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source: branches/help/EDIT4/ed4_class.hxx

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Last change on this file was 18740, checked in by westram, 3 years ago
refactored edit4 column remapper: result of `compile()` now indicates whether mapping has changed (previously returned error which never was set). `mapping_changed` now handled in local variable (previously was stored in class member). changed several method/variable types (int→bool)
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 88.3 KB

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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_LIST
29	#include <list>
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	#ifndef CHARTABLE_H
41	#include "chartable.h"
42	#endif
43
44	#if defined(IMPLEMENT_DUMP) // ------------------------------
45
46	#if 0
47	#define WARN(msg) void dummy_to_produce_a_warning(int msg) {}
48	#else
49	#define WARN(msg)
50	#endif
51
52	#define EMPTY_FUNCTION(name) void name() const {}
53	#define EMPTY_FUNCTION_VERBOSE(name) void name(int je_mappelle_##name) const {}
54
55	#define DERIVABLEFROM(base) concat(prohibited_leafclass_derivation,base)
56
57	#define COMMON_FOR_BASES() \
58	virtual void dump(size_t indent) const = 0; \
59
60	#define COMMON_FOR_DERIVABLE(self) \
61	void dump_base(size_t indent) const; \
62	EMPTY_FUNCTION(DERIVABLEFROM(self)); \
63
64	#define COMMON_FOR_DERIVED(mybase) \
65	void dump_my_base(size_t indent) const { mybase::dump_base(indent); } \
66	virtual const char *baseclassname() const { return #mybase; } \
67
68	#define COMMON_FOR_INSTANCIABLE(mybase) \
69	void dump(size_t indent) const OVERRIDE; \
70
71	#define DECLARE_DUMP_FOR_ROOTCLASS(self) \
72	COMMON_FOR_BASES(); \
73	COMMON_FOR_DERIVABLE(self); \
74
75	#define DECLARE_DUMP_FOR_BASECLASS(self,mybase) \
76	COMMON_FOR_BASES(); \
77	COMMON_FOR_DERIVABLE(self); \
78	COMMON_FOR_DERIVED(mybase); \
79
80	#define DECLARE_DUMP_FOR_MIDCLASS(self,mybase) \
81	WARN(midclass_is_unwanted); \
82	COMMON_FOR_DERIVABLE(self); \
83	COMMON_FOR_DERIVED(mybase); \
84	COMMON_FOR_INSTANCIABLE(mybase); \
85
86	#define DECLARE_DUMP_FOR_LEAFCLASS(mybase) \
87	virtual void leaf() { DERIVABLEFROM(mybase)(); } \
88	COMMON_FOR_DERIVED(mybase); \
89	COMMON_FOR_INSTANCIABLE(mybase); \
90
91	#else
92	#define DECLARE_DUMP_FOR_ROOTCLASS(self)
93	#define DECLARE_DUMP_FOR_BASECLASS(self,mybase)
94	#define DECLARE_DUMP_FOR_MIDCLASS(self,mybase)
95	#define DECLARE_DUMP_FOR_LEAFCLASS(mybase)
96
97	#endif // IMPLEMENT_DUMP ------------------------------
98
99
100
101	// #define LIMIT_TOP_AREA_SPACE // if defined, top area is size-limited
102	#ifdef LIMIT_TOP_AREA_SPACE
103	#define MAX_TOP_AREA_SIZE 10 // size limit for top-area
104	#endif
105
106	#define ed4_beep() do { fputc(char(7), stdout); fflush(stdout); } while (0)
107
108	enum PositionType {
109	ED4_POS_SEQUENCE,
110	ED4_POS_ECOLI,
111	ED4_POS_BASE,
112	};
113
114	// ****************************************
115	// needed prototypes, definitions below
116	// ****************************************
117
118	class ED4_area_manager;
119	class ED4_abstract_group_manager;
120	class ED4_base;
121	class ED4_bracket_terminal;
122	class BaseFrequencies;
123	class ED4_columnStat_terminal;
124	class ED4_consensus_sequence_terminal;
125	class ED4_cursor;
126	class ED4_device_manager;
127	class ED4_folding_line;
128	class ED4_group_manager;
129	class ED4_line_terminal;
130	class ED4_main_manager;
131	class ED4_manager;
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_reference_terminals;
138	class ED4_remap;
139	class ED4_root;
140	class ED4_root_group_manager;
141	class ED4_sequence_info_terminal;
142	class ED4_sequence_manager;
143	class ED4_sequence_terminal;
144	class ED4_orf_terminal;
145	class ED4_spacer_terminal;
146	class ED4_species_manager;
147	class ED4_species_name_terminal;
148	class ED4_species_pointer;
149	class ED4_terminal;
150	class ED4_text_terminal;
151	class ED4_tree_terminal;
152	class ED4_flag_header_terminal;
153	class ED4_flag_terminal;
154	class ED4_window;
155
156	class AP_tree;
157	class ED4_reference;
158	class ED4_seq_colors;
159	class BI_ecoli_ref;
160	class AW_helix;
161	class arb_progress;
162	class ST_ML;
163	class ed_key;
164	class ConsensusBuildParams;
165
166	template <class T> class ED4_list; // derived from Noncopyable
167	template <class T> class ED4_list_elem; // derived from Noncopyable
168
169	typedef ED4_list<ED4_base> ED4_base_list;
170	typedef ED4_list_elem<ED4_base> ED4_base_list_elem;
171
172	typedef ED4_list<ED4_selection_entry> ED4_selected_list;
173	typedef ED4_list_elem<ED4_selection_entry> ED4_selected_elem;
174
175
176	namespace EDB_root_bact {
177	void calc_no_of_all(const char *string_to_scan, // group gets the number of groups in string_to_scan,
178	long *group, // species gets the number of species in string_to_scan
179	long *species);
180
181	ED4_returncode fill_species(ED4_multi_species_manager *multi_species_manager,
182	ED4_reference_terminals& refterms,
183	const char *str,
184	int *index,
185	int group_depth,
186	arb_progress *progress);
187
188	ED4_returncode fill_data(ED4_multi_species_manager *multi_species_manager,
189	ED4_reference_terminals& refterms,
190	char *str,
191	int group_depth,
192	ED4_datamode datamode); // flag only needed for loading a new configuration
193
194	ED4_returncode search_sequence_data_rek(ED4_multi_sequence_manager *multi_sequence_manager,
195	ED4_reference_terminals& refterms,
196	GBDATA *gb_ali_xxx, // alignment-container (or any subcontainer of)
197	int count_too,
198	ED4_index *max_sequence_terminal_length,
199	bool isSAI);
200
201	void scan_string(ED4_multi_species_manager *parent,
202	ED4_reference_terminals& refterms,
203	const char *str,
204	int *index,
205	arb_progress& progress);
206
207	void save_current_config(char *confname);
208	};
209
210	#define SPECIFIED_OBJECT_TYPES 23
211
212	class ED4_objspec : public Noncopyable {
213	static bool object_specs_initialized;
214	static bool descendants_uptodate;
215
216	mutable ED4_level used_children; // in any object of this type
217	mutable ED4_level possible_descendants; // below any object of this type (depends on used_children)
218	mutable ED4_level allowed_descendants; // below any object of this type (depends on allowed_children)
219
220	void calc_descendants() const;
221
222	public:
223	ED4_properties static_prop;
224	ED4_level level;
225	ED4_level allowed_children;
226	ED4_level handled_level;
227	ED4_level restriction_level;
228
229	ED4_objspec(ED4_properties static_prop_, ED4_level level_, ED4_level allowed_children_, ED4_level handled_level_, ED4_level restriction_level_);
230
231	#if defined(IMPLEMENT_DUMP)
232	void dump(size_t indent) const;
233	#endif // IMPLEMENT_DUMP
234
235	static void init_object_specs();
236
237	bool is_manager() const { return static_prop & PROP_IS_MANAGER; }
238	bool is_terminal() const { return static_prop & PROP_IS_TERMINAL; }
239
240	bool allowed_to_contain(ED4_level child_level) const {
241	// e4_assert(object_specs_initialized); // @@@ cant check here.. but where
242	e4_assert(is_manager()); // terminals can't contain anything - your test is senseless
243	return allowed_children & child_level;
244	}
245
246	void announce_added(ED4_level child_level) const {
247	e4_assert(allowed_to_contain(child_level));
248	used_children = ED4_level(used_children\|child_level);
249	descendants_uptodate = false;
250	}
251
252	static void recalc_descendants();
253
254	ED4_level get_possible_descendants() const {
255	e4_assert(is_manager());
256	if (!descendants_uptodate) recalc_descendants();
257	return possible_descendants;
258	}
259	ED4_level get_allowed_descendants() const { // (allowed = possible + those allowed to add, but not added anywhere)
260	e4_assert(is_manager());
261	if (!descendants_uptodate) recalc_descendants();
262	return allowed_descendants;
263	}
264	};
265
266	class ED4_folding_line : virtual Noncopyable {
267	AW_pos dimension; // amount of pixel folded away
268	AW_pos pos; // window position of folding line (x or y, only owner knows which coordinate is folded)
269	ED4_folding_line *next;
270
271	ED4_folding_line insert(ED4_folding_line fl) {
272	e4_assert(!fl->next);
273	if (pos <= fl->pos) { // insert behind
274	next = next ? next->insert(fl) : fl;
275	return this;
276	}
277
278	fl->next = this;
279	return fl;
280	}
281
282	public:
283
284	ED4_folding_line(AW_pos world, AW_pos dim) : dimension(dim), next(NULp) { set_pos(world-dimension); }
285
286	~ED4_folding_line() { delete next; }
287
288	void insertAs(ED4_folding_line*& ptr) {
289	ED4_folding_line *other = ptr;
290	e4_assert(knownNonNull(this));
291	ptr = other ? other->insert(this) : this;
292	}
293
294	ED4_folding_line delete_member(ED4_folding_line fl) {
295	ED4_folding_line *result = this;
296	if (this == fl) {
297	result = next;
298	next = NULp;
299	delete this;
300	}
301	return result;
302	}
303
304	AW_pos get_dimension() const { return dimension; }
305	const ED4_folding_line *get_next() const { return next; }
306
307	void warn_illegal_dimension();
308
309	void set_dimension(AW_pos dim) { dimension = dim; warn_illegal_dimension(); }
310	void add_to_dimension(AW_pos offset) { dimension += offset; warn_illegal_dimension(); }
311
312	void set_pos(AW_pos p) { pos = p; }
313	AW_pos get_pos() const { return pos; }
314
315	AW_pos win2world(AW_pos win) const {
316	if (win<pos) return win;
317	return (next ? next->win2world(win) : win)+dimension;
318	}
319	AW_pos world2win(AW_pos world) const {
320	if (world<pos) return world;
321	world -= dimension;
322	if (!next) return world;
323	return next->world2win(world);
324	}
325	};
326
327	struct ED4_scroll_links {
328	ED4_base *link_for_hor_slider;
329	ED4_base *link_for_ver_slider;
330
331	ED4_scroll_links() : link_for_hor_slider(NULp), link_for_ver_slider(NULp) {}
332	};
333
334	class ED4_foldable : virtual Noncopyable {
335	ED4_folding_line *horizontal_fl;
336	ED4_folding_line *vertical_fl;
337	protected:
338	void reset() {
339	delete horizontal_fl;
340	delete vertical_fl;
341	horizontal_fl = NULp;
342	vertical_fl = NULp;
343	}
344	bool is_reset() const { return !horizontal_fl && !vertical_fl; }
345	public:
346
347	ED4_foldable() : horizontal_fl(NULp), vertical_fl(NULp) {}
348	~ED4_foldable() { reset(); }
349
350	const ED4_folding_line *get_horizontal_folding() { return horizontal_fl; }
351	const ED4_folding_line *get_vertical_folding() { return vertical_fl; }
352
353	void world_to_win_coords(AW_pos xPtr, AW_pos yPtr) const { // @@@ old style
354	// Calculates transformation from world to window coordinates in a given window.
355	// world-coordinates inside folded range result in window coordinates lower than folding line position.
