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ed4_class.hxx

Revision 8631, 91.9 KB (checked in by westram, 5 weeks ago)

merge from e4fix [8443] [8444] [8445] [8604]

new EDIY4-keys
- fold/unfold group using ENTER key
- ALT+up/down jumps between group consensi
- Ctrl-M marks/unmarks current species or group
minor help-fixes
removed "[Ctrl-A]" from aligner menu entry (they do different things)
use ED4_terminal for owner_of_cursor and ED4_base_position

Property svn:eol-style set to native
Property svn:keywords set to Author Date Id Revision

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1	#ifndef ED4_CLASS_HXX
2	#define ED4_CLASS_HXX
3
4	#ifndef AW_FONT_GROUP_HXX
5	#include <aw_font_group.hxx>
6	#endif
7	#ifndef POS_RANGE_H
8	#include <pos_range.h>
9	#endif
10
11	#define e4_assert(bed) arb_assert(bed)
12
13	#define concat(a,b) a##b
14
15	#ifdef DEBUG
16	# define IMPLEMENT_DUMP // comment out this line to skip compilation of the dump() methods
17	#endif
18
19	#ifndef ARB_ERROR_H
20	#include <arb_error.h>
21	#endif
22	#ifndef ED4_DEFS_HXX
23	#include "ed4_defs.hxx"
24	#endif
25	#ifndef ED4_SEARCH_HXX
26	#include "ed4_search.hxx"
27	#endif
28	#ifndef _GLIBCXX_SET
29	#include <set>
30	#endif
31	#ifndef ATTRIBUTES_H
32	#include <attributes.h>
33	#endif
34	#ifndef BI_BASEPOS_HXX
35	#include <BI_basepos.hxx>
36	#endif
37	#ifndef DOWNCAST_H
38	#include <downcast.h>
39	#endif
40
41	#if defined(IMPLEMENT_DUMP) // ------------------------------
42
43	#if 0
44	#define WARN(msg) void dummy_to_produce_a_warning(int msg) {}
45	#else
46	#define WARN(msg)
47	#endif
48
49	#define EMPTY_FUNCTION(name) void name() const {}
50	#define EMPTY_FUNCTION_VERBOSE(name) void name(int je_mappelle_##name) const {}
51
52	#define DERIVABLEFROM(base) concat(prohibited_leafclass_derivation,base)
53
54	#define COMMON_FOR_BASES() \
55	virtual void dump(size_t indent) const = 0; \
56
57	#define COMMON_FOR_DERIVABLE(self) \
58	void dump_base(size_t indent) const; \
59	EMPTY_FUNCTION(DERIVABLEFROM(self)); \
60
61	#define COMMON_FOR_DERIVED(mybase) \
62	void dump_my_base(size_t indent) const { mybase::dump_base(indent); } \
63	virtual const char *baseclassname() const { return #mybase; } \
64
65	#define COMMON_FOR_INSTANCIABLE(mybase) \
66	virtual void dump(size_t indent) const; \
67
68	#define DECLARE_DUMP_FOR_ROOTCLASS(self) \
69	COMMON_FOR_BASES(); \
70	COMMON_FOR_DERIVABLE(self); \
71
72	#define DECLARE_DUMP_FOR_BASECLASS(self,mybase) \
73	COMMON_FOR_BASES(); \
74	COMMON_FOR_DERIVABLE(self); \
75	COMMON_FOR_DERIVED(mybase); \
76
77	#define DECLARE_DUMP_FOR_MIDCLASS(self,mybase) \
78	WARN(midclass_is_unwanted); \
79	COMMON_FOR_DERIVABLE(self); \
80	COMMON_FOR_DERIVED(mybase); \
81	COMMON_FOR_INSTANCIABLE(mybase); \
82
83	#define DECLARE_DUMP_FOR_LEAFCLASS(mybase) \
84	virtual void leaf() { DERIVABLEFROM(mybase)(); } \
85	COMMON_FOR_DERIVED(mybase); \
86	COMMON_FOR_INSTANCIABLE(mybase); \
87
88	#else
89	#define DECLARE_DUMP_FOR_ROOTCLASS(self)
90	#define DECLARE_DUMP_FOR_BASECLASS(self,mybase)
91	#define DECLARE_DUMP_FOR_MIDCLASS(self,mybase)
92	#define DECLARE_DUMP_FOR_LEAFCLASS(mybase)
93
94	#endif // IMPLEMENT_DUMP ------------------------------
95
96
97
98	// #define LIMIT_TOP_AREA_SPACE // if defined, top area is size-limited
99	#ifdef LIMIT_TOP_AREA_SPACE
100	#define MAX_TOP_AREA_SIZE 10 // size limit for top-area
101	#endif
102
103	#define ed4_beep() do { fputc(char(7), stdout); fflush(stdout); } while (0)
104
105	enum PositionType {
106	ED4_POS_SEQUENCE,
107	ED4_POS_ECOLI,
108	ED4_POS_BASE,
109	};
110
111	// ****************************************
112	// needed prototypes, definitions below
113	// ****************************************
114
115	class ED4_Edit_String;
116	class ED4_area_manager;
117	class ED4_abstract_group_manager;
118	class ED4_base;
119	class ED4_bases_table;
120	class ED4_bracket_terminal;
121	class ED4_char_table;
122	class ED4_columnStat_terminal;
123	class ED4_consensus_sequence_terminal;
124	class ED4_cursor;
125	class ED4_device_manager;
126	class ED4_folding_line;
127	class ED4_group_manager;
128	class ED4_line_terminal;
129	class ED4_main_manager;
130	class ED4_manager;
131	class ED4_members;
132	class ED4_multi_name_manager;
133	class ED4_multi_sequence_manager;
134	class ED4_multi_species_manager;
135	class ED4_name_manager;
136	class ED4_pure_text_terminal;
137	class ED4_remap;
138	class ED4_root;
139	class ED4_root_group_manager;
140	class ED4_sequence_info_terminal;
141	class ED4_sequence_manager;
142	class ED4_sequence_terminal;
143	class ED4_orf_terminal;
144	class ED4_spacer_terminal;
145	class ED4_species_manager;
146	class ED4_species_name_terminal;
147	class ED4_species_pointer;
148	class ED4_terminal;
149	class ED4_text_terminal;
150	class ED4_tree_terminal;
151	class ED4_window;
152
153	class AP_tree;
154	class AWT_reference;
155	class AWT_seq_colors;
156	class BI_ecoli_ref;
157	class AW_helix;
158	class arb_progress;
159	class ST_ML;
160	class ed_key;
161
162	template <class T> class ED4_list; // derived from Noncopyable
163	template <class T> class ED4_list_elem; // derived from Noncopyable
164
165	typedef ED4_list<ED4_base> ED4_base_list;
166	typedef ED4_list_elem<ED4_base> ED4_base_list_elem;
167
168	typedef ED4_list<ED4_selection_entry> ED4_selected_list;
169	typedef ED4_list_elem<ED4_selection_entry> ED4_selected_elem;
170
171
172	struct EDB_root_bact {
173	char *make_string();
174	char *make_top_bot_string();
175
176	void calc_no_of_all(char *string_to_scan, // group gets the number of groups in string_to_scan,
177	long *group, // species gets the number of species in string_to_scan
178	long *species);
179
180	ED4_returncode fill_species(ED4_multi_species_manager *multi_species_manager,
181	ED4_sequence_info_terminal *ref_sequence_info_terminal,
182	ED4_sequence_terminal *ref_sequence_terminal,
183	char *string,
184	int *index,
185	ED4_index *y,
186	ED4_index curr_local_position,
187	ED4_index *length_of_terminals,
188	int group_depth,
189	arb_progress *progress);
190
191	ED4_returncode fill_data(ED4_multi_species_manager *multi_species_manager,
192	ED4_sequence_info_terminal *ref_sequence_info_terminal,
193	ED4_sequence_terminal *ref_sequence_terminal,
194	char *string,
195	ED4_index *y,
196	ED4_index curr_local_position,
197	ED4_index *length_of_terminals,
198	int group_depth,
199	ED4_datamode datamode); // flag only needed for loading a new configuration
200
201	ED4_returncode search_sequence_data_rek(ED4_multi_sequence_manager *multi_sequence_manager,
202	ED4_sequence_info_terminal *ref_sequence_info_terminal,
203	ED4_sequence_terminal *ref_sequence_terminal,
204	GBDATA *gb_datamode,
205	int count_too,
206	ED4_index *seq_coords,
207	ED4_index *max_seq_terminal_length,
208	ED4_alignment alignment_flag,
209	bool isSAI);
210
211	ED4_index scan_string(ED4_multi_species_manager *parent,
212	ED4_sequence_info_terminal *ref_sequence_info_terminal,
213	ED4_sequence_terminal *ref_sequence_terminal,
214	char *string,
215	int *index,
216	ED4_index *y,
217	arb_progress& progress);
218
219	ED4_returncode create_group_header(ED4_multi_species_manager *parent,
220	ED4_sequence_info_terminal *ref_sequence_info_terminal,
221	ED4_sequence_terminal *ref_sequence_terminal,
222	ED4_multi_species_manager **multi_species_manager,
223	ED4_bracket_terminal **bracket_terminal,
224	ED4_index *y,
225	char *groupname,
226	int group_depth,
227	bool is_folded,
228	ED4_index local_count_position);
229
230	char generate_config_string(char confname);
231
232
233	EDB_root_bact() {}
234	};
235
236	#define SPECIFIED_OBJECT_TYPES 21
237
238	class ED4_objspec : public Noncopyable {
239	static bool object_specs_initialized;
240	static bool descendants_uptodate;
241
242	mutable ED4_level used_children; // in any object of this type
243	mutable ED4_level possible_descendants; // below any object of this type (depends on used_children)
244	mutable ED4_level allowed_descendants; // below any object of this type (depends on allowed_children)
245
246	void calc_descendants() const;
247
248	public:
249	ED4_properties static_prop;
250	ED4_level level;
251	ED4_level allowed_children;
252	ED4_level handled_level;
253	ED4_level restriction_level;
254
255	ED4_objspec(ED4_properties static_prop_, ED4_level level_, ED4_level allowed_children_, ED4_level handled_level_, ED4_level restriction_level_);
256
257	#if defined(IMPLEMENT_DUMP)
258	void dump(size_t indent) const;
259	#endif // IMPLEMENT_DUMP
260
261	static void init_object_specs();
262
263	bool is_manager() const { return static_prop & ED4_P_IS_MANAGER; }
264	bool is_terminal() const { return static_prop & ED4_P_IS_TERMINAL; }
265
266	bool allowed_to_contain(ED4_level child_level) const {
267	// e4_assert(object_specs_initialized); // @@@ cant check here.. but where
268	e4_assert(is_manager()); // terminals can't contain anything - your test is senseless
269	return allowed_children & child_level;
270	}
271
272	void announce_added(ED4_level child_level) const {
273	e4_assert(allowed_to_contain(child_level));
274	used_children = ED4_level(used_children\|child_level);
275	descendants_uptodate = false;
276	}
277
278	static void recalc_descendants();
279
280	ED4_level get_possible_descendants() const {
281	e4_assert(is_manager());
282	if (!descendants_uptodate) recalc_descendants();
283	return possible_descendants;
284	}
285	ED4_level get_allowed_descendants() const { // (allowed = possible + those allowed to add, but not added anywhere)
286	e4_assert(is_manager());
287	if (!descendants_uptodate) recalc_descendants();
288	return allowed_descendants;
289	}
290	};
291
292	class ED4_folding_line : virtual Noncopyable {
293	AW_pos dimension; // amount of pixel folded away
294	AW_pos pos; // window position of folding line (x or y, only owner knows which coordinate is folded)
295	ED4_folding_line *next;
296
297	ED4_folding_line insert(ED4_folding_line fl) {
298	e4_assert(!fl->next);
299	if (pos <= fl->pos) { // insert behind
300	next = next ? next->insert(fl) : fl;
301	return this;
302	}
303
304	fl->next = this;
305	return fl;
306	}
307
308	public:
309
310	ED4_folding_line(AW_pos world, AW_pos dim) : dimension(dim), next(0) { set_pos(world-dimension); }
311
312	~ED4_folding_line() { delete next; }
313
314	void insertAs(ED4_folding_line*& ptr) {
315	ED4_folding_line *other = ptr;
316	e4_assert(this);
317	ptr = other ? other->insert(this) : this;
318	}
319
320	ED4_folding_line delete_member(ED4_folding_line fl) {
321	ED4_folding_line *result = this;
322	if (this == fl) {
323	result = next;
324	next = NULL;
325	delete this;
326	}
327	return result;
328	}
329
330	AW_pos get_dimension() const { return dimension; }
331	const ED4_folding_line *get_next() const { return next; }
332
333	void warn_illegal_dimension();
334
335	void set_dimension(AW_pos dim) { dimension = dim; warn_illegal_dimension(); }
336	void add_to_dimension(AW_pos offset) { dimension += offset; warn_illegal_dimension(); }
337
338	void set_pos(AW_pos p) { pos = p; }
339	AW_pos get_pos() const { return pos; }
340
341	AW_pos win2world(AW_pos win) const {
342	if (win<pos) return win;
343	return (next ? next->win2world(win) : win)+dimension;
344	}
345	AW_pos world2win(AW_pos world) const {
346	if (world<pos) return world;
347	world -= dimension;
348	if (!next) return world;
349	return next->world2win(world);
350	}
351	};
352
353	struct ED4_scroll_links {
354	ED4_base *link_for_hor_slider;
355	ED4_base *link_for_ver_slider;
356
357	ED4_scroll_links() : link_for_hor_slider(0), link_for_ver_slider(0) {}
358	};
359
360	class ED4_foldable : virtual Noncopyable {
361	ED4_folding_line *horizontal_fl;
362	ED4_folding_line *vertical_fl;
363	protected:
364	void reset() {
365	delete horizontal_fl;
366	delete vertical_fl;
367	horizontal_fl = NULL;
368	vertical_fl = NULL;
369	}
370	bool is_reset() const { return !horizontal_fl && !vertical_fl; }
371	public:
372
373	ED4_foldable() : horizontal_fl(NULL), vertical_fl(NULL) {}
374	~ED4_foldable() { reset(); }
375
376	const ED4_folding_line *get_horizontal_folding() { return horizontal_fl; }
377	const ED4_folding_line *get_vertical_folding() { return vertical_fl; }
378
379	void world_to_win_coords(AW_pos xPtr, AW_pos yPtr) const { // @@@ old style
380	// Calculates transformation from world to window coordinates in a given window.
