	gbtype
	)

static ARB_ERROR force_group_update ( ED4_base * base )

static

Definition at line 529 of file ED4_root.cxx.

References ED4_base::is_multi_species_manager(), and NULp.

Referenced by ED4_root::create_hierarchy().

static void reload_helix_cb ( )

static

Definition at line 806 of file ED4_root.cxx.

References aw_message(), ED4_request_full_refresh(), ED4_ROOT, ED4_root::get_gb_main(), ED4_root::helix, and BI_helix::init().

Referenced by ED4_root::generate_window().

static void reload_ecoli_cb ( )

static

Definition at line 813 of file ED4_root.cxx.

References aw_message(), ED4_root::ecoli_ref, ED4_request_full_refresh(), ED4_ROOT, ED4_root::get_gb_main(), and BI_ecoli_ref::init().

Referenced by ED4_root::generate_window().

DECLARE_CBTYPE_FVV_AND_BUILDERS	(	ED4_Species_Callback	,
		ARB_ERROR	,
		GBDATA *
	)

static ARB_ERROR do_sth_with_species	(	ED4_base *	base,
		const ED4_Species_Callback *	cb
	)

static

Definition at line 824 of file ED4_root.cxx.

References e4_assert, ED4_ROOT, error(), GB_append_exportedError(), GB_read_as_string(), GBS_global_string(), GBT_find_species(), ED4_root::get_gb_main(), ED4_base::is_species_manager(), LEV_SPECIES_NAME, and NULp.

Referenced by ED4_with_all_loaded_species().

static ARB_ERROR ED4_with_all_loaded_species ( const ED4_Species_Callback & cb )

static

Definition at line 849 of file ED4_root.cxx.

References do_sth_with_species(), ED4_ROOT, ED4_root::root_group_man, and ED4_manager::route_down_hierarchy().

Referenced by ED4_remove_faligner_entries().

static bool is_named	(	ED4_base *	base,
		const char *	wanted_name
	)

static

Definition at line 853 of file ED4_root.cxx.

References e4_assert, and GB_read_char_pntr().

Referenced by is_SAI_named(), and is_species_named().

static bool is_species_named	(	ED4_base *	base,
		const char *	species_name
	)

static

Definition at line 865 of file ED4_root.cxx.

References ED4_base::inside_species_seq_manager(), and is_named().

Referenced by ED4_find_species_name_terminal(), and ED4_find_species_or_SAI_name_terminal().

static bool is_SAI_named	(	ED4_base *	base,
		const char *	sai_name
	)

static

Definition at line 869 of file ED4_root.cxx.

References ED4_base::inside_SAI_manager(), and is_named().

Referenced by ED4_find_SAI_name_terminal().

ED4_species_name_terminal* ED4_find_species_or_SAI_name_terminal ( const char * species_name )

Definition at line 873 of file ED4_root.cxx.

References ED4_ROOT, ED4_manager::find_first_that(), is_species_named(), LEV_SPECIES_NAME, NULp, and ED4_root::root_group_man.

Referenced by select_named_sequence_terminal().

ED4_species_name_terminal* ED4_find_species_name_terminal ( const char * species_name )

Definition at line 877 of file ED4_root.cxx.

References ED4_ROOT, ED4_manager::find_first_that(), is_species_named(), LEV_SPECIES_NAME, NULp, and ED4_root::root_group_man.

Referenced by ED4_get_and_jump_to_species(), ED4_get_marked_from_menu(), ED4_jump_to_current_species(), get_group_consensus(), insert_new_species_terminal(), PV_AddOrfTerminalsToLoadedSpecies(), and PV_ManageTerminals().

ED4_species_name_terminal* ED4_find_SAI_name_terminal ( const char * sai_name )

Definition at line 881 of file ED4_root.cxx.

References ED4_ROOT, ED4_manager::find_first_that(), is_SAI_named(), LEV_SPECIES_NAME, NULp, and ED4_root::root_group_man.

Referenced by ED4_get_and_jump_to_selected_SAI(), filter_loadable_SAIs(), and insert_new_species_terminal().

static char* get_group_consensus	(	const char *	species_name,
		PosRange	range
	)

static

Definition at line 886 of file ED4_root.cxx.

