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source: tags/arb-6.0/EDIT4/ed4_class.hxx

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Last change on this file was 12267, checked in by westram, 11 years ago
full update from 'trunk' into 'rc' because i was (nearly) only fixing bugs in the last 5 weeks adds: log:branches/fix@11985,11990:11997,12008:12013,12023:12042,12049:12053,12058:12137,12147:12156 log:branches/gcc@12076:12079 log:branches/tree@12004:12019,12116:12120 log:trunk@11971:11972,11974:11980,11982:11989,11991:12260
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 93.2 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
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 OVERRIDE; \
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(const 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(std::min(dim, scroll_top->get_dimension()));
528	scroll_bottom->set_dimension(std::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(std::min(dim, scroll_left->get_dimension()));
542	scroll_right->set_dimension(std::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; // if calced4term!=NULL => callback is bound to its species manager
581	bool needUpdate;
582
583	void calc4term(const ED4_terminal *term);
584	void set_term(const ED4_terminal *term) {
585	if (calced4term != term \|\| needUpdate) {
586	calc4term(term);
587	}
588	}
589	void remove_changed_cb();
590
591	public:
592
593	ED4_base_position()
594	: calced4term(NULL),
595	needUpdate(true)
596	{}
597
598	~ED4_base_position() {
599	remove_changed_cb();
600	}
601
602	void invalidate() {
603	needUpdate = true;
604	}
605
606	void announce_deletion(const ED4_terminal *term) {
607	if (term == calced4term) {
608	invalidate();
609	remove_changed_cb();
610	}
611	e4_assert(calced4term != term);
612	}
613	void prepare_shutdown() {
614	if (calced4term) announce_deletion(calced4term);
615	}
616
617	int get_base_position(const ED4_terminal *base, int sequence_position);
618	int get_sequence_position(const ED4_terminal *base, int base_position);
619
620	int get_base_count(const ED4_terminal *term) { set_term(term); return base_count(); }
621	int get_abs_len(const ED4_terminal *term) { set_term(term); return abs_count(); }
622	};
623
624	class ED4_CursorShape;
625
626
627	enum ED4_CursorType {
628	ED4_RIGHT_ORIENTED_CURSOR,
629	ED4_RIGHT_ORIENTED_CURSOR_THIN,
630	ED4_TRADITIONAL_CURSOR,
631	ED4_TRADITIONAL_CURSOR_BOTTOM,
632	ED4_TRADITIONAL_CURSOR_CONNECTED,
633	ED4_FUCKING_BIG_CURSOR,
634
635	ED4_CURSOR_TYPES
636
637	};
638
639	extern bool ED4_update_global_cursor_awars_allowed; // update selected species/SAI/cursor position
640
641	struct ED4_TerminalPredicate {
642	virtual ~ED4_TerminalPredicate() {}
643	virtual bool fulfilled_by(const ED4_terminal *) const = 0;
644	};
645
646	class ED4_WinContextFree { // denies usage of the following functions in classes derived from this
647	AW_device *current_device();
648	ED4_window *current_ed4w();
649	AW_window *current_aww();
650	ED4_cursor& current_cursor();
651	public:
652	void avoid_warning() {}
653	};
654
655	class ED4_cursor : virtual Noncopyable, virtual ED4_WinContextFree {
656	ED4_window *win;
657	ED4_index cursor_abs_x; // absolute (to terminal) x-position of cursor (absolute world coordinate of edit window)
658	int screen_position; // number of displayed characters leading the cursor
659	mutable ED4_base_position base_position; // # of bases left of cursor
660	ED4_CursorType ctype;
661	ED4_CursorShape *cursor_shape;
662
663	ED4_returncode draw_cursor(AW_pos x, AW_pos y);
664	ED4_returncode delete_cursor(AW_pos del_mark, ED4_base *target_terminal);
665
666	void updateAwars(bool new_term_selected);
667
668	public:
669
670	bool allowed_to_draw; // needed for cursor handling
671	ED4_terminal *owner_of_cursor;
672
673	bool is_partly_visible() const;
674	bool is_completely_visible() const;
675
676	bool is_hidden_inside_group() const;
677
678	void changeType(ED4_CursorType typ);
679	ED4_CursorType getType() const { return ctype; }
680
681	void redraw() { changeType(getType()); }
682
683	ED4_returncode HideCursor(); // deletes cursor and does refresh
684	ED4_returncode move_cursor(AW_event *event);
685	ED4_returncode show_clicked_cursor(AW_pos click_xpos, ED4_terminal *target_terminal);
686	ED4_returncode show_cursor_at(ED4_terminal *target_terminal, ED4_index what_pos);
687	ED4_returncode ShowCursor(ED4_index offset_x, ED4_cursor_move move, int move_pos = 1);
688
689	int get_sequence_pos() const;
690	int get_screen_pos() const { return screen_position; }
691
692	long get_abs_x() const { return cursor_abs_x; }
693	void set_abs_x();
694
695	int base2sequence_position(int base_pos) const { return base_position.get_sequence_position(owner_of_cursor, base_pos); }
696	int sequence2base_position(int seq_pos) const { return base_position.get_base_position(owner_of_cursor, seq_pos); }
697
698	int get_base_position() const { return sequence2base_position(get_sequence_pos()); }
699
700	void prepare_shutdown() { base_position.prepare_shutdown(); }
701
702	void jump_screen_pos(int screen_pos, ED4_CursorJumpType jump_type);
703	void jump_sequence_pos(int sequence_pos, ED4_CursorJumpType jump_type);
704	void jump_base_pos(int base_pos, ED4_CursorJumpType jump_type);
705
706	int get_screen_relative_pos() const;
707	void set_screen_relative_pos(int scroll_to_relpos);
708
709	void set_to_terminal(ED4_terminal *terminal, int seq_pos, ED4_CursorJumpType jump_type);
710
711	inline bool in_species_seq_terminal() const;
712	inline bool in_consensus_terminal() const;
713	inline bool in_SAI_terminal() const;
714
715	void announce_deletion(ED4_terminal *object) {
716	base_position.announce_deletion(object);
717	if (object == owner_of_cursor) owner_of_cursor = NULL; // no need to delete the cursor (deletion triggers full redraw)
718	}
719
720	void init();
721
722	ED4_window *window() const { return win; }
723
724	ED4_cursor(ED4_window *win);
725	~ED4_cursor();
726	};
727
728	class ED4_window : public ED4_foldable, virtual ED4_WinContextFree { // derived from Noncopyable
729	void set_scrollbar_indents();
730
731	public:
732	AW_window_menu_modes *aww; // Points to Window
733	ED4_window *next;
734	int slider_pos_horizontal;
735	int slider_pos_vertical;
736	ED4_scrolled_rectangle scrolled_rect;
737	int id; // unique id in window-list
738	ED4_coords coords;
739
740	static int no_of_windows;
741
742	char awar_path_for_cursor[50]; // position in current sequence, range = [1;len]
743	char awar_path_for_Ecoli[50]; // position relative to ecoli
744	char awar_path_for_basePos[50]; // base position in current sequence (# of bases left to cursor)
745	char awar_path_for_IUPAC[50]; // IUPAC decoder content for current position
746	char awar_path_for_helixNr[50]; // # of helix (or 0) for current position
747
748	bool is_hidden;
749	ED4_cursor cursor;
750
751	// ED4_window controlling functions
752	static ED4_window insert_window(AW_window_menu_modes new_aww); // append to window list
753
754	void delete_window(ED4_window *window); // delete from window list
755	void reset_all_for_new_config(); // reset structures for loading new config
756	ED4_window get_matching_ed4w(AW_window aww);
757
758	void announce_deletion(ED4_terminal *object) { cursor.announce_deletion(object); }
759
760	// functions concerned the scrolled area
761	void update_scrolled_rectangle();
762	ED4_returncode scroll_rectangle(int dx, int dy);
763	ED4_returncode set_scrolled_rectangle(ED4_base x_link, ED4_base y_link, ED4_base width_link, ED4_base height_link);
764
765	bool scrollbars_and_scrolledRect_inSync() const {
766	// Scrolling in EDIT4 window uses redundant data
767	// - dimension of folding lines
768	// - slider positions in AW_window and ED4_window
769	// This function checks whether they are in sync.
