Context Navigation

source: tags/ms_r16q3/EDIT4/ed4_class.hxx

Visit:

Last change on this file was 15288, checked in by westram, 8 years ago
reintegrates 'flags' into 'trunk' implements #261 adds: log:branches/flags@15225:15230,15232:15238,15240:15241,15243:15246,15248,15250:15287
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 88.8 KB

Line
1	#ifndef ED4_CLASS_HXX
2	#define ED4_CLASS_HXX
3
4	#ifndef AW_FONT_GROUP_HXX
5	#include <aw_font_group.hxx>
6	#endif
7	#ifndef POS_RANGE_H
8	#include <pos_range.h>
9	#endif
10
11	#define e4_assert(bed) arb_assert(bed)
12
13	#define concat(a,b) a##b
14
15	#ifdef DEBUG
16	# define IMPLEMENT_DUMP // comment out this line to skip compilation of the dump() methods
17	#endif
18
19	#ifndef ARB_ERROR_H
20	#include <arb_error.h>
21	#endif
22	#ifndef ED4_DEFS_HXX
23	#include "ed4_defs.hxx"
24	#endif
25	#ifndef ED4_SEARCH_HXX
26	#include "ed4_search.hxx"
27	#endif
28	#ifndef _GLIBCXX_LIST
29	#include <list>
30	#endif
31	#ifndef ATTRIBUTES_H
32	#include <attributes.h>
33	#endif
34	#ifndef BI_BASEPOS_HXX
35	#include <BI_basepos.hxx>
36	#endif
37	#ifndef DOWNCAST_H
38	#include <downcast.h>
39	#endif
40	#ifndef CHARTABLE_H
41	#include "chartable.h"
42	#endif
43
44	#if defined(IMPLEMENT_DUMP) // ------------------------------
45
46	#if 0
47	#define WARN(msg) void dummy_to_produce_a_warning(int msg) {}
48	#else
49	#define WARN(msg)
50	#endif
51
52	#define EMPTY_FUNCTION(name) void name() const {}
53	#define EMPTY_FUNCTION_VERBOSE(name) void name(int je_mappelle_##name) const {}
54
55	#define DERIVABLEFROM(base) concat(prohibited_leafclass_derivation,base)
56
57	#define COMMON_FOR_BASES() \
58	virtual void dump(size_t indent) const = 0; \
59
60	#define COMMON_FOR_DERIVABLE(self) \
61	void dump_base(size_t indent) const; \
62	EMPTY_FUNCTION(DERIVABLEFROM(self)); \
63
64	#define COMMON_FOR_DERIVED(mybase) \
65	void dump_my_base(size_t indent) const { mybase::dump_base(indent); } \
66	virtual const char *baseclassname() const { return #mybase; } \
67
68	#define COMMON_FOR_INSTANCIABLE(mybase) \
69	void dump(size_t indent) const OVERRIDE; \
70
71	#define DECLARE_DUMP_FOR_ROOTCLASS(self) \
72	COMMON_FOR_BASES(); \
73	COMMON_FOR_DERIVABLE(self); \
74
75	#define DECLARE_DUMP_FOR_BASECLASS(self,mybase) \
76	COMMON_FOR_BASES(); \
77	COMMON_FOR_DERIVABLE(self); \
78	COMMON_FOR_DERIVED(mybase); \
79
80	#define DECLARE_DUMP_FOR_MIDCLASS(self,mybase) \
81	WARN(midclass_is_unwanted); \
82	COMMON_FOR_DERIVABLE(self); \
83	COMMON_FOR_DERIVED(mybase); \
84	COMMON_FOR_INSTANCIABLE(mybase); \
85
86	#define DECLARE_DUMP_FOR_LEAFCLASS(mybase) \
87	virtual void leaf() { DERIVABLEFROM(mybase)(); } \
88	COMMON_FOR_DERIVED(mybase); \
89	COMMON_FOR_INSTANCIABLE(mybase); \
90
91	#else
92	#define DECLARE_DUMP_FOR_ROOTCLASS(self)
93	#define DECLARE_DUMP_FOR_BASECLASS(self,mybase)
94	#define DECLARE_DUMP_FOR_MIDCLASS(self,mybase)
95	#define DECLARE_DUMP_FOR_LEAFCLASS(mybase)
96
97	#endif // IMPLEMENT_DUMP ------------------------------
98
99
100
101	// #define LIMIT_TOP_AREA_SPACE // if defined, top area is size-limited
102	#ifdef LIMIT_TOP_AREA_SPACE
103	#define MAX_TOP_AREA_SIZE 10 // size limit for top-area
104	#endif
105
106	#define ed4_beep() do { fputc(char(7), stdout); fflush(stdout); } while (0)
107
108	enum PositionType {
109	ED4_POS_SEQUENCE,
110	ED4_POS_ECOLI,
111	ED4_POS_BASE,
112	};
113
114	// ****************************************
115	// needed prototypes, definitions below
116	// ****************************************
117
118	class ED4_Edit_String;
119	class ED4_area_manager;
120	class ED4_abstract_group_manager;
121	class ED4_base;
122	class ED4_bracket_terminal;
123	class BaseFrequencies;
124	class ED4_columnStat_terminal;
125	class ED4_consensus_sequence_terminal;
126	class ED4_cursor;
127	class ED4_device_manager;
128	class ED4_folding_line;
129	class ED4_group_manager;
130	class ED4_line_terminal;
131	class ED4_main_manager;
132	class ED4_manager;
133	class ED4_multi_name_manager;
134	class ED4_multi_sequence_manager;
135	class ED4_multi_species_manager;
136	class ED4_name_manager;
137	class ED4_pure_text_terminal;
138	class ED4_reference_terminals;
139	class ED4_remap;
140	class ED4_root;
141	class ED4_root_group_manager;
142	class ED4_sequence_info_terminal;
143	class ED4_sequence_manager;
144	class ED4_sequence_terminal;
145	class ED4_orf_terminal;
146	class ED4_spacer_terminal;
147	class ED4_species_manager;
148	class ED4_species_name_terminal;
149	class ED4_species_pointer;
150	class ED4_terminal;
151	class ED4_text_terminal;
152	class ED4_tree_terminal;
153	class ED4_flag_header_terminal;
154	class ED4_flag_terminal;
155	class ED4_window;
156
157	class AP_tree;
158	class ED4_reference;
159	class ED4_seq_colors;
160	class BI_ecoli_ref;
161	class AW_helix;
162	class arb_progress;
163	class ST_ML;
164	class ed_key;
165	class ConsensusBuildParams;
166
167	template <class T> class ED4_list; // derived from Noncopyable
168	template <class T> class ED4_list_elem; // derived from Noncopyable
169
170	typedef ED4_list<ED4_base> ED4_base_list;
171	typedef ED4_list_elem<ED4_base> ED4_base_list_elem;
172
173	typedef ED4_list<ED4_selection_entry> ED4_selected_list;
174	typedef ED4_list_elem<ED4_selection_entry> ED4_selected_elem;
175
176
177	struct EDB_root_bact {
178	char *make_string();
179	char *make_top_bot_string();
180
181	void calc_no_of_all(const char *string_to_scan, // group gets the number of groups in string_to_scan,
182	long *group, // species gets the number of species in string_to_scan
183	long *species);
184
185	ED4_returncode fill_species(ED4_multi_species_manager *multi_species_manager,
186	ED4_reference_terminals& refterms,
187	const char *str,
188	int *index,