References ED4_abstract_group_manager::build_consensus_string(), ED4_find_species_name_terminal(), ED4_base::get_parent(), LEV_GROUP, LEV_ROOTGROUP, and NULp.

Referenced by ED4_get_aligner_data_access().

static bool get_selected_range ( PosRange & range )

static

Definition at line 900 of file ED4_root.cxx.

References ED4_get_highlighted_range(), ED4_ROOT, ED4_list_elem< T >::elem(), ED4_list< T >::head(), and ED4_root::highlighted_objects.

Referenced by ED4_get_aligner_data_access().

static GBDATA* get_next_selected_species ( )

static

Definition at line 911 of file ED4_root.cxx.

References ED4_list_elem< T >::elem(), ED4_list_elem< T >::next(), and NULp.

Referenced by build_reverse_complement(), ED4_get_aligner_data_access(), FastAligner_start(), and get_first_selected_species().

static GBDATA* get_first_selected_species ( int * total_no_of_selected_species )

static

Definition at line 919 of file ED4_root.cxx.

References ED4_ROOT, get_next_selected_species(), ED4_list< T >::head(), ED4_root::highlighted_objects, NULp, and ED4_list< T >::size().

Referenced by build_reverse_complement(), ED4_get_aligner_data_access(), and FastAligner_start().

static ARB_ERROR ED4_delete_temp_entries	(	GBDATA *	species,
		GB_CSTR	alignment_name
	)

static

Definition at line 936 of file ED4_root.cxx.

References FastAligner_delete_temp_entries().

Referenced by ED4_remove_faligner_entries().

static void ED4_remove_faligner_entries ( )

static

Definition at line 940 of file ED4_root.cxx.

References aw_message(), ED4_delete_temp_entries(), ED4_ROOT, ED4_with_all_loaded_species(), error(), GB_begin_transaction(), GB_end_transaction_show_error(), gb_main, ED4_root::get_alignment_name(), and ED4_root::get_gb_main().

Referenced by ED4_root::generate_window().

static void toggle_helix_for_SAI ( AW_window * aww )

static

Definition at line 947 of file ED4_root.cxx.

References aw_message(), current_cursor(), error(), GB_get_grandfather(), GB_read_int(), GB_searchOrCreate_int(), GB_write_int(), ED4_cursor::in_SAI_terminal(), LEV_SEQUENCE_INFO, ED4_cursor::owner_of_cursor, ED4_base::parent, ED4_terminal::request_refresh(), ED4_manager::search_spec_child_rek(), ED4_sequence_terminal::set_secstruct_display(), and ta.

Referenced by ED4_root::generate_window().

static void title_mode_changed	(	AW_root *	aw_root,
		AW_window *	aww
	)

static

Definition at line 974 of file ED4_root.cxx.

References AW_root::awar(), AWAR_EDIT_TITLE_MODE, AW_awar::read_int(), and AW_window::set_info_area_height().

Referenced by ED4_root::generate_window().

static void ED4_undo_redo	(	AW_window *	aww,
		GB_UNDO_TYPE	undo_type
	)

static

Definition at line 985 of file ED4_root.cxx.

References aw_message(), current_cursor(), ED4_ROOT, error(), GB_begin_transaction(), GB_commit_transaction(), gb_main, GB_undo(), ED4_root::get_gb_main(), ED4_cursor::owner_of_cursor, and ED4_terminal::request_refresh().

Referenced by ED4_root::generate_window().

static AW_window* ED4_zoom_message_window ( AW_root * root )

static

Definition at line 1002 of file ED4_root.cxx.

References aw_clear_message_cb(), AW_POPDOWN(), AWAR_ERROR_MESSAGES, and AW_window::load_xfig().

Referenced by ED4_root::generate_window().

static char* cat	(	char *	toBuf,
		const char *	s1,
		const char *	s2
	)

static

Definition at line 1023 of file ED4_root.cxx.

Referenced by insert_search_fields(), and mergeKnownFields().

static void insert_search_fields	(	AW_window_menu_modes *	awmm,
		const char *	label_prefix,
		const char *	macro_prefix,
		const char *	pattern_awar_name,
		const char *	show_awar_name,
		int	short_form,
		ED4_SearchPositionType	type,
		ED4_window *	ed4w
	)