356	e4_assert(!is_reset());
357	xPtr = vertical_fl->world2win(xPtr);
358	yPtr = horizontal_fl->world2win(yPtr);
359	}
360	void win_to_world_coords(AW_pos xPtr, AW_pos yPtr) const { // @@@ old style
361	// calculates transformation from window to world coordinates in a given window
362	e4_assert(!is_reset());
363	xPtr = vertical_fl->win2world(xPtr);
364	yPtr = horizontal_fl->win2world(yPtr);
365	}
366
367	AW::Position world_to_win_coords(const AW::Position& pos) const {
368	e4_assert(!is_reset());
369	return AW::Position(vertical_fl->world2win(pos.xpos()),
370	horizontal_fl->world2win(pos.ypos()));
371	}
372	AW::Position win_to_world_coords(const AW::Position& pos) const {
373	e4_assert(!is_reset());
374	return AW::Position(vertical_fl->win2world(pos.xpos()),
375	horizontal_fl->win2world(pos.ypos()));
376	}
377
378	ED4_folding_line *insert_folding_line(AW_pos pos, AW_pos dimension, ED4_properties prop);
379	void delete_folding_line(ED4_folding_line *fl, ED4_properties prop);
380	};
381
382
383	class ED4_scrolled_rectangle : virtual Noncopyable {
384	ED4_folding_line *scroll_bottom;
385	ED4_folding_line *scroll_right;
386	ED4_folding_line *scroll_top;
387	ED4_folding_line *scroll_left;
388
389	ED4_base *x_link;
390	ED4_base *y_link;
391	ED4_base *width_link;
392	ED4_base *height_link;
393
394	AW::Rectangle world;
395
396	bool folding_dimensions_calculated; // flag to ensure calc_bottomRight_folding_dimensions is called before get_window_rect
397
398	void init_links() {
399	x_link = NULp;
400	y_link = NULp;
401	width_link = NULp;
402	height_link = NULp;
403	}
404
405	void init_folding_lines() {
406	scroll_top = NULp;
407	scroll_bottom = NULp;
408	scroll_left = NULp;
409	scroll_right = NULp;
410
411	folding_dimensions_calculated = false;
412	}
413	void init_pos_size() { world = AW::Rectangle(AW::Origin, AW::ZeroVector); }
414
415	void init() {
416	init_folding_lines();
417	init_pos_size();
418	init_links();
419	}
420
421	void update_folding_line_positions() {
422	scroll_top->set_pos(world.top());
423	scroll_left->set_pos(world.left());
424	}
425
426	public:
427
428	ED4_scrolled_rectangle() { init(); }
429
430	AW_pos bottom() const { return world.bottom(); }
431	AW_pos right() const { return world.right(); }
432
433	void reset(ED4_foldable& owner) {
434	destroy_folding_lines(owner);
435	init_pos_size();
436	}
437
438	AW_pos top_dim() const { return scroll_top->get_dimension(); }
439	AW_pos left_dim() const { return scroll_left->get_dimension(); }
440
441	bool exists() const { return scroll_top && scroll_bottom && scroll_left && scroll_right; }
442	bool is_linked() const {
443	if (x_link) {
444	e4_assert(y_link);
445	e4_assert(width_link);
446	e4_assert(height_link);
447	return true;
448	}
449	e4_assert(!y_link);
450	e4_assert(!width_link);
451	e4_assert(!height_link);
452	return false;
453	}
454	void link(ED4_base x, ED4_base y, ED4_base w, ED4_base h) {
455	e4_assert(x && y && w && h);
456
457	x_link = x;
458	y_link = y;
459	width_link = w;
460	height_link = h;
461	}
462
463	void replace_x_width_link_to(ED4_base old_link, ED4_base new_link) {
464	if (x_link == old_link) x_link = new_link;
465	if (width_link == old_link) width_link = new_link;
466	}
467
468	void add_to_top_left_dimension(int dx, int dy) {
469	scroll_left->add_to_dimension(dx);
470	scroll_top->add_to_dimension(dy);
471	}
472
473	void scroll(int dx, int dy) {
474	scroll_left->add_to_dimension(-dx);
475	scroll_top->add_to_dimension(-dy);
476	scroll_right->add_to_dimension(dx);
477	scroll_bottom->add_to_dimension(dy);
478	}
479
480	AW::Rectangle get_window_rect() const {
481	e4_assert(folding_dimensions_calculated);
482	return AW::Rectangle(scroll_left->get_pos(), scroll_top->get_pos(),
483	scroll_right->get_pos(), scroll_bottom->get_pos());
484	}
485
486	AW::Rectangle get_world_rect() const;
487
488	void set_rect(const AW::Rectangle& rect) { world = rect; }
489	void set_rect_and_update_folding_line_positions(const AW::Rectangle& rect) {
490	set_rect(rect);
491	update_folding_line_positions();
492	}
493
494	void calc_bottomRight_folding_dimensions(int area_width, int area_height) {
495	area_width -= SLIDER_OFFSET;
496	area_height -= SLIDER_OFFSET;
497
498	AW_pos dim;
499	if (bottom() > area_height) { // our world doesn't fit vertically in our window
500	dim = bottom()-area_height; // calc dimension of both horizontal folding lines
501	scroll_top->set_dimension(std::min(dim, scroll_top->get_dimension()));
502	scroll_bottom->set_dimension(std::max(0, int(dim - scroll_top->get_dimension())));
503	}
504	else {
505	dim = 0;
506	scroll_bottom->set_dimension(0);
507	scroll_top->set_dimension(0);
508	}
509
510	e4_assert(dim == (scroll_top->get_dimension()+scroll_bottom->get_dimension()));
511	scroll_bottom->set_pos(world.bottom()-dim+SLIDER_OFFSET);
512
513	if (right()>area_width) { // our world doesn't fit horizontally in our window
514	dim = right()-area_width; // calc dimension of both vertical folding lines
515	scroll_left->set_dimension(std::min(dim, scroll_left->get_dimension()));
516	scroll_right->set_dimension(std::max(0, int(dim - scroll_left->get_dimension())));
517	}
518	else {
519	dim = 0;
520	scroll_right->set_dimension(0);
521	scroll_left->set_dimension(0);
522	}
523
524	e4_assert(dim == (scroll_left->get_dimension()+scroll_right->get_dimension()));
525	scroll_right->set_pos(world.right()-dim+SLIDER_OFFSET);
526
527	folding_dimensions_calculated = true;
528	}
529
530	void create_folding_lines(ED4_foldable& owner, const AW::Rectangle& rect, int area_width, int area_height) {
531	scroll_top = owner.insert_folding_line(rect.top(), 0, PROP_HORIZONTAL);
532	scroll_left = owner.insert_folding_line(rect.left(), 0, PROP_VERTICAL);
533
534	AW_pos dim = 0;
535	if (rect.bottom() > area_height) dim = rect.bottom() - area_height;
536	scroll_bottom = owner.insert_folding_line(rect.bottom(), dim, PROP_HORIZONTAL);
537
538	dim = 0;
539	if (rect.right() > area_width) dim = rect.right() - area_width;
540	scroll_right = owner.insert_folding_line(rect.right(), dim, PROP_VERTICAL);
541	}
542
543	void destroy_folding_lines(ED4_foldable& owner) {
544	if (scroll_top) owner.delete_folding_line(scroll_top, PROP_HORIZONTAL);
545	if (scroll_bottom) owner.delete_folding_line(scroll_bottom, PROP_HORIZONTAL);
546	if (scroll_left) owner.delete_folding_line(scroll_left, PROP_VERTICAL);
547	if (scroll_right) owner.delete_folding_line(scroll_right, PROP_VERTICAL);
548
549	init_folding_lines();
550	}
551	};
552
553	class ED4_base_position : private BasePosition { // derived from a Noncopyable
554	const ED4_terminal *calced4term; // if calced4term => callback is bound to its species manager
555	bool needUpdate;
556
557	void calc4term(const ED4_terminal *term);
558	void set_term(const ED4_terminal *term) {
559	if (calced4term != term \|\| needUpdate) {
560	calc4term(term);
561	}
562	}
563	void remove_changed_cb();
564
565	public:
566
567	ED4_base_position()
568	: calced4term(NULp),
569	needUpdate(true)
570	{}
571
572	~ED4_base_position() {
573	remove_changed_cb();
574	}
575
576	void invalidate() {
577	needUpdate = true;
578	}
579
580	void announce_deletion(const ED4_terminal *term) {
581	if (term == calced4term) {
582	invalidate();
583	remove_changed_cb();
584	}
585	e4_assert(calced4term != term);
586	}
587	void prepare_shutdown() {
588	if (calced4term) announce_deletion(calced4term);
589	}
590
591	int get_base_position(const ED4_terminal *base, int sequence_position);
592	int get_sequence_position(const ED4_terminal *base, int base_position);
593
594	int get_base_count(const ED4_terminal *term) { set_term(term); return base_count(); }
595	int get_abs_len(const ED4_terminal *term) { set_term(term); return abs_count(); }
596	};
597
598	class ED4_CursorShape;
599
600
601	enum ED4_CursorType {
602	ED4_RIGHT_ORIENTED_CURSOR,
603	ED4_RIGHT_ORIENTED_CURSOR_THIN,
604	ED4_TRADITIONAL_CURSOR,
605	ED4_TRADITIONAL_CURSOR_BOTTOM,
606	ED4_TRADITIONAL_CURSOR_CONNECTED,
607	ED4_FUCKING_BIG_CURSOR,
608
609	ED4_CURSOR_TYPES
610
611	};
612
613	struct ED4_TerminalPredicate {
614	virtual ~ED4_TerminalPredicate() {}
615	virtual bool fulfilled_by(const ED4_terminal *) const = 0;
616	};
617
618	class ED4_WinContextFree { // denies usage of the following functions in classes derived from this
619	AW_device *current_device();
620	ED4_window *current_ed4w();
621	AW_window *current_aww();
622	ED4_cursor& current_cursor();
623	public:
624	void avoid_warning() {}
625	};
626
627	class ED4_cursor : virtual Noncopyable, virtual ED4_WinContextFree {
628	ED4_window *win;
629	ED4_index cursor_abs_x; // absolute (to terminal) x-position of cursor (absolute world coordinate of edit window)
630	int screen_position; // number of displayed characters leading the cursor
631	mutable ED4_base_position base_position; // # of bases left of cursor
632	ED4_CursorType ctype;
633	ED4_CursorShape *cursor_shape;
634
635	ED4_returncode draw_cursor(AW_pos x, AW_pos y);
636	ED4_returncode delete_cursor(AW_pos del_mark, ED4_base *target_terminal);
637
638	void updateAwars(bool new_term_selected);
639
640	public:
641
642	bool allowed_to_draw; // needed for cursor handling
643	ED4_terminal *owner_of_cursor;
644
645	bool is_partly_visible() const;
646	bool is_completely_visible() const;
647
648	bool is_hidden_inside_group() const;
649
650	void changeType(ED4_CursorType typ);
651	ED4_CursorType getType() const { return ctype; }
652
653	void redraw() { changeType(getType()); }
654
655	ED4_returncode HideCursor(); // deletes cursor and does refresh
656	ED4_returncode move_cursor(AW_event *event);
657	ED4_returncode show_clicked_cursor(AW_pos click_xpos, ED4_terminal *target_terminal);
658	ED4_returncode show_cursor_at(ED4_terminal *target_terminal, ED4_index what_pos);
659	ED4_returncode ShowCursor(ED4_index offset_x, ED4_cursor_move move, int move_pos = 1);
660
661	int get_sequence_pos() const;
662	int get_screen_pos() const { return screen_position; }
663
664	long get_abs_x() const { return cursor_abs_x; }
665	void set_abs_x();
666
667	int base2sequence_position(int base_pos) const { return base_position.get_sequence_position(owner_of_cursor, base_pos); }
668	int sequence2base_position(int seq_pos) const { return base_position.get_base_position(owner_of_cursor, seq_pos); }
669
670	int get_base_position() const { return sequence2base_position(get_sequence_pos()); }
671
672	void prepare_shutdown() { base_position.prepare_shutdown(); }
673
674	void jump_screen_pos(int screen_pos, ED4_CursorJumpType jump_type);
675	void jump_sequence_pos(int sequence_pos, ED4_CursorJumpType jump_type);
676	void jump_base_pos(int base_pos, ED4_CursorJumpType jump_type);
677
678	int get_screen_relative_pos() const;
679	void set_screen_relative_pos(int scroll_to_relpos);
680
681	void set_to_terminal(ED4_terminal *terminal, int seq_pos, ED4_CursorJumpType jump_type);
682
683	inline bool in_species_seq_terminal() const;
684	inline bool in_consensus_terminal() const;
685	inline bool in_SAI_terminal() const;
686
687	void announce_deletion(ED4_terminal *object) {
688	base_position.announce_deletion(object);
689	if (object == owner_of_cursor) owner_of_cursor = NULp; // no need to delete the cursor (deletion triggers full redraw)
690	}
691
692	void init();
693
694	ED4_window *window() const { return win; }
695
696	ED4_cursor(ED4_window *win);
697	~ED4_cursor();
698	};
699
700	class ED4_window : public ED4_foldable, virtual ED4_WinContextFree { // derived from Noncopyable
701	void set_scrollbar_indents();
702
703	public:
704	AW_window_menu_modes *aww; // Points to Window
705	ED4_window *next;
706	int slider_pos_horizontal;
707	int slider_pos_vertical;
708	ED4_scrolled_rectangle scrolled_rect;
709	int id; // unique id in window-list
710	ED4_coords coords;
711
712	static int no_of_windows;
713
714	char awar_path_for_cursor[50]; // position in current sequence, range = [1;len]
715	char awar_path_for_Ecoli[50]; // position relative to ecoli
716	char awar_path_for_basePos[50]; // base position in current sequence (# of bases left to cursor)
717	char awar_path_for_IUPAC[50]; // IUPAC decoder content for current position
718	char awar_path_for_helixNr[50]; // # of helix (or 0) for current position
719
720	bool is_hidden;
721	ED4_cursor cursor;
722
723	// ED4_window controlling functions
724	static ED4_window insert_window(AW_window_menu_modes new_aww); // append to window list
725
726	void delete_window(ED4_window *window); // delete from window list
727	void reset_all_for_new_config(); // reset structures for loading new config
728	ED4_window get_matching_ed4w(AW_window aww);
729
730	void announce_deletion(ED4_terminal *object) { cursor.announce_deletion(object); }
731
732	// functions concerned the scrolled area
733	void update_scrolled_rectangle();
734	ED4_returncode scroll_rectangle(int dx, int dy);
735	ED4_returncode set_scrolled_rectangle(ED4_base x_link, ED4_base y_link, ED4_base width_link, ED4_base height_link);
736
737	bool scrollbars_and_scrolledRect_inSync() const {
738	// Scrolling in EDIT4 window uses redundant data
739	// - dimension of folding lines
740	// - slider positions in AW_window and ED4_window
741	// This function checks whether they are in sync.