189	int group_depth,
190	arb_progress *progress);
191
192	ED4_returncode fill_data(ED4_multi_species_manager *multi_species_manager,
193	ED4_reference_terminals& refterms,
194	char *str,
195	int group_depth,
196	ED4_datamode datamode); // flag only needed for loading a new configuration
197
198	ED4_returncode search_sequence_data_rek(ED4_multi_sequence_manager *multi_sequence_manager,
199	ED4_reference_terminals& refterms,
200	GBDATA *gb_ali_xxx, // alignment-container (or any subcontainer of)
201	int count_too,
202	ED4_index *max_sequence_terminal_length,
203	bool isSAI);
204
205	void scan_string(ED4_multi_species_manager *parent,
206	ED4_reference_terminals& refterms,
207	const char *str,
208	int *index,
209	arb_progress& progress);
210
211	void save_current_config(char *confname);
212
213	EDB_root_bact() {}
214	};
215
216	#define SPECIFIED_OBJECT_TYPES 23
217
218	class ED4_objspec : public Noncopyable {
219	static bool object_specs_initialized;
220	static bool descendants_uptodate;
221
222	mutable ED4_level used_children; // in any object of this type
223	mutable ED4_level possible_descendants; // below any object of this type (depends on used_children)
224	mutable ED4_level allowed_descendants; // below any object of this type (depends on allowed_children)
225
226	void calc_descendants() const;
227
228	public:
229	ED4_properties static_prop;
230	ED4_level level;
231	ED4_level allowed_children;
232	ED4_level handled_level;
233	ED4_level restriction_level;
234
235	ED4_objspec(ED4_properties static_prop_, ED4_level level_, ED4_level allowed_children_, ED4_level handled_level_, ED4_level restriction_level_);
236
237	#if defined(IMPLEMENT_DUMP)
238	void dump(size_t indent) const;
239	#endif // IMPLEMENT_DUMP
240
241	static void init_object_specs();
242
243	bool is_manager() const { return static_prop & PROP_IS_MANAGER; }
244	bool is_terminal() const { return static_prop & PROP_IS_TERMINAL; }
245
246	bool allowed_to_contain(ED4_level child_level) const {
247	// e4_assert(object_specs_initialized); // @@@ cant check here.. but where
248	e4_assert(is_manager()); // terminals can't contain anything - your test is senseless
249	return allowed_children & child_level;
250	}
251
252	void announce_added(ED4_level child_level) const {
253	e4_assert(allowed_to_contain(child_level));
254	used_children = ED4_level(used_children\|child_level);
255	descendants_uptodate = false;
256	}
257
258	static void recalc_descendants();
259
260	ED4_level get_possible_descendants() const {
261	e4_assert(is_manager());
262	if (!descendants_uptodate) recalc_descendants();
263	return possible_descendants;
264	}
265	ED4_level get_allowed_descendants() const { // (allowed = possible + those allowed to add, but not added anywhere)
266	e4_assert(is_manager());
267	if (!descendants_uptodate) recalc_descendants();
268	return allowed_descendants;
269	}
270	};
271
272	class ED4_folding_line : virtual Noncopyable {
273	AW_pos dimension; // amount of pixel folded away
274	AW_pos pos; // window position of folding line (x or y, only owner knows which coordinate is folded)
275	ED4_folding_line *next;
276
277	ED4_folding_line insert(ED4_folding_line fl) {
278	e4_assert(!fl->next);
279	if (pos <= fl->pos) { // insert behind
280	next = next ? next->insert(fl) : fl;
281	return this;
282	}
283
284	fl->next = this;
285	return fl;
286	}
287
288	public:
289
290	ED4_folding_line(AW_pos world, AW_pos dim) : dimension(dim), next(0) { set_pos(world-dimension); }
291
292	~ED4_folding_line() { delete next; }
293
294	void insertAs(ED4_folding_line*& ptr) {
295	ED4_folding_line *other = ptr;
296	e4_assert(knownNonNull(this));
297	ptr = other ? other->insert(this) : this;
298	}
299
300	ED4_folding_line delete_member(ED4_folding_line fl) {
301	ED4_folding_line *result = this;
302	if (this == fl) {
303	result = next;
304	next = NULL;
305	delete this;
306	}
307	return result;
308	}
309
310	AW_pos get_dimension() const { return dimension; }
311	const ED4_folding_line *get_next() const { return next; }
312
313	void warn_illegal_dimension();
314
315	void set_dimension(AW_pos dim) { dimension = dim; warn_illegal_dimension(); }
316	void add_to_dimension(AW_pos offset) { dimension += offset; warn_illegal_dimension(); }
317
318	void set_pos(AW_pos p) { pos = p; }
319	AW_pos get_pos() const { return pos; }
320
321	AW_pos win2world(AW_pos win) const {
322	if (win<pos) return win;
323	return (next ? next->win2world(win) : win)+dimension;
324	}
325	AW_pos world2win(AW_pos world) const {
326	if (world<pos) return world;
327	world -= dimension;
328	if (!next) return world;
329	return next->world2win(world);
330	}
331	};
332
333	struct ED4_scroll_links {
334	ED4_base *link_for_hor_slider;
335	ED4_base *link_for_ver_slider;
336
337	ED4_scroll_links() : link_for_hor_slider(0), link_for_ver_slider(0) {}
338	};
339
340	class ED4_foldable : virtual Noncopyable {
341	ED4_folding_line *horizontal_fl;
342	ED4_folding_line *vertical_fl;
343	protected:
344	void reset() {
345	delete horizontal_fl;
346	delete vertical_fl;
347	horizontal_fl = NULL;
348	vertical_fl = NULL;
349	}
350	bool is_reset() const { return !horizontal_fl && !vertical_fl; }
351	public:
352
353	ED4_foldable() : horizontal_fl(NULL), vertical_fl(NULL) {}
354	~ED4_foldable() { reset(); }
355
356	const ED4_folding_line *get_horizontal_folding() { return horizontal_fl; }
357	const ED4_folding_line *get_vertical_folding() { return vertical_fl; }
358
359	void world_to_win_coords(AW_pos xPtr, AW_pos yPtr) const { // @@@ old style
360	// Calculates transformation from world to window coordinates in a given window.
361	// world-coordinates inside folded range result in window coordinates lower than folding line position.