381	// world-coordinates inside folded range result in window coordinates lower than folding line position.
382	e4_assert(!is_reset());
383	xPtr = vertical_fl->world2win(xPtr);
384	yPtr = horizontal_fl->world2win(yPtr);
385	}
386	void win_to_world_coords(AW_pos xPtr, AW_pos yPtr) const { // @@@ old style
387	// calculates transformation from window to world coordinates in a given window
388	e4_assert(!is_reset());
389	xPtr = vertical_fl->win2world(xPtr);
390	yPtr = horizontal_fl->win2world(yPtr);
391	}
392
393	AW::Position world_to_win_coords(const AW::Position& pos) const {
394	e4_assert(!is_reset());
395	return AW::Position(vertical_fl->world2win(pos.xpos()),
396	horizontal_fl->world2win(pos.ypos()));
397	}
398	AW::Position win_to_world_coords(const AW::Position& pos) const {
399	e4_assert(!is_reset());
400	return AW::Position(vertical_fl->win2world(pos.xpos()),
401	horizontal_fl->win2world(pos.ypos()));
402	}
403
404	ED4_folding_line *insert_folding_line(AW_pos pos, AW_pos dimension, ED4_properties prop);
405	void delete_folding_line(ED4_folding_line *fl, ED4_properties prop);
406	};
407
408
409	class ED4_scrolled_rectangle : virtual Noncopyable {
410	ED4_folding_line *scroll_bottom;
411	ED4_folding_line *scroll_right;
412	ED4_folding_line *scroll_top;
413	ED4_folding_line *scroll_left;
414
415	ED4_base *x_link;
416	ED4_base *y_link;
417	ED4_base *width_link;
418	ED4_base *height_link;
419
420	AW::Rectangle world;
421
422	bool folding_dimensions_calculated; // flag to ensure calc_bottomRight_folding_dimensions is called before get_window_rect
423
424	void init_links() {
425	x_link = 0;
426	y_link = 0;
427	width_link = 0;
428	height_link = 0;
429	}
430
431	void init_folding_lines() {
432	scroll_top = 0;
433	scroll_bottom = 0;
434	scroll_left = 0;
435	scroll_right = 0;
436
437	folding_dimensions_calculated = false;
438	}
439	void init_pos_size() { world = AW::Rectangle(AW::Origin, AW::ZeroVector); }
440
441	void init() {
442	init_folding_lines();
443	init_pos_size();
444	init_links();
445	}
446
447	void update_folding_line_positions() {
448	scroll_top->set_pos(world.top());
449	scroll_left->set_pos(world.left());
450	}
451
452	public:
453
454	ED4_scrolled_rectangle() { init(); }
455
456	AW_pos bottom() const { return world.bottom(); }
457	AW_pos right() const { return world.right(); }
458
459	void reset(ED4_foldable& owner) {
460	destroy_folding_lines(owner);
461	init_pos_size();
462	}
463
464	AW_pos top_dim() const { return scroll_top->get_dimension(); }
465	AW_pos left_dim() const { return scroll_left->get_dimension(); }
466
467	bool exists() const { return scroll_top && scroll_bottom && scroll_left && scroll_right; }
468	bool is_linked() const {
469	if (x_link) {
470	e4_assert(y_link);
471	e4_assert(width_link);
472	e4_assert(height_link);
473	return true;
474	}
475	e4_assert(!y_link);
476	e4_assert(!width_link);
477	e4_assert(!height_link);
478	return false;
479	}
480	void link(ED4_base x, ED4_base y, ED4_base w, ED4_base h) {
481	e4_assert(x && y && w && h);
482
483	x_link = x;
484	y_link = y;
485	width_link = w;
486	height_link = h;
487	}
488
489	void replace_x_width_link_to(ED4_base old_link, ED4_base new_link) {
490	if (x_link == old_link) x_link = new_link;
491	if (width_link == old_link) width_link = new_link;
492	}
493
494	void add_to_top_left_dimension(int dx, int dy) {
495	scroll_left->add_to_dimension(dx);
496	scroll_top->add_to_dimension(dy);
497	}
498
499	void scroll(int dx, int dy) {
500	scroll_left->add_to_dimension(-dx);
501	scroll_top->add_to_dimension(-dy);
502	scroll_right->add_to_dimension(dx);
503	scroll_bottom->add_to_dimension(dy);
504	}
505
506	AW::Rectangle get_window_rect() const {
507	e4_assert(folding_dimensions_calculated);
508	return AW::Rectangle(scroll_left->get_pos(), scroll_top->get_pos(),
509	scroll_right->get_pos(), scroll_bottom->get_pos());
510	}
511
512	AW::Rectangle get_world_rect() const;
513
514	void set_rect(const AW::Rectangle& rect) { world = rect; }
515	void set_rect_and_update_folding_line_positions(const AW::Rectangle& rect) {
516	set_rect(rect);
517	update_folding_line_positions();
518	}
519
520	void calc_bottomRight_folding_dimensions(int area_width, int area_height) {
521	area_width -= SLIDER_OFFSET;
522	area_height -= SLIDER_OFFSET;
523
524	AW_pos dim;
525	if (bottom() > area_height) { // our world doesn't fit vertically in our window
526	dim = bottom()-area_height; // calc dimension of both horizontal folding lines
527	scroll_top->set_dimension(min(dim, scroll_top->get_dimension()));
528	scroll_bottom->set_dimension(max(0, int(dim - scroll_top->get_dimension())));
529	}
530	else {
531	dim = 0;
532	scroll_bottom->set_dimension(0);
533	scroll_top->set_dimension(0);
534	}
535
536	e4_assert(dim == (scroll_top->get_dimension()+scroll_bottom->get_dimension()));
537	scroll_bottom->set_pos(world.bottom()-dim+SLIDER_OFFSET);
538
539	if (right()>area_width) { // our world doesn't fit horizontally in our window
540	dim = right()-area_width; // calc dimension of both vertical folding lines
541	scroll_left->set_dimension(min(dim, scroll_left->get_dimension()));
542	scroll_right->set_dimension(max(0, int(dim - scroll_left->get_dimension())));
543	}
544	else {
545	dim = 0;
546	scroll_right->set_dimension(0);
547	scroll_left->set_dimension(0);
548	}
549
550	e4_assert(dim == (scroll_left->get_dimension()+scroll_right->get_dimension()));
551	scroll_right->set_pos(world.right()-dim+SLIDER_OFFSET);
552
553	folding_dimensions_calculated = true;
554	}
555
556	void create_folding_lines(ED4_foldable& owner, const AW::Rectangle& rect, int area_width, int area_height) {
557	scroll_top = owner.insert_folding_line(rect.top(), 0, ED4_P_HORIZONTAL);
558	scroll_left = owner.insert_folding_line(rect.left(), 0, ED4_P_VERTICAL);
559
560	AW_pos dim = 0;
561	if (rect.bottom() > area_height) dim = rect.bottom() - area_height;
562	scroll_bottom = owner.insert_folding_line(rect.bottom(), dim, ED4_P_HORIZONTAL);
563
564	dim = 0;
565	if (rect.right() > area_width) dim = rect.right() - area_width;
566	scroll_right = owner.insert_folding_line(rect.right(), dim, ED4_P_VERTICAL);
567	}
568
569	void destroy_folding_lines(ED4_foldable& owner) {
570	if (scroll_top) owner.delete_folding_line(scroll_top, ED4_P_HORIZONTAL);
571	if (scroll_bottom) owner.delete_folding_line(scroll_bottom, ED4_P_HORIZONTAL);
572	if (scroll_left) owner.delete_folding_line(scroll_left, ED4_P_VERTICAL);
573	if (scroll_right) owner.delete_folding_line(scroll_right, ED4_P_VERTICAL);
574
575	init_folding_lines();
576	}
577	};
578
579	class ED4_base_position : private BasePosition { // derived from a Noncopyable
580	const ED4_terminal *calced4term;
581
582	void calc4term(const ED4_terminal *term);
583	void set_term(const ED4_terminal *term) { if (calced4term != term) calc4term(term); }
584
585	public:
586
587	ED4_base_position();
588	~ED4_base_position();
589
590	void invalidate();
591
592	void announce_deletion(const ED4_terminal *term) {
593	if (term == calced4term) invalidate();
594	e4_assert(calced4term != term);
595	}
596
597	int get_base_position(const ED4_terminal *base, int sequence_position);
598	int get_sequence_position(const ED4_terminal *base, int base_position);
599
600	int get_base_count(const ED4_terminal *term) { set_term(term); return base_count(); }
601	int get_abs_len(const ED4_terminal *term) { set_term(term); return abs_count(); }
602	};
603
604	class ED4_CursorShape;
605
606
607	enum ED4_CursorType {
608	ED4_RIGHT_ORIENTED_CURSOR,
609	ED4_RIGHT_ORIENTED_CURSOR_THIN,
610	ED4_TRADITIONAL_CURSOR,
611	ED4_TRADITIONAL_CURSOR_BOTTOM,
612	ED4_TRADITIONAL_CURSOR_CONNECTED,
613	ED4_FUCKING_BIG_CURSOR,
614
615	ED4_CURSOR_TYPES
616
617	};
618
619	extern bool ED4_update_global_cursor_awars_allowed; // update selected species/SAI/cursor position
620
621	struct ED4_TerminalPredicate {
622	virtual ~ED4_TerminalPredicate() {}
623	virtual bool fulfilled_by(const ED4_terminal *) const = 0;
624	};
625
626	class ED4_WinContextFree { // denies usage of the following functions in classes derived from this
627	AW_device *current_device();
628	ED4_window *current_ed4w();
629	AW_window *current_aww();
630	ED4_cursor& current_cursor();
631	public:
632	void avoid_warning() {}
633	};
634
635	class ED4_cursor : virtual Noncopyable, virtual ED4_WinContextFree {
636	ED4_window *win;
637	ED4_index cursor_abs_x; // absolute (to terminal) x-position of cursor (absolute world coordinate of edit window)
638	int screen_position; // number of displayed characters leading the cursor
639	mutable ED4_base_position base_position; // # of bases left of cursor
640	ED4_CursorType ctype;
641	ED4_CursorShape *cursor_shape;
642
643	ED4_returncode draw_cursor(AW_pos x, AW_pos y);
644	ED4_returncode delete_cursor(AW_pos del_mark, ED4_base *target_terminal);
645
646	void updateAwars(bool new_term_selected);
647
648	public:
649
650	bool allowed_to_draw; // needed for cursor handling
651	ED4_terminal *owner_of_cursor;
652
653	bool is_partly_visible() const;
654	bool is_completely_visible() const;
655
656	bool is_hidden_inside_group() const;
657
658	void changeType(ED4_CursorType typ);
659	ED4_CursorType getType() const { return ctype; }
660
661	void redraw() { changeType(getType()); }
662
663	ED4_returncode HideCursor(); // deletes cursor and does refresh
664	ED4_returncode move_cursor(AW_event *event);
665	ED4_returncode show_clicked_cursor(AW_pos click_xpos, ED4_terminal *target_terminal);
666	ED4_returncode show_cursor_at(ED4_terminal *target_terminal, ED4_index what_pos);
667	ED4_returncode ShowCursor(ED4_index offset_x, ED4_cursor_move move, int move_pos = 1);
668
669	int get_sequence_pos() const;
670	int get_screen_pos() const { return screen_position; }
671
672	long get_abs_x() const { return cursor_abs_x; }
673	void set_abs_x();
674
675	int base2sequence_position(int base_pos) const { return base_position.get_sequence_position(owner_of_cursor, base_pos); }
676	int sequence2base_position(int seq_pos) const { return base_position.get_base_position(owner_of_cursor, seq_pos); }
677
678	int get_base_position() const { return sequence2base_position(get_sequence_pos()); }
679
680	void invalidate_base_position() { base_position.invalidate(); }
681
682	void jump_screen_pos(int screen_pos, ED4_CursorJumpType jump_type);
683	void jump_sequence_pos(int sequence_pos, ED4_CursorJumpType jump_type);
684	void jump_base_pos(int base_pos, ED4_CursorJumpType jump_type);
685
686	int get_screen_relative_pos() const;
687	void set_screen_relative_pos(int scroll_to_relpos);
688
689	void set_to_terminal(ED4_terminal *terminal, int seq_pos, ED4_CursorJumpType jump_type);
690
691	inline bool in_species_seq_terminal() const;
692	inline bool in_consensus_terminal() const;
693	inline bool in_SAI_terminal() const;
694
695	void announce_deletion(ED4_terminal *object) {
696	base_position.announce_deletion(object);
697	if (object == owner_of_cursor) owner_of_cursor = NULL; // no need to delete the cursor (deletion triggers full redraw)
698	}
699
700	void init();
701
702	ED4_window *window() const { return win; }
703
704	ED4_cursor(ED4_window *win);
705	~ED4_cursor();
706	};
707
708	class ED4_window : public ED4_foldable, virtual ED4_WinContextFree { // derived from Noncopyable
709	void set_scrollbar_indents();
710
711	public:
712	AW_window *aww; // Points to Window
713	ED4_window *next;
714	int slider_pos_horizontal;
715	int slider_pos_vertical;
716	ED4_scrolled_rectangle scrolled_rect;
717	int id; // unique id in window-list
718	ED4_coords coords;
719
720	static int no_of_windows;
721
722	char awar_path_for_cursor[50]; // position in current sequence, range = [1;len]
723	char awar_path_for_Ecoli[50]; // position relative to ecoli
724	char awar_path_for_basePos[50]; // base position in current sequence (# of bases left to cursor)
725	char awar_path_for_IUPAC[50]; // IUPAC decoder content for current position
726	char awar_path_for_helixNr[50]; // # of helix (or 0) for current position
727
728	bool is_hidden;
729	ED4_cursor cursor;
730
731	// ED4_window controlling functions
732	static ED4_window insert_window(AW_window new_aww); // append to window list
733
734	void delete_window(ED4_window *window); // delete from window list
735	void reset_all_for_new_config(); // reset structures for loading new config
736	ED4_window get_matching_ed4w(AW_window aww);
737
738	void announce_deletion(ED4_terminal *object) { cursor.announce_deletion(object); }
739
740	// functions concerned the scrolled area
741	void update_scrolled_rectangle();
742	ED4_returncode scroll_rectangle(int dx, int dy);
743	ED4_returncode set_scrolled_rectangle(ED4_base x_link, ED4_base y_link, ED4_base width_link, ED4_base height_link);
744
745	bool scrollbars_and_scrolledRect_inSync() const {
746	// Scrolling in EDIT4 window uses redundant data
747	// - dimension of folding lines
748	// - slider positions in AW_window and ED4_window
749	// This function checks whether they are in sync.