770
771	bool inSync =
772	(scrolled_rect.top_dim() == aww->slider_pos_vertical) &&
773	(scrolled_rect.left_dim() == aww->slider_pos_horizontal);
774
775	#if defined(DEBUG)
776	if (!inSync) {
777	fputs("scrollbars not in sync with scrolled_rect:\n", stderr);
778	#if defined(ARB_GTK)
779	#define POSTYPE "%zu"
780	#else
781	#define POSTYPE "%i"
782	#endif
783	fprintf(stderr, " aww->slider_pos_vertical =" POSTYPE " scrolled_rect->top_dim() =%f\n", aww->slider_pos_vertical, scrolled_rect.top_dim());
784	fprintf(stderr, " aww->slider_pos_horizontal=" POSTYPE " scrolled_rect->left_dim()=%f\n", aww->slider_pos_horizontal, scrolled_rect.left_dim());
785	}
786	#endif
787
788	return inSync;
789	}
790
791	void check_valid_scrollbar_values() { e4_assert(scrollbars_and_scrolledRect_inSync()); }
792
793	bool shows_xpos(int x) const { return x >= coords.window_left_clip_point && x <= coords.window_right_clip_point; }
794	bool partly_shows(int x1, int y1, int x2, int y2) const;
795	bool completely_shows(int x1, int y1, int x2, int y2) const;
796
797	void update_window_coords();
798
799	AW_device *get_device() const { return aww->get_device(AW_MIDDLE_AREA); }
800
801	ED4_window(AW_window_menu_modes *window);
802	~ED4_window();
803	};
804
805	class ED4_members : virtual Noncopyable {
806	// contains children related functions from members of a manager
807
808	ED4_manager *my_owner; // who is controlling this object
809	ED4_base **memberList;
810	ED4_index no_of_members; // How much members are in the list
811	ED4_index size_of_list;
812
813	public:
814
815	ED4_manager* owner() const { return my_owner; }
816	ED4_base* member(ED4_index i) const { e4_assert(i>=0 && i<size_of_list); return memberList[i]; }
817	ED4_index members() const { return no_of_members; }
818
819	ED4_returncode insert_member(ED4_base *new_member); // only used to move members with mouse
820	ED4_returncode append_member(ED4_base *new_member);
821
822	// an array is chosen instead of a linked list, because destructorhandling is more comfortable in various destructors (manager-destructors)
823
824	ED4_returncode remove_member(ED4_base *member);
825	ED4_index search_member(ED4_extension *location, ED4_properties prop); // search member
826	ED4_returncode shift_list(ED4_index start_index, int length);
827	// list has to be shifted because member_list is an array and not a linked list
828
829	ED4_returncode search_target_species (ED4_extension location, ED4_properties prop, ED4_base *found_member, ED4_level return_level);
830
831	ED4_returncode move_member (ED4_index old_pos, ED4_index new_pos);
832
833	#if defined(IMPLEMENT_DUMP)
834	void dump(size_t indent) const;
835	#endif // IMPLEMENT_DUMP
836
837	#if defined(ASSERTION_USED)
838	int members_ok() const;
839	#endif // ASSERTION_USED
840
841	ED4_members(ED4_manager *the_owner);
842	~ED4_members();
843	};
844
845	#ifdef DEBUG
846	// # define TEST_BASES_TABLE
847	#endif
848
849	#if defined(DEBUG) && !defined(DEVEL_RELEASE)
850	# define TEST_CHAR_TABLE_INTEGRITY
851	#endif
852
853	#define SHORT_TABLE_ELEM_SIZE 1
854	#define SHORT_TABLE_MAX_VALUE 0xff
855	#define LONG_TABLE_ELEM_SIZE 4
856
857	class ED4_bases_table : virtual Noncopyable {
858	int table_entry_size; // how many bytes are used for each element of 'no_of_bases' (1 or 4 bytes)
859	union {
860	unsigned char *shortTable;
861	int *longTable;
862	} no_of_bases; // counts bases for each sequence position
863	int no_of_entries; // length of bases table
864
865	int legal(int offset) const { return offset>=0 && offset<no_of_entries; }
866
867	void set_elem_long(int offset, int value) {
868	#ifdef TEST_BASES_TABLE
869	e4_assert(legal(offset));
870	e4_assert(table_entry_size==LONG_TABLE_ELEM_SIZE);
871	#endif
872	no_of_bases.longTable[offset] = value;
873	}
874
875	void set_elem_short(int offset, int value) {
876	#ifdef TEST_BASES_TABLE
877	e4_assert(legal(offset));
878	e4_assert(table_entry_size==SHORT_TABLE_ELEM_SIZE);
879	e4_assert(value>=0 && value<=SHORT_TABLE_MAX_VALUE);
880	#endif
881	no_of_bases.shortTable[offset] = value;
882	}
883
884	int get_elem_long(int offset) const {
885	#ifdef TEST_BASES_TABLE
886	e4_assert(legal(offset));
887	e4_assert(table_entry_size==LONG_TABLE_ELEM_SIZE);
888	#endif
889	return no_of_bases.longTable[offset];
890	}
891
892	int get_elem_short(int offset) const {
893	#ifdef TEST_BASES_TABLE
894	e4_assert(legal(offset));
895	e4_assert(table_entry_size==SHORT_TABLE_ELEM_SIZE);
896	#endif
897	return no_of_bases.shortTable[offset];
898	}
899
900	public:
901
902	ED4_bases_table(int maxseqlength);
903	~ED4_bases_table();
904
905	void init(int length);
906	int size() const { return no_of_entries; }
907
908	int get_table_entry_size() const { return table_entry_size; }
909	void expand_table_entry_size();
910	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; }
911
912	int operator[](int offset) const { return table_entry_size==SHORT_TABLE_ELEM_SIZE ? get_elem_short(offset) : get_elem_long(offset); }
913
914	void inc_short(int offset) {
915	int old = get_elem_short(offset);
916	e4_assert(old<255);
917	set_elem_short(offset, old+1);
918	}
919	void dec_short(int offset) {
920	int old = get_elem_short(offset);
921	e4_assert(old>0);
922	set_elem_short(offset, old-1);
923	}
924	void inc_long(int offset) {
925	int old = get_elem_long(offset);
926	set_elem_long(offset, old+1);
927	}
928	void dec_long(int offset) {
929	int old = get_elem_long(offset);
930	e4_assert(old>0);
931	set_elem_long(offset, old-1);
932	}
933
934	int firstDifference(const ED4_bases_table& other, int start, int end, int *firstDifferentPos) const;
935	int lastDifference(const ED4_bases_table& other, int start, int end, int *lastDifferentPos) const;
936
937	void add(const ED4_bases_table& other, int start, int end);
938	void sub(const ED4_bases_table& other, int start, int end);
939	void sub_and_add(const ED4_bases_table& Sub, const ED4_bases_table& Add, PosRange range);
940
941	void change_table_length(int new_length, int default_entry);
942
943
944	#if defined(TEST_CHAR_TABLE_INTEGRITY) \|\| defined(ASSERTION_USED)
945	int empty() const;
946	#endif // TEST_CHAR_TABLE_INTEGRITY
947	};
948
949	typedef ED4_bases_table *ED4_bases_table_ptr;
950
951	class ED4_char_table : virtual Noncopyable {
952	ED4_bases_table_ptr *bases_table;
953	int sequences; // # of sequences added to the table
954	int ignore; // this table will be ignored when calculating tables higher in hierarchy
955	// (used to suppress SAI in root_group_man tables)
956
957	// @@@ move statics into own class:
958	static bool initialized;
959	static unsigned char char_to_index_tab[MAXCHARTABLE];
960	static unsigned char *upper_index_chars;
961	static unsigned char *lower_index_chars;
962	static int used_bases_tables; // size of 'bases_table'
963	static GB_alignment_type ali_type;
964
965	static inline void set_char_to_index(unsigned char c, int index);
966
967	void add(const ED4_char_table& other, int start, int end);
968	void sub(const ED4_char_table& other, int start, int end);
969
970	void expand_tables();
971	int get_table_entry_size() const {
972	return linear_table(0).get_table_entry_size();
973	}
974	void prepare_to_add_elements(int new_sequences) {
975	e4_assert(used_bases_tables);
976	if (linear_table(0).bigger_table_entry_size_needed(sequences+new_sequences)) {
977	expand_tables();
978	}
979	}
980
981	public:
982
983	#if defined(TEST_CHAR_TABLE_INTEGRITY) \|\| defined(ASSERTION_USED)
984	bool ok() const;
985	bool empty() const;
986	#endif
987
988	#if defined(TEST_CHAR_TABLE_INTEGRITY)
989	void test() const; // test if table is valid (dumps core if invalid)
990	#else
991	void test() const {}
992	#endif
993
994	ED4_char_table(int maxseqlength=0);
995	~ED4_char_table();
996
997	static void initial_setup(const char *gap_chars, GB_alignment_type ali_type_);
998
999	void ignore_me() { ignore = 1; }
1000	int is_ignored() const { return ignore; }
1001
1002	void init(int maxseqlength);
1003	int size() const { return bases_table[0]->size(); }
1004	int added_sequences() const { return sequences; }
1005
1006	void bases_and_gaps_at(int column, int bases, int gaps) const;
1007
1008	unsigned char index_to_upperChar(int index) const;
1009	unsigned char index_to_lowerChar(int index) const;
1010
1011	// linear access to all tables
1012	ED4_bases_table& linear_table(int c) { e4_assert(c<used_bases_tables); return *bases_table[c]; }
1013	const ED4_bases_table& linear_table(int c) const { e4_assert(c<used_bases_tables); return *bases_table[c]; }
1014
1015	// access via character
1016	ED4_bases_table& table(int c) { e4_assert(c>0 && c<MAXCHARTABLE); return linear_table(char_to_index_tab[c]); }
1017	const ED4_bases_table& table(int c) const { e4_assert(c>0 && c<MAXCHARTABLE); return linear_table(char_to_index_tab[c]); }
1018
1019	const PosRange *changed_range(const ED4_char_table& other) const;
1020	static const PosRange changed_range(const char string1, const char *string2, int min_len);
1021
1022	void add(const ED4_char_table& other);
1023	void sub(const ED4_char_table& other);