362	e4_assert(!is_reset());
363	xPtr = vertical_fl->world2win(xPtr);
364	yPtr = horizontal_fl->world2win(yPtr);
365	}
366	void win_to_world_coords(AW_pos xPtr, AW_pos yPtr) const { // @@@ old style
367	// calculates transformation from window to world coordinates in a given window
368	e4_assert(!is_reset());
369	xPtr = vertical_fl->win2world(xPtr);
370	yPtr = horizontal_fl->win2world(yPtr);
371	}
372
373	AW::Position world_to_win_coords(const AW::Position& pos) const {
374	e4_assert(!is_reset());
375	return AW::Position(vertical_fl->world2win(pos.xpos()),
376	horizontal_fl->world2win(pos.ypos()));
377	}
378	AW::Position win_to_world_coords(const AW::Position& pos) const {
379	e4_assert(!is_reset());
380	return AW::Position(vertical_fl->win2world(pos.xpos()),
381	horizontal_fl->win2world(pos.ypos()));
382	}
383
384	ED4_folding_line *insert_folding_line(AW_pos pos, AW_pos dimension, ED4_properties prop);
385	void delete_folding_line(ED4_folding_line *fl, ED4_properties prop);
386	};
387
388
389	class ED4_scrolled_rectangle : virtual Noncopyable {
390	ED4_folding_line *scroll_bottom;
391	ED4_folding_line *scroll_right;
392	ED4_folding_line *scroll_top;
393	ED4_folding_line *scroll_left;
394
395	ED4_base *x_link;
396	ED4_base *y_link;
397	ED4_base *width_link;
398	ED4_base *height_link;
399
400	AW::Rectangle world;
401
402	bool folding_dimensions_calculated; // flag to ensure calc_bottomRight_folding_dimensions is called before get_window_rect
403
404	void init_links() {
405	x_link = 0;
406	y_link = 0;
407	width_link = 0;
408	height_link = 0;
409	}
410
411	void init_folding_lines() {
412	scroll_top = 0;
413	scroll_bottom = 0;
414	scroll_left = 0;
415	scroll_right = 0;
416
417	folding_dimensions_calculated = false;
418	}
419	void init_pos_size() { world = AW::Rectangle(AW::Origin, AW::ZeroVector); }
420
421	void init() {
422	init_folding_lines();
423	init_pos_size();
424	init_links();
425	}
426
427	void update_folding_line_positions() {
428	scroll_top->set_pos(world.top());
429	scroll_left->set_pos(world.left());
430	}
431
432	public:
433
434	ED4_scrolled_rectangle() { init(); }
435
436	AW_pos bottom() const { return world.bottom(); }
437	AW_pos right() const { return world.right(); }
438
439	void reset(ED4_foldable& owner) {
440	destroy_folding_lines(owner);
441	init_pos_size();
442	}
443
444	AW_pos top_dim() const { return scroll_top->get_dimension(); }
445	AW_pos left_dim() const { return scroll_left->get_dimension(); }
446
447	bool exists() const { return scroll_top && scroll_bottom && scroll_left && scroll_right; }
448	bool is_linked() const {
449	if (x_link) {
450	e4_assert(y_link);
451	e4_assert(width_link);
452	e4_assert(height_link);
453	return true;
454	}
455	e4_assert(!y_link);
456	e4_assert(!width_link);
457	e4_assert(!height_link);
458	return false;
459	}
460	void link(ED4_base x, ED4_base y, ED4_base w, ED4_base h) {
461	e4_assert(x && y && w && h);
462
463	x_link = x;
464	y_link = y;
465	width_link = w;
466	height_link = h;
467	}
468
469	void replace_x_width_link_to(ED4_base old_link, ED4_base new_link) {
470	if (x_link == old_link) x_link = new_link;
471	if (width_link == old_link) width_link = new_link;
472	}
473
474	void add_to_top_left_dimension(int dx, int dy) {
475	scroll_left->add_to_dimension(dx);
476	scroll_top->add_to_dimension(dy);
477	}
478
479	void scroll(int dx, int dy) {
480	scroll_left->add_to_dimension(-dx);
481	scroll_top->add_to_dimension(-dy);
482	scroll_right->add_to_dimension(dx);
483	scroll_bottom->add_to_dimension(dy);
484	}
485
486	AW::Rectangle get_window_rect() const {
487	e4_assert(folding_dimensions_calculated);
488	return AW::Rectangle(scroll_left->get_pos(), scroll_top->get_pos(),
489	scroll_right->get_pos(), scroll_bottom->get_pos());
490	}
491
492	AW::Rectangle get_world_rect() const;
493
494	void set_rect(const AW::Rectangle& rect) { world = rect; }
495	void set_rect_and_update_folding_line_positions(const AW::Rectangle& rect) {
496	set_rect(rect);
497	update_folding_line_positions();
498	}
499
500	void calc_bottomRight_folding_dimensions(int area_width, int area_height) {
501	area_width -= SLIDER_OFFSET;
502	area_height -= SLIDER_OFFSET;
503
504	AW_pos dim;
505	if (bottom() > area_height) { // our world doesn't fit vertically in our window
506	dim = bottom()-area_height; // calc dimension of both horizontal folding lines
507	scroll_top->set_dimension(std::min(dim, scroll_top->get_dimension()));
508	scroll_bottom->set_dimension(std::max(0, int(dim - scroll_top->get_dimension())));
509	}
510	else {
511	dim = 0;
512	scroll_bottom->set_dimension(0);
513	scroll_top->set_dimension(0);
514	}
515
516	e4_assert(dim == (scroll_top->get_dimension()+scroll_bottom->get_dimension()));
517	scroll_bottom->set_pos(world.bottom()-dim+SLIDER_OFFSET);
518
519	if (right()>area_width) { // our world doesn't fit horizontally in our window
520	dim = right()-area_width; // calc dimension of both vertical folding lines
521	scroll_left->set_dimension(std::min(dim, scroll_left->get_dimension()));
522	scroll_right->set_dimension(std::max(0, int(dim - scroll_left->get_dimension())));
523	}
524	else {
525	dim = 0;
526	scroll_right->set_dimension(0);
527	scroll_left->set_dimension(0);
528	}
529
530	e4_assert(dim == (scroll_left->get_dimension()+scroll_right->get_dimension()));
531	scroll_right->set_pos(world.right()-dim+SLIDER_OFFSET);
532
533	folding_dimensions_calculated = true;
534	}
535
536	void create_folding_lines(ED4_foldable& owner, const AW::Rectangle& rect, int area_width, int area_height) {
537	scroll_top = owner.insert_folding_line(rect.top(), 0, PROP_HORIZONTAL);
538	scroll_left = owner.insert_folding_line(rect.left(), 0, PROP_VERTICAL);
539
540	AW_pos dim = 0;
541	if (rect.bottom() > area_height) dim = rect.bottom() - area_height;
542	scroll_bottom = owner.insert_folding_line(rect.bottom(), dim, PROP_HORIZONTAL);
543
544	dim = 0;
545	if (rect.right() > area_width) dim = rect.right() - area_width;
546	scroll_right = owner.insert_folding_line(rect.right(), dim, PROP_VERTICAL);
547	}
548
549	void destroy_folding_lines(ED4_foldable& owner) {
550	if (scroll_top) owner.delete_folding_line(scroll_top, PROP_HORIZONTAL);
551	if (scroll_bottom) owner.delete_folding_line(scroll_bottom, PROP_HORIZONTAL);
552	if (scroll_left) owner.delete_folding_line(scroll_left, PROP_VERTICAL);
553	if (scroll_right) owner.delete_folding_line(scroll_right, PROP_VERTICAL);
554
555	init_folding_lines();
556	}
557	};
558
559	class ED4_base_position : private BasePosition { // derived from a Noncopyable
560	const ED4_terminal *calced4term; // if calced4term!=NULL => callback is bound to its species manager
561	bool needUpdate;
562
563	void calc4term(const ED4_terminal *term);
564	void set_term(const ED4_terminal *term) {
565	if (calced4term != term \|\| needUpdate) {
566	calc4term(term);
567	}
568	}
569	void remove_changed_cb();
570
571	public:
572
573	ED4_base_position()
574	: calced4term(NULL),
575	needUpdate(true)
576	{}
577
578	~ED4_base_position() {
579	remove_changed_cb();
580	}
581
582	void invalidate() {
583	needUpdate = true;
584	}
585
586	void announce_deletion(const ED4_terminal *term) {
587	if (term == calced4term) {
588	invalidate();
589	remove_changed_cb();
590	}
591	e4_assert(calced4term != term);
592	}
593	void prepare_shutdown() {
594	if (calced4term) announce_deletion(calced4term);
595	}
596
597	int get_base_position(const ED4_terminal *base, int sequence_position);
598	int get_sequence_position(const ED4_terminal *base, int base_position);
599
600	int get_base_count(const ED4_terminal *term) { set_term(term); return base_count(); }
601	int get_abs_len(const ED4_terminal *term) { set_term(term); return abs_count(); }
602	};
603
604	class ED4_CursorShape;
605
606
607	enum ED4_CursorType {
608	ED4_RIGHT_ORIENTED_CURSOR,
609	ED4_RIGHT_ORIENTED_CURSOR_THIN,
610	ED4_TRADITIONAL_CURSOR,
611	ED4_TRADITIONAL_CURSOR_BOTTOM,
612	ED4_TRADITIONAL_CURSOR_CONNECTED,
613	ED4_FUCKING_BIG_CURSOR,
614
615	ED4_CURSOR_TYPES
616
617	};
618
619	extern bool ED4_update_global_cursor_awars_allowed; // update selected species/SAI/cursor position
620
621	struct ED4_TerminalPredicate {
622	virtual ~ED4_TerminalPredicate() {}
623	virtual bool fulfilled_by(const ED4_terminal *) const = 0;
624	};
625
626	class ED4_WinContextFree { // denies usage of the following functions in classes derived from this
627	AW_device *current_device();
628	ED4_window *current_ed4w();
629	AW_window *current_aww();
630	ED4_cursor& current_cursor();
631	public:
632	void avoid_warning() {}
633	};
634
635	class ED4_cursor : virtual Noncopyable, virtual ED4_WinContextFree {
636	ED4_window *win;