750
751	bool inSync =
752	(scrolled_rect.top_dim() == aww->slider_pos_vertical) &&
753	(scrolled_rect.left_dim() == aww->slider_pos_horizontal);
754
755	#if defined(DEBUG)
756	if (!inSync) {
757	fputs("scrollbars not in sync with scrolled_rect:\n", stderr);
758	fprintf(stderr, " aww->slider_pos_vertical =%i scrolled_rect->top_dim() =%f\n", aww->slider_pos_vertical, scrolled_rect.top_dim());
759	fprintf(stderr, " aww->slider_pos_horizontal=%i scrolled_rect->left_dim()=%f\n", aww->slider_pos_horizontal, scrolled_rect.left_dim());
760	}
761	#endif
762
763	return inSync;
764	}
765
766	void check_valid_scrollbar_values() { e4_assert(scrollbars_and_scrolledRect_inSync()); }
767
768	bool shows_xpos(int x) const { return x >= coords.window_left_clip_point && x <= coords.window_right_clip_point; }
769	bool partly_shows(int x1, int y1, int x2, int y2) const;
770	bool completely_shows(int x1, int y1, int x2, int y2) const;
771
772	void update_window_coords();
773
774	AW_device *get_device() const { return aww->get_device(AW_MIDDLE_AREA); }
775
776	ED4_window(AW_window *window);
777	~ED4_window();
778	};
779
780	class ED4_members : virtual Noncopyable {
781	// contains children related functions from members of a manager
782
783	ED4_manager *my_owner; // who is controlling this object
784	ED4_base **memberList;
785	ED4_index no_of_members; // How much members are in the list
786	ED4_index size_of_list;
787
788	public:
789
790	ED4_manager* owner() const { return my_owner; }
791	ED4_base* member(ED4_index i) const { e4_assert(i>=0 && i<size_of_list); return memberList[i]; }
792	ED4_index members() const { return no_of_members; }
793
794	ED4_returncode insert_member(ED4_base *new_member); // only used to move members with mouse
795	ED4_returncode append_member(ED4_base *new_member);
796
797	// an array is chosen instead of a linked list, because destructorhandling is more comfortable in various destructors (manager-destructors)
798
799	ED4_returncode remove_member(ED4_base *member);
800	ED4_index search_member(ED4_extension *location, ED4_properties prop); // search member
801	ED4_returncode shift_list(ED4_index start_index, int length);
802	// list has to be shifted because member_list is an array and not a linked list
803
804	ED4_returncode search_target_species (ED4_extension location, ED4_properties prop, ED4_base *found_member, ED4_level return_level);
805
806	ED4_returncode move_member (ED4_index old_pos, ED4_index new_pos);
807
808	#if defined(IMPLEMENT_DUMP)
809	void dump(size_t indent) const;
810	#endif // IMPLEMENT_DUMP
811
812	#if defined(ASSERTION_USED)
813	int members_ok() const;
814	#endif // ASSERTION_USED
815
816	ED4_members(ED4_manager *the_owner);
817	~ED4_members();
818	};
819
820	#ifdef DEBUG
821	// # define TEST_BASES_TABLE
822	#endif
823
824	#define SHORT_TABLE_ELEM_SIZE 1
825	#define SHORT_TABLE_MAX_VALUE 0xff
826	#define LONG_TABLE_ELEM_SIZE 4
827
828	class ED4_bases_table : virtual Noncopyable {
829	int table_entry_size; // how many bytes are used for each element of 'no_of_bases' (1 or 4 bytes)
830	union {
831	unsigned char *shortTable;
832	int *longTable;
833	} no_of_bases; // counts bases for each sequence position
834	int no_of_entries; // length of bases table
835
836	int legal(int offset) const { return offset>=0 && offset<no_of_entries; }
837
838	void set_elem_long(int offset, int value) {
839	#ifdef TEST_BASES_TABLE
840	e4_assert(legal(offset));
841	e4_assert(table_entry_size==LONG_TABLE_ELEM_SIZE);
842	#endif
843	no_of_bases.longTable[offset] = value;
844	}
845
846	void set_elem_short(int offset, int value) {
847	#ifdef TEST_BASES_TABLE
848	e4_assert(legal(offset));
849	e4_assert(table_entry_size==SHORT_TABLE_ELEM_SIZE);
850	e4_assert(value>=0 && value<=SHORT_TABLE_MAX_VALUE);
851	#endif
852	no_of_bases.shortTable[offset] = value;
853	}
854
855	int get_elem_long(int offset) const {
856	#ifdef TEST_BASES_TABLE
857	e4_assert(legal(offset));
858	e4_assert(table_entry_size==LONG_TABLE_ELEM_SIZE);
859	#endif
860	return no_of_bases.longTable[offset];
861	}
862
863	int get_elem_short(int offset) const {
864	#ifdef TEST_BASES_TABLE
865	e4_assert(legal(offset));
866	e4_assert(table_entry_size==SHORT_TABLE_ELEM_SIZE);
867	#endif
868	return no_of_bases.shortTable[offset];
869	}
870
871	public:
872
873	ED4_bases_table(int maxseqlength);
874	~ED4_bases_table();
875
876	void init(int length);
877	int size() const { return no_of_entries; }
878
879	int get_table_entry_size() const { return table_entry_size; }
880	void expand_table_entry_size();
881	int bigger_table_entry_size_needed(int new_no_of_sequences) { return table_entry_size==SHORT_TABLE_ELEM_SIZE ? (new_no_of_sequences>SHORT_TABLE_MAX_VALUE) : 0; }
882
883	int operator[](int offset) const { return table_entry_size==SHORT_TABLE_ELEM_SIZE ? get_elem_short(offset) : get_elem_long(offset); }
884
885	void inc_short(int offset) {
886	int old = get_elem_short(offset);
887	e4_assert(old<255);
888	set_elem_short(offset, old+1);
889	}
890	void dec_short(int offset) {
891	int old = get_elem_short(offset);
892	e4_assert(old>0);
893	set_elem_short(offset, old-1);
894	}
895	void inc_long(int offset) {
896	int old = get_elem_long(offset);
897	set_elem_long(offset, old+1);
898	}
899	void dec_long(int offset) {
900	int old = get_elem_long(offset);
901	e4_assert(old>0);
902	set_elem_long(offset, old-1);
903	}
904
905	int firstDifference(const ED4_bases_table& other, int start, int end, int *firstDifferentPos) const;
906	int lastDifference(const ED4_bases_table& other, int start, int end, int *lastDifferentPos) const;
907
908	void add(const ED4_bases_table& other, int start, int end);
909	void sub(const ED4_bases_table& other, int start, int end);
910	void sub_and_add(const ED4_bases_table& Sub, const ED4_bases_table& Add, PosRange range);
911
912	void change_table_length(int new_length, int default_entry);
913
914
915	#ifdef ASSERTION_USED
916	int empty() const;
917	#endif // ASSERTION_USED
918	};
919
920	typedef ED4_bases_table *ED4_bases_table_ptr;
921
922	#if defined(DEBUG) && !defined(DEVEL_RELEASE)
923	# define TEST_CHAR_TABLE_INTEGRITY // uncomment to remove tests for ED4_char_table
924	#endif // DEBUG
925
926	class ED4_char_table : virtual Noncopyable {
927	ED4_bases_table_ptr *bases_table;
928	int sequences; // # of sequences added to the table
929	int ignore; // this table will be ignored when calculating tables higher in hierarchy
930	// (used to suppress SAI in root_group_man tables)
931
932	// @@@ move statics into own class:
933	static bool initialized;
934	static unsigned char char_to_index_tab[MAXCHARTABLE];
935	static unsigned char *upper_index_chars;
936	static unsigned char *lower_index_chars;
937	static int used_bases_tables; // size of 'bases_table'
938	static GB_alignment_type ali_type;
939
940	static inline void set_char_to_index(unsigned char c, int index);
941
942	void add(const ED4_char_table& other, int start, int end);
943	void sub(const ED4_char_table& other, int start, int end);
944
945	void expand_tables();
946	int get_table_entry_size() const {
947	return linear_table(0).get_table_entry_size();
948	}
949	void prepare_to_add_elements(int new_sequences) {
950	e4_assert(used_bases_tables);
951	if (linear_table(0).bigger_table_entry_size_needed(sequences+new_sequences)) {
952	expand_tables();
953	}
954	}
955
956	public:
957
958	#if defined(TEST_CHAR_TABLE_INTEGRITY) \|\| defined(ASSERTION_USED)
959	bool ok() const;
960	bool empty() const;
961	#endif
962
963	#if defined(TEST_CHAR_TABLE_INTEGRITY)
964	void test() const; // test if table is valid (dumps core if invalid)
965	#else
966	void test() const {}
967	#endif
968
969	ED4_char_table(int maxseqlength=0);
970	~ED4_char_table();
971
972	static void initial_setup(const char *gap_chars, GB_alignment_type ali_type_);
973
974	void ignore_me() { ignore = 1; }
975	int is_ignored() const { return ignore; }
976
977	void init(int maxseqlength);
978	int size() const { return bases_table[0]->size(); }
979	int added_sequences() const { return sequences; }
980
981	void bases_and_gaps_at(int column, int bases, int gaps) const;
982
983	unsigned char index_to_upperChar(int index) const;
984	unsigned char index_to_lowerChar(int index) const;
985
986	// linear access to all tables
987	ED4_bases_table& linear_table(int c) { e4_assert(c<used_bases_tables); return *bases_table[c]; }
988	const ED4_bases_table& linear_table(int c) const { e4_assert(c<used_bases_tables); return *bases_table[c]; }
989
990	// access via character
991	ED4_bases_table& table(int c) { e4_assert(c>0 && c<MAXCHARTABLE); return linear_table(char_to_index_tab[c]); }
992	const ED4_bases_table& table(int c) const { e4_assert(c>0 && c<MAXCHARTABLE); return linear_table(char_to_index_tab[c]); }
993
994	const PosRange *changed_range(const ED4_char_table& other) const;
995	static const PosRange changed_range(const char string1, const char *string2, int min_len);
996
997	void add(const ED4_char_table& other);
998	void sub(const ED4_char_table& other);
999	void sub_and_add(const ED4_char_table& Sub, const ED4_char_table& Add);
1000	void sub_and_add(const ED4_char_table& Sub, const ED4_char_table& Add, PosRange range);
1001
1002	void add(const char *string, int len);
1003	void sub(const char *string, int len);
1004	void sub_and_add(const char old_string, const char new_string, PosRange range);
1005
1006	void build_consensus_string_to(char *buffer, ExplicitRange range) const;
1007	char *build_consensus_string(PosRange range) const;
1008	char *build_consensus_string() const { return build_consensus_string(PosRange::whole()); }
1009
1010	void change_table_length(int new_length);
1011	};
1012
1013	// ----------------------------
1014	// ED4_species_pointer
1015
1016	class ED4_species_pointer : virtual Noncopyable {
1017	// @@@ shall be renamed into ED4_gbdata_pointer to reflect general usage
1018
1019	GBDATA *species_pointer; // points to database
1020
1021	void add_callback(int *clientdata);
1022	void remove_callback(int *clientdata);
1023
1024	public:
1025
1026	ED4_species_pointer();
1027	~ED4_species_pointer();
1028
1029	GBDATA *Get() const { return species_pointer; }
1030	void Set(GBDATA gbd, int clientdata);
1031	void notify_deleted() {
1032	species_pointer=0;
1033	}
1034	};
1035
1036	// -----------------
1037	// ED4_base
1038
1039	class ED4_base;
1040	typedef ARB_ERROR (ED4_cb)(ED4_base , AW_CL, AW_CL);
1041	typedef ARB_ERROR (ED4_cb1)(ED4_base , AW_CL);
1042	typedef ARB_ERROR (ED4_cb0)(ED4_base );
1043
1044	enum ED4_species_type {
1045	ED4_SP_NONE,
1046	ED4_SP_SPECIES,
1047	ED4_SP_SAI,
1048	ED4_SP_CONSENSUS,
1049	};
1050
1051	class ED4_base : virtual Noncopyable {
1052	// base object
1053
1054	ED4_species_pointer my_species_pointer;
1055
1056	// cache world coordinates:
1057
1058	static int currTimestamp;
1059	mutable AW::Position lastPos;
1060	mutable int timestamp;
1061
1062	ED4_base_list *linked_objects; // linked list of objects which are depending from this object
1063
1064	public:
1065	const ED4_objspec& spec; // contains information about Objectproperties
1066
1067	ED4_manager *parent; // Points to parent
1068
1069
1070	ED4_properties dynamic_prop; // contains info about what i am, what i can do, what i should do
1071	char *id; // globally unique name in hierarchy
1072	ED4_index index; // defines the order of child objects
1073	ED4_base *width_link; // concerning the hierarchy
1074	ED4_base *height_link; // concerning the hierarchy
1075	ED4_extension extension; // contains relative info about graphical properties
1076	ED4_update_info update_info; // info about things to be done for the object, i.e. refresh; flag structure
1077	struct {
1078	unsigned int hidden : 1; // flag whether object is hidden or not
1079	} flag;
1080
1081	void draw_bb(int color);
1082
1083	DECLARE_DUMP_FOR_ROOTCLASS(ED4_base);
1084
1085	// function for species_pointer
1086
1087	GBDATA *get_species_pointer() const { return my_species_pointer.Get(); }
1088	void set_species_pointer(GBDATA gbd) { my_species_pointer.Set(gbd, (int)(this)); }
1089	int has_callback() const { return get_species_pointer()!=0; }
1090
1091	// callbacks
1092
1093	virtual void changed_by_database();
1094	virtual void deleted_from_database();
1095
1096	// functions concerned with graphic output
1097	int adjust_clipping_rectangle();
1098	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) = 0;
1099	virtual bool calc_bounding_box() = 0;
1100
1101	ED4_returncode clear_background(int color=0);
1102
1103	void set_links(ED4_base width_link, ED4_base height_link);
1104
1105	// functions concerned with special initialization
1106	void set_property(ED4_properties prop) { dynamic_prop = (ED4_properties) (dynamic_prop \| prop); }
1107	void clr_property(ED4_properties prop) { dynamic_prop = (ED4_properties) (dynamic_prop & ~prop); }
1108
1109	// functions concerned with coordinate transformation
1110
1111	void calc_rel_coords(AW_pos x, AW_pos y);
1112
1113	void calc_world_coords(AW_pos x, AW_pos y) const {
1114	update_world_coords_cache();
1115	*x = lastPos.xpos();
1116	*y = lastPos.ypos();
1117	}
1118	const AW::Position& calc_world_coords() const {
1119	update_world_coords_cache();
1120	return lastPos;
1121	}
1122
1123	void update_world_coords_cache() const {
1124	bool cache_up_to_date = timestamp == currTimestamp;
1125	if (!cache_up_to_date) {
1126	if (parent) {
1127	ED4_base pab = (ED4_base)parent;
1128	lastPos = pab->calc_world_coords();
1129	}
1130	else {
1131	lastPos = AW::Origin;
1132	}
1133	lastPos.move(extension.get_parent_offset());
1134	timestamp = currTimestamp;
1135	}
1136	}
1137
1138	static void touch_world_cache() {
1139	currTimestamp++;
1140	}
1141
1142	AW::Rectangle get_win_area(ED4_window *ed4w) const {
1143	AW::Position pos = ed4w->world_to_win_coords(calc_world_coords());
1144	return AW::Rectangle(pos, extension.get_size()-AW::Vector(1, 1));
1145	}
1146
1147	// functions which refer to the object as a child, i.e. travelling down the hierarchy
1148	virtual void request_refresh(int clear=1) = 0;
1149
1150	inline void request_resize();
1151	void request_resize_of_linked();
1152	void resize_requested_by_link(ED4_base *link);
1153	virtual void resize_requested_children() = 0;
1154
1155	virtual void delete_requested_children() = 0;
1156	virtual void Delete() = 0;
1157
1158	inline void set_update();
1159	virtual void update_requested_children() = 0;
1160
1161	virtual ED4_returncode move_requested_by_parent(ED4_move_info *mi)=0;
1162	virtual ED4_returncode event_sent_by_parent(AW_event event, AW_window aww);
1163	virtual ED4_returncode move_requested_by_child(ED4_move_info *moveinfo)=0;
1164
1165
1166	virtual ED4_returncode handle_move(ED4_move_info *moveinfo) = 0;
1167
1168	virtual ARB_ERROR route_down_hierarchy(ED4_cb cb, AW_CL cd1, AW_CL cd2);
1169	virtual ARB_ERROR route_down_hierarchy(ED4_cb1 cb, AW_CL cd) { return route_down_hierarchy(ED4_cb(cb), cd, 0); }
1170	virtual ARB_ERROR route_down_hierarchy(ED4_cb0 cb) { return route_down_hierarchy(ED4_cb(cb), 0, 0); }
1171
1172	int calc_group_depth();
1173
1174	// general purpose functions
1175	virtual ED4_base search_ID(const char id) = 0;
1176
1177	void check_all();
1178	short in_border(AW_pos abs_x, AW_pos abs_y, ED4_movemode mode);
1179	ED4_returncode set_width();
1180
1181
1182	ED4_AREA_LEVEL get_area_level(ED4_multi_species_manager **multi_species_manager=0) const; // returns area we belong to and the next multi species manager of the area
1183
1184	ED4_base *get_parent(ED4_level lev) const;
1185	void unlink_from_parent();
1186	bool has_parent(ED4_manager *Parent);
1187	bool is_child_of(ED4_manager *Parent) { return has_parent(Parent); }
1188
1189	virtual char resolve_pointer_to_string_copy(int str_len = 0) const;
1190	virtual const char resolve_pointer_to_char_pntr(int str_len = 0) const;
1191
1192	ED4_group_manager *is_in_folded_group() const;
1193	virtual bool is_hidden() const = 0;
1194
1195	char *get_name_of_species(); // go from terminal to name of species
1196
1197	// functions which refer to the selected object(s), i.e. across the hierarchy
1198	virtual ED4_base *get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop)=0;
1199	virtual ED4_base *get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop)=0;
1200	virtual ED4_base *search_spec_child_rek(ED4_level level); // recursive search for level
1201
1202	ED4_terminal *get_next_terminal();
1203	ED4_terminal *get_prev_terminal();
1204
1205	ED4_returncode generate_configuration_string(char **generated_string);
1206
1207	virtual ED4_returncode remove_callbacks();
1208
1209	const ED4_terminal *get_consensus_relevant_terminal() const;
1210
1211	ED4_base(const ED4_objspec& spec_, GB_CSTR id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
1212	virtual ~ED4_base();
1213
1214	// use the following functions to test which derived class we have
1215
1216	int is_terminal() const { e4_assert(this); return spec.static_prop & ED4_P_IS_TERMINAL; }
1217
1218	int is_text_terminal() const { e4_assert(this); return spec.level & (ED4_L_SPECIES_NAME\|ED4_L_SEQUENCE_INFO\|ED4_L_SEQUENCE_STRING\|ED4_L_PURE_TEXT\|ED4_L_COL_STAT); }
1219
1220	int is_species_name_terminal() const { e4_assert(this); return spec.level & ED4_L_SPECIES_NAME; }
1221
1222	int is_sequence_info_terminal() const { e4_assert(this); return spec.level & ED4_L_SEQUENCE_INFO; }
1223	int is_sequence_terminal() const { e4_assert(this); return spec.level & ED4_L_SEQUENCE_STRING; }
1224	int is_orf_terminal() const { e4_assert(this); return spec.level & ED4_L_ORF; }
1225
1226	int is_pure_text_terminal() const { e4_assert(this); return spec.level & ED4_L_PURE_TEXT; }
1227	int is_columnStat_terminal() const { e4_assert(this); return spec.level & ED4_L_COL_STAT; }
1228
1229	int is_bracket_terminal() const { e4_assert(this); return spec.level & ED4_L_BRACKET; }
1230	int is_spacer_terminal() const { e4_assert(this); return spec.level & ED4_L_SPACER; }
1231	int is_line_terminal() const { e4_assert(this); return spec.level & ED4_L_LINE; }
1232
1233	int is_manager() const { e4_assert(this); return spec.static_prop & ED4_P_IS_MANAGER; }
1234
1235	int is_sequence_manager() const { e4_assert(this); return spec.level & ED4_L_SEQUENCE; }
1236	int is_multi_name_manager() const { e4_assert(this); return spec.level & ED4_L_MULTI_NAME; }
1237	int is_name_manager() const { e4_assert(this); return spec.level & ED4_L_NAME_MANAGER; }
1238	int is_multi_species_manager() const { e4_assert(this); return spec.level & ED4_L_MULTI_SPECIES; }
1239	int is_multi_sequence_manager() const { e4_assert(this); return spec.level & ED4_L_MULTI_SEQUENCE; }
1240	int is_device_manager() const { e4_assert(this); return spec.level & ED4_L_DEVICE; }
1241
1242	int is_group_manager() const { e4_assert(this); return spec.level & ED4_L_GROUP; }
1243	int is_root_group_manager() const { e4_assert(this); return spec.level & ED4_L_ROOTGROUP; }
1244	int is_abstract_group_manager() const { e4_assert(this); return spec.level & (ED4_L_GROUP\|ED4_L_ROOTGROUP); }
1245
1246	int is_species_manager() const { e4_assert(this); return spec.level & ED4_L_SPECIES; }
1247	int is_area_manager() const { e4_assert(this); return spec.level & ED4_L_AREA; }
1248
1249	// use the following functions to cast ED4_base to derived classes:
1250
1251	#define E4B_DECL_CASTOP_helper(Class,toName) \
1252	inline const Class *toName() const; \
1253	inline Class *toName();
1254
1255	#define E4B_AVOID_CAST__helper(Class,toName,isName) \
1256	const Class *toName() const; \
1257	Class *toName(); \
1258	int isName() const;
1259
1260	#define E4B_IMPL_CASTOP_helper(Class,toName,isName) \
1261	const Class *ED4_base::toName() const { \
1262	e4_assert(isName()); \
1263	return DOWNCAST(const Class*, this); \
1264	} \
1265	Class *ED4_base::toName() { \
1266	return const_cast<Class>(const_cast<const ED4_base>(this)->toName()); \
1267	}
1268
1269	#define E4B_DECL_CASTOP(name) E4B_DECL_CASTOP_helper(concat(ED4_,name), concat(to_,name))
1270	#define E4B_AVOID_UNNEEDED_CASTS(name) E4B_AVOID_CAST__helper(concat(ED4_,name), concat(to_,name), concat(is_,name))
1271	#define E4B_IMPL_CASTOP(name) E4B_IMPL_CASTOP_helper(concat(ED4_,name), concat(to_,name), concat(is_,name))
1272
1273	E4B_DECL_CASTOP(area_manager); // to_area_manager
1274	E4B_DECL_CASTOP(abstract_group_manager); // to_abstract_group_manager
1275	E4B_DECL_CASTOP(bracket_terminal); // to_bracket_terminal
1276	E4B_DECL_CASTOP(columnStat_terminal); // to_columnStat_terminal
1277	E4B_DECL_CASTOP(device_manager); // to_device_manager
1278	E4B_DECL_CASTOP(group_manager); // to_group_manager
1279	E4B_DECL_CASTOP(line_terminal); // to_line_terminal
1280	E4B_DECL_CASTOP(manager); // to_manager
1281	E4B_DECL_CASTOP(multi_name_manager); // to_multi_name_manager
1282	E4B_DECL_CASTOP(multi_sequence_manager); // to_multi_sequence_manager
1283	E4B_DECL_CASTOP(multi_species_manager); // to_multi_species_manager
1284	E4B_DECL_CASTOP(name_manager); // to_name_manager
1285	E4B_DECL_CASTOP(orf_terminal); // to_orf_terminal
1286	E4B_DECL_CASTOP(pure_text_terminal); // to_pure_text_terminal
1287	E4B_DECL_CASTOP(root_group_manager); // to_root_group_manager
1288	E4B_DECL_CASTOP(sequence_info_terminal); // to_sequence_info_terminal
1289	E4B_DECL_CASTOP(sequence_manager); // to_sequence_manager
1290	E4B_DECL_CASTOP(sequence_terminal); // to_sequence_terminal
1291	E4B_DECL_CASTOP(spacer_terminal); // to_spacer_terminal
1292	E4B_DECL_CASTOP(species_manager); // to_species_manager
1293	E4B_DECL_CASTOP(species_name_terminal); // to_species_name_terminal
1294	E4B_DECL_CASTOP(terminal); // to_terminal
1295	E4B_DECL_CASTOP(text_terminal); // to_text_terminal
1296
1297	// simple access to containing managers
1298	inline ED4_species_manager *containing_species_manager() const;
1299
1300	// discriminate between different sequence managers:
1301
1302	inline bool is_consensus_manager() const;
1303	inline bool is_SAI_manager() const;
1304	inline bool is_species_seq_manager() const;
1305