1024	void sub_and_add(const ED4_char_table& Sub, const ED4_char_table& Add);
1025	void sub_and_add(const ED4_char_table& Sub, const ED4_char_table& Add, PosRange range);
1026
1027	void add(const char *string, int len);
1028	void sub(const char *string, int len);
1029	void sub_and_add(const char old_string, const char new_string, PosRange range);
1030
1031	void build_consensus_string_to(char *buffer, ExplicitRange range) const;
1032	char *build_consensus_string(PosRange range) const;
1033	char *build_consensus_string() const { return build_consensus_string(PosRange::whole()); }
1034
1035	void change_table_length(int new_length);
1036	};
1037
1038	// ----------------------------
1039	// ED4_species_pointer
1040
1041	class ED4_species_pointer : virtual Noncopyable {
1042	// @@@ shall be renamed into ED4_gbdata_pointer to reflect general usage
1043
1044	GBDATA *species_pointer; // points to database
1045
1046	void addCallback(ED4_base *base);
1047	void removeCallback(ED4_base *base);
1048
1049	public:
1050
1051	ED4_species_pointer();
1052	~ED4_species_pointer();
1053
1054	GBDATA *Get() const { return species_pointer; }
1055	void Set(GBDATA gbd, ED4_base base);
1056	void notify_deleted() {
1057	species_pointer=0;
1058	}
1059	};
1060
1061	// -----------------
1062	// ED4_base
1063
1064	class ED4_base;
1065	typedef ARB_ERROR (ED4_cb)(ED4_base , AW_CL, AW_CL);
1066	typedef ARB_ERROR (ED4_cb1)(ED4_base , AW_CL);
1067	typedef ARB_ERROR (ED4_cb0)(ED4_base );
1068
1069	enum ED4_species_type {
1070	ED4_SP_NONE,
1071	ED4_SP_SPECIES,
1072	ED4_SP_SAI,
1073	ED4_SP_CONSENSUS,
1074	};
1075
1076	class ED4_base : virtual Noncopyable {
1077	// base object
1078
1079	ED4_species_pointer my_species_pointer;
1080
1081	// cache world coordinates:
1082
1083	static int currTimestamp;
1084	mutable AW::Position lastPos;
1085	mutable int timestamp;
1086
1087	ED4_base_list *linked_objects; // linked list of objects which are depending from this object
1088
1089	public:
1090	const ED4_objspec& spec; // contains information about Objectproperties
1091
1092	ED4_manager *parent; // Points to parent
1093
1094
1095	ED4_properties dynamic_prop; // contains info about what i am, what i can do, what i should do
1096	char *id; // globally unique name in hierarchy
1097	ED4_index index; // defines the order of child objects
1098	ED4_base *width_link; // concerning the hierarchy
1099	ED4_base *height_link; // concerning the hierarchy
1100	ED4_extension extension; // contains relative info about graphical properties
1101	ED4_update_info update_info; // info about things to be done for the object, i.e. refresh; flag structure
1102	struct {
1103	unsigned int hidden : 1; // flag whether object is hidden or not
1104	} flag;
1105
1106	void draw_bb(int color);
1107
1108	DECLARE_DUMP_FOR_ROOTCLASS(ED4_base);
1109
1110	// function for species_pointer
1111
1112	GBDATA *get_species_pointer() const { return my_species_pointer.Get(); }
1113	void set_species_pointer(GBDATA *gbd) { my_species_pointer.Set(gbd, this); }
1114	int has_callback() const { return get_species_pointer()!=0; }
1115
1116	// callbacks
1117
1118	virtual void changed_by_database();
1119	virtual void deleted_from_database();
1120
1121	// functions concerned with graphic output
1122	int adjust_clipping_rectangle();
1123	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) = 0;
1124	virtual bool calc_bounding_box() = 0;
1125
1126	ED4_returncode clear_background(int color=0);
1127
1128	void set_links(ED4_base width_link, ED4_base height_link);
1129
1130	// functions concerned with special initialization
1131	void set_property(ED4_properties prop) { dynamic_prop = (ED4_properties) (dynamic_prop \| prop); }
1132	void clr_property(ED4_properties prop) { dynamic_prop = (ED4_properties) (dynamic_prop & ~prop); }
1133
1134	// functions concerned with coordinate transformation
1135
1136	void calc_rel_coords(AW_pos x, AW_pos y);
1137
1138	void calc_world_coords(AW_pos x, AW_pos y) const {
1139	update_world_coords_cache();
1140	*x = lastPos.xpos();
1141	*y = lastPos.ypos();
1142	}
1143	const AW::Position& calc_world_coords() const {
1144	update_world_coords_cache();
1145	return lastPos;
1146	}
1147
1148	void update_world_coords_cache() const {
1149	bool cache_up_to_date = timestamp == currTimestamp;
1150	if (!cache_up_to_date) {
1151	if (parent) {
1152	ED4_base pab = (ED4_base)parent;
1153	lastPos = pab->calc_world_coords();
1154	}
1155	else {
1156	lastPos = AW::Origin;
1157	}
1158	lastPos.move(extension.get_parent_offset());
1159	timestamp = currTimestamp;
1160	}
1161	}
1162
1163	static void touch_world_cache() {
1164	currTimestamp++;
1165	}
1166
1167	AW::Rectangle get_win_area(ED4_window *ed4w) const {
1168	AW::Position pos = ed4w->world_to_win_coords(calc_world_coords());
1169	return AW::Rectangle(pos, extension.get_size()-AW::Vector(1, 1));
1170	}
1171
1172	// functions which refer to the object as a child, i.e. travelling down the hierarchy
1173	virtual void request_refresh(int clear=1) = 0;
1174
1175	inline void request_resize();
1176	void request_resize_of_linked();
1177	void resize_requested_by_link(ED4_base *link);
1178	virtual void resize_requested_children() = 0;
1179
1180	virtual void delete_requested_children() = 0;
1181	virtual void Delete() = 0;
1182
1183	inline void set_update();
1184	virtual void update_requested_children() = 0;
1185
1186	virtual ED4_returncode move_requested_by_parent(ED4_move_info *mi) = 0;
1187	virtual ED4_returncode event_sent_by_parent(AW_event event, AW_window aww);
1188	virtual ED4_returncode move_requested_by_child(ED4_move_info *moveinfo) = 0;
1189
1190
1191	virtual ED4_returncode handle_move(ED4_move_info *moveinfo) = 0;
1192
1193	virtual ARB_ERROR route_down_hierarchy(ED4_cb cb, AW_CL cd1, AW_CL cd2);
1194	virtual ARB_ERROR route_down_hierarchy(ED4_cb1 cb, AW_CL cd) { return route_down_hierarchy(ED4_cb(cb), cd, 0); }
1195	virtual ARB_ERROR route_down_hierarchy(ED4_cb0 cb) { return route_down_hierarchy(ED4_cb(cb), 0, 0); }
1196
1197	int calc_group_depth();
1198
1199	// general purpose functions
1200	virtual ED4_base search_ID(const char id) = 0;
1201
1202	void check_all();
1203	short in_border(AW_pos abs_x, AW_pos abs_y, ED4_movemode mode);
1204	ED4_returncode set_width();
1205
1206
1207	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
1208
1209	ED4_base *get_parent(ED4_level lev) const;
1210	void unlink_from_parent();
1211	bool has_parent(ED4_manager *Parent);
1212	bool is_child_of(ED4_manager *Parent) { return has_parent(Parent); }
1213
1214	virtual char resolve_pointer_to_string_copy(int str_len = 0) const;
1215	virtual const char resolve_pointer_to_char_pntr(int str_len = 0) const;
1216
1217	ED4_group_manager *is_in_folded_group() const;
1218	virtual bool is_hidden() const = 0;
1219
1220	char *get_name_of_species(); // go from terminal to name of species
1221
1222	// functions which refer to the selected object(s), i.e. across the hierarchy
1223	virtual ED4_base *get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop)=0;
1224	virtual ED4_base *get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop)=0;
1225	virtual ED4_base *search_spec_child_rek(ED4_level level); // recursive search for level
1226
1227	ED4_terminal *get_next_terminal();
1228	ED4_terminal *get_prev_terminal();
1229
1230	ED4_returncode generate_configuration_string(char **generated_string);
1231
1232	virtual ED4_returncode remove_callbacks();
1233
1234	const ED4_terminal *get_consensus_relevant_terminal() const;
1235
1236	ED4_base(const ED4_objspec& spec_, GB_CSTR id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
1237	virtual ~ED4_base();
1238
1239	// use the following functions to test which derived class we have
1240
1241	int is_terminal() const { e4_assert(this); return spec.static_prop & ED4_P_IS_TERMINAL; }
1242
1243	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); }
1244
1245	int is_species_name_terminal() const { e4_assert(this); return spec.level & ED4_L_SPECIES_NAME; }
1246
1247	int is_sequence_info_terminal() const { e4_assert(this); return spec.level & ED4_L_SEQUENCE_INFO; }
1248	int is_sequence_terminal() const { e4_assert(this); return spec.level & ED4_L_SEQUENCE_STRING; }
1249	int is_orf_terminal() const { e4_assert(this); return spec.level & ED4_L_ORF; }
1250
1251	int is_pure_text_terminal() const { e4_assert(this); return spec.level & ED4_L_PURE_TEXT; }
1252	int is_columnStat_terminal() const { e4_assert(this); return spec.level & ED4_L_COL_STAT; }
1253
1254	int is_bracket_terminal() const { e4_assert(this); return spec.level & ED4_L_BRACKET; }
1255	int is_spacer_terminal() const { e4_assert(this); return spec.level & ED4_L_SPACER; }
1256	int is_line_terminal() const { e4_assert(this); return spec.level & ED4_L_LINE; }
1257
1258	int is_manager() const { e4_assert(this); return spec.static_prop & ED4_P_IS_MANAGER; }
1259
1260	int is_sequence_manager() const { e4_assert(this); return spec.level & ED4_L_SEQUENCE; }
1261	int is_multi_name_manager() const { e4_assert(this); return spec.level & ED4_L_MULTI_NAME; }