637	ED4_index cursor_abs_x; // absolute (to terminal) x-position of cursor (absolute world coordinate of edit window)
638	int screen_position; // number of displayed characters leading the cursor
639	mutable ED4_base_position base_position; // # of bases left of cursor
640	ED4_CursorType ctype;
641	ED4_CursorShape *cursor_shape;
642
643	ED4_returncode draw_cursor(AW_pos x, AW_pos y);
644	ED4_returncode delete_cursor(AW_pos del_mark, ED4_base *target_terminal);
645
646	void updateAwars(bool new_term_selected);
647
648	public:
649
650	bool allowed_to_draw; // needed for cursor handling
651	ED4_terminal *owner_of_cursor;
652
653	bool is_partly_visible() const;
654	bool is_completely_visible() const;
655
656	bool is_hidden_inside_group() const;
657
658	void changeType(ED4_CursorType typ);
659	ED4_CursorType getType() const { return ctype; }
660
661	void redraw() { changeType(getType()); }
662
663	ED4_returncode HideCursor(); // deletes cursor and does refresh
664	ED4_returncode move_cursor(AW_event *event);
665	ED4_returncode show_clicked_cursor(AW_pos click_xpos, ED4_terminal *target_terminal);
666	ED4_returncode show_cursor_at(ED4_terminal *target_terminal, ED4_index what_pos);
667	ED4_returncode ShowCursor(ED4_index offset_x, ED4_cursor_move move, int move_pos = 1);
668
669	int get_sequence_pos() const;
670	int get_screen_pos() const { return screen_position; }
671
672	long get_abs_x() const { return cursor_abs_x; }
673	void set_abs_x();
674
675	int base2sequence_position(int base_pos) const { return base_position.get_sequence_position(owner_of_cursor, base_pos); }
676	int sequence2base_position(int seq_pos) const { return base_position.get_base_position(owner_of_cursor, seq_pos); }
677
678	int get_base_position() const { return sequence2base_position(get_sequence_pos()); }
679
680	void prepare_shutdown() { base_position.prepare_shutdown(); }
681
682	void jump_screen_pos(int screen_pos, ED4_CursorJumpType jump_type);
683	void jump_sequence_pos(int sequence_pos, ED4_CursorJumpType jump_type);
684	void jump_base_pos(int base_pos, ED4_CursorJumpType jump_type);
685
686	int get_screen_relative_pos() const;
687	void set_screen_relative_pos(int scroll_to_relpos);
688
689	void set_to_terminal(ED4_terminal *terminal, int seq_pos, ED4_CursorJumpType jump_type);
690
691	inline bool in_species_seq_terminal() const;
692	inline bool in_consensus_terminal() const;
693	inline bool in_SAI_terminal() const;
694
695	void announce_deletion(ED4_terminal *object) {
696	base_position.announce_deletion(object);
697	if (object == owner_of_cursor) owner_of_cursor = NULL; // no need to delete the cursor (deletion triggers full redraw)
698	}
699
700	void init();
701
702	ED4_window *window() const { return win; }
703
704	ED4_cursor(ED4_window *win);
705	~ED4_cursor();
706	};
707
708	class ED4_window : public ED4_foldable, virtual ED4_WinContextFree { // derived from Noncopyable
709	void set_scrollbar_indents();
710
711	public:
712	AW_window_menu_modes *aww; // Points to Window
713	ED4_window *next;
714	int slider_pos_horizontal;
715	int slider_pos_vertical;
716	ED4_scrolled_rectangle scrolled_rect;
717	int id; // unique id in window-list
718	ED4_coords coords;
719
720	static int no_of_windows;
721
722	char awar_path_for_cursor[50]; // position in current sequence, range = [1;len]
723	char awar_path_for_Ecoli[50]; // position relative to ecoli
724	char awar_path_for_basePos[50]; // base position in current sequence (# of bases left to cursor)
725	char awar_path_for_IUPAC[50]; // IUPAC decoder content for current position
726	char awar_path_for_helixNr[50]; // # of helix (or 0) for current position
727
728	bool is_hidden;
729	ED4_cursor cursor;
730
731	// ED4_window controlling functions
732	static ED4_window insert_window(AW_window_menu_modes new_aww); // append to window list
733
734	void delete_window(ED4_window *window); // delete from window list
735	void reset_all_for_new_config(); // reset structures for loading new config
736	ED4_window get_matching_ed4w(AW_window aww);
737
738	void announce_deletion(ED4_terminal *object) { cursor.announce_deletion(object); }
739
740	// functions concerned the scrolled area
741	void update_scrolled_rectangle();
742	ED4_returncode scroll_rectangle(int dx, int dy);
743	ED4_returncode set_scrolled_rectangle(ED4_base x_link, ED4_base y_link, ED4_base width_link, ED4_base height_link);
744
745	bool scrollbars_and_scrolledRect_inSync() const {
746	// Scrolling in EDIT4 window uses redundant data
747	// - dimension of folding lines
748	// - slider positions in AW_window and ED4_window
749	// This function checks whether they are in sync.
750
751	bool inSync =
752	(scrolled_rect.top_dim() == aww->slider_pos_vertical) &&
753	(scrolled_rect.left_dim() == aww->slider_pos_horizontal);
754
755	#if defined(DEBUG)
756	if (!inSync) {
757	fputs("scrollbars not in sync with scrolled_rect:\n", stderr);
758	#if defined(ARB_GTK)
759	#define POSTYPE "%zu"
760	#else // ARB_MOTIF
761	#define POSTYPE "%i"
762	#endif
763	fprintf(stderr, " aww->slider_pos_vertical =" POSTYPE " scrolled_rect->top_dim() =%f\n", aww->slider_pos_vertical, scrolled_rect.top_dim());
764	fprintf(stderr, " aww->slider_pos_horizontal=" POSTYPE " scrolled_rect->left_dim()=%f\n", aww->slider_pos_horizontal, scrolled_rect.left_dim());
765	}
766	#endif
767
768	return inSync;
769	}
770
771	void check_valid_scrollbar_values() { e4_assert(scrollbars_and_scrolledRect_inSync()); }
772
773	bool shows_xpos(int x) const { return x >= coords.window_left_clip_point && x <= coords.window_right_clip_point; }
774	bool partly_shows(int x1, int y1, int x2, int y2) const;
775	bool completely_shows(int x1, int y1, int x2, int y2) const;
776
777	void update_window_coords();
778
779	AW_device *get_device() const { return aww->get_device(AW_MIDDLE_AREA); }
780
781	ED4_window(AW_window_menu_modes *window);
782	~ED4_window();
783	};
784
785	class ED4_container : virtual Noncopyable {
786	// contains children of a manager
787
788	ED4_base **memberList;
789	ED4_index no_of_members; // How much members are in the list
790	ED4_index size_of_list; // allocated size
791
792	void correct_insert_position(ED4_index& index);
793	void resize(ED4_index needed_size);
794
795	void shift_list(ED4_index start_index, int length);
796
797	protected:
798
799	bool valid_index(ED4_index idx) const { return idx >= 0 && idx<size_of_list; }
800	bool existing_index(ED4_index idx) const { return idx >= 0 && idx<no_of_members; }
801
802	public:
803
804	ED4_manager owner() { return DOWNCAST(ED4_manager, this); }
805	const ED4_manager owner() const { return const_cast<ED4_container>(this)->owner(); }
806
807	ED4_base* member(ED4_index i) const { e4_assert(i>=0 && i<size_of_list); return memberList[i]; }
808
809	ED4_index members() const { return no_of_members; }
810	bool empty() const { return !members(); }
811	void clear();
812
813	void insert_member(ED4_base *new_member); // only used to move members with mouse
814	void append_member(ED4_base *new_member);
815
816	// an array is chosen instead of a linked list, because destructorhandling is more comfortable in various destructors (manager-destructors)
817
818	ED4_returncode remove_member(ED4_base *member);
819	ED4_index search_member(ED4_extension *location, ED4_properties prop); // search member
820
821	ED4_returncode search_target_species(ED4_extension location, ED4_properties prop, ED4_base *found_member, ED4_level return_level);
822
823	ED4_returncode move_member(ED4_index old_pos, ED4_index new_pos);
824
825	#if defined(IMPLEMENT_DUMP)
826	void dump_container(size_t indent) const;
827	#endif // IMPLEMENT_DUMP
828
829	#if defined(ASSERTION_USED)
830	bool members_ok() const;
831	#endif // ASSERTION_USED
832
833	ED4_container();
834	virtual ~ED4_container();
835	};
836
837	// ----------------------------
838	// ED4_species_pointer
839
840	class ED4_species_pointer : virtual Noncopyable {
841	// @@@ shall be renamed into ED4_gbdata_pointer to reflect general usage
842
843	GBDATA *species_pointer; // points to database
844
845	void addCallback(ED4_base *base);
846	void removeCallback(ED4_base *base);
847
848	public:
849
850	ED4_species_pointer();
851	~ED4_species_pointer();
852
853	GBDATA *Get() const { return species_pointer; }
854	void Set(GBDATA gbd, ED4_base base);
855	void notify_deleted() {
856	species_pointer=0;
857	}
858	};
859
860	// ------------------------
861	// callback types
862
863	template <class BASE, class BASECB>
864	class ED4_cb_list {
865	std::list<BASECB> callbacks;
866	public:
867	#if defined(ASSERTION_USED)
868	ED4_cb_list() {}
869	~ED4_cb_list() {
870	e4_assert(empty()); // calling ED4_root::remove_all_callbacks() did not remove all callbacks!