742
743	bool inSync =
744	(scrolled_rect.top_dim() == aww->slider_pos_vertical) &&
745	(scrolled_rect.left_dim() == aww->slider_pos_horizontal);
746
747	#if defined(DEBUG)
748	if (!inSync) {
749	fputs("scrollbars not in sync with scrolled_rect:\n", stderr);
750	fprintf(stderr, " aww->slider_pos_vertical =%i scrolled_rect->top_dim() =%f\n", aww->slider_pos_vertical, scrolled_rect.top_dim());
751	fprintf(stderr, " aww->slider_pos_horizontal=%i scrolled_rect->left_dim()=%f\n", aww->slider_pos_horizontal, scrolled_rect.left_dim());
752	}
753	#endif
754
755	return inSync;
756	}
757
758	void check_valid_scrollbar_values() { e4_assert(scrollbars_and_scrolledRect_inSync()); }
759
760	bool shows_xpos(int x) const { return x >= coords.window_left_clip_point && x <= coords.window_right_clip_point; }
761	bool partly_shows(int x1, int y1, int x2, int y2) const;
762	bool completely_shows(int x1, int y1, int x2, int y2) const;
763
764	void update_window_coords();
765
766	AW_device *get_device() const { return aww->get_device(AW_MIDDLE_AREA); }
767
768	ED4_window(AW_window_menu_modes *window);
769	~ED4_window();
770	};
771
772	class ED4_container : virtual Noncopyable {
773	// contains children of a manager
774
775	ED4_base **memberList;
776	ED4_index no_of_members; // How much members are in the list
777	ED4_index size_of_list; // allocated size
778
779	void correct_insert_position(ED4_index& index);
780	void resize(ED4_index needed_size);
781
782	void shift_list(ED4_index start_index, int length);
783
784	protected:
785
786	bool valid_index(ED4_index idx) const { return idx >= 0 && idx<size_of_list; }
787	bool existing_index(ED4_index idx) const { return idx >= 0 && idx<no_of_members; }
788
789	public:
790
791	ED4_manager owner() { return DOWNCAST(ED4_manager, this); }
792	const ED4_manager owner() const { return const_cast<ED4_container>(this)->owner(); }
793
794	ED4_base* member(ED4_index i) const { e4_assert(i>=0 && i<size_of_list); return memberList[i]; }
795
796	ED4_index members() const { return no_of_members; }
797	bool empty() const { return !members(); }
798	void clear();
799
800	void insert_member(ED4_base *new_member); // only used to move members with mouse
801	void append_member(ED4_base *new_member);
802
803	// an array is chosen instead of a linked list, because destructorhandling is more comfortable in various destructors (manager-destructors)
804
805	ED4_returncode remove_member(ED4_base *member);
806	ED4_index search_member(ED4_extension *location, ED4_properties prop); // search member
807
808	ED4_returncode search_target_species(ED4_extension location, ED4_properties prop, ED4_base *found_member, ED4_level return_level);
809
810	ED4_returncode move_member(ED4_index old_pos, ED4_index new_pos);
811
812	#if defined(IMPLEMENT_DUMP)
813	void dump_container(size_t indent) const;
814	#endif // IMPLEMENT_DUMP
815
816	#if defined(ASSERTION_USED)
817	bool members_ok() const;
818	#endif // ASSERTION_USED
819
820	ED4_container();
821	virtual ~ED4_container();
822	};
823
824	// ----------------------------
825	// ED4_species_pointer
826
827	class ED4_species_pointer : virtual Noncopyable {
828	// @@@ shall be renamed into ED4_gbdata_pointer to reflect general usage
829
830	GBDATA *species_pointer; // points to database
831
832	void addCallback(ED4_base *base);
833	void removeCallback(ED4_base *base);
834
835	public:
836
837	ED4_species_pointer();
838	~ED4_species_pointer();
839
840	GBDATA *Get() const { return species_pointer; }
841	void Set(GBDATA gbd, ED4_base base);
842	void notify_deleted() {
843	species_pointer=NULp;
844	}
845	};
846
847	// ------------------------
848	// callback types
849
850	template <class BASE, class BASECB>
851	class ED4_cb_list {
852	std::list<BASECB> callbacks;
853	public:
854	#if defined(ASSERTION_USED)
855	ED4_cb_list() {}
856	~ED4_cb_list() {
857	e4_assert(empty()); // calling ED4_root::remove_all_callbacks() did not remove all callbacks!
858	}
859	#endif
860	void add_cb(BASECB cb) { callbacks.push_back(cb); }
861	void remove_cb(BASECB cb) { callbacks.remove(cb); }
862
863	void call(BASE *b) {
864	for (typename std::list<BASECB>::iterator cb = callbacks.begin(); cb != callbacks.end();) {
865	typename std::list<BASECB>::iterator curr = cb;
866	++cb;
867	(*curr)(b); // Note: may be removed while called
868	}
869	}
870	void clear() { callbacks.clear(); }
871	bool empty() const { return callbacks.empty(); }
872	};
873
874	// declare callback types used in ED4_cb_list:
875	DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_managerCallback, void, ED4_manager*); // generates makeED4_managerCallback
876	DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_species_managerCallback, void, ED4_species_manager*); // generates makeED4_species_managerCallback
877
878	// -----------------
879	// ED4_base
880
881	class ED4_base;
882
883	DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_route_cb, ARB_ERROR, ED4_base*); // generates makeED4_route_cb
884
885	enum ED4_species_type {
886	ED4_SP_NONE,
887	ED4_SP_SPECIES,
888	ED4_SP_SAI,
889	ED4_SP_CONSENSUS,
890	};
891
892	class ED4_base : virtual Noncopyable {
893	// base object
894
895	ED4_species_pointer my_species_pointer;
896
897	// cache world coordinates:
898
899	static int currTimestamp;
900	mutable AW::Position lastPos;
901	mutable int timestamp;
902
903	ED4_base_list *linked_objects; // linked list of objects which are depending from this object
904
905	virtual bool set_dynamic_size() {
906	// default behavior: keep size
907	// (overload to implement dynamic sizing; also set static_prop!)
908	e4_assert(!(spec.static_prop & PROP_DYNA_RESIZE)); // forgot to overload set_dynamic_size?
909	return false; // = "nothing changed"
910	}
911
912	public:
913	const ED4_objspec& spec; // contains information about Objectproperties
914
915	ED4_manager *parent; // Points to parent
916
917
918	ED4_properties dynamic_prop; // contains info about what i am, what i can do, what i should do
919	char *id; // globally unique name in hierarchy
920	ED4_index index; // defines the order of child objects
921	ED4_base *width_link; // concerning the hierarchy
922	ED4_base *height_link; // concerning the hierarchy
923	ED4_extension extension; // contains relative info about graphical properties
924	ED4_update_info update_info; // info about things to be done for the object, i.e. refresh; flag structure
925	struct {
926	unsigned int hidden : 1; // flag whether object is hidden or not
927	} flag;
928
929	void draw_bb(int color);
930
931	DECLARE_DUMP_FOR_ROOTCLASS(ED4_base);
932
933	// function for species_pointer
934	//
935	// Notes:
936	//
937	// * design is broken @@@
938	// - my_species_pointer should be member of those derived classes, where it's used
939	// - accessor functions should tell what we get (eg. ED4_species_name_terminal::get_name_entry() or similar)
940	//
941	// * current uses of my_species_pointer (grepped for 'set_species_pointer' to detect):
942	// - ED4_species_manager [holds pointer to] species/SAI container
943	// - ED4_species_name_terminal [holds pointer to] the 'name' entry of species/SAI
944	// - ED4_sequence_info_terminal [holds pointer to] the displayed sub-entry of the alignment-container of species/SAI (multiple may exist per species)
945	// - ED4_text_terminal [holds pointer to] same as ED4_sequence_info_terminal (Caution: not true for all text terminals!)
946
947	GBDATA *get_species_pointer() const { return my_species_pointer.Get(); }
948	void set_species_pointer(GBDATA *gbd) { my_species_pointer.Set(gbd, this); }
949	bool has_callback() const { return get_species_pointer(); }
950
951	// callbacks
952
953	virtual void changed_by_database();
954	virtual void deleted_from_database();
955
956	// functions concerned with graphic output
957	int adjust_clipping_rectangle();
958	virtual void Show(bool refresh_all, bool is_cleared) = 0;
959
960	virtual bool calc_bounding_box() = 0;
961	void resize_dynamic() {
962	if (set_dynamic_size()) {
963	e4_assert(has_property(PROP_DYNA_RESIZE)); // object dynamically changed size (but isn't allowed to!)