1306	inline ED4_species_type get_species_type() const; // works for all items (recursively) contained in ED4_species_manager
1307
1308	inline bool inside_consensus_manager() const;
1309	inline bool inside_SAI_manager() const;
1310	inline bool inside_species_seq_manager() const;
1311
1312	inline bool is_consensus_terminal() const;
1313	inline bool is_SAI_terminal() const;
1314	inline bool is_species_seq_terminal() const;
1315	};
1316
1317	struct ED4_manager : public ED4_base { // derived from a Noncopyable
1318	ED4_members *children;
1319
1320	E4B_AVOID_UNNEEDED_CASTS(manager);
1321	DECLARE_DUMP_FOR_BASECLASS(ED4_manager, ED4_base);
1322
1323	int refresh_flag_ok();
1324
1325	virtual void changed_by_database();
1326	virtual void deleted_from_database();
1327
1328	// functions concerned with graphics
1329	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0);
1330	virtual bool calc_bounding_box();
1331
1332	ED4_returncode distribute_children();
1333
1334	// top-down functions, means travelling down the hierarchy
1335	virtual ED4_returncode event_sent_by_parent(AW_event event, AW_window aww);
1336
1337	virtual void request_refresh(int clear=1);
1338	ED4_returncode clear_refresh();
1339
1340	virtual void resize_requested_children();
1341
1342	virtual void update_requested_children();
1343
1344	virtual void delete_requested_children();
1345	virtual void Delete();
1346
1347	virtual ED4_returncode move_requested_by_parent(ED4_move_info *mi);
1348
1349	void create_consensus(ED4_abstract_group_manager upper_group_manager, arb_progress progress);
1350
1351	virtual ARB_ERROR route_down_hierarchy(ED4_cb cb, AW_CL cd1, AW_CL cd2);
1352	virtual ARB_ERROR route_down_hierarchy(ED4_cb1 cb, AW_CL cd) { return route_down_hierarchy(ED4_cb(cb), cd, 0); }
1353	virtual ARB_ERROR route_down_hierarchy(ED4_cb0 cb) { return route_down_hierarchy(ED4_cb(cb), 0, 0); }
1354
1355	ED4_base* find_first_that(ED4_level level, bool (condition)(ED4_base to_test, AW_CL arg), AW_CL arg);
1356	ED4_base* find_first_that(ED4_level level, bool (condition)(ED4_base to_test)) {
1357	return find_first_that(level, (bool()(ED4_base, AW_CL))condition, (AW_CL)0);
1358	}
1359
1360	// bottom-up functions
1361	virtual ED4_returncode move_requested_by_child(ED4_move_info *moveinfo);
1362	inline void resize_requested_by_child();
1363	virtual ED4_returncode refresh_requested_by_child();
1364	void delete_requested_by_child();
1365	void update_requested_by_child();
1366
1367	ED4_base *get_defined_level(ED4_level lev) const;
1368
1369	// functions referring the consensus
1370
1371	ED4_returncode create_group(ED4_group_manager **group_manager, GB_CSTR group_name);
1372
1373	void update_consensus(ED4_manager old_parent, ED4_manager new_parent, ED4_base *sequence);
1374	ED4_returncode rebuild_consensi(ED4_base *start_species, ED4_update_flag update_flag);
1375
1376	ED4_returncode check_in_bases(ED4_base *added_base);
1377	ED4_returncode check_out_bases(ED4_base *subbed_base);
1378
1379	ED4_returncode update_bases(const ED4_base old_base, const ED4_base new_base, PosRange range = PosRange::whole());
1380	ED4_returncode update_bases(const char old_seq, int old_len, const char new_seq, int new_len, PosRange range = PosRange::whole());
1381	ED4_returncode update_bases(const char old_seq, int old_len, const ED4_base new_base, PosRange range = PosRange::whole());
1382	ED4_returncode update_bases(const ED4_char_table old_table, const ED4_char_table new_table, PosRange range = PosRange::whole());
1383
1384	ED4_returncode update_bases_and_rebuild_consensi(const char old_seq, int old_len, ED4_base species, ED4_update_flag update_flag, PosRange range = PosRange::whole());
1385
1386	// handle moves across the hierarchy
1387	virtual ED4_returncode handle_move(ED4_move_info *moveinfo);
1388
1389	virtual ED4_base *get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop);
1390	virtual ED4_base *get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop);
1391	virtual ED4_base *search_spec_child_rek(ED4_level level); // recursive search for level
1392
1393	// general purpose functions
1394	virtual ED4_base search_ID(const char id);
1395	virtual ED4_returncode remove_callbacks();
1396
1397	ED4_terminal *get_first_terminal(int start_index=0) const;
1398	ED4_terminal *get_last_terminal(int start_index=-1) const;
1399
1400	void hide_children();
1401	void unhide_children();
1402
1403	bool is_hidden() const {
1404	if (flag.hidden) return true;
1405	if (!parent) return false;
1406	return parent->is_hidden();
1407	}
1408
1409	ED4_manager(const ED4_objspec& spec_, const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1410	virtual ~ED4_manager();
1411	};
1412
1413	struct ED4_terminal : public ED4_base { // derived from a Noncopyable
1414	E4B_AVOID_UNNEEDED_CASTS(terminal);
1415
1416	struct { unsigned int deleted : 1; } tflag; // @@@ go bool
1417
1418	long curr_timestamp;
1419
1420	DECLARE_DUMP_FOR_BASECLASS(ED4_terminal,ED4_base);
1421
1422	// callbacks
1423
1424	virtual void changed_by_database();
1425	virtual void deleted_from_database();
1426
1427	// functions concerning graphic output
1428	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) = 0;
1429	virtual ED4_returncode draw() = 0;
1430
1431	virtual bool calc_bounding_box();
1432
1433	ED4_returncode draw_drag_box(AW_pos x, AW_pos y, GB_CSTR text = NULL, int cursor_y=-1);
1434
1435	// functions which concern the object as a child
1436	virtual void request_refresh(int clear=1);
1437
1438	virtual void resize_requested_children();
1439
1440	virtual void update_requested_children();
1441	virtual void delete_requested_children();
1442	virtual void Delete();
1443
1444	virtual ED4_returncode move_requested_by_parent(ED4_move_info *mi);
1445	virtual ED4_returncode event_sent_by_parent(AW_event event, AW_window aww);
1446	virtual ED4_base *get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop);
1447	virtual ED4_base *get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop);
1448	virtual ED4_returncode move_requested_by_child(ED4_move_info *moveinfo);
1449	virtual ED4_returncode handle_move(ED4_move_info *moveinfo);
1450
1451	ED4_returncode kill_object();
1452
1453	// general purpose functions
1454	virtual ED4_base search_ID(const char id);
1455	virtual char resolve_pointer_to_string_copy(int str_len = 0) const;
1456	virtual const char resolve_pointer_to_char_pntr(int str_len = 0) const;
1457	virtual ED4_returncode remove_callbacks();
1458
1459	GB_ERROR write_sequence(const char *seq, int seq_len);
1460
1461	void scroll_into_view(ED4_window *ed4w);
1462	inline bool setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfoldGroups, ED4_CursorJumpType jump_type);
1463
1464	bool is_hidden() const { return parent && parent->is_hidden(); }
1465
1466	ED4_terminal(const ED4_objspec& spec_, GB_CSTR id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
1467	virtual ~ED4_terminal();
1468	};
1469
1470	enum ED4_species_mode {
1471	ED4_SM_MOVE,
1472	ED4_SM_KILL,
1473	ED4_SM_MARK
1474	};
1475
1476	class ED4_reference_terminals : virtual Noncopyable {
1477	ED4_sequence_info_terminal *ref_sequence_info;
1478	ED4_sequence_terminal *ref_sequence;
1479	ED4_sequence_info_terminal *ref_column_stat_info;
1480	ED4_columnStat_terminal *ref_column_stat;
1481
1482	void null() { ref_sequence_info = 0; ref_sequence = 0; ref_column_stat = 0; ref_column_stat_info = 0; }
1483	public:
1484	void clear();
1485	void init(ED4_sequence_info_terminal , ED4_sequence_terminal , ED4_sequence_info_terminal , ED4_columnStat_terminal );
1486
1487	ED4_sequence_info_terminal *get_ref_sequence_info() { return ref_sequence_info; }
1488	ED4_sequence_terminal *get_ref_sequence() { return ref_sequence; }
1489	ED4_sequence_info_terminal *get_ref_column_stat_info() { return ref_column_stat_info; }
1490	ED4_columnStat_terminal *get_ref_column_stat() { return ref_column_stat; }
1491
1492	ED4_reference_terminals() { null(); }
1493	~ED4_reference_terminals() { clear(); }
1494	};
1495
1496	class ED4_WinContext {
1497	ED4_window *ed4w;
1498	AW_device *device;
1499
1500	bool is_set() const { return ed4w; }
1501	void init(ED4_window *ew) {
1502	e4_assert(ew);
1503	ed4w = ew;
1504	device = ed4w->get_device();
1505	}
1506
1507	void warn_missing_context() const;
1508	void expect_context() const { if (!is_set()) warn_missing_context(); }
1509
1510	protected:
1511	ED4_WinContext() : ed4w(0), device(0) {}
1512	static ED4_WinContext current_context;
1513
1514	public:
1515	inline ED4_WinContext(AW_window *aww_);
1516	ED4_WinContext(ED4_window *ed4w_) { init(ed4w_); }
1517
1518	AW_device *get_device() const { expect_context(); return device; }
1519	ED4_window *get_ed4w() const { expect_context(); return ed4w; }
1520
1521	static const ED4_WinContext& get_current_context() { return current_context; }
1522	static bool have_context() { return current_context.is_set(); }
1523	};
1524
1525	// accessors for current context (see also ED4_WinContextFree)
1526	inline AW_device *current_device() { return ED4_WinContext::get_current_context().get_device(); }
1527	inline ED4_window *current_ed4w() { return ED4_WinContext::get_current_context().get_ed4w(); }
1528	inline AW_window *current_aww() { return current_ed4w()->aww; }
1529	inline ED4_cursor& current_cursor() { return current_ed4w()->cursor; }
1530
1531
1532	class ED4_root : virtual Noncopyable {
1533	void ED4_ROOT() const { e4_assert(0); } // avoid ED4_root-members use global ED4_ROOT
1534
1535	void refresh_window_simple(bool redraw);
1536	void handle_update_requests(bool& redraw);
1537
1538	ED4_window *most_recently_used_window;
1539
1540	public:
1541	char *db_name; // name of Default Properties database (complete path)
1542	AW_root *aw_root; // Points to 'AW-Window-Controller'
1543	AW_default props_db; // Default Properties database
1544
1545	ED4_window *first_window; // Points to List of Main Windows of ED4
1546	ED4_main_manager *main_manager; // Points to Main manager of ED4
1547	ED4_area_manager *middle_area_man; // Points to middle area
1548	ED4_area_manager *top_area_man;
1549	ED4_root_group_manager *root_group_man;
1550	EDB_root_bact *database; // Points to Object which controls Data
1551	ED4_selected_list *selected_objects;
1552	ED4_scroll_links scroll_links;
1553	bool folding_action; // flag tells whether action was folding action or not
1554	ED4_reference_terminals ref_terminals;
1555	ED4_species_mode species_mode;
1556	ED4_scroll_picture scroll_picture;
1557	BI_ecoli_ref *ecoli_ref;
1558	char *alignment_name;
1559	GB_alignment_type alignment_type;
1560	AWT_reference *reference;
1561	AWT_seq_colors *sequence_colors;
1562	AW_gc_manager aw_gc_manager;
1563	ST_ML *st_ml;
1564	AW_helix *helix;
1565	int helix_spacing;
1566	long helix_add_spacing;
1567	long terminal_add_spacing;
1568	char *protstruct; // protein structure summary
1569	long protstruct_len; // protein structure summary
1570	ed_key *edk;
1571	ED4_Edit_String *edit_string;
1572
1573	bool column_stat_activated;
1574	bool column_stat_initialized;
1575	bool visualizeSAI;