871	}
872	#endif
873	void add_cb(BASECB cb) { callbacks.push_back(cb); }
874	void remove_cb(BASECB cb) { callbacks.remove(cb); }
875
876	void call(BASE *b) {
877	for (typename std::list<BASECB>::iterator cb = callbacks.begin(); cb != callbacks.end();) {
878	typename std::list<BASECB>::iterator curr = cb;
879	++cb;
880	(*curr)(b); // Note: may be removed while called
881	}
882	}
883	void clear() { callbacks.clear(); }
884	bool empty() const { return callbacks.empty(); }
885	};
886
887	// declare callback types used in ED4_cb_list:
888	DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_managerCallback, void, ED4_manager*); // generates makeED4_managerCallback
889	DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_species_managerCallback, void, ED4_species_manager*); // generates makeED4_species_managerCallback
890
891	// -----------------
892	// ED4_base
893
894	class ED4_base;
895
896	DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_route_cb, ARB_ERROR, ED4_base*); // generates makeED4_route_cb
897
898	enum ED4_species_type {
899	ED4_SP_NONE,
900	ED4_SP_SPECIES,
901	ED4_SP_SAI,
902	ED4_SP_CONSENSUS,
903	};
904
905	class ED4_base : virtual Noncopyable {
906	// base object
907
908	ED4_species_pointer my_species_pointer;
909
910	// cache world coordinates:
911
912	static int currTimestamp;
913	mutable AW::Position lastPos;
914	mutable int timestamp;
915
916	ED4_base_list *linked_objects; // linked list of objects which are depending from this object
917
918	virtual bool set_dynamic_size() {
919	// default behavior: keep size
920	// (overload to implement dynamic sizing; also set static_prop!)
921	e4_assert(!(spec.static_prop & PROP_DYNA_RESIZE)); // forgot to overload set_dynamic_size?
922	return false; // = "nothing changed"
923	}
924
925	public:
926	const ED4_objspec& spec; // contains information about Objectproperties
927
928	ED4_manager *parent; // Points to parent
929
930
931	ED4_properties dynamic_prop; // contains info about what i am, what i can do, what i should do
932	char *id; // globally unique name in hierarchy
933	ED4_index index; // defines the order of child objects
934	ED4_base *width_link; // concerning the hierarchy
935	ED4_base *height_link; // concerning the hierarchy
936	ED4_extension extension; // contains relative info about graphical properties
937	ED4_update_info update_info; // info about things to be done for the object, i.e. refresh; flag structure
938	struct {
939	unsigned int hidden : 1; // flag whether object is hidden or not
940	} flag;
941
942	void draw_bb(int color);
943
944	DECLARE_DUMP_FOR_ROOTCLASS(ED4_base);
945
946	// function for species_pointer
947	//
948	// Notes:
949	//
950	// * design is broken @@@
951	// - my_species_pointer should be member of those derived classes, where it's used
952	// - accessor functions should tell what we get (eg. ED4_species_name_terminal::get_name_entry() or similar)
953	//
954	// * current uses of my_species_pointer (grepped for 'set_species_pointer' to detect):
955	// - ED4_species_manager [holds pointer to] species/SAI container
956	// - ED4_species_name_terminal [holds pointer to] the 'name' entry of species/SAI
957	// - ED4_sequence_info_terminal [holds pointer to] the displayed sub-entry of the alignment-container of species/SAI (multiple may exist per species)
958	// - ED4_text_terminal [holds pointer to] same as ED4_sequence_info_terminal (Caution: not true for all text terminals!)
959
960	GBDATA *get_species_pointer() const { return my_species_pointer.Get(); }
961	void set_species_pointer(GBDATA *gbd) { my_species_pointer.Set(gbd, this); }
962	int has_callback() const { return get_species_pointer()!=0; }
963
964	// callbacks
965
966	virtual void changed_by_database();
967	virtual void deleted_from_database();
968
969	// functions concerned with graphic output
970	int adjust_clipping_rectangle();
971	virtual void Show(bool refresh_all, bool is_cleared) = 0;
972
973	virtual bool calc_bounding_box() = 0;
974	void resize_dynamic() {
975	if (set_dynamic_size()) {
976	e4_assert(has_property(PROP_DYNA_RESIZE)); // object dynamically changed size (but isn't allowed to!)