1262	int is_name_manager() const { e4_assert(this); return spec.level & ED4_L_NAME_MANAGER; }
1263	int is_multi_species_manager() const { e4_assert(this); return spec.level & ED4_L_MULTI_SPECIES; }
1264	int is_multi_sequence_manager() const { e4_assert(this); return spec.level & ED4_L_MULTI_SEQUENCE; }
1265	int is_device_manager() const { e4_assert(this); return spec.level & ED4_L_DEVICE; }
1266
1267	int is_group_manager() const { e4_assert(this); return spec.level & ED4_L_GROUP; }
1268	int is_root_group_manager() const { e4_assert(this); return spec.level & ED4_L_ROOTGROUP; }
1269	int is_abstract_group_manager() const { e4_assert(this); return spec.level & (ED4_L_GROUP\|ED4_L_ROOTGROUP); }
1270
1271	int is_species_manager() const { e4_assert(this); return spec.level & ED4_L_SPECIES; }
1272	int is_area_manager() const { e4_assert(this); return spec.level & ED4_L_AREA; }
1273
1274	// use the following functions to cast ED4_base to derived classes:
1275
1276	#define E4B_DECL_CASTOP_helper(Class,toName) \
1277	inline const Class *toName() const; \
1278	inline Class *toName();
1279
1280	#define E4B_AVOID_CAST__helper(Class,toName,isName) \
1281	const Class *toName() const; \
1282	Class *toName(); \
1283	int isName() const;
1284
1285	#define E4B_IMPL_CASTOP_helper(Class,toName,isName) \
1286	const Class *ED4_base::toName() const { \
1287	e4_assert(isName()); \
1288	return DOWNCAST(const Class*, this); \
1289	} \
1290	Class *ED4_base::toName() { \
1291	return const_cast<Class>(const_cast<const ED4_base>(this)->toName()); \
1292	}
1293
1294	#define E4B_DECL_CASTOP(name) E4B_DECL_CASTOP_helper(concat(ED4_,name), concat(to_,name))
1295	#define E4B_AVOID_UNNEEDED_CASTS(name) E4B_AVOID_CAST__helper(concat(ED4_,name), concat(to_,name), concat(is_,name))
1296	#define E4B_IMPL_CASTOP(name) E4B_IMPL_CASTOP_helper(concat(ED4_,name), concat(to_,name), concat(is_,name))
1297
1298	E4B_DECL_CASTOP(area_manager); // to_area_manager
1299	E4B_DECL_CASTOP(abstract_group_manager); // to_abstract_group_manager
1300	E4B_DECL_CASTOP(bracket_terminal); // to_bracket_terminal
1301	E4B_DECL_CASTOP(columnStat_terminal); // to_columnStat_terminal
1302	E4B_DECL_CASTOP(device_manager); // to_device_manager
1303	E4B_DECL_CASTOP(group_manager); // to_group_manager
1304	E4B_DECL_CASTOP(line_terminal); // to_line_terminal
1305	E4B_DECL_CASTOP(manager); // to_manager
1306	E4B_DECL_CASTOP(multi_name_manager); // to_multi_name_manager
1307	E4B_DECL_CASTOP(multi_sequence_manager); // to_multi_sequence_manager
1308	E4B_DECL_CASTOP(multi_species_manager); // to_multi_species_manager
1309	E4B_DECL_CASTOP(name_manager); // to_name_manager
1310	E4B_DECL_CASTOP(orf_terminal); // to_orf_terminal
1311	E4B_DECL_CASTOP(pure_text_terminal); // to_pure_text_terminal
1312	E4B_DECL_CASTOP(root_group_manager); // to_root_group_manager
1313	E4B_DECL_CASTOP(sequence_info_terminal); // to_sequence_info_terminal
1314	E4B_DECL_CASTOP(sequence_manager); // to_sequence_manager
1315	E4B_DECL_CASTOP(sequence_terminal); // to_sequence_terminal
1316	E4B_DECL_CASTOP(spacer_terminal); // to_spacer_terminal
1317	E4B_DECL_CASTOP(species_manager); // to_species_manager
1318	E4B_DECL_CASTOP(species_name_terminal); // to_species_name_terminal
1319	E4B_DECL_CASTOP(terminal); // to_terminal
1320	E4B_DECL_CASTOP(text_terminal); // to_text_terminal
1321
1322	// simple access to containing managers
1323	inline ED4_species_manager *containing_species_manager() const;
1324
1325	// discriminate between different sequence managers:
1326
1327	inline bool is_consensus_manager() const;
1328	inline bool is_SAI_manager() const;
1329	inline bool is_species_seq_manager() const;
1330
1331	inline ED4_species_type get_species_type() const; // works for all items (recursively) contained in ED4_species_manager
1332
1333	inline bool inside_consensus_manager() const;
1334	inline bool inside_SAI_manager() const;
1335	inline bool inside_species_seq_manager() const;
1336
1337	inline bool is_consensus_terminal() const;
1338	inline bool is_SAI_terminal() const;
1339	inline bool is_species_seq_terminal() const;
1340	};
1341
1342	struct ED4_manager : public ED4_base { // derived from a Noncopyable
1343	ED4_members *children;
1344
1345	E4B_AVOID_UNNEEDED_CASTS(manager);
1346	DECLARE_DUMP_FOR_BASECLASS(ED4_manager, ED4_base);
1347
1348	int refresh_flag_ok();
1349
1350	virtual void changed_by_database() OVERRIDE;
1351	virtual void deleted_from_database() OVERRIDE;
1352
1353	// functions concerned with graphics
1354	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) OVERRIDE;
1355	virtual bool calc_bounding_box() OVERRIDE;
1356
1357	ED4_returncode distribute_children();
1358
1359	// top-down functions, means travelling down the hierarchy
1360	virtual ED4_returncode event_sent_by_parent(AW_event event, AW_window aww) OVERRIDE;
1361
1362	virtual void request_refresh(int clear=1) OVERRIDE;
1363	ED4_returncode clear_refresh();
1364
1365	virtual void resize_requested_children() OVERRIDE;
1366
1367	virtual void update_requested_children() OVERRIDE;
1368
1369	virtual void delete_requested_children() OVERRIDE;
1370	virtual void Delete() OVERRIDE;
1371
1372	virtual ED4_returncode move_requested_by_parent(ED4_move_info *mi) OVERRIDE;
1373
1374	void create_consensus(ED4_abstract_group_manager upper_group_manager, arb_progress progress);
1375
1376	virtual ARB_ERROR route_down_hierarchy(ED4_cb cb, AW_CL cd1, AW_CL cd2) OVERRIDE;
1377	virtual ARB_ERROR route_down_hierarchy(ED4_cb1 cb, AW_CL cd) OVERRIDE { return route_down_hierarchy(ED4_cb(cb), cd, 0); }
1378	virtual ARB_ERROR route_down_hierarchy(ED4_cb0 cb) OVERRIDE { return route_down_hierarchy(ED4_cb(cb), 0, 0); }
1379
1380	ED4_base* find_first_that(ED4_level level, bool (condition)(ED4_base to_test, AW_CL arg), AW_CL arg);
1381	ED4_base* find_first_that(ED4_level level, bool (condition)(ED4_base to_test)) {
1382	return find_first_that(level, (bool()(ED4_base, AW_CL))condition, (AW_CL)0);
1383	}
1384
1385	// bottom-up functions
1386	virtual ED4_returncode move_requested_by_child(ED4_move_info *moveinfo) OVERRIDE;
1387	inline void resize_requested_by_child();
1388	ED4_returncode refresh_requested_by_child();
1389	void delete_requested_by_child();
1390	void update_requested_by_child();
1391
1392	ED4_base *get_defined_level(ED4_level lev) const;
1393
1394	// functions referring the consensus
1395
1396	ED4_returncode create_group(ED4_group_manager **group_manager, GB_CSTR group_name);
1397
1398	void update_consensus(ED4_manager old_parent, ED4_manager new_parent, ED4_base *sequence);
1399	ED4_returncode rebuild_consensi(ED4_base *start_species, ED4_update_flag update_flag);
1400
1401	ED4_returncode check_in_bases(ED4_base *added_base);
1402	ED4_returncode check_out_bases(ED4_base *subbed_base);
1403
1404	ED4_returncode update_bases(const ED4_base old_base, const ED4_base new_base, PosRange range = PosRange::whole());
1405	ED4_returncode update_bases(const char old_seq, int old_len, const char new_seq, int new_len, PosRange range = PosRange::whole());
1406	ED4_returncode update_bases(const char old_seq, int old_len, const ED4_base new_base, PosRange range = PosRange::whole());
1407	ED4_returncode update_bases(const ED4_char_table old_table, const ED4_char_table new_table, PosRange range = PosRange::whole());
1408
1409	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());
1410
1411	// handle moves across the hierarchy
1412	virtual ED4_returncode handle_move(ED4_move_info *moveinfo) OVERRIDE;
1413
1414	virtual ED4_base *get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop) OVERRIDE;
1415	virtual ED4_base *get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop) OVERRIDE;
1416	virtual ED4_base *search_spec_child_rek(ED4_level level) OVERRIDE; // recursive search for level
1417
1418	// general purpose functions
1419	virtual ED4_base search_ID(const char id) OVERRIDE;
1420	virtual ED4_returncode remove_callbacks() OVERRIDE;
1421
1422	ED4_terminal *get_first_terminal(int start_index=0) const;
1423	ED4_terminal *get_last_terminal(int start_index=-1) const;
1424
1425	void hide_children();
1426	void unhide_children();
1427
1428	bool is_hidden() const OVERRIDE {
1429	if (flag.hidden) return true;
1430	if (!parent) return false;
1431	return parent->is_hidden();
1432	}
1433
1434	ED4_manager(const ED4_objspec& spec_, const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1435	virtual ~ED4_manager() OVERRIDE;
1436	};
1437
1438	struct ED4_terminal : public ED4_base { // derived from a Noncopyable
1439	E4B_AVOID_UNNEEDED_CASTS(terminal);
1440
1441	struct { unsigned int deleted : 1; } tflag; // @@@ go bool
1442
1443	long curr_timestamp;
1444
1445	DECLARE_DUMP_FOR_BASECLASS(ED4_terminal,ED4_base);
1446
1447	// callbacks
1448
1449	virtual void changed_by_database() OVERRIDE;
1450	virtual void deleted_from_database() OVERRIDE;
1451
1452	// functions concerning graphic output
1453	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) OVERRIDE = 0;
1454	virtual ED4_returncode draw() = 0;