964	request_resize();
965	}
966	}
967
968	ED4_returncode clear_background(int color=0);
969
970	void set_links(ED4_base width_ref, ED4_base height_ref);
971	void set_both_links(ED4_base *ref) { set_links(ref, ref); }
972
973	// functions concerned with special initialization
974	void set_property(ED4_properties prop) { dynamic_prop = (ED4_properties) (dynamic_prop \| prop); }
975	void clr_property(ED4_properties prop) { dynamic_prop = (ED4_properties) (dynamic_prop & ~prop); }
976	bool has_property(ED4_properties prop) const { return dynamic_prop & prop; }
977
978	// functions concerned with coordinate transformation
979
980	void calc_rel_coords(AW_pos x, AW_pos y);
981
982	void calc_world_coords(AW_pos x, AW_pos y) const {
983	update_world_coords_cache();
984	*x = lastPos.xpos();
985	*y = lastPos.ypos();
986	}
987	const AW::Position& calc_world_coords() const {
988	update_world_coords_cache();
989	return lastPos;
990	}
991
992	void update_world_coords_cache() const {
993	bool cache_up_to_date = timestamp == currTimestamp;
994	if (!cache_up_to_date) {
995	if (parent) {
996	ED4_base pab = (ED4_base)parent;
997	lastPos = pab->calc_world_coords();
998	}
999	else {
1000	lastPos = AW::Origin;
1001	}
1002	lastPos.move(extension.get_parent_offset());
1003	timestamp = currTimestamp;
1004	}
1005	}
1006
1007	static void touch_world_cache() {
1008	currTimestamp++;
1009	}
1010
1011	AW::Rectangle get_win_area(ED4_window *ed4w) const {
1012	AW::Position pos = ed4w->world_to_win_coords(calc_world_coords());
1013	return AW::Rectangle(pos, extension.get_size()-AW::Vector(1, 1));
1014	}
1015
1016	// functions which refer to the object as a child, i.e. travelling down the hierarchy
1017	virtual void request_refresh(int clear=1) = 0;
1018
1019	inline void request_resize();
1020	void request_resize_of_linked();
1021	void resize_requested_by_link(ED4_base *link);
1022	virtual void resize_requested_children() = 0;
1023
1024	virtual void delete_requested_children() = 0;
1025	virtual void Delete() = 0;
1026
1027	inline void set_update();
1028	virtual void update_requested_children() = 0;
1029
1030	virtual ED4_returncode event_sent_by_parent(AW_event event, AW_window aww) = 0;
1031
1032	virtual ARB_ERROR route_down_hierarchy(const ED4_route_cb& cb);
1033
1034	int calc_group_depth();
1035
1036	// general purpose functions
1037	virtual ED4_base search_ID(const char id) = 0;
1038
1039	void check_all();
1040	short in_border(AW_pos abs_x, AW_pos abs_y, ED4_movemode mode);
1041	ED4_returncode set_width();
1042
1043
1044	ED4_AREA_LEVEL get_area_level(ED4_multi_species_manager **multi_species_manager=NULp) const; // returns area we belong to and the next multi species manager of the area
1045
1046	inline ED4_manager *get_parent(ED4_level lev) const;
1047	void unlink_from_parent();
1048	bool has_parent(ED4_manager *Parent);
1049	bool is_child_of(ED4_manager *Parent) { return has_parent(Parent); }
1050
1051	virtual char resolve_pointer_to_string_copy(int str_len = NULp) const;
1052	virtual const char resolve_pointer_to_char_pntr(int str_len = NULp) const;
1053
1054	ED4_group_manager *is_in_folded_group() const;
1055	virtual bool is_hidden() const = 0;
1056
1057	char *get_name_of_species(); // go from terminal to name of species
1058
1059	// functions which refer to the selected object(s), i.e. across the hierarchy
1060
1061	ED4_terminal *get_next_terminal();
1062	ED4_terminal *get_prev_terminal();
1063
1064	void generate_configuration_string(GBS_strstruct& buffer);
1065
1066	virtual void remove_callbacks() = 0;
1067
1068	const ED4_terminal *get_consensus_relevant_terminal() const;
1069
1070	ED4_base(const ED4_objspec& spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
1071	virtual ~ED4_base();
1072
1073	// use the following functions to test which derived class we have
1074
1075	int is_terminal() const { e4_assert(knownNonNull(this)); return spec.static_prop & PROP_IS_TERMINAL; }
1076
1077	int is_text_terminal() const { e4_assert(knownNonNull(this)); return spec.level & (LEV_SPECIES_NAME\|LEV_SEQUENCE_INFO\|LEV_SEQUENCE_STRING\|LEV_PURE_TEXT\|LEV_COL_STAT); }
1078
1079	int is_species_name_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SPECIES_NAME; }
1080
1081	int is_sequence_info_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SEQUENCE_INFO; }
1082	int is_sequence_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SEQUENCE_STRING; }
1083	int is_orf_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_ORF; }
1084
1085	int is_pure_text_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_PURE_TEXT; }
1086	int is_columnStat_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_COL_STAT; }
1087
1088	int is_bracket_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_BRACKET; }
1089	int is_spacer_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SPACER; }
1090	int is_line_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_LINE; }
1091
1092	int is_flag_header_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_FLAG_HEADER; }
1093	int is_flag_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_FLAG; }
1094
1095	int is_manager() const { e4_assert(knownNonNull(this)); return spec.static_prop & PROP_IS_MANAGER; }
1096
1097	int is_sequence_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SEQUENCE; }
1098	int is_multi_name_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_MULTI_NAME; }
1099	int is_name_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_NAME_MANAGER; }
1100	int is_multi_species_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_MULTI_SPECIES; }
1101	int is_multi_sequence_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_MULTI_SEQUENCE; }
1102	int is_device_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_DEVICE; }
1103
1104	int is_group_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_GROUP; }
1105	int is_root_group_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_ROOTGROUP; }
1106	int is_abstract_group_manager() const { e4_assert(knownNonNull(this)); return spec.level & (LEV_GROUP\|LEV_ROOTGROUP); }
1107
1108	int is_species_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SPECIES; }
1109	int is_area_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_AREA; }
1110
1111	// use the following functions to cast ED4_base to derived classes:
1112
1113	#define E4B_DECL_CASTOP_helper(Class,toName) \
1114	inline const Class *toName() const; \
1115	inline Class *toName();
1116
1117	#define E4B_AVOID_CAST__helper(Class,toName,isName) \
1118	const Class *toName() const; \
1119	Class *toName(); \
1120	int isName() const;
1121
1122	#define E4B_IMPL_CASTOP_helper(Class,toName,isName) \
1123	const Class *ED4_base::toName() const { \
1124	e4_assert(isName()); \
1125	return DOWNCAST(const Class*, this); \
1126	} \
1127	Class *ED4_base::toName() { \
1128	return const_cast<Class>(const_cast<const ED4_base>(this)->toName()); \
1129	}
1130
1131	#define E4B_DECL_CASTOP(name) E4B_DECL_CASTOP_helper(concat(ED4_,name), concat(to_,name))
1132	#define E4B_AVOID_UNNEEDED_CASTS(name) E4B_AVOID_CAST__helper(concat(ED4_,name), concat(to_,name), concat(is_,name))
1133	#define E4B_IMPL_CASTOP(name) E4B_IMPL_CASTOP_helper(concat(ED4_,name), concat(to_,name), concat(is_,name))
1134
1135	E4B_DECL_CASTOP(area_manager); // to_area_manager
1136	E4B_DECL_CASTOP(abstract_group_manager); // to_abstract_group_manager
1137	E4B_DECL_CASTOP(bracket_terminal); // to_bracket_terminal
1138	E4B_DECL_CASTOP(columnStat_terminal); // to_columnStat_terminal
1139	E4B_DECL_CASTOP(consensus_sequence_terminal); // to_consensus_sequence_terminal
1140	E4B_DECL_CASTOP(device_manager); // to_device_manager
1141	E4B_DECL_CASTOP(group_manager); // to_group_manager
1142	E4B_DECL_CASTOP(line_terminal); // to_line_terminal
1143	E4B_DECL_CASTOP(manager); // to_manager
1144	E4B_DECL_CASTOP(multi_name_manager); // to_multi_name_manager
1145	E4B_DECL_CASTOP(multi_sequence_manager); // to_multi_sequence_manager
1146	E4B_DECL_CASTOP(multi_species_manager); // to_multi_species_manager
1147	E4B_DECL_CASTOP(name_manager); // to_name_manager
1148	E4B_DECL_CASTOP(orf_terminal); // to_orf_terminal
1149	E4B_DECL_CASTOP(pure_text_terminal); // to_pure_text_terminal
1150	E4B_DECL_CASTOP(root_group_manager); // to_root_group_manager
1151	E4B_DECL_CASTOP(sequence_info_terminal); // to_sequence_info_terminal
1152	E4B_DECL_CASTOP(sequence_manager); // to_sequence_manager
1153	E4B_DECL_CASTOP(sequence_terminal); // to_sequence_terminal
1154	E4B_DECL_CASTOP(spacer_terminal); // to_spacer_terminal
1155	E4B_DECL_CASTOP(species_manager); // to_species_manager
1156	E4B_DECL_CASTOP(species_name_terminal); // to_species_name_terminal
1157	E4B_DECL_CASTOP(terminal); // to_terminal
1158	E4B_DECL_CASTOP(text_terminal); // to_text_terminal
1159	E4B_DECL_CASTOP(flag_header_terminal); // to_flag_header_terminal
1160	E4B_DECL_CASTOP(flag_terminal); // to_flag_terminal
1161
1162	// simple access to containing managers
1163	inline ED4_species_manager *containing_species_manager() const;
1164
1165	// discriminate between different sequence managers:
1166
1167	inline bool is_consensus_manager() const;
1168	inline bool is_SAI_manager() const;
1169	inline bool is_species_seq_manager() const;
1170
1171	inline ED4_species_type get_species_type() const; // works for all items (recursively) contained in ED4_species_manager
1172
1173	inline bool inside_consensus_manager() const;
1174	inline bool inside_SAI_manager() const;
1175	inline bool inside_species_seq_manager() const;
1176
1177	inline bool is_consensus_terminal() const;
1178	inline bool is_SAI_terminal() const;
1179	inline bool is_species_seq_terminal() const;
1180
1181	inline bool is_consensus_sequence_terminal() const { // alias for CASTOP
1182	return is_consensus_terminal();
1183	}
1184	};
1185	MARK_NONFINAL_FUNCTION(ED4_base,bool,set_dynamic_size,(),false);
1186
1187	DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_basePredicate, bool, ED4_base*); // generates makeED4_basePredicate
1188
1189	class ED4_manager : public ED4_base, public ED4_container { // derived from a Noncopyable
1190	ED4_cb_list<ED4_manager, ED4_managerCallback> delete_cbs;
1191	public:
1192
1193	E4B_AVOID_UNNEEDED_CASTS(manager);
1194	DECLARE_DUMP_FOR_BASECLASS(ED4_manager, ED4_base);
1195
1196	void add_delete_callback(const ED4_managerCallback& cb) { delete_cbs.add_cb(cb); }
1197	void remove_delete_callback(const ED4_managerCallback& cb) { delete_cbs.remove_cb(cb); }
1198
1199	int refresh_flag_ok();
1200
1201	void changed_by_database() OVERRIDE;
1202	void deleted_from_database() OVERRIDE;
1203
1204	// functions concerned with graphics
1205	void Show(bool refresh_all, bool is_cleared) OVERRIDE;
1206	bool calc_bounding_box() FINAL_OVERRIDE;
1207
1208	ED4_returncode distribute_children();
1209
1210	// top-down functions, means travelling down the hierarchy
1211	ED4_returncode event_sent_by_parent(AW_event event, AW_window aww) FINAL_OVERRIDE;
1212
1213	void request_refresh(int clear=1) FINAL_OVERRIDE;
1214	ED4_returncode clear_refresh();
1215
1216	void resize_requested_children() OVERRIDE;
1217
1218	void update_requested_children() OVERRIDE;
1219
1220	void delete_requested_children() OVERRIDE;
1221	void Delete() FINAL_OVERRIDE;
1222
1223	ED4_returncode move_requested_by_parent(ED4_move_info *mi);
1224
1225	void create_consensus(ED4_abstract_group_manager upper_group_manager, arb_progress progress);
1226
1227	ARB_ERROR route_down_hierarchy(const ED4_route_cb& cb) FINAL_OVERRIDE;
1228
1229	ED4_base *find_first_that(ED4_level level, const ED4_basePredicate& fulfills_predicate);
1230
1231	// bottom-up functions
1232	ED4_returncode move_requested_by_child(ED4_move_info *moveinfo);
1233	inline void resize_requested_by_child();
1234	ED4_returncode refresh_requested_by_child();
1235	void delete_requested_by_child();