1576	bool visualizeSAI_allSpecies;
1577
1578	int temp_gc;
1579	AW_font_group font_group;
1580
1581	void announce_useraction_in(AW_window *aww);
1582	ED4_window *get_most_recently_used_window() const { return most_recently_used_window; }
1583
1584	inline ED4_device_manager *get_device_manager();
1585
1586	// Initializing functions
1587	ED4_returncode create_hierarchy(char area_string_middle, char area_string_top);
1588	ED4_returncode init_alignment();
1589	void recalc_font_group();
1590
1591	AW_window *create_new_window();
1592	ED4_returncode generate_window(AW_device device, ED4_window new_window);
1593	void copy_window_struct(ED4_window source, ED4_window destination);
1594
1595	// functions concerned with global refresh and resize
1596	void resize_all();
1597
1598	void special_window_refresh(bool handle_updates);
1599	ED4_returncode refresh_all_windows(bool redraw);
1600
1601	void request_refresh_for_all_terminals();
1602	void request_refresh_for_specific_terminals(ED4_level lev);
1603	void request_refresh_for_consensus_terminals();
1604	void request_refresh_for_sequence_terminals();
1605
1606	inline void announce_deletion(ED4_base *object); // before deleting an object, use this to announce
1607
1608	// functions concerned with list of selected objects
1609	ED4_returncode add_to_selected(ED4_species_name_terminal *object);
1610	void remove_from_selected(ED4_species_name_terminal *object);
1611	ED4_returncode deselect_all();
1612
1613	ED4_returncode get_area_rectangle(AW_screen_area *rect, AW_pos x, AW_pos y);
1614
1615	ED4_index pixel2pos(AW_pos click_x);
1616
1617	void remove_all_callbacks();
1618
1619	ED4_root();
1620	~ED4_root();
1621	};
1622
1623	ED4_WinContext::ED4_WinContext(AW_window *aww_) { init(ED4_ROOT->first_window->get_matching_ed4w(aww_)); }
1624
1625	struct ED4_LocalWinContext : private ED4_WinContext {
1626	ED4_LocalWinContext(AW_window *aww) : ED4_WinContext(current_context) { current_context = ED4_WinContext(aww); }
1627	ED4_LocalWinContext(ED4_window *ew) : ED4_WinContext(current_context) { current_context = ED4_WinContext(ew); }
1628	~ED4_LocalWinContext() { current_context = *this; }
1629	};
1630
1631	class ED4_MostRecentWinContext : virtual Noncopyable {
1632	ED4_LocalWinContext *most_recent;
1633	public:
1634	ED4_MostRecentWinContext() : most_recent(0) {
1635	if (!ED4_WinContext::have_context()) {
1636	most_recent = new ED4_LocalWinContext(ED4_ROOT->get_most_recently_used_window());
1637	}
1638	}
1639	~ED4_MostRecentWinContext() {
1640	delete most_recent;
1641	}
1642	};
1643
1644	inline void ED4_root::announce_deletion(ED4_base *object) {
1645	if (object->is_terminal()) {
1646	ED4_terminal *term = object->to_terminal();
1647	for (ED4_window *win = first_window; win; win = win->next) {
1648	ED4_LocalWinContext uses(win);
1649	win->announce_deletion(term);
1650	}
1651	}
1652	}
1653
1654	// ------------------------
1655	// manager classes
1656	//
1657	// All manager classes only differ in their static properties.
1658	// This kind of construction was chosen for using a minimum of RAM
1659
1660	class ED4_main_manager : public ED4_manager { // derived from a Noncopyable
1661	// first in hierarchy
1662
1663	E4B_AVOID_UNNEEDED_CASTS(main_manager);
1664
1665	// these terminals are redrawn after refresh (with increase clipping area)
1666	// to revert text from middle area drawn into top area:
1667	ED4_terminal *top_middle_line;
1668	ED4_terminal *top_middle_spacer;
1669
1670	public:
1671	ED4_main_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1672
1673	void set_top_middle_spacer_terminal(ED4_terminal *top_middle_spacer_) { top_middle_spacer = top_middle_spacer_; }
1674	void set_top_middle_line_terminal(ED4_terminal *top_middle_line_) { top_middle_line = top_middle_line_; }
1675
1676	ED4_terminal *get_top_middle_spacer_terminal() const { return top_middle_spacer; }
1677	ED4_terminal *get_top_middle_line_terminal() const { return top_middle_line; }
1678
1679	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1680
1681	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0);
1682	virtual void resize_requested_children();
1683
1684	void clear_whole_background();
1685	};
1686
1687	struct ED4_device_manager : public ED4_manager {
1688	E4B_AVOID_UNNEEDED_CASTS(device_manager);
1689	ED4_device_manager (const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1690	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1691	};
1692
1693	struct ED4_area_manager : public ED4_manager {
1694	E4B_AVOID_UNNEEDED_CASTS(area_manager);
1695	ED4_area_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1696	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1697
1698	ED4_multi_species_manager *get_multi_species_manager() const {
1699	return get_defined_level(ED4_L_MULTI_SPECIES)->to_multi_species_manager();
1700	}
1701	};
1702
1703	class ED4_multi_species_manager : public ED4_manager {
1704	E4B_AVOID_UNNEEDED_CASTS(multi_species_manager);
1705
1706	int species; // # of species (-1 == unknown)
1707	int selected_species; // # of selected species (-1 == unknown)
1708
1709	void set_species_counters(int no_of_species, int no_of_selected);
1710	#ifdef DEBUG
1711	void count_species(int speciesPtr, int selectedPtr) const;
1712	#endif
1713	void update_species_counters();
1714
1715	public:
1716	ED4_multi_species_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1717
1718	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1719
1720	virtual void update_requested_children();
1721	virtual void delete_requested_children();
1722
1723	int count_visible_children(); // is called by a multi_species_manager
1724
1725	ED4_species_manager *get_consensus_manager() const; // returns the consensus-manager or NULL
1726	ED4_species_name_terminal *get_consensus_name_terminal() const; // returns the consensus-name-terminal or NULL
1727
1728	// functions concerned with selection
1729	int get_no_of_selected_species();
1730	int get_no_of_species();
1731
1732	void update_group_id();
1733
1734	void invalidate_species_counters();
1735	int has_valid_counters() const { return species != -1 && selected_species!=-1; }
1736	bool all_are_selected() const { e4_assert(has_valid_counters()); return species == selected_species; }
1737
1738	void select_all(bool only_species);
1739	void deselect_all_species_and_SAI();
1740	void invert_selection_of_all_species();
1741	void marked_species_select(bool select);
1742	void selected_species_mark(bool mark);
1743
1744	void toggle_selected_species();
1745	};
1746
1747	class ED4_abstract_group_manager : public ED4_manager {
1748	E4B_AVOID_UNNEEDED_CASTS(abstract_group_manager);
1749	protected:
1750	ED4_char_table my_table; // table concerning Consensusfunction
1751
1752	public:
1753	ED4_abstract_group_manager(const ED4_objspec& spec_, const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1754
1755	DECLARE_DUMP_FOR_BASECLASS(ED4_abstract_group_manager, ED4_manager);
1756
1757	ED4_char_table& table() { return my_table; }
1758	const ED4_char_table& table() const { return my_table; }
1759
1760	ED4_bases_table& table(unsigned char c) { return table().table(c); }
1761	const ED4_bases_table& table(unsigned char c) const { return table().table(c); }
1762
1763	ED4_multi_species_manager *get_multi_species_manager() const {
1764	return get_defined_level(ED4_L_MULTI_SPECIES)->to_multi_species_manager();
1765	}
1766	};
1767
1768	struct ED4_group_manager : public ED4_abstract_group_manager {
1769	E4B_AVOID_UNNEEDED_CASTS(group_manager);
1770	ED4_group_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1771	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_group_manager);
1772	void reinit_char_table();
1773	};
1774
1775	enum ED4_remap_mode {
1776	ED4_RM_NONE, // no remapping (normal mode)
1777	ED4_RM_SHOW_ABOVE, // Show all positions, where xxx% of all edited sequences have any base
1778	ED4_RM_MAX_ALIGN, // ------------------------- any edited sequence has a base
1779	ED4_RM_MAX_EDIT, // like ED4_RM_MAX_ALIGN, but bases are pushed OVER remapped gaps (not INTO)
1780	ED4_RM_DYNAMIC_GAPS, // gaps shown as spaces (more gaps => more spaces)
1781
1782	ED4_RM_MODES
1783
1784	};
1785
1786	class ED4_remap : virtual Noncopyable {
1787
1788	ED4_remap_mode mode;
1789	int show_above_percent; // used only for ED4_RM_SHOW_ABOVE
1790
1791	size_t sequence_table_len; // allocated size of sequence_to_screen_tab
1792	size_t screen_table_len; // allocated size of screen_to_sequence_tab
1793
1794	size_t sequence_len; // size of recently compiled part of sequence_to_screen_tab
1795	size_t screen_len; // size of recently compiled part of screen_to_sequence_tab
1796
1797	int *screen_to_sequence_tab;
1798	int *sequence_to_screen_tab; // <0 means position is not mapped (last displayed sequence position)
1799
1800	int changed; // remap-table changed at last compile
1801	int update_needed; // remapping should be recompiled
1802
1803	inline void set_sequence_to_screen(int pos, int newVal);
1804
1805	public:
1806
1807	ED4_remap();
1808	~ED4_remap();
1809
1810	int screen_to_sequence(int screen_pos) const;
1811
1812	int sequence_to_screen_PLAIN(int sequence_pos) const {
1813	e4_assert(sequence_pos>=0 && size_t(sequence_pos)<=sequence_len);
1814	return sequence_to_screen_tab[sequence_pos];
1815	}
1816	int shown_sequence_to_screen(int sequence_pos) const {
1817	// as well works for sequence_pos == MAXSEQUENCECHARACTERLENGTH
1818	int screen_pos = sequence_to_screen_PLAIN(sequence_pos);
1819	e4_assert(screen_pos >= 0); // sequence_pos expected to be visible (i.e. not folded away)
1820	return screen_pos;
1821	}
1822
1823	int clipped_sequence_to_screen_PLAIN(int sequence_pos) const;
1824	int sequence_to_screen(int sequence_pos) const;
1825
1826	PosRange sequence_to_screen(PosRange range) const {
1827	e4_assert(!range.is_empty());
1828	return PosRange(sequence_to_screen(range.start()), sequence_to_screen(range.end()));
1829	}
1830	PosRange screen_to_sequence(PosRange range) const {
1831	e4_assert(!range.is_empty());
1832	if (range.is_unlimited()) return PosRange::from(screen_to_sequence(range.start()));
1833	return PosRange(screen_to_sequence(range.start()), screen_to_sequence(range.end()));
1834	}
1835
1836	size_t get_max_screen_pos() const { return screen_len-1; }
1837
1838	ED4_remap_mode get_mode() const { return mode; }
1839	void set_mode(ED4_remap_mode Mode, int above_percent) {
1840	if (Mode<0 \|\| Mode>=ED4_RM_MODES) {
1841	Mode = ED4_RM_NONE;
1842	}
1843	if (mode!=Mode) {
1844	mode = Mode;
1845	update_needed = 1;
1846	}
1847
1848	if (show_above_percent!=above_percent) {
1849	show_above_percent = above_percent;
1850	if (mode==ED4_RM_SHOW_ABOVE) {
1851	update_needed = 1;
1852	}
1853	}
1854	}
1855
1856	void mark_compile_needed(); // recompile if mode != none
1857	void mark_compile_needed_force(); // always recompile
1858	int compile_needed() const { return update_needed; }
1859
1860	GB_ERROR compile(ED4_root_group_manager *gm);
1861	int was_changed() const { return changed; } // mapping changed by last compile ?