977	request_resize();
978	}
979	}
980
981	ED4_returncode clear_background(int color=0);
982
983	void set_links(ED4_base width_ref, ED4_base height_ref);
984	void set_both_links(ED4_base *ref) { set_links(ref, ref); }
985
986	// functions concerned with special initialization
987	void set_property(ED4_properties prop) { dynamic_prop = (ED4_properties) (dynamic_prop \| prop); }
988	void clr_property(ED4_properties prop) { dynamic_prop = (ED4_properties) (dynamic_prop & ~prop); }
989	bool has_property(ED4_properties prop) const { return dynamic_prop & prop; }
990
991	// functions concerned with coordinate transformation
992
993	void calc_rel_coords(AW_pos x, AW_pos y);
994
995	void calc_world_coords(AW_pos x, AW_pos y) const {
996	update_world_coords_cache();
997	*x = lastPos.xpos();
998	*y = lastPos.ypos();
999	}
1000	const AW::Position& calc_world_coords() const {
1001	update_world_coords_cache();
1002	return lastPos;
1003	}
1004
1005	void update_world_coords_cache() const {
1006	bool cache_up_to_date = timestamp == currTimestamp;
1007	if (!cache_up_to_date) {
1008	if (parent) {
1009	ED4_base pab = (ED4_base)parent;
1010	lastPos = pab->calc_world_coords();
1011	}
1012	else {
1013	lastPos = AW::Origin;
1014	}
1015	lastPos.move(extension.get_parent_offset());
1016	timestamp = currTimestamp;
1017	}
1018	}
1019
1020	static void touch_world_cache() {
1021	currTimestamp++;
1022	}
1023
1024	AW::Rectangle get_win_area(ED4_window *ed4w) const {
1025	AW::Position pos = ed4w->world_to_win_coords(calc_world_coords());
1026	return AW::Rectangle(pos, extension.get_size()-AW::Vector(1, 1));
1027	}
1028
1029	// functions which refer to the object as a child, i.e. travelling down the hierarchy
1030	virtual void request_refresh(int clear=1) = 0;
1031
1032	inline void request_resize();
1033	void request_resize_of_linked();
1034	void resize_requested_by_link(ED4_base *link);
1035	virtual void resize_requested_children() = 0;
1036
1037	virtual void delete_requested_children() = 0;
1038	virtual void Delete() = 0;
1039
1040	inline void set_update();
1041	virtual void update_requested_children() = 0;
1042
1043	virtual ED4_returncode move_requested_by_parent(ED4_move_info *mi) = 0;
1044	virtual ED4_returncode event_sent_by_parent(AW_event event, AW_window aww);
1045	virtual ED4_returncode move_requested_by_child(ED4_move_info *moveinfo) = 0;
1046
1047
1048	virtual ED4_returncode handle_move(ED4_move_info *moveinfo) = 0;
1049
1050	virtual ARB_ERROR route_down_hierarchy(const ED4_route_cb& cb);
1051
1052	int calc_group_depth();
1053
1054	// general purpose functions
1055	virtual ED4_base search_ID(const char id) = 0;
1056
1057	void check_all();
1058	short in_border(AW_pos abs_x, AW_pos abs_y, ED4_movemode mode);
1059	ED4_returncode set_width();
1060
1061
1062	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
1063
1064	ED4_base *get_parent(ED4_level lev) const;
1065	void unlink_from_parent();
1066	bool has_parent(ED4_manager *Parent);
1067	bool is_child_of(ED4_manager *Parent) { return has_parent(Parent); }
1068
1069	virtual char resolve_pointer_to_string_copy(int str_len = 0) const;
1070	virtual const char resolve_pointer_to_char_pntr(int str_len = 0) const;
1071
1072	ED4_group_manager *is_in_folded_group() const;
1073	virtual bool is_hidden() const = 0;
1074
1075	char *get_name_of_species(); // go from terminal to name of species
1076
1077	// functions which refer to the selected object(s), i.e. across the hierarchy
1078	virtual ED4_base *get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop)=0;
1079	virtual ED4_base *get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop)=0;
1080	virtual ED4_base *search_spec_child_rek(ED4_level level); // recursive search for level
1081
1082	ED4_terminal *get_next_terminal();
1083	ED4_terminal *get_prev_terminal();
1084
1085	void generate_configuration_string(GBS_strstruct& buffer);
1086
1087	virtual ED4_returncode remove_callbacks();
1088
1089	const ED4_terminal *get_consensus_relevant_terminal() const;
1090
1091	ED4_base(const ED4_objspec& spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
1092	virtual ~ED4_base();
1093
1094	// use the following functions to test which derived class we have
1095
1096	int is_terminal() const { e4_assert(knownNonNull(this)); return spec.static_prop & PROP_IS_TERMINAL; }
1097
1098	int is_text_terminal() const { e4_assert(knownNonNull(this)); return spec.level & (LEV_SPECIES_NAME\|LEV_SEQUENCE_INFO\|LEV_SEQUENCE_STRING\|LEV_PURE_TEXT\|LEV_COL_STAT); }
1099
1100	int is_species_name_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SPECIES_NAME; }
1101
1102	int is_sequence_info_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SEQUENCE_INFO; }
1103	int is_sequence_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SEQUENCE_STRING; }
1104	int is_orf_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_ORF; }
1105
1106	int is_pure_text_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_PURE_TEXT; }
1107	int is_columnStat_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_COL_STAT; }
1108
1109	int is_bracket_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_BRACKET; }
1110	int is_spacer_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SPACER; }
1111	int is_line_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_LINE; }
1112
1113	int is_flag_header_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_FLAG_HEADER; }
1114	int is_flag_terminal() const { e4_assert(knownNonNull(this)); return spec.level & LEV_FLAG; }
1115
1116	int is_manager() const { e4_assert(knownNonNull(this)); return spec.static_prop & PROP_IS_MANAGER; }
1117
1118	int is_sequence_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SEQUENCE; }
1119	int is_multi_name_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_MULTI_NAME; }
1120	int is_name_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_NAME_MANAGER; }
1121	int is_multi_species_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_MULTI_SPECIES; }
1122	int is_multi_sequence_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_MULTI_SEQUENCE; }
1123	int is_device_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_DEVICE; }
1124
1125	int is_group_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_GROUP; }
1126	int is_root_group_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_ROOTGROUP; }
1127	int is_abstract_group_manager() const { e4_assert(knownNonNull(this)); return spec.level & (LEV_GROUP\|LEV_ROOTGROUP); }
1128
1129	int is_species_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_SPECIES; }
1130	int is_area_manager() const { e4_assert(knownNonNull(this)); return spec.level & LEV_AREA; }
1131
1132	// use the following functions to cast ED4_base to derived classes:
1133
1134	#define E4B_DECL_CASTOP_helper(Class,toName) \
1135	inline const Class *toName() const; \
1136	inline Class *toName();
1137
1138	#define E4B_AVOID_CAST__helper(Class,toName,isName) \
1139	const Class *toName() const; \
1140	Class *toName(); \
1141	int isName() const;
1142
1143	#define E4B_IMPL_CASTOP_helper(Class,toName,isName) \
1144	const Class *ED4_base::toName() const { \
1145	e4_assert(isName()); \
1146	return DOWNCAST(const Class*, this); \
1147	} \
1148	Class *ED4_base::toName() { \
1149	return const_cast<Class>(const_cast<const ED4_base>(this)->toName()); \
1150	}
1151
1152	#define E4B_DECL_CASTOP(name) E4B_DECL_CASTOP_helper(concat(ED4_,name), concat(to_,name))
1153	#define E4B_AVOID_UNNEEDED_CASTS(name) E4B_AVOID_CAST__helper(concat(ED4_,name), concat(to_,name), concat(is_,name))
1154	#define E4B_IMPL_CASTOP(name) E4B_IMPL_CASTOP_helper(concat(ED4_,name), concat(to_,name), concat(is_,name))
1155
1156	E4B_DECL_CASTOP(area_manager); // to_area_manager
1157	E4B_DECL_CASTOP(abstract_group_manager); // to_abstract_group_manager