1455
1456	virtual bool calc_bounding_box() OVERRIDE;
1457
1458	ED4_returncode draw_drag_box(AW_pos x, AW_pos y, GB_CSTR text = NULL, int cursor_y=-1);
1459
1460	// functions which concern the object as a child
1461	virtual void request_refresh(int clear=1) OVERRIDE;
1462
1463	virtual void resize_requested_children() OVERRIDE;
1464
1465	virtual void update_requested_children() OVERRIDE;
1466	virtual void delete_requested_children() OVERRIDE;
1467	virtual void Delete() OVERRIDE;
1468
1469	virtual ED4_returncode move_requested_by_parent(ED4_move_info *mi) OVERRIDE;
1470	virtual ED4_returncode event_sent_by_parent(AW_event event, AW_window aww) OVERRIDE;
1471	virtual ED4_base *get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop) OVERRIDE;
1472	virtual ED4_base *get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop) OVERRIDE;
1473	virtual ED4_returncode move_requested_by_child(ED4_move_info *moveinfo) OVERRIDE;
1474	virtual ED4_returncode handle_move(ED4_move_info *moveinfo) OVERRIDE;
1475
1476	ED4_returncode kill_object();
1477
1478	// general purpose functions
1479	virtual ED4_base search_ID(const char id) OVERRIDE;
1480	virtual char resolve_pointer_to_string_copy(int str_len = 0) const OVERRIDE;
1481	virtual const char resolve_pointer_to_char_pntr(int str_len = 0) const OVERRIDE;
1482	virtual ED4_returncode remove_callbacks() OVERRIDE;
1483
1484	GB_ERROR write_sequence(const char *seq, int seq_len);
1485
1486	void scroll_into_view(ED4_window *ed4w);
1487	inline bool setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfoldGroups, ED4_CursorJumpType jump_type);
1488
1489	bool is_hidden() const OVERRIDE { return parent && parent->is_hidden(); }
1490
1491	ED4_terminal(const ED4_objspec& spec_, GB_CSTR id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
1492	virtual ~ED4_terminal() OVERRIDE;
1493	};
1494
1495	enum ED4_species_mode {
1496	ED4_SM_MOVE,
1497	ED4_SM_KILL,
1498	ED4_SM_MARK
1499	};
1500
1501	class ED4_reference_terminals : virtual Noncopyable {
1502	ED4_sequence_info_terminal *ref_sequence_info;
1503	ED4_sequence_terminal *ref_sequence;
1504	ED4_sequence_info_terminal *ref_column_stat_info;
1505	ED4_columnStat_terminal *ref_column_stat;
1506
1507	void null() { ref_sequence_info = 0; ref_sequence = 0; ref_column_stat = 0; ref_column_stat_info = 0; }
1508	public:
1509	void clear();
1510	void init(ED4_sequence_info_terminal , ED4_sequence_terminal , ED4_sequence_info_terminal , ED4_columnStat_terminal );
1511
1512	ED4_sequence_info_terminal *get_ref_sequence_info() { return ref_sequence_info; }
1513	ED4_sequence_terminal *get_ref_sequence() { return ref_sequence; }
1514	ED4_sequence_info_terminal *get_ref_column_stat_info() { return ref_column_stat_info; }
1515	ED4_columnStat_terminal *get_ref_column_stat() { return ref_column_stat; }
1516
1517	ED4_reference_terminals() { null(); }
1518	~ED4_reference_terminals() { clear(); }
1519	};
1520
1521	class ED4_WinContext {
1522	ED4_window *ed4w;
1523	AW_device *device;
1524
1525	bool is_set() const { return ed4w; }
1526	void init(ED4_window *ew) {
1527	e4_assert(ew);
1528	ed4w = ew;
1529	device = ed4w->get_device();
1530	}
1531
1532	void warn_missing_context() const;
1533	void expect_context() const { if (!is_set()) warn_missing_context(); }
1534
1535	protected:
1536	ED4_WinContext() : ed4w(0), device(0) {}
1537	static ED4_WinContext current_context;
1538
1539	public:
1540	inline ED4_WinContext(AW_window *aww_);
1541	ED4_WinContext(ED4_window *ed4w_) { init(ed4w_); }
1542
1543	AW_device *get_device() const { expect_context(); return device; }
1544	ED4_window *get_ed4w() const { expect_context(); return ed4w; }
1545
1546	static const ED4_WinContext& get_current_context() { return current_context; }
1547	static bool have_context() { return current_context.is_set(); }
1548	};
1549
1550	// accessors for current context (see also ED4_WinContextFree)
1551	inline AW_device *current_device() { return ED4_WinContext::get_current_context().get_device(); }
1552	inline ED4_window *current_ed4w() { return ED4_WinContext::get_current_context().get_ed4w(); }
1553	inline AW_window *current_aww() { return current_ed4w()->aww; }
1554	inline ED4_cursor& current_cursor() { return current_ed4w()->cursor; }
1555
1556
1557	class ED4_root : virtual Noncopyable {
1558	void ED4_ROOT() const { e4_assert(0); } // avoid ED4_root-members use global ED4_ROOT
1559
1560	void refresh_window_simple(bool redraw);
1561	void handle_update_requests(bool& redraw);
1562
1563	ED4_window *most_recently_used_window;
1564
1565	public:
1566	char *db_name; // name of Default Properties database (complete path)
1567	AW_root *aw_root; // Points to 'AW-Window-Controller'
1568	AW_default props_db; // Default Properties database
1569
1570	ED4_window *first_window; // Points to List of Main Windows of ED4
1571	ED4_main_manager *main_manager; // Points to Main manager of ED4
1572	ED4_area_manager *middle_area_man; // Points to middle area
1573	ED4_area_manager *top_area_man;
1574	ED4_root_group_manager *root_group_man;
1575	EDB_root_bact *database; // Points to Object which controls Data
1576	ED4_selected_list *selected_objects;
1577	ED4_scroll_links scroll_links;
1578	bool folding_action; // flag tells whether action was folding action or not
1579	ED4_reference_terminals ref_terminals;
1580	ED4_species_mode species_mode;
1581	ED4_scroll_picture scroll_picture;
1582	BI_ecoli_ref *ecoli_ref;
1583	char *alignment_name;
1584	GB_alignment_type alignment_type;
1585	AWT_reference *reference;
1586	AWT_seq_colors *sequence_colors;
1587	AW_gc_manager gc_manager;
1588	ST_ML *st_ml;
1589	AW_helix *helix;
1590	int helix_spacing;
1591	long helix_add_spacing;
1592	long terminal_add_spacing;
1593	char *protstruct; // protein structure summary
1594	long protstruct_len; // protein structure summary
1595	ed_key *edk;
1596	ED4_Edit_String *edit_string;
1597
1598	bool column_stat_activated;
1599	bool column_stat_initialized;
1600	bool visualizeSAI;
1601	bool visualizeSAI_allSpecies;
1602
1603	int temp_gc;
1604	AW_font_group font_group;
1605
1606	void announce_useraction_in(AW_window *aww);
1607	ED4_window *get_most_recently_used_window() const {
1608	e4_assert(most_recently_used_window);
1609	return most_recently_used_window;
1610	}
1611
1612	inline ED4_device_manager *get_device_manager();
1613
1614	// Initializing functions
1615	ED4_returncode create_hierarchy(char area_string_middle, char area_string_top);
1616	ED4_returncode init_alignment();
1617	void recalc_font_group();
1618
1619	AW_window *create_new_window();
1620	ED4_returncode generate_window(AW_device device, ED4_window new_window);
1621	void copy_window_struct(ED4_window source, ED4_window destination);
1622
1623	// functions concerned with global refresh and resize
1624	void resize_all();
1625
1626	void special_window_refresh(bool handle_updates);
1627	ED4_returncode refresh_all_windows(bool redraw);
1628
1629	void request_refresh_for_all_terminals();
1630	void request_refresh_for_specific_terminals(ED4_level lev);
1631	void request_refresh_for_consensus_terminals();
1632	void request_refresh_for_sequence_terminals();
1633
1634	inline void announce_deletion(ED4_base *object); // before deleting an object, use this to announce
1635
1636	// functions concerned with list of selected objects
1637	ED4_returncode add_to_selected(ED4_species_name_terminal *object);
1638	void remove_from_selected(ED4_species_name_terminal *object);
1639	ED4_returncode deselect_all();
1640
1641	ED4_returncode get_area_rectangle(AW_screen_area *rect, AW_pos x, AW_pos y);
1642
1643	ED4_index pixel2pos(AW_pos click_x);
1644
1645	void remove_all_callbacks();
1646
1647	ED4_root(int argc, char** argv);
1648	~ED4_root();
1649	};
1650
1651	ED4_WinContext::ED4_WinContext(AW_window *aww_) { init(ED4_ROOT->first_window->get_matching_ed4w(aww_)); }
1652
1653	struct ED4_LocalWinContext : private ED4_WinContext {
1654	ED4_LocalWinContext(AW_window *aww) : ED4_WinContext(current_context) { current_context = ED4_WinContext(aww); }
1655	ED4_LocalWinContext(ED4_window *ew) : ED4_WinContext(current_context) { current_context = ED4_WinContext(ew); }
1656	~ED4_LocalWinContext() { current_context = *this; }
1657	};
1658
1659	class ED4_MostRecentWinContext : virtual Noncopyable {
1660	ED4_LocalWinContext *most_recent;
1661	public:
1662	ED4_MostRecentWinContext() : most_recent(0) {
1663	if (!ED4_WinContext::have_context()) {
1664	most_recent = new ED4_LocalWinContext(ED4_ROOT->get_most_recently_used_window());
1665	}
1666	}
1667	~ED4_MostRecentWinContext() {
1668	delete most_recent;
1669	}
1670	};
1671
1672	inline void ED4_root::announce_deletion(ED4_base *object) {
1673	if (object->is_terminal()) {
1674	ED4_terminal *term = object->to_terminal();
1675	for (ED4_window *win = first_window; win; win = win->next) {
1676	ED4_LocalWinContext uses(win);
1677	win->announce_deletion(term);
1678	}
1679	}
1680	}
1681
1682	// ------------------------
1683	// manager classes
1684	//
1685	// All manager classes only differ in their static properties.