1862
1863	int is_shown(int position) const { return sequence_to_screen_PLAIN(position)>=0; }
1864
1865	ExplicitRange clip_screen_range(PosRange screen_range) const { return ExplicitRange(screen_range, screen_len-1); }
1866	};
1867
1868	class ED4_root_group_manager : public ED4_abstract_group_manager {
1869	E4B_AVOID_UNNEEDED_CASTS(root_group_manager);
1870	ED4_remap my_remap;
1871	public:
1872	ED4_root_group_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1873
1874	bool update_remap(); // 'true' if mapping has changed
1875
1876	const ED4_remap *remap() const { return &my_remap; }
1877	ED4_remap *remap() { return &my_remap; }
1878
1879	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0);
1880	virtual void resize_requested_children();
1881
1882	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_group_manager);
1883	};
1884
1885	typedef void (ED4_species_manager_cb)(ED4_species_manager, AW_CL);
1886
1887	class ED4_species_manager_cb_data {
1888	ED4_species_manager_cb cb;
1889	AW_CL cd; // client data
1890
1891	public:
1892	ED4_species_manager_cb_data(ED4_species_manager_cb cb_, AW_CL cd_) : cb(cb_), cd(cd_) {}
1893
1894	void call(ED4_species_manager *man) const { cb(man, cd); }
1895	bool operator<(const ED4_species_manager_cb_data& other) const {
1896	return (char)cb < (char)other.cb &&
1897	(char)cd < (char)other.cd;
1898	}
1899	};
1900
1901	class ED4_species_manager : public ED4_manager {
1902	E4B_AVOID_UNNEEDED_CASTS(species_manager);
1903
1904	std::set<ED4_species_manager_cb_data> callbacks;
1905
1906	ED4_species_type type;
1907	bool selected;
1908
1909	public:
1910	ED4_species_manager(ED4_species_type type_, const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1911	~ED4_species_manager ();
1912
1913	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1914
1915	ED4_species_type get_type() const { return type; }
1916
1917	bool is_selected() const { return selected; }
1918	void set_selected(bool select) {
1919	// e4_assert(type != ED4_SP_CONSENSUS); // it's not allowed to select a consensus // @@@ happens atm when moving a group
1920	selected = select;
1921	}
1922
1923	bool setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfold_groups, ED4_CursorJumpType jump_type);
1924
1925	void add_sequence_changed_cb(ED4_species_manager_cb cb, AW_CL cd);
1926	void remove_sequence_changed_cb(ED4_species_manager_cb cb, AW_CL cd);
1927	void remove_all_callbacks();
1928
1929	void do_callbacks();
1930
1931	ED4_species_name_terminal *get_name_terminal() const { return children->member(0)->to_species_name_terminal(); }
1932	};
1933
1934	inline ED4_species_manager *ED4_base::containing_species_manager() const {
1935	ED4_base *sman = get_parent(ED4_L_SPECIES);
1936	return sman ? sman->to_species_manager() : NULL;
1937	}
1938
1939	inline bool ED4_base::is_consensus_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_CONSENSUS; }
1940	inline bool ED4_base::is_SAI_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_SAI; }
1941	inline bool ED4_base::is_species_seq_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_SPECIES; }
1942
1943	inline ED4_species_type ED4_base::get_species_type() const {
1944	ED4_species_manager *sman = containing_species_manager();
1945	return sman ? sman->get_type() : ED4_SP_NONE;
1946	}
1947
1948	inline bool ED4_base::inside_consensus_manager() const { return get_species_type() == ED4_SP_CONSENSUS; }
1949	inline bool ED4_base::inside_SAI_manager() const { return get_species_type() == ED4_SP_SAI; }
1950	inline bool ED4_base::inside_species_seq_manager() const { return get_species_type() == ED4_SP_SPECIES; }
1951
1952	inline bool ED4_base::is_consensus_terminal() const { return is_sequence_terminal() && inside_consensus_manager(); }
1953	inline bool ED4_base::is_SAI_terminal() const { return is_sequence_terminal() && inside_SAI_manager(); }
1954	inline bool ED4_base::is_species_seq_terminal() const { return is_sequence_terminal() && inside_species_seq_manager(); }
1955
1956	inline bool ED4_cursor::in_species_seq_terminal() const { return owner_of_cursor && owner_of_cursor->is_species_seq_terminal(); }
1957	inline bool ED4_cursor::in_consensus_terminal() const { return owner_of_cursor && owner_of_cursor->is_consensus_terminal(); }
1958	inline bool ED4_cursor::in_SAI_terminal() const { return owner_of_cursor && owner_of_cursor->is_SAI_terminal(); }
1959
1960
1961	struct ED4_multi_sequence_manager : public ED4_manager {
1962	E4B_AVOID_UNNEEDED_CASTS(multi_sequence_manager);
1963	ED4_multi_sequence_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1964	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1965	};
1966
1967	struct ED4_sequence_manager : public ED4_manager {
1968	E4B_AVOID_UNNEEDED_CASTS(sequence_manager);
1969	ED4_sequence_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1970	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1971	};
1972
1973	struct ED4_multi_name_manager : public ED4_manager {
1974	E4B_AVOID_UNNEEDED_CASTS(multi_name_manager);
1975	// member of ED4_species_manager (contains ED4_name_manager for name and info)
1976	ED4_multi_name_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1977	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1978	};
1979
1980
1981	struct ED4_name_manager : public ED4_manager {
1982	E4B_AVOID_UNNEEDED_CASTS(name_manager);
1983	// member of ED4_multi_name_manager (contains speciesname or other info concerning the species)
1984	ED4_name_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1985	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1986	};
1987
1988
1989	// -------------------------
1990	// terminal classes
1991
1992
1993	struct ED4_tree_terminal : public ED4_terminal {
1994	E4B_AVOID_UNNEEDED_CASTS(tree_terminal);
1995
1996	virtual ED4_returncode draw();
1997	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0);
1998
1999	ED4_tree_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2000
2001	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2002	};
2003
2004	struct ED4_bracket_terminal : public ED4_terminal {
2005	E4B_AVOID_UNNEEDED_CASTS(bracket_terminal);
2006
2007	virtual ED4_returncode draw();
2008	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0);
2009
2010	void fold();
2011	void unfold();
2012
2013	ED4_bracket_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2014
2015	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2016	};
2017
2018	struct ED4_text_terminal : public ED4_terminal {
2019	E4B_AVOID_UNNEEDED_CASTS(text_terminal);
2020
2021	// functions concerning graphic output
2022	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0);
2023	virtual ED4_returncode draw();
2024
2025	virtual int get_length() const = 0;
2026	virtual void deleted_from_database();
2027
2028	ED4_text_terminal(const ED4_objspec& spec_, GB_CSTR id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
2029	virtual ~ED4_text_terminal() {}
2030
2031	DECLARE_DUMP_FOR_BASECLASS(ED4_text_terminal, ED4_terminal);
2032	};
2033
2034	class ED4_abstract_sequence_terminal : public ED4_text_terminal { // derived from a Noncopyable
2035
2036	PosRange pixel2index(PosRange pixel_range);
2037
2038	E4B_AVOID_UNNEEDED_CASTS(abstract_sequence_terminal);
2039	public:
2040	char *species_name; // @@@ wrong place (may be member of ED4_sequence_manager)
2041
2042
2043	ED4_abstract_sequence_terminal(const ED4_objspec& spec_, const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2044	virtual ~ED4_abstract_sequence_terminal();
2045
2046	virtual GB_alignment_type GetAliType() = 0;
2047	virtual int get_length() const { int len; resolve_pointer_to_char_pntr(&len); return len; }
2048
2049	ED4_species_name_terminal *corresponding_species_name_terminal() const {
2050	return get_parent(ED4_L_SPECIES)->search_spec_child_rek(ED4_L_SPECIES_NAME)->to_species_name_terminal();
2051	}
2052	PosRange calc_interval_displayed_in_rectangle(AW_screen_area *area_rect);
2053	PosRange calc_update_interval();
2054
2055	DECLARE_DUMP_FOR_BASECLASS(ED4_abstract_sequence_terminal, ED4_text_terminal);
2056	};
2057
2058	class ED4_orf_terminal : public ED4_abstract_sequence_terminal { // derived from a Noncopyable
2059	// NOTE: ED4_orf_terminal is a separate terminal class used to display Open Reading Frames (ORFs)
2060	// for the corresponding gene (DNA) sequence. It is used in ProteinViewer Module and should not be
2061	// used for drawing aminoacid sequence alone as in protein alignment. Aminoacid sequences are
2062	// handled by the standard "ED4_sequence_terminal" class.
