#include <cctype>
#include <climits>
#include <arbdbt.h>
#include <aw_awars.hxx>
#include <AW_helix.hxx>
#include <BI_basepos.hxx>
#include <aw_msg.hxx>
#include <arb_progress.h>
#include <aw_root.hxx>
#include <iupac.h>
#include <ed4_extern.hxx>
#include "ed4_class.hxx"
#include "ed4_edit_string.hxx"
#include "ed4_tools.hxx"
#include "ed4_awars.hxx"
#include "ed4_ProteinViewer.hxx"
#include "ed4_seq_colors.hxx"
#include <arb_strbuf.h>
#include <arb_defs.h>

Include dependency graph for ED4_cursor.cxx:

Classes
class	ED4_CursorShape

class	has_base_at

struct	acceptAnyTerminal

struct	acceptConsensusTerminal

class	CursorPos

Macros
#define	MAXLINES 30

#define	MAXPOINTS (2*MAXLINES)

#define	UPPER_OFFSET (-1)

#define	LOWER_OFFSET (term_height-1)

#define	CWIDTH (character_width)

#define	UPPER_OFFSET 0

#define	LOWER_OFFSET (term_height-1)

#define	CWIDTH 3

#define	OUTER_HEIGHT (term_height/4)

#define	INNER_HEIGHT (term_height-1)

#define	CWIDTH 12

#define	STEPS 6

#define	THICKNESS 2

#define	EXPAND_SIZE 0

#define	BUFFERSIZE 1000

#define	MAXIUPAC 6

Functions
static void	jump_to_corresponding_seq_terminal (ED4_species_name_terminal *name_term, bool unfold_groups)

static void	select_named_sequence_terminal (const char *name)

void	ED4_selected_SAI_changed_cb (AW_root *)

void	ED4_selected_species_changed_cb (AW_root *)

void	ED4_jump_to_current_species (AW_window *aww)

static bool	multi_species_man_consensus_id_starts_with (ED4_base base, const char start)

ED4_multi_species_manager *	ED4_find_MoreSequences_manager ()

void	ED4_init_notFoundMessage ()

void	ED4_finish_and_show_notFoundMessage ()

static ED4_species_name_terminal *	insert_new_species_terminal (GB_CSTR species_name, bool is_SAI)

void	ED4_get_and_jump_to_selected_SAI (AW_window *aww)

void	ED4_get_and_jump_to_species (GB_CSTR species_name)

void	ED4_get_and_jump_to_current (AW_window *aww)

void	ED4_get_marked_from_menu (AW_window *)

static void	trace_termChange_in_global_awar (ED4_terminal term, char &last_value, bool &ignore_flag, const char *awar_name)

static ED4_terminal *	get_upper_lower_cursor_pos (ED4_manager *starting_point, ED4_cursor_move cursor_move, AW_pos current_y, bool isScreen, const ED4_TerminalPredicate &predicate)

static void	ed4_bp_sequence_changed_cb (ED4_species_manager , ED4_base_position base_pos)

static bool	is_consensus_gap (char c)

void	ED4_store_curpos (AW_window *aww)

void	ED4_restore_curpos (AW_window *aww)

void	ED4_clear_stored_curpos ()

void	ED4_helix_jump_opposite (AW_window *aww)

void	ED4_change_cursor (AW_window *aww)

Variables
static bool	allow_update_global_cursorpos = true

static bool	ignore_selected_species_changes_cb = false

static bool	ignore_selected_SAI_changes_cb = false

Macro Definition Documentation

#define MAXLINES 30

Definition at line 29 of file ED4_cursor.cxx.

#define MAXPOINTS (2*MAXLINES)

Definition at line 30 of file ED4_cursor.cxx.

#define UPPER_OFFSET (-1)

Referenced by ED4_CursorShape::ED4_CursorShape().

#define LOWER_OFFSET (term_height-1)

Referenced by ED4_CursorShape::ED4_CursorShape().

#define CWIDTH (character_width)

Referenced by ED4_CursorShape::ED4_CursorShape().