1236	void update_requested_by_child();
1237
1238	ED4_base *get_defined_level(ED4_level lev) const;
1239
1240	// functions referring the consensus
1241
1242	void update_consensus(ED4_manager old_parent, ED4_manager new_parent, ED4_base *sequence);
1243	ED4_returncode rebuild_consensi(ED4_base *start_species, ED4_update_flag update_flag);
1244
1245	ED4_returncode check_in_bases(ED4_base *added_base);
1246	ED4_returncode check_out_bases(ED4_base *subbed_base);
1247
1248	ED4_returncode update_bases(const ED4_base old_base, const ED4_base new_base, PosRange range = PosRange::whole());
1249	ED4_returncode update_bases(const char old_seq, int old_len, const char new_seq, int new_len, PosRange range = PosRange::whole());
1250	ED4_returncode update_bases(const char old_seq, int old_len, const ED4_base new_base, PosRange range = PosRange::whole());
1251	ED4_returncode update_bases(const BaseFrequencies old_table, const BaseFrequencies new_table, PosRange range = PosRange::whole());
1252
1253	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());
1254
1255	// handle moves across the hierarchy
1256	ED4_returncode handle_move(ED4_move_info *moveinfo);
1257
1258	ED4_base *get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop);
1259	ED4_base *get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop);
1260	ED4_base *search_spec_child_rek(ED4_level level); // recursive search for level
1261
1262	// general purpose functions
1263	ED4_base search_ID(const char id) FINAL_OVERRIDE;
1264	void remove_callbacks() OVERRIDE;
1265
1266	ED4_terminal *get_first_terminal(int start_index=0) const;
1267	ED4_terminal *get_last_terminal(int start_index=-1) const;
1268
1269	void hide_children();
1270	void unhide_children();
1271
1272	bool is_hidden() const FINAL_OVERRIDE {
1273	if (flag.hidden) return true;
1274	if (!parent) return false;
1275	return parent->is_hidden();
1276	}
1277
1278	ED4_manager(const ED4_objspec& spec_, const char id, AW_pos width, AW_pos height, ED4_manager parent);
1279	~ED4_manager() OVERRIDE;
1280	};
1281	MARK_NONFINAL_METHOD(ED4_manager,update_requested_children,());
1282	MARK_NONFINAL_METHOD(ED4_manager,delete_requested_children,());
1283
1284	class ED4_terminal : public ED4_base { // derived from a Noncopyable
1285	E4B_AVOID_UNNEEDED_CASTS(terminal);
1286
1287	public:
1288
1289	struct { unsigned int deleted : 1; } tflag; // @@@ go bool
1290
1291	long curr_timestamp;
1292
1293	DECLARE_DUMP_FOR_BASECLASS(ED4_terminal,ED4_base);
1294
1295	// callbacks
1296
1297	void changed_by_database() OVERRIDE;
1298	void deleted_from_database() OVERRIDE;
1299
1300	// functions concerning graphic output
1301	void Show(bool refresh_all, bool is_cleared) OVERRIDE;
1302	virtual void draw() = 0;
1303
1304	bool calc_bounding_box() FINAL_OVERRIDE;
1305
1306	ED4_returncode draw_drag_box(AW_pos x, AW_pos y, GB_CSTR text = NULp, int cursor_y=-1);
1307
1308	// functions which concern the object as a child
1309	void request_refresh(int clear=1) FINAL_OVERRIDE;
1310
1311	void resize_requested_children() OVERRIDE;
1312
1313	void update_requested_children() OVERRIDE;
1314	void delete_requested_children() OVERRIDE;
1315	void Delete() OVERRIDE;
1316
1317	ED4_returncode event_sent_by_parent(AW_event event, AW_window aww) OVERRIDE;
1318
1319	ED4_returncode kill_object();
1320
1321	// general purpose functions
1322	ED4_base search_ID(const char id) OVERRIDE;
1323	char resolve_pointer_to_string_copy(int str_len = NULp) const FINAL_OVERRIDE;
1324	const char resolve_pointer_to_char_pntr(int str_len = NULp) const FINAL_OVERRIDE;
1325	void remove_callbacks() FINAL_OVERRIDE;
1326
1327	GB_ERROR write_sequence(const char *seq, int seq_len);
1328
1329	void scroll_into_view(ED4_window *ed4w);
1330	inline bool setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfoldGroups, ED4_CursorJumpType jump_type);
1331
1332	bool is_hidden() const FINAL_OVERRIDE { return parent && parent->is_hidden(); }
1333
1334	ED4_terminal(const ED4_objspec& spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
1335	~ED4_terminal() OVERRIDE;
1336	};
1337	MARK_NONFINAL_METHOD(ED4_terminal,Show,(bool,bool));
1338
1339	enum ED4_species_mode {
1340	ED4_SM_MOVE,
1341	ED4_SM_KILL,
1342	ED4_SM_MARK,
1343	ED4_SM_INFO // same functionality as AWT_MODE_INFO
1344	};
1345
1346	class ED4_reference_terminals : virtual Noncopyable {
1347	ED4_sequence_info_terminal *ref_sequence_info;
1348	ED4_sequence_terminal *ref_sequence;
1349	ED4_sequence_info_terminal *ref_column_stat_info;
1350	ED4_columnStat_terminal *ref_column_stat;
1351
1352	void null() { ref_sequence_info = NULp; ref_sequence = NULp; ref_column_stat = NULp; ref_column_stat_info = NULp; }
1353	public:
1354	void clear();
1355	void init(ED4_sequence_info_terminal , ED4_sequence_terminal , ED4_sequence_info_terminal , ED4_columnStat_terminal );
1356
1357	ED4_sequence_terminal *sequence() { return ref_sequence; }
1358	ED4_sequence_info_terminal *sequence_info() { return ref_sequence_info; }
1359	ED4_columnStat_terminal *column_stat() { return ref_column_stat; }
1360	ED4_sequence_info_terminal *column_stat_info() { return ref_column_stat_info; }
1361
1362	ED4_reference_terminals() { null(); }
1363	~ED4_reference_terminals() { clear(); }
1364	};
1365
1366	class ED4_WinContext {
1367	ED4_window *ed4w;
1368	AW_device *device;
1369
1370	bool is_set() const { return ed4w; }
1371	void init(ED4_window *ew) {
1372	e4_assert(ew);
1373	ed4w = ew;
1374	device = ed4w->get_device();
1375	}
1376
1377	void warn_missing_context() const;
1378	void expect_context() const { if (!is_set()) warn_missing_context(); }
1379
1380	protected:
1381	ED4_WinContext() : ed4w(NULp), device(NULp) {}
1382	static ED4_WinContext current_context;
1383
1384	public:
1385	inline ED4_WinContext(AW_window *aww_);
1386	ED4_WinContext(ED4_window *ed4w_) { init(ed4w_); }
1387
1388	AW_device *get_device() const { expect_context(); return device; }
1389	ED4_window *get_ed4w() const { expect_context(); return ed4w; }
1390
1391	static const ED4_WinContext& get_current_context() { return current_context; }
1392	static bool have_context() { return current_context.is_set(); }
1393	};
1394
1395	// accessors for current context (see also ED4_WinContextFree)
1396	inline AW_device *current_device() { return ED4_WinContext::get_current_context().get_device(); }
1397	inline ED4_window *current_ed4w() { return ED4_WinContext::get_current_context().get_ed4w(); }
1398	inline AW_window *current_aww() { return current_ed4w()->aww; }
1399	inline ED4_cursor& current_cursor() { return current_ed4w()->cursor; }
1400
1401	enum LoadableSaiState {
1402	LSAI_UNUSED,
1403	LSAI_UPTODATE,
1404	LSAI_OUTDATED,
1405	};
1406
1407	class ED4_root : virtual Noncopyable {
1408	void ED4_ROOT() const { e4_assert(0); } // avoid ED4_root-members use global ED4_ROOT
1409
1410	void refresh_window_simple(bool redraw);
1411	void handle_update_requests(bool& redraw);
1412
1413	ED4_window *most_recently_used_window;
1414	ConsensusBuildParams *cons_param;
1415
1416	GBDATA *gb_main;
1417
1418	public:
1419
1420	GBDATA *get_gb_main() const { return gb_main; }
1421
1422	char *db_name; // name of Default Properties database (complete path)
1423	AW_root *aw_root; // Points to 'AW-Window-Controller'
1424	AW_default props_db; // Default Properties database
1425
1426	ED4_window *first_window; // Points to List of Main Windows of ED4
1427	ED4_main_manager *main_manager; // Points to Main manager of ED4
1428	ED4_area_manager *middle_area_man; // Points to middle area
1429	ED4_area_manager *top_area_man;
1430	ED4_root_group_manager *root_group_man;
1431	ED4_selected_list *selected_objects;
1432	ED4_scroll_links scroll_links;
1433	bool folding_action; // flag tells whether action was folding action or not
1434	ED4_reference_terminals ref_terminals;
1435	ED4_species_mode species_mode;
1436	ED4_scroll_picture scroll_picture;
1437	BI_ecoli_ref *ecoli_ref;
1438	char *alignment_name;
1439	GB_alignment_type alignment_type;
1440	ED4_reference *reference;
1441	ED4_seq_colors *sequence_colors;
1442	AW_gc_manager *gc_manager;
1443	ST_ML *st_ml;
1444	AW_helix *helix;
1445	int helix_spacing;
1446	long helix_add_spacing;
1447	long terminal_add_spacing;
1448	char *protstruct; // protein structure summary
1449	long protstruct_len; // protein structure summary
1450	ed_key *edk;
1451
1452	bool column_stat_activated;
1453	bool column_stat_initialized;
1454	bool visualizeSAI;
1455	bool visualizeSAI_allSpecies;
1456
1457	const ConsensusBuildParams& get_consensus_params();
1458	void reset_consensus_params();
1459
1460	LoadableSaiState loadable_SAIs; // maintain proper refresh of list of loadable SAIs
1461	void loadable_SAIs_may_have_changed() { if (loadable_SAIs == LSAI_UPTODATE) loadable_SAIs = LSAI_OUTDATED; }
1462
1463	int temp_gc;
1464	AW_font_group font_group;
1465
1466	void announce_useraction_in(AW_window *aww);
1467	ED4_window *get_most_recently_used_window() const {
1468	e4_assert(most_recently_used_window);
1469	return most_recently_used_window;
1470	}
1471
1472	inline ED4_device_manager *get_device_manager();
1473
1474	// Initializing functions
1475	ED4_returncode create_hierarchy(const char area_string_middle, const char area_string_top);
1476	ARB_ERROR init_alignment();
1477	void recalc_font_group();
1478
1479	AW_window *create_first_window();
1480	ED4_returncode generate_window(AW_device device, ED4_window new_window);
1481	void copy_window_struct(ED4_window source, ED4_window destination);
1482
1483	// functions concerned with global refresh and resize
1484	void resize_all_requesting_childs();
1485
1486	void special_window_refresh(bool handle_updates);
1487	ED4_returncode refresh_all_windows(bool redraw);
1488
1489	void request_refresh_for_all_terminals();
1490	void request_refresh_for_specific_terminals(ED4_level lev);
1491	void request_refresh_for_consensus_terminals();
1492	void request_refresh_for_sequence_terminals();
1493
1494	inline void announce_deletion(ED4_base *object); // before deleting an object, use this to announce
1495
1496	// functions concerned with list of selected objects
1497	ED4_returncode add_to_selected(ED4_species_name_terminal *object);
1498	void remove_from_selected(ED4_species_name_terminal *object);
1499	ED4_returncode deselect_all();
1500
1501	ED4_returncode get_area_rectangle(AW_screen_area *rect, AW_pos x, AW_pos y);
1502
1503	ED4_index pixel2pos(AW_pos click_x);
1504
1505	void remove_all_callbacks();
1506
1507	ED4_root(GBDATA *gb_main_);
1508	~ED4_root();
1509	};
1510
1511	ED4_WinContext::ED4_WinContext(AW_window *aww_) { init(ED4_ROOT->first_window->get_matching_ed4w(aww_)); }
1512
1513	struct ED4_LocalWinContext : private ED4_WinContext {
1514	ED4_LocalWinContext(AW_window *aww) : ED4_WinContext(current_context) { current_context = ED4_WinContext(aww); }
1515	ED4_LocalWinContext(ED4_window *ew) : ED4_WinContext(current_context) { current_context = ED4_WinContext(ew); }
1516	~ED4_LocalWinContext() { current_context = *this; }
1517	};
1518
1519	class ED4_MostRecentWinContext : virtual Noncopyable {
1520	ED4_LocalWinContext *most_recent;
1521	public:
1522	ED4_MostRecentWinContext() : most_recent(NULp) {
1523	if (!ED4_WinContext::have_context()) {
1524	most_recent = new ED4_LocalWinContext(ED4_ROOT->get_most_recently_used_window());
1525	}
1526	}
1527	~ED4_MostRecentWinContext() {
1528	delete most_recent;
1529	}
1530	};
1531
1532	inline void ED4_root::announce_deletion(ED4_base *object) {
1533	if (object->is_terminal()) {
1534	ED4_terminal *term = object->to_terminal();
1535	for (ED4_window *win = first_window; win; win = win->next) {
1536	ED4_LocalWinContext uses(win);
1537	win->announce_deletion(term);
1538	}
1539	}
1540	}
1541
1542	// ------------------------
1543	// manager classes
1544	//
1545	// All manager classes only differ in their static properties.