1686	// This kind of construction was chosen for using a minimum of RAM
1687
1688	class ED4_main_manager : public ED4_manager { // derived from a Noncopyable
1689	// first in hierarchy
1690
1691	E4B_AVOID_UNNEEDED_CASTS(main_manager);
1692
1693	// these terminals are redrawn after refresh (with increase clipping area)
1694	// to revert text from middle area drawn into top area:
1695	ED4_terminal *top_middle_line;
1696	ED4_terminal *top_middle_spacer;
1697
1698	public:
1699	ED4_main_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1700
1701	void set_top_middle_spacer_terminal(ED4_terminal *top_middle_spacer_) { top_middle_spacer = top_middle_spacer_; }
1702	void set_top_middle_line_terminal(ED4_terminal *top_middle_line_) { top_middle_line = top_middle_line_; }
1703
1704	ED4_terminal *get_top_middle_spacer_terminal() const { return top_middle_spacer; }
1705	ED4_terminal *get_top_middle_line_terminal() const { return top_middle_line; }
1706
1707	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1708
1709	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) OVERRIDE;
1710	virtual void resize_requested_children() OVERRIDE;
1711
1712	void clear_whole_background();
1713	};
1714
1715	struct ED4_device_manager : public ED4_manager {
1716	E4B_AVOID_UNNEEDED_CASTS(device_manager);
1717	ED4_device_manager (const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1718	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1719	};
1720
1721	struct ED4_area_manager : public ED4_manager {
1722	E4B_AVOID_UNNEEDED_CASTS(area_manager);
1723	ED4_area_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1724	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1725
1726	ED4_multi_species_manager *get_multi_species_manager() const {
1727	return get_defined_level(ED4_L_MULTI_SPECIES)->to_multi_species_manager();
1728	}
1729	};
1730
1731	class ED4_multi_species_manager : public ED4_manager {
1732	E4B_AVOID_UNNEEDED_CASTS(multi_species_manager);
1733
1734	int species; // # of species (-1 == unknown)
1735	int selected_species; // # of selected species (-1 == unknown)
1736
1737	void set_species_counters(int no_of_species, int no_of_selected);
1738	#ifdef DEBUG
1739	void count_species(int speciesPtr, int selectedPtr) const;
1740	#endif
1741	void update_species_counters();
1742
1743	public:
1744	ED4_multi_species_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1745
1746	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1747
1748	virtual void update_requested_children() OVERRIDE;
1749	virtual void delete_requested_children() OVERRIDE;
1750
1751	int count_visible_children(); // is called by a multi_species_manager
1752
1753	ED4_species_manager *get_consensus_manager() const; // returns the consensus-manager or NULL
1754	ED4_species_name_terminal *get_consensus_name_terminal() const; // returns the consensus-name-terminal or NULL
1755
1756	// functions concerned with selection
1757	int get_no_of_selected_species();
1758	int get_no_of_species();
1759
1760	void update_group_id();
1761
1762	void invalidate_species_counters();
1763	int has_valid_counters() const { return species != -1 && selected_species!=-1; }
1764	bool all_are_selected() const { e4_assert(has_valid_counters()); return species == selected_species; }
1765
1766	void select_all(bool only_species);
1767	void deselect_all_species_and_SAI();
1768	void invert_selection_of_all_species();
1769	void marked_species_select(bool select);
1770	void selected_species_mark(bool mark);
1771
1772	void toggle_selected_species();
1773	};
1774
1775	class ED4_abstract_group_manager : public ED4_manager {
1776	E4B_AVOID_UNNEEDED_CASTS(abstract_group_manager);
1777	protected:
1778	ED4_char_table my_table; // table concerning Consensusfunction
1779
1780	public:
1781	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);
1782
1783	DECLARE_DUMP_FOR_BASECLASS(ED4_abstract_group_manager, ED4_manager);
1784
1785	ED4_char_table& table() { return my_table; }
1786	const ED4_char_table& table() const { return my_table; }
1787
1788	ED4_bases_table& table(unsigned char c) { return table().table(c); }
1789	const ED4_bases_table& table(unsigned char c) const { return table().table(c); }
1790
1791	ED4_multi_species_manager *get_multi_species_manager() const {
1792	return get_defined_level(ED4_L_MULTI_SPECIES)->to_multi_species_manager();
1793	}
1794	};
1795
1796	struct ED4_group_manager : public ED4_abstract_group_manager {
1797	E4B_AVOID_UNNEEDED_CASTS(group_manager);
1798	ED4_group_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1799	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_group_manager);
1800	void reinit_char_table();
1801	};
1802
1803	enum ED4_remap_mode {
1804	ED4_RM_NONE, // no remapping (normal mode)
1805	ED4_RM_SHOW_ABOVE, // Show all positions, where xxx% of all edited sequences have any base
1806	ED4_RM_MAX_ALIGN, // ------------------------- any edited sequence has a base
1807	ED4_RM_MAX_EDIT, // like ED4_RM_MAX_ALIGN, but bases are pushed OVER remapped gaps (not INTO)
1808	ED4_RM_DYNAMIC_GAPS, // gaps shown as spaces (more gaps => more spaces)
1809
1810	ED4_RM_MODES
1811
1812	};
1813
1814	class ED4_remap : virtual Noncopyable {
1815
1816	ED4_remap_mode mode;
1817	int show_above_percent; // used only for ED4_RM_SHOW_ABOVE
1818
1819	size_t sequence_table_len; // allocated size of sequence_to_screen_tab
1820	size_t screen_table_len; // allocated size of screen_to_sequence_tab
1821
1822	size_t sequence_len; // size of recently compiled part of sequence_to_screen_tab
1823	size_t screen_len; // size of recently compiled part of screen_to_sequence_tab
1824
1825	int *screen_to_sequence_tab;
1826	int *sequence_to_screen_tab; // <0 means position is not mapped (last displayed sequence position)
1827
1828	int changed; // remap-table changed at last compile
1829	int update_needed; // remapping should be recompiled
1830
1831	inline void set_sequence_to_screen(int pos, int newVal);
1832
1833	public:
1834
1835	ED4_remap();
1836	~ED4_remap();
1837
1838	int screen_to_sequence(int screen_pos) const;
1839
1840	int sequence_to_screen_PLAIN(int sequence_pos) const {
1841	e4_assert(sequence_pos>=0 && size_t(sequence_pos)<=sequence_len);
1842	return sequence_to_screen_tab[sequence_pos];
1843	}
1844	int shown_sequence_to_screen(int sequence_pos) const {
1845	// as well works for sequence_pos == MAXSEQUENCECHARACTERLENGTH
1846	int screen_pos = sequence_to_screen_PLAIN(sequence_pos);
1847	e4_assert(screen_pos >= 0); // sequence_pos expected to be visible (i.e. not folded away)
1848	return screen_pos;
1849	}
1850
1851	int clipped_sequence_to_screen_PLAIN(int sequence_pos) const;
1852	int sequence_to_screen(int sequence_pos) const;
1853
1854	PosRange sequence_to_screen(PosRange range) const {
1855	e4_assert(!range.is_empty());
1856	return PosRange(sequence_to_screen(range.start()), sequence_to_screen(range.end()));
1857	}
1858	PosRange screen_to_sequence(PosRange range) const {
1859	e4_assert(!range.is_empty());
1860	if (range.is_unlimited()) return PosRange::from(screen_to_sequence(range.start()));
1861	return PosRange(screen_to_sequence(range.start()), screen_to_sequence(range.end()));
1862	}
1863
1864	size_t get_max_screen_pos() const { return screen_len-1; }
1865
1866	ED4_remap_mode get_mode() const { return mode; }
1867	void set_mode(ED4_remap_mode Mode, int above_percent) {
1868	if (Mode<0 \|\| Mode>=ED4_RM_MODES) {
1869	Mode = ED4_RM_NONE;
1870	}
1871	if (mode!=Mode) {
1872	mode = Mode;
1873	update_needed = 1;
1874	}
1875
1876	if (show_above_percent!=above_percent) {
1877	show_above_percent = above_percent;
1878	if (mode==ED4_RM_SHOW_ABOVE) {
1879	update_needed = 1;
1880	}
1881	}
1882	}
1883
1884	void mark_compile_needed(); // recompile if mode != none
1885	void mark_compile_needed_force(); // always recompile
1886	int compile_needed() const { return update_needed; }
1887
1888	GB_ERROR compile(ED4_root_group_manager *gm);
1889	int was_changed() const { return changed; } // mapping changed by last compile ?
1890
1891	int is_shown(int position) const { return sequence_to_screen_PLAIN(position)>=0; }
1892
1893	ExplicitRange clip_screen_range(PosRange screen_range) const { return ExplicitRange(screen_range, screen_len-1); }
1894	};
1895
1896	class ED4_root_group_manager : public ED4_abstract_group_manager {
1897	E4B_AVOID_UNNEEDED_CASTS(root_group_manager);
1898	ED4_remap my_remap;
1899	public:
1900	ED4_root_group_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1901
1902	bool update_remap(); // 'true' if mapping has changed
1903
1904	const ED4_remap *remap() const { return &my_remap; }
1905	ED4_remap *remap() { return &my_remap; }
1906
1907	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) OVERRIDE;
1908	virtual void resize_requested_children() OVERRIDE;
1909
1910	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_group_manager);
1911	};
1912
1913	typedef void (ED4_species_manager_cb)(ED4_species_manager, AW_CL);
1914
1915	class ED4_species_manager_cb_data {
1916	ED4_species_manager_cb cb;
1917	AW_CL cd; // client data
1918
1919	public:
1920	ED4_species_manager_cb_data(ED4_species_manager_cb cb_, AW_CL cd_) : cb(cb_), cd(cd_) {}
1921
1922	void call(ED4_species_manager *man) const { cb(man, cd); }
1923	bool operator == (const ED4_species_manager_cb_data& other) const {
1924	return
1925	(char)cb == (char)other.cb &&
1926	(char)cd == (char)other.cd;
1927	}
1928	};
1929
1930	class ED4_species_manager : public ED4_manager {
1931	E4B_AVOID_UNNEEDED_CASTS(species_manager);
1932
1933	std::list<ED4_species_manager_cb_data> callbacks;
1934
1935	ED4_species_type type;
1936	bool selected;
1937
1938	public:
1939	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);
1940	~ED4_species_manager() OVERRIDE;
1941
1942	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1943
1944	ED4_species_type get_type() const { return type; }
1945
1946	bool is_selected() const { return selected; }
1947	void set_selected(bool select) {
1948	// e4_assert(type != ED4_SP_CONSENSUS); // it's not allowed to select a consensus // @@@ happens atm when moving a group
1949	selected = select;
1950	}
1951