#define UPPER_OFFSET 0

#define LOWER_OFFSET (term_height-1)

#define CWIDTH 3

#define OUTER_HEIGHT (term_height/4)

Referenced by ED4_CursorShape::ED4_CursorShape().

#define INNER_HEIGHT (term_height-1)

Referenced by ED4_CursorShape::ED4_CursorShape().

#define CWIDTH 12

#define STEPS 6

Referenced by ED4_CursorShape::ED4_CursorShape().

#define THICKNESS 2

Referenced by ED4_CursorShape::ED4_CursorShape().

#define EXPAND_SIZE 0

#define BUFFERSIZE 1000

Referenced by ED4_get_marked_from_menu().

#define MAXIUPAC 6

Function Documentation

static void jump_to_corresponding_seq_terminal	(	ED4_species_name_terminal *	name_term,
		bool	unfold_groups
	)

static

Definition at line 427 of file ED4_cursor.cxx.

References current_cursor(), ED4_JUMP_KEEP_POSITION, ED4_cursor::HideCursor(), and LEV_SPECIES.

Referenced by ED4_get_and_jump_to_selected_SAI(), ED4_get_and_jump_to_species(), ED4_jump_to_current_species(), and select_named_sequence_terminal().

static void select_named_sequence_terminal ( const char * name )

static

Definition at line 439 of file ED4_cursor.cxx.

References ED4_abstract_sequence_terminal::corresponding_species_name_terminal(), current_cursor(), ED4_find_species_or_SAI_name_terminal(), ED4_ROOT, ED4_root::get_gb_main(), ED4_base::get_parent(), ED4_base::is_sequence_terminal(), jump_to_corresponding_seq_terminal(), LEV_MULTI_SEQUENCE, LEV_SEQUENCE_STRING, NULp, ED4_cursor::owner_of_cursor, ED4_manager::search_spec_child_rek(), and ta.

Referenced by ED4_selected_SAI_changed_cb(), and ED4_selected_species_changed_cb().

void ED4_selected_SAI_changed_cb ( AW_root * )

Definition at line 484 of file ED4_cursor.cxx.

References allow_update_global_cursorpos, AWAR_SAI_NAME, ED4_ROOT, GBT_read_string(), ED4_root::get_gb_main(), and select_named_sequence_terminal().

Referenced by ed4_bind_mainDB_awar_callbacks().

void ED4_selected_species_changed_cb ( AW_root * )

Definition at line 499 of file ED4_cursor.cxx.

References allow_update_global_cursorpos, AWAR_SPECIES_NAME, ED4_ROOT, GBT_read_string(), ED4_root::get_gb_main(), and select_named_sequence_terminal().

Referenced by ed4_bind_mainDB_awar_callbacks().

void ED4_jump_to_current_species ( AW_window * aww )

Definition at line 518 of file ED4_cursor.cxx.

References aw_message(), AWAR_SPECIES_NAME, ED4_find_species_name_terminal(), ED4_ROOT, gb_main, GBS_global_string(), GBT_read_string(), ED4_root::get_gb_main(), jump_to_corresponding_seq_terminal(), and ta.

Referenced by ED4_root::generate_window().

static bool multi_species_man_consensus_id_starts_with	(	ED4_base *	base,
		const char *	start
	)

static

Definition at line 542 of file ED4_cursor.cxx.

References ED4_base::get_parent(), ED4_base::id, LEV_MULTI_SPECIES, LEV_SPECIES, LEV_SPECIES_NAME, and ED4_manager::search_spec_child_rek().

Referenced by ED4_find_MoreSequences_manager().

ED4_multi_species_manager* ED4_find_MoreSequences_manager ( )

Definition at line 560 of file ED4_cursor.cxx.

References ED4_ROOT, ED4_manager::find_first_that(), LEV_MULTI_SPECIES, multi_species_man_consensus_id_starts_with(), NULp, and ED4_root::root_group_man.