2063
2064	char *aaSequence;
2065	size_t aaSeqLen;
2066	char *aaColor;
2067	int aaStartPos;
2068	int aaStrandType;
2069
2070	virtual ED4_returncode draw();
2071	E4B_AVOID_UNNEEDED_CASTS(orf_terminal);
2072	public:
2073	ED4_orf_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2074	virtual ~ED4_orf_terminal();
2075
2076	virtual GB_alignment_type GetAliType();
2077
2078	void SET_aaSeqFlags (int startPos, int strandType) { aaStartPos = startPos; aaStrandType = strandType; }
2079	void SET_aaSequence(const char *aaSeq) { freedup(aaSequence, aaSeq); aaSeqLen = strlen(aaSequence); }
2080	void SET_aaColor(const char *aaSeq) { freedup(aaColor, aaSeq); }
2081
2082	int GET_aaStartPos () { return aaStartPos; }
2083	int GET_aaStrandType () { return aaStrandType; }
2084
2085	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_sequence_terminal);
2086	};
2087
2088	class ED4_sequence_terminal : public ED4_abstract_sequence_terminal { // derived from a Noncopyable
2089	mutable ED4_SearchResults searchResults;
2090	bool shall_display_secstruct_info; // helix or protstruct
2091
2092	virtual ED4_returncode draw();
2093
2094	E4B_AVOID_UNNEEDED_CASTS(sequence_terminal);
2095
2096	public:
2097
2098	AP_tree *st_ml_node;
2099
2100	ED4_sequence_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent, bool shall_display_secstruct_info_);
2101
2102	virtual GB_alignment_type GetAliType();
2103
2104	virtual void deleted_from_database();
2105	virtual int get_length() const { return ED4_abstract_sequence_terminal::get_length(); }
2106
2107	void set_secstruct_display(bool show) { shall_display_secstruct_info = show; }
2108
2109	ED4_SearchResults& results() const { return searchResults; }
2110
2111	ED4_columnStat_terminal *corresponding_columnStat_terminal() const {
2112	ED4_base *col_term = get_parent(ED4_L_MULTI_SEQUENCE)->search_spec_child_rek(ED4_L_COL_STAT);
2113	return col_term ? col_term->to_columnStat_terminal() : 0;
2114	}
2115
2116	DECLARE_DUMP_FOR_MIDCLASS(ED4_sequence_terminal,ED4_abstract_sequence_terminal);
2117	};
2118
2119	class ED4_columnStat_terminal : public ED4_text_terminal { // derived from a Noncopyable
2120	char *likelihood[4]; // likelihood-array for each base (ACGU) [length of array = alignment_length]
2121	int latest_update;
2122
2123	static double threshold;
2124
2125	int update_likelihood();
2126
2127	E4B_AVOID_UNNEEDED_CASTS(columnStat_terminal);
2128
2129	public:
2130	// functions concerning graphic output
2131	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0);
2132	virtual ED4_returncode draw();
2133	virtual int get_length() const { return corresponding_sequence_terminal()->get_length(); }
2134
2135	static int threshold_is_set();
2136	static void set_threshold(double aThreshold);
2137	static double get_threshold() { return threshold; }
2138
2139	ED4_sequence_terminal *corresponding_sequence_terminal() const { return get_parent(ED4_L_MULTI_SEQUENCE)->search_spec_child_rek(ED4_L_SEQUENCE_STRING)->to_sequence_terminal(); }
2140
2141	GB_CSTR build_probe_match_string(PosRange range) const;
2142
2143	ED4_columnStat_terminal(GB_CSTR id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
2144	~ED4_columnStat_terminal();
2145
2146	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2147	};
2148
2149	struct ED4_species_name_terminal : public ED4_text_terminal { // derived from a Noncopyable
2150	ED4_species_name_terminal(GB_CSTR id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
2151	~ED4_species_name_terminal() { delete selection_info; }
2152
2153	E4B_AVOID_UNNEEDED_CASTS(species_name_terminal);
2154
2155	ED4_selection_entry *selection_info; // Info about i.e. Position
2156	bool dragged;
2157
2158	GB_CSTR get_displayed_text() const;
2159	virtual int get_length() const { return strlen(get_displayed_text()); }
2160
2161	ED4_sequence_terminal *corresponding_sequence_terminal() const {
2162	ED4_base *seq_term = get_parent(ED4_L_SPECIES)->search_spec_child_rek(ED4_L_SEQUENCE_STRING);
2163	return seq_term ? seq_term->to_sequence_terminal() : 0;
2164	}
2165
2166	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2167	};
2168
2169	struct ED4_sequence_info_terminal : public ED4_text_terminal {
2170	E4B_AVOID_UNNEEDED_CASTS(sequence_info_terminal);
2171
2172	ED4_sequence_info_terminal(const char id, / GBDATA gbd, / AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
2173
2174	ED4_species_name_terminal *corresponding_species_name_terminal() const {
2175	return get_parent(ED4_L_SPECIES)->search_spec_child_rek(ED4_L_SPECIES_NAME)->to_species_name_terminal();
2176	}
2177
2178	virtual ED4_returncode draw();
2179
2180	GBDATA *data() { return get_species_pointer(); } // DB-entry ("ali_xxx/data")
2181	const GBDATA *data() const { return get_species_pointer(); }
2182
2183	virtual int get_length() const { return 1+strlen(id); }
2184
2185	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2186	};
2187
2188	struct ED4_pure_text_terminal : public ED4_text_terminal {
2189	E4B_AVOID_UNNEEDED_CASTS(pure_text_terminal);
2190
2191	ED4_pure_text_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2192
2193	virtual int get_length() const { int len; resolve_pointer_to_char_pntr(&len); return len; }
2194
2195	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2196	};
2197
2198	class ED4_consensus_sequence_terminal : public ED4_sequence_terminal {
2199	E4B_AVOID_UNNEEDED_CASTS(consensus_sequence_terminal);
2200
2201	virtual ED4_returncode draw();
2202	ED4_char_table& get_char_table() const { return get_parent(ED4_L_GROUP)->to_group_manager()->table(); }
2203	public:
2204	ED4_consensus_sequence_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2205
2206	virtual int get_length() const;
2207
2208	DECLARE_DUMP_FOR_LEAFCLASS(ED4_sequence_terminal);
2209	};
2210
2211	class ED4_spacer_terminal : public ED4_terminal {
2212	E4B_AVOID_UNNEEDED_CASTS(spacer_terminal);
2213	bool shallDraw; // true -> spacer is really drawn (otherwise it's only a placeholder)
2214
2215	public:
2216	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0);
2217	virtual ED4_returncode draw();
2218
2219	ED4_spacer_terminal(const char id, bool shallDraw_, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2220
2221	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2222	};
2223
2224	struct ED4_line_terminal : public ED4_terminal {
2225	E4B_AVOID_UNNEEDED_CASTS(line_terminal);
2226
2227	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0);
2228	virtual ED4_returncode draw();
2229
2230	ED4_line_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2231
2232	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2233	};
2234
2235
2236	// ----------------------------------------------
2237	// inlines which need complete classdefs
2238
2239	inline void ED4_base::set_update() { // @@@ rename into request_update
2240	if (!update_info.update_requested) {
2241	update_info.update_requested = 1;
2242	if (parent) parent->update_requested_by_child();
2243	}
2244	}
2245
2246	inline void ED4_base::request_resize() {
2247	update_info.set_resize(1);
2248	if (parent) parent->resize_requested_by_child();
2249	}
2250
2251	void ED4_manager::resize_requested_by_child() {
2252	if (!update_info.resize) request_resize();
2253	}
2254
2255
2256	inline bool ED4_terminal::setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfoldGroups, ED4_CursorJumpType jump_type) {
2257	ED4_species_manager *sm = get_parent(ED4_L_SPECIES)->to_species_manager();
2258	return sm->setCursorTo(cursor, seq_pos, unfoldGroups, jump_type);
2259	}
2260
2261	E4B_IMPL_CASTOP(area_manager); // to_area_manager
2262	E4B_IMPL_CASTOP(abstract_group_manager); // to_abstract_group_manager
2263	E4B_IMPL_CASTOP(bracket_terminal); // to_bracket_terminal
2264	E4B_IMPL_CASTOP(columnStat_terminal); // to_columnStat_terminal
2265	E4B_IMPL_CASTOP(device_manager); // to_device_manager
2266	E4B_IMPL_CASTOP(group_manager); // to_group_manager
2267	E4B_IMPL_CASTOP(line_terminal); // to_line_terminal
2268	E4B_IMPL_CASTOP(manager); // to_manager
2269	E4B_IMPL_CASTOP(multi_name_manager); // to_multi_name_manager
2270	E4B_IMPL_CASTOP(multi_sequence_manager); // to_multi_sequence_manager
2271	E4B_IMPL_CASTOP(multi_species_manager); // to_multi_species_manager
2272	E4B_IMPL_CASTOP(name_manager); // to_name_manager
2273	E4B_IMPL_CASTOP(orf_terminal); // to_orf_terminal
2274	E4B_IMPL_CASTOP(pure_text_terminal); // to_pure_text_terminal
2275	E4B_IMPL_CASTOP(root_group_manager); // to_root_group_manager
2276	E4B_IMPL_CASTOP(sequence_info_terminal); // to_sequence_info_terminal
2277	E4B_IMPL_CASTOP(sequence_manager); // to_sequence_manager
2278	E4B_IMPL_CASTOP(sequence_terminal); // to_sequence_terminal
2279	E4B_IMPL_CASTOP(spacer_terminal); // to_spacer_terminal
2280	E4B_IMPL_CASTOP(species_manager); // to_species_manager
2281	E4B_IMPL_CASTOP(species_name_terminal); // to_species_name_terminal
2282	E4B_IMPL_CASTOP(terminal); // to_terminal
2283	E4B_IMPL_CASTOP(text_terminal); // to_text_terminal
2284
2285	inline ED4_device_manager *ED4_root::get_device_manager() {
2286	return main_manager->search_spec_child_rek(ED4_L_DEVICE)->to_device_manager();
2287	}
2288
2289	inline ED4_species_name_terminal *ED4_multi_species_manager::get_consensus_name_terminal() const {
2290	ED4_species_manager *consensus_man = get_consensus_manager();
2291	return consensus_man ? consensus_man->get_name_terminal() : NULL;
2292	}
2293
2294	// --------------------------------------------
2295	// Prototype functions without a class
2296
2297	extern ST_ML *st_ml;
2298
2299	void ED4_with_all_edit_windows(void (cb)(ED4_window ));
2300
2301	void ED4_expose_recalculations();
2302	void ED4_calc_terminal_extentions();
2303
2304	void ED4_input_cb (AW_window *aww, AW_CL cd1, AW_CL cd2);
2305
2306	void ED4_remote_event(AW_event *faked_event);
2307
2308	void ED4_quit(AW_window *aww, AW_CL cd1, AW_CL cd2);
2309
2310	void ED4_motion_cb (AW_window *aww, AW_CL cd1, AW_CL cd2);
2311	void ED4_vertical_change_cb (AW_window *aww, AW_CL cd1, AW_CL cd2);
2312	void ED4_horizontal_change_cb (AW_window *aww, AW_CL cd1, AW_CL cd2);
2313	void ED4_scrollbar_change_cb (AW_window *aww, AW_CL cd1, AW_CL cd2);
2314
2315	void ED4_no_dangerous_modes ();
2316	void group_species_cb (AW_window *aww, AW_CL cd1, AW_CL cd2);
2317	AW_window ED4_create_group_species_by_field_window(AW_root aw_root);
2318
2319	void ED4_trigger_instant_refresh();
2320	void ED4_request_relayout();
2321	void ED4_request_full_refresh();
2322	void ED4_request_full_instant_refresh();
2323
2324	ARB_ERROR update_terminal_extension(ED4_base *this_object);
2325
2326	AW_window ED4_start_editor_on_old_configuration (AW_root awr);
2327	void ED4_restart_editor (AW_window *aww, AW_CL, AW_CL);
2328	void ED4_save_configuration (AW_window *aww, AW_CL close_flag);
2329	AW_window ED4_save_configuration_as_open_window (AW_root awr);
2330
2331	void ED4_set_iupac (AW_window aww, char awar_name, bool callback_flag);
2332	void ED4_set_helixnr (AW_window aww, char awar_name, bool callback_flag);
2333	void ed4_changesecurity (AW_root *root, AW_CL cd1);
2334	void ed4_change_edit_mode (AW_root *root, AW_CL cd1);
2335
2336	ARB_ERROR rebuild_consensus(ED4_base *object);
2337
2338	void ED4_exit() __ATTR__NORETURN;
2339
2340	void ED4_quit_editor (AW_window *aww, AW_CL cd1, AW_CL cd2); // Be Careful: Is this the last window?
2341
2342	void ED4_store_curpos (AW_window *aww, AW_CL cd1, AW_CL cd2);
2343	void ED4_restore_curpos (AW_window *aww, AW_CL cd1, AW_CL cd2);
2344	void ED4_clear_stored_curpos (AW_window *aww, AW_CL cd1, AW_CL cd2);
2345	void ED4_helix_jump_opposite (AW_window aww, AW_CL / cd1 /, AW_CL / cd2 */);
2346	void ED4_jump_to_cursor_position (AW_window *aww, AW_CL cl_awar_name, AW_CL cl_pos_type);
2347	void ED4_remote_set_cursor_cb (AW_root *awr, AW_CL, AW_CL);
2348	void ED4_change_cursor (AW_window * /* aww /, AW_CL / cd1 /, AW_CL / cd2 */);
2349	void ED4_set_reference_species (AW_window *aww, AW_CL cd1, AW_CL cd2);
2350
2351	void ED4_toggle_detailed_column_stats (AW_window *aww, AW_CL, AW_CL);
2352	void ED4_set_col_stat_threshold (AW_window *aww, AW_CL, AW_CL);
2353
2354	void ED4_new_editor_window (AW_window *aww, AW_CL cd1, AW_CL cd2);
2355
2356	AW_window ED4_create_consensus_definition_window (AW_root root);
2357	void ED4_create_consensus_awars (AW_root *aw_root);
2358	void ED4_consensus_definition_changed (AW_root*, AW_CL, AW_CL);
2359	void ED4_consensus_display_changed (AW_root*, AW_CL, AW_CL);
2360
2361	AW_window ED4_create_level_1_options_window (AW_root root);
2362	void ED4_compression_toggle_changed_cb (AW_root *root, AW_CL cd1, AW_CL cd2);
2363
2364	AW_window ED4_create_new_seq_window (AW_root root, AW_CL cl_creation_mode);
2365
2366	void ED4_jump_to_current_species (AW_window *, AW_CL);
2367	void ED4_get_and_jump_to_current (AW_window *, AW_CL);
2368	void ED4_get_and_jump_to_current_from_menu (AW_window *aw, AW_CL cl, AW_CL);
2369	void ED4_get_and_jump_to_species (GB_CSTR species_name);
2370	void ED4_get_marked_from_menu (AW_window *, AW_CL, AW_CL);
2371	void ED4_selected_species_changed_cb (AW_root *aw_root);
2372	void ED4_selected_SAI_changed_cb (AW_root *aw_root);
2373
2374	void ED4_init_notFoundMessage();
2375	void ED4_finish_and_show_notFoundMessage();
2376
2377	ED4_species_name_terminal ED4_find_species_name_terminal(const char species_name);
2378	ED4_multi_species_manager *ED4_new_species_multi_species_manager(); // returns manager into which new species should be inserted
2379
2380	void ED4_compression_changed_cb(AW_root *awr);
2381
2382	// functions passed to external c-functions (i.e. as callbacks) have to be declared as 'extern "C"'
2383
2384	extern "C" {
2385	void ED4_alignment_length_changed(GBDATA gb_alignment_len, int dummy, GB_CB_TYPE gbtype);
2386	}
2387
2388	struct AlignDataAccess;
2389	void ED4_init_aligner_data_access(AlignDataAccess *data_access);
2390
2391	#else
2392	#error ed4_class included twice
2393	#endif
2394

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