1158	E4B_DECL_CASTOP(bracket_terminal); // to_bracket_terminal
1159	E4B_DECL_CASTOP(columnStat_terminal); // to_columnStat_terminal
1160	E4B_DECL_CASTOP(consensus_sequence_terminal); // to_consensus_sequence_terminal
1161	E4B_DECL_CASTOP(device_manager); // to_device_manager
1162	E4B_DECL_CASTOP(group_manager); // to_group_manager
1163	E4B_DECL_CASTOP(line_terminal); // to_line_terminal
1164	E4B_DECL_CASTOP(manager); // to_manager
1165	E4B_DECL_CASTOP(multi_name_manager); // to_multi_name_manager
1166	E4B_DECL_CASTOP(multi_sequence_manager); // to_multi_sequence_manager
1167	E4B_DECL_CASTOP(multi_species_manager); // to_multi_species_manager
1168	E4B_DECL_CASTOP(name_manager); // to_name_manager
1169	E4B_DECL_CASTOP(orf_terminal); // to_orf_terminal
1170	E4B_DECL_CASTOP(pure_text_terminal); // to_pure_text_terminal
1171	E4B_DECL_CASTOP(root_group_manager); // to_root_group_manager
1172	E4B_DECL_CASTOP(sequence_info_terminal); // to_sequence_info_terminal
1173	E4B_DECL_CASTOP(sequence_manager); // to_sequence_manager
1174	E4B_DECL_CASTOP(sequence_terminal); // to_sequence_terminal
1175	E4B_DECL_CASTOP(spacer_terminal); // to_spacer_terminal
1176	E4B_DECL_CASTOP(species_manager); // to_species_manager
1177	E4B_DECL_CASTOP(species_name_terminal); // to_species_name_terminal
1178	E4B_DECL_CASTOP(terminal); // to_terminal
1179	E4B_DECL_CASTOP(text_terminal); // to_text_terminal
1180	E4B_DECL_CASTOP(flag_header_terminal); // to_flag_header_terminal
1181	E4B_DECL_CASTOP(flag_terminal); // to_flag_terminal
1182
1183	// simple access to containing managers
1184	inline ED4_species_manager *containing_species_manager() const;
1185
1186	// discriminate between different sequence managers:
1187
1188	inline bool is_consensus_manager() const;
1189	inline bool is_SAI_manager() const;
1190	inline bool is_species_seq_manager() const;
1191
1192	inline ED4_species_type get_species_type() const; // works for all items (recursively) contained in ED4_species_manager
1193
1194	inline bool inside_consensus_manager() const;
1195	inline bool inside_SAI_manager() const;
1196	inline bool inside_species_seq_manager() const;
1197
1198	inline bool is_consensus_terminal() const;
1199	inline bool is_SAI_terminal() const;
1200	inline bool is_species_seq_terminal() const;
1201
1202	inline bool is_consensus_sequence_terminal() const { // alias for CASTOP
1203	return is_consensus_terminal();
1204	}
1205	};
1206
1207	DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_basePredicate, bool, ED4_base*); // generates makeED4_basePredicate
1208
1209	class ED4_manager : public ED4_base, public ED4_container { // derived from a Noncopyable
1210	ED4_cb_list<ED4_manager, ED4_managerCallback> delete_cbs;
1211	public:
1212
1213	E4B_AVOID_UNNEEDED_CASTS(manager);
1214	DECLARE_DUMP_FOR_BASECLASS(ED4_manager, ED4_base);
1215
1216	void add_delete_callback(const ED4_managerCallback& cb) { delete_cbs.add_cb(cb); }
1217	void remove_delete_callback(const ED4_managerCallback& cb) { delete_cbs.remove_cb(cb); }
1218
1219	int refresh_flag_ok();
1220
1221	void changed_by_database() OVERRIDE;
1222	void deleted_from_database() OVERRIDE;
1223
1224	// functions concerned with graphics
1225	void Show(bool refresh_all, bool is_cleared) OVERRIDE;
1226	bool calc_bounding_box() OVERRIDE;
1227
1228	ED4_returncode distribute_children();
1229
1230	// top-down functions, means travelling down the hierarchy
1231	ED4_returncode event_sent_by_parent(AW_event event, AW_window aww) OVERRIDE;
1232
1233	void request_refresh(int clear=1) OVERRIDE;
1234	ED4_returncode clear_refresh();
1235
1236	void resize_requested_children() OVERRIDE;
1237
1238	void update_requested_children() OVERRIDE;
1239
1240	void delete_requested_children() OVERRIDE;
1241	void Delete() OVERRIDE;
1242
1243	ED4_returncode move_requested_by_parent(ED4_move_info *mi) OVERRIDE;
1244
1245	void create_consensus(ED4_abstract_group_manager upper_group_manager, arb_progress progress);
1246
1247	ARB_ERROR route_down_hierarchy(const ED4_route_cb& cb) OVERRIDE;
1248
1249	ED4_base *find_first_that(ED4_level level, const ED4_basePredicate& fulfills_predicate);
1250
1251	// bottom-up functions
1252	ED4_returncode move_requested_by_child(ED4_move_info *moveinfo) OVERRIDE;
1253	inline void resize_requested_by_child();
1254	ED4_returncode refresh_requested_by_child();
1255	void delete_requested_by_child();
1256	void update_requested_by_child();
1257
1258	ED4_base *get_defined_level(ED4_level lev) const;
1259
1260	// functions referring the consensus
1261
1262	void update_consensus(ED4_manager old_parent, ED4_manager new_parent, ED4_base *sequence);
1263	ED4_returncode rebuild_consensi(ED4_base *start_species, ED4_update_flag update_flag);
1264
1265	ED4_returncode check_in_bases(ED4_base *added_base);
1266	ED4_returncode check_out_bases(ED4_base *subbed_base);
1267
1268	ED4_returncode update_bases(const ED4_base old_base, const ED4_base new_base, PosRange range = PosRange::whole());
1269	ED4_returncode update_bases(const char old_seq, int old_len, const char new_seq, int new_len, PosRange range = PosRange::whole());
1270	ED4_returncode update_bases(const char old_seq, int old_len, const ED4_base new_base, PosRange range = PosRange::whole());
1271	ED4_returncode update_bases(const BaseFrequencies old_table, const BaseFrequencies new_table, PosRange range = PosRange::whole());
1272
1273	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());
1274
1275	// handle moves across the hierarchy
1276	ED4_returncode handle_move(ED4_move_info *moveinfo) OVERRIDE;
1277
1278	ED4_base *get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop) OVERRIDE;
1279	ED4_base *get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop) OVERRIDE;
1280	ED4_base *search_spec_child_rek(ED4_level level) OVERRIDE; // recursive search for level
1281
1282	// general purpose functions
1283	ED4_base search_ID(const char id) OVERRIDE;
1284	ED4_returncode remove_callbacks() OVERRIDE;
1285
1286	ED4_terminal *get_first_terminal(int start_index=0) const;
1287	ED4_terminal *get_last_terminal(int start_index=-1) const;
1288
1289	void hide_children();
1290	void unhide_children();
1291
1292	bool is_hidden() const OVERRIDE {
1293	if (flag.hidden) return true;
1294	if (!parent) return false;
1295	return parent->is_hidden();
1296	}
1297
1298	ED4_manager(const ED4_objspec& spec_, const char id, AW_pos width, AW_pos height, ED4_manager parent);
1299	~ED4_manager() OVERRIDE;
1300	};
1301
1302	class ED4_terminal : public ED4_base { // derived from a Noncopyable
1303	E4B_AVOID_UNNEEDED_CASTS(terminal);
1304
1305	public:
1306
1307	struct { unsigned int deleted : 1; } tflag; // @@@ go bool
1308
1309	long curr_timestamp;
1310
1311	DECLARE_DUMP_FOR_BASECLASS(ED4_terminal,ED4_base);
1312
1313	// callbacks
1314
1315	void changed_by_database() OVERRIDE;
1316	void deleted_from_database() OVERRIDE;
1317
1318	// functions concerning graphic output
1319	void Show(bool refresh_all, bool is_cleared) OVERRIDE;
1320	virtual void draw() = 0;
1321
1322	bool calc_bounding_box() OVERRIDE;
1323
1324	ED4_returncode draw_drag_box(AW_pos x, AW_pos y, GB_CSTR text = NULL, int cursor_y=-1);
1325
1326	// functions which concern the object as a child
1327	void request_refresh(int clear=1) OVERRIDE;
1328
1329	void resize_requested_children() OVERRIDE;
1330
1331	void update_requested_children() OVERRIDE;
1332	void delete_requested_children() OVERRIDE;
1333	void Delete() OVERRIDE;
1334
1335	ED4_returncode move_requested_by_parent(ED4_move_info *mi) OVERRIDE;
1336	ED4_returncode event_sent_by_parent(AW_event event, AW_window aww) OVERRIDE;
1337	ED4_base *get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop) OVERRIDE;
1338	ED4_base *get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop) OVERRIDE;
1339	ED4_returncode move_requested_by_child(ED4_move_info *moveinfo) OVERRIDE;