Referenced by ED4_get_marked_from_menu(), insert_new_species_terminal(), and ED4_terminal::kill_object().

void ED4_init_notFoundMessage ( )

Definition at line 566 of file ED4_cursor.cxx.

References not_found_counter, and not_found_message.

Referenced by ED4_root::create_first_window(), ED4_get_marked_from_menu(), ED4_load_new_config(), and insert_new_species_terminal().

void ED4_finish_and_show_notFoundMessage ( )

Definition at line 570 of file ED4_cursor.cxx.

References aw_message(), GBS_global_string(), GBS_strstruct::get_data(), MAX_SHOWN_MISSING_SPECIES, not_found_counter, not_found_message, GBS_strstruct::nprintf(), and NULp.

Referenced by ED4_root::create_hierarchy(), ED4_get_marked_from_menu(), and insert_new_species_terminal().

static ED4_species_name_terminal* insert_new_species_terminal	(	GB_CSTR	species_name,
		bool	is_SAI
	)

static

void ED4_get_and_jump_to_selected_SAI ( AW_window * aww )

Definition at line 629 of file ED4_cursor.cxx.

References aw_message(), AW_root::awar(), AWAR_SAI_NAME, ED4_find_SAI_name_terminal(), ED4_ROOT, GBS_global_string(), ED4_root::get_gb_main(), AW_window::get_root(), insert_new_species_terminal(), jump_to_corresponding_seq_terminal(), AW_awar::read_char_pntr(), and ta.

Referenced by ED4_create_loadSAI_window().

void ED4_get_and_jump_to_species ( GB_CSTR species_name )

Definition at line 652 of file ED4_cursor.cxx.

References aw_message(), e4_assert, ED4_find_species_name_terminal(), ED4_ROOT, GBS_global_string(), ED4_root::get_gb_main(), insert_new_species_terminal(), jump_to_corresponding_seq_terminal(), and ta.

Referenced by create_new_species(), and ED4_get_and_jump_to_current().

void ED4_get_and_jump_to_current ( AW_window * aww )

Definition at line 672 of file ED4_cursor.cxx.

References aw_message(), AWAR_SPECIES_NAME, ED4_get_and_jump_to_species(), ED4_ROOT, GBT_read_string(), and ED4_root::get_gb_main().

Referenced by ED4_root::generate_window().

void ED4_get_marked_from_menu ( AW_window * )

Definition at line 683 of file ED4_cursor.cxx.

References ED4_root::alignment_type, aw_message(), buffer, BUFFERSIZE, ED4_base::calc_group_depth(), ED4_find_MoreSequences_manager(), ED4_find_species_name_terminal(), ED4_finish_and_show_notFoundMessage(), ED4_init_notFoundMessage(), ED4_ROOT, EDB_root_bact::fill_species(), GB_AT_DNA, gb_main, GB_read_string(), GB_read_string_count(), GBS_global_string(), GBT_count_marked_species(), GBT_find_sequence(), GBT_first_marked_species(), GBT_get_name_or_description(), GBT_next_marked_species(), ED4_root::get_alignment_name(), ED4_root::get_gb_main(), ED4_base::get_parent(), arb_progress::inc(), LEV_GROUP, ED4_root::main_manager, NULp, PV_AddOrfTerminalsToLoadedSpecies(), ED4_root::ref_terminals, ta, and ED4_abstract_group_manager::table().

Referenced by ED4_root::generate_window().

static void trace_termChange_in_global_awar	(	ED4_terminal *	term,
		char *&	last_value,
		bool &	ignore_flag,
		const char *	awar_name
	)

static

Definition at line 797 of file ED4_cursor.cxx.

References ED4_ROOT, GBT_write_string(), ED4_root::get_gb_main(), and ED4_base::get_name_of_species().

static ED4_terminal* get_upper_lower_cursor_pos	(	ED4_manager *	starting_point,
		ED4_cursor_move	cursor_move,
		AW_pos	current_y,
		bool	isScreen,
		const ED4_TerminalPredicate &	predicate
	)