1546	// This kind of construction was chosen for using a minimum of RAM
1547
1548	class ED4_main_manager FINAL_TYPE : public ED4_manager { // derived from a Noncopyable
1549	// first in hierarchy
1550
1551	E4B_AVOID_UNNEEDED_CASTS(main_manager);
1552
1553	// these terminals are redrawn after refresh (with increase clipping area)
1554	// to revert text from middle area drawn into top area:
1555	ED4_terminal *top_middle_line;
1556	ED4_terminal *top_middle_spacer;
1557
1558	public:
1559	ED4_main_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1560
1561	void set_top_middle_spacer_terminal(ED4_terminal *top_middle_spacer_) { top_middle_spacer = top_middle_spacer_; }
1562	void set_top_middle_line_terminal(ED4_terminal *top_middle_line_) { top_middle_line = top_middle_line_; }
1563
1564	ED4_terminal *get_top_middle_spacer_terminal() const { return top_middle_spacer; }
1565	ED4_terminal *get_top_middle_line_terminal() const { return top_middle_line; }
1566
1567	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1568
1569	void Show(bool refresh_all, bool is_cleared) OVERRIDE;
1570	void resize_requested_children() OVERRIDE;
1571
1572	void clear_whole_background();
1573	};
1574
1575	struct ED4_device_manager : public ED4_manager {
1576	E4B_AVOID_UNNEEDED_CASTS(device_manager);
1577	ED4_device_manager (const char id, AW_pos width, AW_pos height, ED4_manager parent);
1578	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1579	};
1580
1581	struct ED4_area_manager : public ED4_manager {
1582	E4B_AVOID_UNNEEDED_CASTS(area_manager);
1583	ED4_area_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1584	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1585
1586	ED4_multi_species_manager *get_multi_species_manager() const {
1587	return get_defined_level(LEV_MULTI_SPECIES)->to_multi_species_manager();
1588	}
1589	};
1590
1591	class ED4_multi_species_manager : public ED4_manager {
1592	E4B_AVOID_UNNEEDED_CASTS(multi_species_manager);
1593
1594	int species; // # of species (-1 == unknown)
1595	int selected_species; // # of selected species (-1 == unknown)
1596
1597	void set_species_counters(int no_of_species, int no_of_selected);
1598	#ifdef DEBUG
1599	void count_species(int speciesPtr, int selectedPtr) const;
1600	#endif
1601	void update_species_counters();
1602
1603	public:
1604	ED4_multi_species_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1605
1606	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1607
1608	void update_requested_children() OVERRIDE;
1609	void delete_requested_children() OVERRIDE;
1610
1611	int count_visible_children(); // is called by a multi_species_manager
1612
1613	ED4_species_manager *get_consensus_manager() const; // returns the consensus-manager or NULp
1614	ED4_species_name_terminal *get_consensus_name_terminal() const; // returns the consensus-name-terminal or NULp
1615
1616	// functions concerned with selection
1617	int get_no_of_selected_species();
1618	int get_no_of_species();
1619
1620	void update_group_id();
1621
1622	void invalidate_species_counters();
1623	int has_valid_counters() const { return species != -1 && selected_species!=-1; }
1624	bool all_are_selected() const { e4_assert(has_valid_counters()); return species == selected_species; }
1625
1626	void select_all(bool only_species);
1627	void deselect_all_species_and_SAI();
1628	void invert_selection_of_all_species();
1629	void marked_species_select(bool select);
1630	void selected_species_mark(bool mark);
1631
1632	void toggle_selected_species();
1633	};
1634
1635	class ED4_abstract_group_manager : public ED4_manager {
1636	E4B_AVOID_UNNEEDED_CASTS(abstract_group_manager);
1637	protected:
1638	BaseFrequencies my_table; // table concerning Consensusfunction
1639
1640	public:
1641	ED4_abstract_group_manager(const ED4_objspec& spec_, const char id, AW_pos width, AW_pos height, ED4_manager parent);
1642
1643	DECLARE_DUMP_FOR_BASECLASS(ED4_abstract_group_manager, ED4_manager);
1644
1645	BaseFrequencies& table() { return my_table; }
1646	const BaseFrequencies& table() const { return my_table; }
1647
1648	ED4_multi_species_manager *get_multi_species_manager() const {
1649	return get_defined_level(LEV_MULTI_SPECIES)->to_multi_species_manager();
1650	}
1651
1652	char *build_consensus_string(PosRange range) const { return table().build_consensus_string(range, ED4_ROOT->get_consensus_params()); }
1653	char build_consensus_string(int cons_length = NULp) const {
1654	if (cons_length) *cons_length = table().size();
1655	return table().build_consensus_string(ED4_ROOT->get_consensus_params());
1656	}
1657	};
1658
1659	struct ED4_group_manager : public ED4_abstract_group_manager {
1660	E4B_AVOID_UNNEEDED_CASTS(group_manager);
1661	ED4_group_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1662	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_group_manager);
1663	void reinit_char_table();
1664
1665	void fold();
1666	void unfold();
1667	void toggle_folding();
1668	};
1669
1670	enum ED4_remap_mode {
1671	ED4_RM_NONE, // no remapping (normal mode = 'show all gaps')
1672	ED4_RM_SHOW_ABOVE, // Show all positions, where xxx% of all edited sequences have any base
1673	ED4_RM_MAX_ALIGN, // ------------------------- any edited sequence has a base
1674	ED4_RM_MAX_EDIT, // like ED4_RM_MAX_ALIGN, but bases are pushed OVER remapped gaps (not INTO)
1675	ED4_RM_DYNAMIC_GAPS, // gaps shown as spaces (more gaps => more spaces)
1676
1677	ED4_RM_MODES
1678
1679	};
1680
1681	class ED4_remap : virtual Noncopyable {
1682
1683	ED4_remap_mode mode;
1684	int show_above_percent; // used only for ED4_RM_SHOW_ABOVE
1685
1686	size_t sequence_table_len; // allocated size of sequence_to_screen_tab
1687	size_t screen_table_len; // allocated size of screen_to_sequence_tab
1688
1689	size_t sequence_len; // size of recently compiled part of sequence_to_screen_tab
1690	size_t screen_len; // size of recently compiled part of screen_to_sequence_tab
1691
1692	int *screen_to_sequence_tab;
1693	int *sequence_to_screen_tab; // <0 means position is not mapped (last displayed sequence position); 0 may be mapped or not; see is_shown() below
1694
1695	bool update_needed; // remapping should be recompiled
1696
1697	inline void set_sequence_to_screen(int pos, int newVal, bool& mapping_changed);
1698
1699	public:
1700
1701	ED4_remap();
1702	~ED4_remap();
1703
1704	int screen_to_sequence(int screen_pos) const;
1705
1706	int sequence_to_screen_PLAIN(int sequence_pos) const {
1707	e4_assert(sequence_pos>=0 && size_t(sequence_pos)<=sequence_len);
1708	return sequence_to_screen_tab[sequence_pos];
1709	}
1710	int shown_sequence_to_screen(int sequence_pos) const {
1711	// as well works for sequence_pos == MAXSEQUENCECHARACTERLENGTH
1712	int screen_pos = sequence_to_screen_PLAIN(sequence_pos);
1713	e4_assert(screen_pos >= 0); // sequence_pos expected to be visible (i.e. not folded away)
1714	return screen_pos;
1715	}
1716
1717	int clipped_sequence_to_screen_PLAIN(int sequence_pos) const;
1718	int sequence_to_screen(int sequence_pos) const;
1719
1720	PosRange sequence_to_screen(PosRange range) const {
1721	e4_assert(!range.is_empty());
1722	return PosRange(sequence_to_screen(range.start()), sequence_to_screen(range.end()));
1723	}
1724	PosRange screen_to_sequence(PosRange range) const {
1725	e4_assert(!range.is_empty());
1726	if (range.is_unlimited()) return PosRange::from(screen_to_sequence(range.start()));
1727	return PosRange(screen_to_sequence(range.start()), screen_to_sequence(range.end()));
1728	}
1729
1730	size_t get_max_screen_pos() const { return screen_len-1; }
1731
1732	void adjacent_screen_positions(int seq_pos, int& screen_pos_left, int& screen_pos_right);
1733
1734	ED4_remap_mode get_mode() const { return mode; }
1735	void set_mode(ED4_remap_mode Mode, int above_percent) {
1736	if (Mode<0 \|\| Mode>=ED4_RM_MODES) {
1737	Mode = ED4_RM_NONE;
1738	}
1739	if (mode!=Mode) {
1740	mode = Mode;
1741	update_needed = true;
1742	}
1743
1744	if (show_above_percent!=above_percent) {
1745	show_above_percent = above_percent;
1746	if (mode==ED4_RM_SHOW_ABOVE) {
1747	update_needed = true;
1748	}
1749	}
1750	}
1751
1752	void mark_compile_needed(); // recompile if mode != none
1753	void mark_compile_needed_force(); // always recompile
1754	bool compile_needed() const { return update_needed; }
1755
1756	bool compile(ED4_root_group_manager *gm); // returns true if mapping did change
1757
1758	bool is_shown(int seq_pos) const {
1759	int scr_pos = sequence_to_screen_PLAIN(seq_pos);
1760	if (scr_pos<0) return false;
1761	if (scr_pos>0) return true;
1762
1763	int seq_pos2 = screen_to_sequence_tab[0];
1764	return seq_pos == seq_pos2;
1765	}
1766
1767	ExplicitRange clip_screen_range(PosRange screen_range) const { return ExplicitRange(screen_range, screen_len-1); }
1768	};
1769
1770	class ED4_root_group_manager : public ED4_abstract_group_manager {
1771	E4B_AVOID_UNNEEDED_CASTS(root_group_manager);
1772	ED4_remap my_remap;
1773	public:
1774	ED4_root_group_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1775
1776	bool update_remap(); // 'true' if mapping has changed
1777
1778	const ED4_remap *remap() const { return &my_remap; }
1779	ED4_remap *remap() { return &my_remap; }
1780
1781	void Show(bool refresh_all, bool is_cleared) OVERRIDE;
1782	void resize_requested_children() OVERRIDE;
1783
1784	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_group_manager);
1785	};
1786
1787	class ED4_species_manager FINAL_TYPE : public ED4_manager {
1788	E4B_AVOID_UNNEEDED_CASTS(species_manager);
1789
1790	ED4_cb_list<ED4_species_manager, ED4_species_managerCallback> changed_cbs; // called when sequence changes
1791
1792	ED4_species_type type;
1793	bool selected;
1794
1795	public:
1796	ED4_species_manager(ED4_species_type type_, const char id, AW_pos width, AW_pos height, ED4_manager parent);
1797	~ED4_species_manager() OVERRIDE;
1798
1799	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1800
1801	ED4_species_type get_type() const { return type; }
1802
1803	bool is_selected() const { return selected; }
1804	void set_selected(bool select) {
1805	// e4_assert(type != ED4_SP_CONSENSUS); // it's not allowed to select a consensus // @@@ happens atm when moving a group
1806	selected = select;
1807	}
1808
1809	bool setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfold_groups, ED4_CursorJumpType jump_type);
1810
1811	void add_sequence_changed_cb(const ED4_species_managerCallback& cb) { changed_cbs.add_cb(cb); }
1812	void remove_sequence_changed_cb(const ED4_species_managerCallback& cb) { changed_cbs.remove_cb(cb); }
1813	void do_callbacks() { changed_cbs.call(this); }
1814
1815	ED4_species_name_terminal *get_name_terminal() const { return member(0)->to_species_name_terminal(); }
1816	};
1817
1818	inline ED4_manager *ED4_base::get_parent(ED4_level lev) const {
1819	ED4_manager *temp_parent = parent;
1820	while (temp_parent && !(temp_parent->spec.level & lev)) {
1821	temp_parent = temp_parent->parent;
1822	}