1952	bool setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfold_groups, ED4_CursorJumpType jump_type);
1953
1954	void add_sequence_changed_cb(ED4_species_manager_cb cb, AW_CL cd);
1955	void remove_sequence_changed_cb(ED4_species_manager_cb cb, AW_CL cd);
1956	void remove_all_callbacks();
1957
1958	void do_callbacks();
1959
1960	ED4_species_name_terminal *get_name_terminal() const { return children->member(0)->to_species_name_terminal(); }
1961	};
1962
1963	inline ED4_species_manager *ED4_base::containing_species_manager() const {
1964	ED4_base *sman = get_parent(ED4_L_SPECIES);
1965	return sman ? sman->to_species_manager() : NULL;
1966	}
1967
1968	inline bool ED4_base::is_consensus_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_CONSENSUS; }
1969	inline bool ED4_base::is_SAI_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_SAI; }
1970	inline bool ED4_base::is_species_seq_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_SPECIES; }
1971
1972	inline ED4_species_type ED4_base::get_species_type() const {
1973	ED4_species_manager *sman = containing_species_manager();
1974	return sman ? sman->get_type() : ED4_SP_NONE;
1975	}
1976
1977	inline bool ED4_base::inside_consensus_manager() const { return get_species_type() == ED4_SP_CONSENSUS; }
1978	inline bool ED4_base::inside_SAI_manager() const { return get_species_type() == ED4_SP_SAI; }
1979	inline bool ED4_base::inside_species_seq_manager() const { return get_species_type() == ED4_SP_SPECIES; }
1980
1981	inline bool ED4_base::is_consensus_terminal() const { return is_sequence_terminal() && inside_consensus_manager(); }
1982	inline bool ED4_base::is_SAI_terminal() const { return is_sequence_terminal() && inside_SAI_manager(); }
1983	inline bool ED4_base::is_species_seq_terminal() const { return is_sequence_terminal() && inside_species_seq_manager(); }
1984
1985	inline bool ED4_cursor::in_species_seq_terminal() const { return owner_of_cursor && owner_of_cursor->is_species_seq_terminal(); }
1986	inline bool ED4_cursor::in_consensus_terminal() const { return owner_of_cursor && owner_of_cursor->is_consensus_terminal(); }
1987	inline bool ED4_cursor::in_SAI_terminal() const { return owner_of_cursor && owner_of_cursor->is_SAI_terminal(); }
1988
1989
1990	struct ED4_multi_sequence_manager : public ED4_manager {
1991	E4B_AVOID_UNNEEDED_CASTS(multi_sequence_manager);
1992	ED4_multi_sequence_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1993	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1994	};
1995
1996	struct ED4_sequence_manager : public ED4_manager {
1997	E4B_AVOID_UNNEEDED_CASTS(sequence_manager);
1998	ED4_sequence_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
1999	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
2000	};
2001
2002	struct ED4_multi_name_manager : public ED4_manager {
2003	E4B_AVOID_UNNEEDED_CASTS(multi_name_manager);
2004	// member of ED4_species_manager (contains ED4_name_manager for name and info)
2005	ED4_multi_name_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2006	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
2007	};
2008
2009
2010	struct ED4_name_manager : public ED4_manager {
2011	E4B_AVOID_UNNEEDED_CASTS(name_manager);
2012	// member of ED4_multi_name_manager (contains speciesname or other info concerning the species)
2013	ED4_name_manager(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2014	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
2015	};
2016
2017
2018	// -------------------------
2019	// terminal classes
2020
2021
2022	struct ED4_tree_terminal : public ED4_terminal {
2023	E4B_AVOID_UNNEEDED_CASTS(tree_terminal);
2024
2025	virtual ED4_returncode draw() OVERRIDE;
2026	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) OVERRIDE;
2027
2028	ED4_tree_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2029
2030	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2031	};
2032
2033	struct ED4_bracket_terminal : public ED4_terminal {
2034	E4B_AVOID_UNNEEDED_CASTS(bracket_terminal);
2035
2036	virtual ED4_returncode draw() OVERRIDE;
2037	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) OVERRIDE;
2038
2039	void fold();
2040	void unfold();
2041
2042	ED4_bracket_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2043
2044	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2045	};
2046
2047	struct ED4_text_terminal : public ED4_terminal {
2048	E4B_AVOID_UNNEEDED_CASTS(text_terminal);
2049
2050	// functions concerning graphic output
2051	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) OVERRIDE;
2052	virtual ED4_returncode draw() OVERRIDE;
2053
2054	virtual int get_length() const = 0;
2055	virtual void deleted_from_database() OVERRIDE;
2056
2057	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);
2058	virtual ~ED4_text_terminal() OVERRIDE {}
2059
2060	DECLARE_DUMP_FOR_BASECLASS(ED4_text_terminal, ED4_terminal);
2061	};
2062
2063	class ED4_abstract_sequence_terminal : public ED4_text_terminal { // derived from a Noncopyable
2064
2065	PosRange pixel2index(PosRange pixel_range);
2066
2067	E4B_AVOID_UNNEEDED_CASTS(abstract_sequence_terminal);
2068	public:
2069	char *species_name; // @@@ wrong place (may be member of ED4_sequence_manager)
2070
2071
2072	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);
2073	virtual ~ED4_abstract_sequence_terminal() OVERRIDE;
2074
2075	virtual GB_alignment_type GetAliType() = 0;
2076	virtual int get_length() const OVERRIDE { int len; resolve_pointer_to_char_pntr(&len); return len; }
2077
2078	ED4_species_name_terminal *corresponding_species_name_terminal() const {
2079	return get_parent(ED4_L_SPECIES)->search_spec_child_rek(ED4_L_SPECIES_NAME)->to_species_name_terminal();
2080	}
2081	PosRange calc_interval_displayed_in_rectangle(AW_screen_area *area_rect);
2082	PosRange calc_update_interval();
2083
2084	DECLARE_DUMP_FOR_BASECLASS(ED4_abstract_sequence_terminal, ED4_text_terminal);
2085	};
2086
2087	class ED4_orf_terminal : public ED4_abstract_sequence_terminal { // derived from a Noncopyable
2088	// NOTE: ED4_orf_terminal is a separate terminal class used to display Open Reading Frames (ORFs)
2089	// for the corresponding gene (DNA) sequence. It is used in ProteinViewer Module and should not be
2090	// used for drawing aminoacid sequence alone as in protein alignment. Aminoacid sequences are
2091	// handled by the standard "ED4_sequence_terminal" class.
2092
2093	char *aaSequence;
2094	size_t aaSeqLen;
2095	char *aaColor;
2096	int aaStartPos;
2097	int aaStrandType;
2098
2099	virtual ED4_returncode draw() OVERRIDE;
2100	E4B_AVOID_UNNEEDED_CASTS(orf_terminal);
2101	public:
2102	ED4_orf_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2103	virtual ~ED4_orf_terminal() OVERRIDE;
2104
2105	virtual GB_alignment_type GetAliType() OVERRIDE;
2106
2107	void SET_aaSeqFlags (int startPos, int strandType) { aaStartPos = startPos; aaStrandType = strandType; }
2108	void SET_aaSequence(const char *aaSeq) { freedup(aaSequence, aaSeq); aaSeqLen = strlen(aaSequence); }
2109	void SET_aaColor(const char *aaSeq) { freedup(aaColor, aaSeq); }
2110
2111	int GET_aaStartPos () { return aaStartPos; }
2112	int GET_aaStrandType () { return aaStrandType; }
2113
2114	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_sequence_terminal);
2115	};
2116
2117	class ED4_sequence_terminal : public ED4_abstract_sequence_terminal { // derived from a Noncopyable
2118	mutable ED4_SearchResults searchResults;
2119	bool shall_display_secstruct_info; // helix or protstruct
2120
2121	virtual ED4_returncode draw() OVERRIDE;
2122
2123	E4B_AVOID_UNNEEDED_CASTS(sequence_terminal);
2124
2125	public:
2126
2127	AP_tree *st_ml_node;
2128
2129	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_);
2130
2131	virtual GB_alignment_type GetAliType() OVERRIDE;
2132
2133	virtual void deleted_from_database() OVERRIDE;
2134	virtual int get_length() const OVERRIDE { return ED4_abstract_sequence_terminal::get_length(); }
2135
2136	void set_secstruct_display(bool show) { shall_display_secstruct_info = show; }
2137
2138	ED4_SearchResults& results() const { return searchResults; }
2139
2140	ED4_columnStat_terminal *corresponding_columnStat_terminal() const {
2141	ED4_base *col_term = get_parent(ED4_L_MULTI_SEQUENCE)->search_spec_child_rek(ED4_L_COL_STAT);
2142	return col_term ? col_term->to_columnStat_terminal() : 0;
2143	}
2144
2145	DECLARE_DUMP_FOR_MIDCLASS(ED4_sequence_terminal,ED4_abstract_sequence_terminal);
2146	};
2147
2148	class ED4_columnStat_terminal : public ED4_text_terminal { // derived from a Noncopyable
2149	char *likelihood[4]; // likelihood-array for each base (ACGU) [length of array = alignment_length]
2150	int latest_update;
2151
2152	static double threshold;
2153
2154	int update_likelihood();
2155
2156	E4B_AVOID_UNNEEDED_CASTS(columnStat_terminal);
2157
2158	public:
2159	// functions concerning graphic output
2160	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) OVERRIDE;
2161	virtual ED4_returncode draw() OVERRIDE;
2162	virtual int get_length() const OVERRIDE { return corresponding_sequence_terminal()->get_length(); }
2163
2164	static int threshold_is_set();
2165	static void set_threshold(double aThreshold);
2166	static double get_threshold() { return threshold; }
2167
2168	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(); }
2169
2170	GB_CSTR build_probe_match_string(PosRange range) const;
2171
2172	ED4_columnStat_terminal(GB_CSTR id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
2173	~ED4_columnStat_terminal() OVERRIDE;
2174
2175	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2176	};
2177
2178	struct ED4_species_name_terminal : public ED4_text_terminal { // derived from a Noncopyable
2179	ED4_species_name_terminal(GB_CSTR id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
2180	~ED4_species_name_terminal() OVERRIDE { delete selection_info; }
2181
2182	E4B_AVOID_UNNEEDED_CASTS(species_name_terminal);
2183
2184	ED4_selection_entry *selection_info; // Info about i.e. Position
2185	bool dragged;
2186
2187	GB_CSTR get_displayed_text() const;
2188	virtual int get_length() const OVERRIDE { return strlen(get_displayed_text()); }
2189
2190	ED4_sequence_terminal *corresponding_sequence_terminal() const {