1823	return temp_parent;
1824	}
1825
1826
1827	inline ED4_species_manager *ED4_base::containing_species_manager() const {
1828	ED4_base *sman = get_parent(LEV_SPECIES);
1829	return sman ? sman->to_species_manager() : NULp;
1830	}
1831
1832	inline bool ED4_base::is_consensus_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_CONSENSUS; }
1833	inline bool ED4_base::is_SAI_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_SAI; }
1834	inline bool ED4_base::is_species_seq_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_SPECIES; }
1835
1836	inline ED4_species_type ED4_base::get_species_type() const {
1837	ED4_species_manager *sman = containing_species_manager();
1838	return sman ? sman->get_type() : ED4_SP_NONE;
1839	}
1840
1841	inline bool ED4_base::inside_consensus_manager() const { return get_species_type() == ED4_SP_CONSENSUS; }
1842	inline bool ED4_base::inside_SAI_manager() const { return get_species_type() == ED4_SP_SAI; }
1843	inline bool ED4_base::inside_species_seq_manager() const { return get_species_type() == ED4_SP_SPECIES; }
1844
1845	inline bool ED4_base::is_consensus_terminal() const { return is_sequence_terminal() && inside_consensus_manager(); }
1846	inline bool ED4_base::is_SAI_terminal() const { return is_sequence_terminal() && inside_SAI_manager(); }
1847	inline bool ED4_base::is_species_seq_terminal() const { return is_sequence_terminal() && inside_species_seq_manager(); }
1848
1849	inline bool ED4_cursor::in_species_seq_terminal() const { return owner_of_cursor && owner_of_cursor->is_species_seq_terminal(); }
1850	inline bool ED4_cursor::in_consensus_terminal() const { return owner_of_cursor && owner_of_cursor->is_consensus_terminal(); }
1851	inline bool ED4_cursor::in_SAI_terminal() const { return owner_of_cursor && owner_of_cursor->is_SAI_terminal(); }
1852
1853
1854	struct ED4_multi_sequence_manager : public ED4_manager {
1855	E4B_AVOID_UNNEEDED_CASTS(multi_sequence_manager);
1856	ED4_multi_sequence_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1857	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1858	};
1859
1860	struct ED4_sequence_manager : public ED4_manager {
1861	E4B_AVOID_UNNEEDED_CASTS(sequence_manager);
1862	ED4_sequence_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1863	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1864	};
1865
1866	struct ED4_multi_name_manager : public ED4_manager {
1867	E4B_AVOID_UNNEEDED_CASTS(multi_name_manager);
1868	// member of ED4_species_manager (contains ED4_name_manager for name and info)
1869	ED4_multi_name_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1870	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1871	};
1872
1873
1874	struct ED4_name_manager : public ED4_manager {
1875	E4B_AVOID_UNNEEDED_CASTS(name_manager);
1876	// member of ED4_multi_name_manager (contains speciesname or other info concerning the species)
1877	ED4_name_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1878	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1879	};
1880
1881
1882	// -------------------------
1883	// terminal classes
1884
1885
1886	struct ED4_tree_terminal FINAL_TYPE : public ED4_terminal {
1887	E4B_AVOID_UNNEEDED_CASTS(tree_terminal);
1888
1889	void draw() OVERRIDE;
1890
1891	ED4_tree_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1892
1893	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
1894	};
1895
1896	struct ED4_bracket_terminal : public ED4_terminal {
1897	E4B_AVOID_UNNEEDED_CASTS(bracket_terminal);
1898
1899	void draw() OVERRIDE;
1900
1901	void toggle_folding();
1902
1903	ED4_bracket_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1904
1905	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
1906	};
1907
1908	struct ED4_text_terminal : public ED4_terminal {
1909	E4B_AVOID_UNNEEDED_CASTS(text_terminal);
1910
1911	// functions concerning graphic output
1912	void draw() OVERRIDE;
1913
1914	virtual int get_length() const = 0;
1915	void deleted_from_database() OVERRIDE;
1916
1917	ED4_text_terminal(const ED4_objspec& spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
1918	~ED4_text_terminal() OVERRIDE {}
1919
1920	DECLARE_DUMP_FOR_BASECLASS(ED4_text_terminal, ED4_terminal);
1921	};
1922
1923	class ED4_abstract_sequence_terminal : public ED4_text_terminal { // derived from a Noncopyable
1924
1925	PosRange pixel2index(PosRange pixel_range);
1926
1927	E4B_AVOID_UNNEEDED_CASTS(abstract_sequence_terminal);
1928	public:
1929	char *species_name; // @@@ wrong place (may be member of ED4_sequence_manager)
1930
1931
1932	ED4_abstract_sequence_terminal(const ED4_objspec& spec_, const char id, AW_pos width, AW_pos height, ED4_manager parent);
1933	~ED4_abstract_sequence_terminal() OVERRIDE;
1934
1935	virtual GB_alignment_type GetAliType() = 0;
1936	int get_length() const OVERRIDE { int len; resolve_pointer_to_char_pntr(&len); return len; }
1937
1938	ED4_species_name_terminal *corresponding_species_name_terminal() const {
1939	return get_parent(LEV_SPECIES)->search_spec_child_rek(LEV_SPECIES_NAME)->to_species_name_terminal();
1940	}
1941	PosRange calc_interval_displayed_in_rectangle(AW_screen_area *area_rect);
1942	PosRange calc_update_interval();
1943
1944	DECLARE_DUMP_FOR_BASECLASS(ED4_abstract_sequence_terminal, ED4_text_terminal);
1945	};
1946
1947	class ED4_orf_terminal : public ED4_abstract_sequence_terminal { // derived from a Noncopyable
1948	// NOTE: ED4_orf_terminal is a separate terminal class used to display Open Reading Frames (ORFs)
1949	// for the corresponding gene (DNA) sequence. It is used in ProteinViewer Module and should not be
1950	// used for drawing aminoacid sequence alone as in protein alignment. Aminoacid sequences are
1951	// handled by the standard "ED4_sequence_terminal" class.
1952
1953	char *aaSequence;
1954	size_t aaSeqLen;
1955	char *aaColor;
1956	int aaStartPos;
1957	int aaStrandType;
1958
1959	void draw() OVERRIDE;
1960	E4B_AVOID_UNNEEDED_CASTS(orf_terminal);
1961	public:
1962	ED4_orf_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1963	~ED4_orf_terminal() OVERRIDE;
1964
1965	GB_alignment_type GetAliType() OVERRIDE { return GB_AT_AA; }
1966
1967	void SET_aaSeqFlags (int startPos, int strandType) { aaStartPos = startPos; aaStrandType = strandType; }
1968	void SET_aaSequence(const char *aaSeq) { freedup(aaSequence, aaSeq); aaSeqLen = strlen(aaSequence); }
1969	void SET_aaColor(const char *aaSeq) { freedup(aaColor, aaSeq); }
1970
1971	int GET_aaStartPos () { return aaStartPos; }
1972	int GET_aaStrandType () { return aaStrandType; }
1973
1974	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_sequence_terminal);
1975	};
1976
1977	class ED4_sequence_terminal : public ED4_abstract_sequence_terminal { // derived from a Noncopyable
1978	mutable ED4_SearchResults searchResults;
1979	bool shall_display_secstruct_info; // helix or protstruct
1980
1981	void draw() OVERRIDE;
1982
1983	E4B_AVOID_UNNEEDED_CASTS(sequence_terminal);
1984
1985	public:
1986
1987	AP_tree *st_ml_node;
1988
1989	ED4_sequence_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent, bool shall_display_secstruct_info_);
1990
1991	GB_alignment_type GetAliType() FINAL_OVERRIDE { return ED4_ROOT->alignment_type; }
1992
1993	void deleted_from_database() OVERRIDE;
1994	int get_length() const OVERRIDE { return ED4_abstract_sequence_terminal::get_length(); }
1995
1996	virtual char get_sequence_copy(int str_len = NULp) const { return resolve_pointer_to_string_copy(str_len); }
1997
1998	void set_secstruct_display(bool show) { shall_display_secstruct_info = show; }
1999
2000	ED4_SearchResults& results() const { return searchResults; }
2001
2002	ED4_columnStat_terminal *corresponding_columnStat_terminal() const {
2003	ED4_base *col_term = get_parent(LEV_MULTI_SEQUENCE)->search_spec_child_rek(LEV_COL_STAT);
2004	return col_term ? col_term->to_columnStat_terminal() : NULp;
2005	}
2006
2007	DECLARE_DUMP_FOR_MIDCLASS(ED4_sequence_terminal,ED4_abstract_sequence_terminal);
2008	PREPARE_MARK_NONFINAL_CLASS(ED4_sequence_terminal);
2009	};
2010	MARK_NONFINAL_CLASS(ED4_sequence_terminal);
2011	MARK_NONFINAL_FUNCTION(ED4_sequence_terminal,int,get_length,()const,0);
2012	MARK_NONFINAL_FUNCTION(ED4_sequence_terminal,char,get_sequence_copy,(int)const,NULp);
2013
2014	class ED4_columnStat_terminal FINAL_TYPE : public ED4_text_terminal { // derived from a Noncopyable
2015	char *likelihood[4]; // likelihood-array for each base (ACGU) [length of array = alignment_length]
2016	int latest_update;
2017
2018	static double threshold;
2019
2020	int update_likelihood();
2021
2022	E4B_AVOID_UNNEEDED_CASTS(columnStat_terminal);
2023
2024	public:
2025	// functions concerning graphic output
2026	void draw() OVERRIDE;
2027	int get_length() const OVERRIDE { return corresponding_sequence_terminal()->get_length(); }
2028
2029	static int threshold_is_set();
2030	static void set_threshold(double aThreshold);
2031	static double get_threshold() { return threshold; }
2032
2033	ED4_sequence_terminal *corresponding_sequence_terminal() const { return get_parent(LEV_MULTI_SEQUENCE)->search_spec_child_rek(LEV_SEQUENCE_STRING)->to_sequence_terminal(); }
2034
2035	ED4_columnStat_terminal(GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
2036	~ED4_columnStat_terminal() OVERRIDE;
2037
2038	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2039	};
2040
2041	class ED4_species_name_terminal FINAL_TYPE : public ED4_text_terminal { // derived from a Noncopyable
2042	E4B_AVOID_UNNEEDED_CASTS(species_name_terminal);
2043	bool set_dynamic_size() OVERRIDE;
2044
2045	public:
2046	ED4_species_name_terminal(GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
2047	~ED4_species_name_terminal() OVERRIDE { delete selection_info; }
2048
2049
2050	ED4_selection_entry *selection_info; // Info about i.e. Position
2051	bool dragged;
2052
2053	GB_CSTR get_displayed_text() const;
2054	int get_length() const OVERRIDE { return strlen(get_displayed_text()); }
2055
2056	ED4_sequence_terminal *corresponding_sequence_terminal() const {
2057	ED4_base *seq_term = get_parent(LEV_SPECIES)->search_spec_child_rek(LEV_SEQUENCE_STRING);
2058	return seq_term ? seq_term->to_sequence_terminal() : NULp;
2059	}
2060
2061	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2062	};
2063
2064	class ED4_flag_header_terminal FINAL_TYPE : public ED4_text_terminal { // derived from a Noncopyable
2065	// displays header of flags
2066
2067	E4B_AVOID_UNNEEDED_CASTS(flag_header_terminal);
2068	bool set_dynamic_size() OVERRIDE;
2069
2070	public:
2071	ED4_flag_header_terminal(GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
2072
2073	GB_CSTR get_displayed_text() const;
2074	int get_length() const OVERRIDE;
2075
2076	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2077	};
2078
2079	class ED4_sequence_info_terminal FINAL_TYPE : public ED4_text_terminal {
2080	E4B_AVOID_UNNEEDED_CASTS(sequence_info_terminal);
2081	bool set_dynamic_size() OVERRIDE;
2082
2083	public:
2084	ED4_sequence_info_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
2085
2086	ED4_species_name_terminal *corresponding_species_name_terminal() const {
2087	return get_parent(LEV_SPECIES)->search_spec_child_rek(LEV_SPECIES_NAME)->to_species_name_terminal();
2088	}
2089
2090	void draw() OVERRIDE;
2091
2092	GBDATA *data() { return get_species_pointer(); } // DB-entry ("ali_xxx/data")
2093	const GBDATA *data() const { return get_species_pointer(); }
2094
2095	int get_length() const OVERRIDE { return 1+strlen(id); }
2096
2097	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2098	};
2099
2100	struct ED4_pure_text_terminal FINAL_TYPE : public ED4_text_terminal {
2101	E4B_AVOID_UNNEEDED_CASTS(pure_text_terminal);
2102
2103	ED4_pure_text_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
2104
2105	int get_length() const OVERRIDE { int len; resolve_pointer_to_char_pntr(&len); return len; }
2106
2107	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2108	};
2109
2110	class ED4_consensus_sequence_terminal : public ED4_sequence_terminal { // derived from a Noncopyable
2111	E4B_AVOID_UNNEEDED_CASTS(consensus_sequence_terminal);
2112
2113	void draw() OVERRIDE;
2114	const ED4_abstract_group_manager *get_group_manager() const { return get_parent(LEV_GROUP)->to_group_manager(); }
2115	const BaseFrequencies& get_char_table() const { return get_group_manager()->table(); }
2116
2117	public:
2118	char *temp_cons_seq; // used for editing consensus (normally NULp)
2119
2120	ED4_consensus_sequence_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
2121	#if defined(ASSERTION_USED)
2122	virtual ~ED4_consensus_sequence_terminal() { e4_assert(!temp_cons_seq); }
2123	#endif
2124
2125	int get_length() const OVERRIDE;
2126	char get_sequence_copy(int str_len = NULp) const FINAL_OVERRIDE { return get_group_manager()->build_consensus_string(str_len); }
2127
2128	DECLARE_DUMP_FOR_LEAFCLASS(ED4_sequence_terminal);
2129	};
2130
2131	class ED4_spacer_terminal FINAL_TYPE : public ED4_terminal {
2132	E4B_AVOID_UNNEEDED_CASTS(spacer_terminal);
2133	bool shallDraw; // true -> spacer is really drawn (otherwise it's only a placeholder)
2134
2135	bool set_dynamic_size() OVERRIDE;
2136
2137	public:
2138	void Show(bool refresh_all, bool is_cleared) OVERRIDE;
2139	void draw() OVERRIDE;
2140
2141	ED4_spacer_terminal(const char id, bool shallDraw_, AW_pos width, AW_pos height, ED4_manager parent);
2142
2143	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2144	};
2145
2146	class ED4_line_terminal : public ED4_terminal {
2147	E4B_AVOID_UNNEEDED_CASTS(line_terminal);
2148	bool set_dynamic_size() OVERRIDE;
2149
2150	public:
2151	void draw() OVERRIDE;
2152
2153	ED4_line_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
2154
2155	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2156	};
2157
2158	class ED4_flag_terminal FINAL_TYPE : public ED4_terminal {
2159	E4B_AVOID_UNNEEDED_CASTS(flag_terminal);
2160	bool set_dynamic_size() OVERRIDE;
2161
2162	public:
2163	void draw() OVERRIDE;
2164
2165	ED4_flag_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
2166
2167	GBDATA *get_species() const { return get_parent(LEV_SPECIES)->get_species_pointer(); }
2168	void handle_left_click(const AW::Position& click);
2169
2170	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2171	};
2172
2173
2174	// ----------------------------------------------
2175	// inlines which need complete classdefs
2176
2177	inline void ED4_base::set_update() { // @@@ rename into request_update
2178	if (!update_info.update_requested) {
2179	update_info.update_requested = 1;
2180	if (parent) parent->update_requested_by_child();
2181	}
2182	}
2183
2184	inline void ED4_base::request_resize() {
2185	update_info.set_resize(1);
2186	if (parent) parent->resize_requested_by_child();
2187	}
2188
2189	void ED4_manager::resize_requested_by_child() {
2190	if (!update_info.resize) request_resize();
2191	}
2192
2193	inline bool ED4_terminal::setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfoldGroups, ED4_CursorJumpType jump_type) {
2194	ED4_species_manager *sm = get_parent(LEV_SPECIES)->to_species_manager();
2195	return sm->setCursorTo(cursor, seq_pos, unfoldGroups, jump_type);
2196	}
2197
2198	E4B_IMPL_CASTOP(area_manager); // to_area_manager
2199	E4B_IMPL_CASTOP(abstract_group_manager); // to_abstract_group_manager
2200	E4B_IMPL_CASTOP(bracket_terminal); // to_bracket_terminal
2201	E4B_IMPL_CASTOP(columnStat_terminal); // to_columnStat_terminal
2202	E4B_IMPL_CASTOP(consensus_sequence_terminal); // to_consensus_sequence_terminal
2203	E4B_IMPL_CASTOP(device_manager); // to_device_manager
2204	E4B_IMPL_CASTOP(group_manager); // to_group_manager
2205	E4B_IMPL_CASTOP(line_terminal); // to_line_terminal
2206	E4B_IMPL_CASTOP(manager); // to_manager
2207	E4B_IMPL_CASTOP(multi_name_manager); // to_multi_name_manager
2208	E4B_IMPL_CASTOP(multi_sequence_manager); // to_multi_sequence_manager
2209	E4B_IMPL_CASTOP(multi_species_manager); // to_multi_species_manager
2210	E4B_IMPL_CASTOP(name_manager); // to_name_manager
2211	E4B_IMPL_CASTOP(orf_terminal); // to_orf_terminal
2212	E4B_IMPL_CASTOP(pure_text_terminal); // to_pure_text_terminal
2213	E4B_IMPL_CASTOP(root_group_manager); // to_root_group_manager
2214	E4B_IMPL_CASTOP(sequence_info_terminal); // to_sequence_info_terminal
2215	E4B_IMPL_CASTOP(sequence_manager); // to_sequence_manager
2216	E4B_IMPL_CASTOP(sequence_terminal); // to_sequence_terminal
2217	E4B_IMPL_CASTOP(spacer_terminal); // to_spacer_terminal
2218	E4B_IMPL_CASTOP(species_manager); // to_species_manager
2219	E4B_IMPL_CASTOP(species_name_terminal); // to_species_name_terminal
2220	E4B_IMPL_CASTOP(terminal); // to_terminal
2221	E4B_IMPL_CASTOP(text_terminal); // to_text_terminal
2222	E4B_IMPL_CASTOP(flag_header_terminal); // to_flag_header_terminal
2223	E4B_IMPL_CASTOP(flag_terminal); // to_flag_terminal
2224
2225	inline ED4_device_manager *ED4_root::get_device_manager() {
2226	return main_manager->search_spec_child_rek(LEV_DEVICE)->to_device_manager();
2227	}
2228
2229
2230	inline ED4_species_name_terminal *ED4_multi_species_manager::get_consensus_name_terminal() const {
2231	ED4_species_manager *consensus_man = get_consensus_manager();
2232	return consensus_man ? consensus_man->get_name_terminal() : NULp;
2233	}
2234
2235	// ----------------------------------------
2236
2237	enum SpeciesCreationMode {
2238	CREATE_NEW_SPECIES,
2239	CREATE_FROM_CONSENSUS, // create new species from group consensus (of surrounding group)
2240	COPY_SPECIES, // copy current species
2241	};
2242
2243	#if defined(ASSERTION_USED)
2244	CONSTEXPR_INLINE bool valid(SpeciesCreationMode m) { return m>=CREATE_NEW_SPECIES && m<=COPY_SPECIES; }
2245	#endif
2246
2247	extern ST_ML *st_ml;
2248	struct AlignDataAccess;
2249
2250	// -------------------------------------------------
2251	// factory functions (hierarchy builders):
2252
2253	ED4_group_manager ED4_build_group_manager_start(ED4_manager group_parent,
2254	GB_CSTR group_name,
2255	int group_depth,
2256	bool is_folded,
2257	ED4_reference_terminals& refterms,
2258	ED4_multi_species_manager*& multi_species_manager);
2259
2260	void ED4_build_group_manager_end(ED4_multi_species_manager *multi_species_manager);
2261
2262	// -------------------------------------
2263	// hierarchy access functions:
2264
2265	ED4_species_name_terminal ED4_find_species_name_terminal(const char species_name);
2266	ED4_species_name_terminal ED4_find_SAI_name_terminal(const char sai_name);
2267	ED4_species_name_terminal ED4_find_species_or_SAI_name_terminal(const char species_name);
2268
2269	ED4_multi_species_manager *ED4_find_MoreSequences_manager();
2270
2271	// --------------------------
2272	// other functions:
2273
2274	void ED4_new_editor_window(AW_window *aww);
2275	void ED4_with_all_edit_windows(void (cb)(ED4_window ));
2276
2277	void ED4_resize_all_extensions();
2278	void ED4_calc_terminal_extentions();
2279
2280	void ED4_input_cb(AW_window *aww);
2281	void ED4_remote_event(AW_event *faked_event);
2282	void ED4_motion_cb(AW_window *aww);
2283	void ED4_vertical_change_cb(AW_window *aww);
2284	void ED4_horizontal_change_cb(AW_window *aww);
2285	void ED4_scrollbar_change_cb(AW_window *aww);
2286	void ED4_trigger_instant_refresh();
2287	void ED4_request_relayout();
2288	void ED4_request_full_refresh();
2289	void ED4_request_full_instant_refresh();
2290
2291	void ED4_store_curpos(AW_window *aww);
2292	void ED4_restore_curpos(AW_window *aww);
2293	void ED4_clear_stored_curpos();
2294	void ED4_helix_jump_opposite(AW_window *aww);
2295	void ED4_jump_to_cursor_position(AW_window aww, const char awar_name, PositionType posType);
2296	void ED4_remote_set_cursor_cb(AW_root *awr);
2297	void ED4_change_cursor(AW_window *aww);
2298
2299	void ED4_set_iupac(AW_window aww, const char awar_name);
2300	void ED4_set_helixnr(AW_window aww, const char awar_name);
2301	void ed4_changesecurity(AW_root *root);
2302	void ed4_change_edit_mode(AW_root *root);
2303
2304	void ED4_jump_to_current_species(AW_window *);
2305	void ED4_get_and_jump_to_current(AW_window *);
2306	void ED4_get_and_jump_to_species(GB_CSTR species_name);
2307
2308	void ED4_get_marked_from_menu(AW_window *);
2309	void ED4_selected_species_changed_cb(AW_root *aw_root);
2310
2311	AW_window ED4_create_loadSAI_window(AW_root awr);
2312	void ED4_get_and_jump_to_selected_SAI(AW_window *aww);
2313	void ED4_selected_SAI_changed_cb(AW_root *aw_root);
2314
2315	void ED4_init_notFoundMessage();
2316	void ED4_finish_and_show_notFoundMessage();
2317
2318	const AlignDataAccess *ED4_get_aligner_data_access();
2319
2320	void ED4_popup_gc_window(AW_window awp, AW_gc_manager gcman);
2321	void ED4_no_dangerous_modes();
2322
2323	void group_species_cb(AW_window *aww, bool use_fields);
2324	AW_window ED4_create_group_species_by_field_window(AW_root aw_root);
2325
2326	AW_window ED4_create_loadConfiguration_window(AW_root awr);
2327	void ED4_reloadConfiguration(AW_window *aww);
2328	void ED4_saveConfiguration(AW_window *aww, bool hide_aww);
2329	AW_window ED4_create_saveConfigurationAs_window(AW_root awr);
2330
2331	ARB_ERROR rebuild_consensus(ED4_base *object);
2332
2333	void ED4_create_consensus_awars(AW_root *aw_root);
2334	AW_window ED4_create_consensus_definition_window(AW_root root);
2335	void ED4_consensus_definition_changed(AW_root*);
2336	void ED4_consensus_display_changed(AW_root *root);
2337
2338	AW_window ED4_create_editor_options_window(AW_root root);
2339	void ED4_compression_toggle_changed_cb(AW_root *root, bool hideChanged);
2340	void ED4_compression_changed_cb(AW_root *awr);
2341	void ED4_alignment_length_changed(GBDATA *gb_alignment_len, GB_CB_TYPE gbtype);
2342
2343	AW_window ED4_create_new_seq_window(AW_root root, SpeciesCreationMode creation_mode);
2344
2345	void ED4_quit_editor(AW_window *aww);
2346	void ED4_exit() __ATTR__NORETURN;
2347
2348
2349	#else
2350	#error ed4_class included twice
2351	#endif

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