2191	ED4_base *seq_term = get_parent(ED4_L_SPECIES)->search_spec_child_rek(ED4_L_SEQUENCE_STRING);
2192	return seq_term ? seq_term->to_sequence_terminal() : 0;
2193	}
2194
2195	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2196	};
2197
2198	struct ED4_sequence_info_terminal : public ED4_text_terminal {
2199	E4B_AVOID_UNNEEDED_CASTS(sequence_info_terminal);
2200
2201	ED4_sequence_info_terminal(const char id, / GBDATA gbd, / AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager *parent);
2202
2203	ED4_species_name_terminal *corresponding_species_name_terminal() const {
2204	return get_parent(ED4_L_SPECIES)->search_spec_child_rek(ED4_L_SPECIES_NAME)->to_species_name_terminal();
2205	}
2206
2207	virtual ED4_returncode draw() OVERRIDE;
2208
2209	GBDATA *data() { return get_species_pointer(); } // DB-entry ("ali_xxx/data")
2210	const GBDATA *data() const { return get_species_pointer(); }
2211
2212	virtual int get_length() const OVERRIDE { return 1+strlen(id); }
2213
2214	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2215	};
2216
2217	struct ED4_pure_text_terminal : public ED4_text_terminal {
2218	E4B_AVOID_UNNEEDED_CASTS(pure_text_terminal);
2219
2220	ED4_pure_text_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2221
2222	virtual int get_length() const OVERRIDE { int len; resolve_pointer_to_char_pntr(&len); return len; }
2223
2224	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2225	};
2226
2227	class ED4_consensus_sequence_terminal : public ED4_sequence_terminal {
2228	E4B_AVOID_UNNEEDED_CASTS(consensus_sequence_terminal);
2229
2230	virtual ED4_returncode draw() OVERRIDE;
2231	ED4_char_table& get_char_table() const { return get_parent(ED4_L_GROUP)->to_group_manager()->table(); }
2232	public:
2233	ED4_consensus_sequence_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2234
2235	virtual int get_length() const OVERRIDE;
2236
2237	DECLARE_DUMP_FOR_LEAFCLASS(ED4_sequence_terminal);
2238	};
2239
2240	class ED4_spacer_terminal : public ED4_terminal {
2241	E4B_AVOID_UNNEEDED_CASTS(spacer_terminal);
2242	bool shallDraw; // true -> spacer is really drawn (otherwise it's only a placeholder)
2243
2244	public:
2245	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) OVERRIDE;
2246	virtual ED4_returncode draw() OVERRIDE;
2247
2248	ED4_spacer_terminal(const char id, bool shallDraw_, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2249
2250	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2251	};
2252
2253	struct ED4_line_terminal : public ED4_terminal {
2254	E4B_AVOID_UNNEEDED_CASTS(line_terminal);
2255
2256	virtual ED4_returncode Show(int refresh_all=0, int is_cleared=0) OVERRIDE;
2257	virtual ED4_returncode draw() OVERRIDE;
2258
2259	ED4_line_terminal(const char id, AW_pos x, AW_pos y, AW_pos width, AW_pos height, ED4_manager parent);
2260
2261	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2262	};
2263
2264
2265	// ----------------------------------------------
2266	// inlines which need complete classdefs
2267
2268	inline void ED4_base::set_update() { // @@@ rename into request_update
2269	if (!update_info.update_requested) {
2270	update_info.update_requested = 1;
2271	if (parent) parent->update_requested_by_child();
2272	}
2273	}
2274
2275	inline void ED4_base::request_resize() {
2276	update_info.set_resize(1);
2277	if (parent) parent->resize_requested_by_child();
2278	}
2279
2280	void ED4_manager::resize_requested_by_child() {
2281	if (!update_info.resize) request_resize();
2282	}
2283
2284
2285	inline bool ED4_terminal::setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfoldGroups, ED4_CursorJumpType jump_type) {
2286	ED4_species_manager *sm = get_parent(ED4_L_SPECIES)->to_species_manager();
2287	return sm->setCursorTo(cursor, seq_pos, unfoldGroups, jump_type);
2288	}
2289
2290	E4B_IMPL_CASTOP(area_manager); // to_area_manager
2291	E4B_IMPL_CASTOP(abstract_group_manager); // to_abstract_group_manager
2292	E4B_IMPL_CASTOP(bracket_terminal); // to_bracket_terminal
2293	E4B_IMPL_CASTOP(columnStat_terminal); // to_columnStat_terminal
2294	E4B_IMPL_CASTOP(device_manager); // to_device_manager
2295	E4B_IMPL_CASTOP(group_manager); // to_group_manager
2296	E4B_IMPL_CASTOP(line_terminal); // to_line_terminal
2297	E4B_IMPL_CASTOP(manager); // to_manager
2298	E4B_IMPL_CASTOP(multi_name_manager); // to_multi_name_manager
2299	E4B_IMPL_CASTOP(multi_sequence_manager); // to_multi_sequence_manager
2300	E4B_IMPL_CASTOP(multi_species_manager); // to_multi_species_manager
2301	E4B_IMPL_CASTOP(name_manager); // to_name_manager
2302	E4B_IMPL_CASTOP(orf_terminal); // to_orf_terminal
2303	E4B_IMPL_CASTOP(pure_text_terminal); // to_pure_text_terminal
2304	E4B_IMPL_CASTOP(root_group_manager); // to_root_group_manager
2305	E4B_IMPL_CASTOP(sequence_info_terminal); // to_sequence_info_terminal
2306	E4B_IMPL_CASTOP(sequence_manager); // to_sequence_manager
2307	E4B_IMPL_CASTOP(sequence_terminal); // to_sequence_terminal
2308	E4B_IMPL_CASTOP(spacer_terminal); // to_spacer_terminal
2309	E4B_IMPL_CASTOP(species_manager); // to_species_manager
2310	E4B_IMPL_CASTOP(species_name_terminal); // to_species_name_terminal
2311	E4B_IMPL_CASTOP(terminal); // to_terminal
2312	E4B_IMPL_CASTOP(text_terminal); // to_text_terminal
2313
2314	inline ED4_device_manager *ED4_root::get_device_manager() {
2315	return main_manager->search_spec_child_rek(ED4_L_DEVICE)->to_device_manager();
2316	}
2317
2318	inline ED4_species_name_terminal *ED4_multi_species_manager::get_consensus_name_terminal() const {
2319	ED4_species_manager *consensus_man = get_consensus_manager();
2320	return consensus_man ? consensus_man->get_name_terminal() : NULL;
2321	}
2322
2323	// --------------------------------------------
2324	// Prototype functions without a class
2325
2326	extern ST_ML *st_ml;
2327
2328	void ED4_with_all_edit_windows(void (cb)(ED4_window ));
2329
2330	void ED4_expose_recalculations();
2331	void ED4_calc_terminal_extentions();
2332
2333	void ED4_input_cb (AW_window *aww);
2334
2335	void ED4_remote_event(AW_event *faked_event);
2336
2337	void ED4_quit (AW_window *aww, AW_CL cd1, AW_CL cd2);
2338	void ED4_motion_cb (AW_window *aww);
2339	void ED4_vertical_change_cb (AW_window *aww);
2340	void ED4_horizontal_change_cb (AW_window *aww);
2341	void ED4_scrollbar_change_cb (AW_window *aww);
2342
2343	void ED4_no_dangerous_modes ();
2344	void group_species_cb (AW_window *aww, AW_CL cd1, AW_CL cd2);
2345	AW_window ED4_create_group_species_by_field_window(AW_root aw_root);
2346
2347	void ED4_trigger_instant_refresh();
2348	void ED4_request_relayout();
2349	void ED4_request_full_refresh();
2350	void ED4_request_full_instant_refresh();
2351
2352	AW_window ED4_start_editor_on_old_configuration (AW_root awr);
2353	void ED4_restart_editor (AW_window *aww, AW_CL, AW_CL);
2354	void ED4_save_configuration(AW_window *aww, bool hide_aww);
2355	AW_window ED4_save_configuration_as_open_window (AW_root awr);
2356
2357	void ED4_set_iupac (AW_window aww, char awar_name, bool callback_flag);
2358	void ED4_set_helixnr (AW_window aww, char awar_name, bool callback_flag);
2359	void ed4_changesecurity (AW_root *root, AW_CL cd1);
2360	void ed4_change_edit_mode (AW_root *root, AW_CL cd1);
2361
2362	ARB_ERROR rebuild_consensus(ED4_base *object);
2363
2364	void ED4_exit() __ATTR__NORETURN;
2365
2366	void ED4_quit_editor (AW_window *aww); // Be Careful: Is this the last window?
2367
2368	void ED4_store_curpos (AW_window *aww);
2369	void ED4_restore_curpos (AW_window *aww);
2370	void ED4_clear_stored_curpos ();
2371	void ED4_helix_jump_opposite (AW_window *aww);
2372	void ED4_jump_to_cursor_position (AW_window *aww, AW_CL cl_awar_name, AW_CL cl_pos_type);
2373	void ED4_remote_set_cursor_cb (AW_root *awr);
2374	void ED4_change_cursor (AW_window *aww);
2375	void ED4_set_reference_species (AW_window *aww, AW_CL cd1, AW_CL cd2);
2376
2377	void ED4_new_editor_window (AW_window *aww);
2378
2379	AW_window ED4_create_consensus_definition_window(AW_root root);
2380	void ED4_create_consensus_awars(AW_root *aw_root);
2381	void ED4_consensus_definition_changed(AW_root*);
2382	void ED4_consensus_display_changed(AW_root *root);
2383
2384	AW_window ED4_create_level_1_options_window (AW_root root);
2385	void ED4_compression_toggle_changed_cb (AW_root *root, AW_CL cd1, AW_CL cd2);
2386
2387	enum SpeciesCreationMode {
2388	CREATE_NEW_SPECIES,
2389	CREATE_FROM_CONSENSUS, // create new species from group consensus (of surrounding group)
2390	COPY_SPECIES, // copy current species
2391	};
2392
2393	#if defined(ASSERTION_USED)
2394	CONSTEXPR_RETURN inline bool valid(SpeciesCreationMode m) { return m>=CREATE_NEW_SPECIES && m<=COPY_SPECIES; }
2395	#endif
2396
2397	AW_window ED4_create_new_seq_window(AW_root root, SpeciesCreationMode creation_mode);
2398
2399	void ED4_jump_to_current_species (AW_window *, AW_CL);
2400	void ED4_get_and_jump_to_current (AW_window *, AW_CL);
2401	void ED4_get_and_jump_to_current_from_menu (AW_window *aw, AW_CL cl, AW_CL);
2402	void ED4_get_and_jump_to_species (GB_CSTR species_name);
2403	void ED4_get_marked_from_menu (AW_window *, AW_CL, AW_CL);
2404	void ED4_selected_species_changed_cb (AW_root *aw_root);
2405	void ED4_selected_SAI_changed_cb (AW_root *aw_root);
2406
2407	void ED4_init_notFoundMessage();
2408	void ED4_finish_and_show_notFoundMessage();
2409
2410	ED4_species_name_terminal ED4_find_species_name_terminal(const char species_name);
2411	ED4_multi_species_manager *ED4_new_species_multi_species_manager(); // returns manager into which new species should be inserted
2412
2413	void ED4_compression_changed_cb(AW_root *awr);
2414
2415	// functions passed to external c-functions (i.e. as callbacks) have to be declared as 'extern "C"'
2416
2417	extern "C" {
2418	void ED4_alignment_length_changed(GBDATA *gb_alignment_len, GB_CB_TYPE gbtype);
2419	}
2420
2421	struct AlignDataAccess;
2422	void ED4_init_aligner_data_access(AlignDataAccess *data_access);
2423
2424	void ED4_popup_gc_window(AW_window *awp, AW_gc_manager gcman);
2425
2426	#else
2427	#error ed4_class included twice
2428	#endif
2429

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