1340	ED4_returncode handle_move(ED4_move_info *moveinfo) OVERRIDE;
1341
1342	ED4_returncode kill_object();
1343
1344	// general purpose functions
1345	ED4_base search_ID(const char id) OVERRIDE;
1346	char resolve_pointer_to_string_copy(int str_len = 0) const OVERRIDE;
1347	const char resolve_pointer_to_char_pntr(int str_len = 0) const OVERRIDE;
1348	ED4_returncode remove_callbacks() OVERRIDE;
1349
1350	GB_ERROR write_sequence(const char *seq, int seq_len);
1351
1352	void scroll_into_view(ED4_window *ed4w);
1353	inline bool setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfoldGroups, ED4_CursorJumpType jump_type);
1354
1355	bool is_hidden() const OVERRIDE { return parent && parent->is_hidden(); }
1356
1357	ED4_terminal(const ED4_objspec& spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
1358	~ED4_terminal() OVERRIDE;
1359	};
1360
1361	enum ED4_species_mode {
1362	ED4_SM_MOVE,
1363	ED4_SM_KILL,
1364	ED4_SM_MARK,
1365	ED4_SM_INFO // same functionality as AWT_MODE_INFO
1366	};
1367
1368	class ED4_reference_terminals : virtual Noncopyable {
1369	ED4_sequence_info_terminal *ref_sequence_info;
1370	ED4_sequence_terminal *ref_sequence;
1371	ED4_sequence_info_terminal *ref_column_stat_info;
1372	ED4_columnStat_terminal *ref_column_stat;
1373
1374	void null() { ref_sequence_info = 0; ref_sequence = 0; ref_column_stat = 0; ref_column_stat_info = 0; }
1375	public:
1376	void clear();
1377	void init(ED4_sequence_info_terminal , ED4_sequence_terminal , ED4_sequence_info_terminal , ED4_columnStat_terminal );
1378
1379	ED4_sequence_terminal *sequence() { return ref_sequence; }
1380	ED4_sequence_info_terminal *sequence_info() { return ref_sequence_info; }
1381	ED4_columnStat_terminal *column_stat() { return ref_column_stat; }
1382	ED4_sequence_info_terminal *column_stat_info() { return ref_column_stat_info; }
1383
1384	ED4_reference_terminals() { null(); }
1385	~ED4_reference_terminals() { clear(); }
1386	};
1387
1388	class ED4_WinContext {
1389	ED4_window *ed4w;
1390	AW_device *device;
1391
1392	bool is_set() const { return ed4w; }
1393	void init(ED4_window *ew) {
1394	e4_assert(ew);
1395	ed4w = ew;
1396	device = ed4w->get_device();
1397	}
1398
1399	void warn_missing_context() const;
1400	void expect_context() const { if (!is_set()) warn_missing_context(); }
1401
1402	protected:
1403	ED4_WinContext() : ed4w(0), device(0) {}
1404	static ED4_WinContext current_context;
1405
1406	public:
1407	inline ED4_WinContext(AW_window *aww_);
1408	ED4_WinContext(ED4_window *ed4w_) { init(ed4w_); }
1409
1410	AW_device *get_device() const { expect_context(); return device; }
1411	ED4_window *get_ed4w() const { expect_context(); return ed4w; }
1412
1413	static const ED4_WinContext& get_current_context() { return current_context; }
1414	static bool have_context() { return current_context.is_set(); }
1415	};
1416
1417	// accessors for current context (see also ED4_WinContextFree)
1418	inline AW_device *current_device() { return ED4_WinContext::get_current_context().get_device(); }
1419	inline ED4_window *current_ed4w() { return ED4_WinContext::get_current_context().get_ed4w(); }
1420	inline AW_window *current_aww() { return current_ed4w()->aww; }
1421	inline ED4_cursor& current_cursor() { return current_ed4w()->cursor; }
1422
1423	enum LoadableSaiState {
1424	LSAI_UNUSED,
1425	LSAI_UPTODATE,
1426	LSAI_OUTDATED,
1427	};
1428
1429	class ED4_root : virtual Noncopyable {
1430	void ED4_ROOT() const { e4_assert(0); } // avoid ED4_root-members use global ED4_ROOT
1431
1432	void refresh_window_simple(bool redraw);
1433	void handle_update_requests(bool& redraw);
1434
1435	ED4_window *most_recently_used_window;
1436	ConsensusBuildParams *cons_param;
1437
1438	public:
1439	char *db_name; // name of Default Properties database (complete path)
1440	AW_root *aw_root; // Points to 'AW-Window-Controller'
1441	AW_default props_db; // Default Properties database
1442
1443	ED4_window *first_window; // Points to List of Main Windows of ED4
1444	ED4_main_manager *main_manager; // Points to Main manager of ED4
1445	ED4_area_manager *middle_area_man; // Points to middle area
1446	ED4_area_manager *top_area_man;
1447	ED4_root_group_manager *root_group_man;
1448	EDB_root_bact *database; // Points to Object which controls Data
1449	ED4_selected_list *selected_objects;
1450	ED4_scroll_links scroll_links;
1451	bool folding_action; // flag tells whether action was folding action or not
1452	ED4_reference_terminals ref_terminals;
1453	ED4_species_mode species_mode;
1454	ED4_scroll_picture scroll_picture;
1455	BI_ecoli_ref *ecoli_ref;
1456	char *alignment_name;
1457	GB_alignment_type alignment_type;
1458	ED4_reference *reference;
1459	ED4_seq_colors *sequence_colors;
1460	AW_gc_manager *gc_manager;
1461	ST_ML *st_ml;
1462	AW_helix *helix;
1463	int helix_spacing;
1464	long helix_add_spacing;
1465	long terminal_add_spacing;
1466	char *protstruct; // protein structure summary
1467	long protstruct_len; // protein structure summary
1468	ed_key *edk;
1469	ED4_Edit_String *edit_string;
1470
1471	bool column_stat_activated;
1472	bool column_stat_initialized;
1473	bool visualizeSAI;
1474	bool visualizeSAI_allSpecies;
1475
1476	const ConsensusBuildParams& get_consensus_params();
1477	void reset_consensus_params();
1478
1479	LoadableSaiState loadable_SAIs; // maintain proper refresh of list of loadable SAIs
1480	void loadable_SAIs_may_have_changed() { if (loadable_SAIs == LSAI_UPTODATE) loadable_SAIs = LSAI_OUTDATED; }
1481
1482	int temp_gc;
1483	AW_font_group font_group;
1484
1485	void announce_useraction_in(AW_window *aww);
1486	ED4_window *get_most_recently_used_window() const {
1487	e4_assert(most_recently_used_window);
1488	return most_recently_used_window;
1489	}
1490
1491	inline ED4_device_manager *get_device_manager();
1492
1493	// Initializing functions
1494	ED4_returncode create_hierarchy(const char area_string_middle, const char area_string_top);
1495	ARB_ERROR init_alignment();
1496	void recalc_font_group();
1497
1498	AW_window *create_first_window();
1499	ED4_returncode generate_window(AW_device device, ED4_window new_window);
1500	void copy_window_struct(ED4_window source, ED4_window destination);
1501
1502	// functions concerned with global refresh and resize
1503	void resize_all_requesting_childs();
1504
1505	void special_window_refresh(bool handle_updates);
1506	ED4_returncode refresh_all_windows(bool redraw);
1507
1508	void request_refresh_for_all_terminals();
1509	void request_refresh_for_specific_terminals(ED4_level lev);
1510	void request_refresh_for_consensus_terminals();
1511	void request_refresh_for_sequence_terminals();
1512
1513	inline void announce_deletion(ED4_base *object); // before deleting an object, use this to announce
1514
1515	// functions concerned with list of selected objects
1516	ED4_returncode add_to_selected(ED4_species_name_terminal *object);
1517	void remove_from_selected(ED4_species_name_terminal *object);
1518	ED4_returncode deselect_all();
1519
1520	ED4_returncode get_area_rectangle(AW_screen_area *rect, AW_pos x, AW_pos y);
1521
1522	ED4_index pixel2pos(AW_pos click_x);
1523
1524	void remove_all_callbacks();
1525
1526	ED4_root(int argc, char** argv);
1527	~ED4_root();
1528	};
1529
1530	ED4_WinContext::ED4_WinContext(AW_window *aww_) { init(ED4_ROOT->first_window->get_matching_ed4w(aww_)); }
1531
1532	struct ED4_LocalWinContext : private ED4_WinContext {
1533	ED4_LocalWinContext(AW_window *aww) : ED4_WinContext(current_context) { current_context = ED4_WinContext(aww); }
1534	ED4_LocalWinContext(ED4_window *ew) : ED4_WinContext(current_context) { current_context = ED4_WinContext(ew); }
1535	~ED4_LocalWinContext() { current_context = *this; }
1536	};
1537
1538	class ED4_MostRecentWinContext : virtual Noncopyable {
1539	ED4_LocalWinContext *most_recent;
1540	public:
1541	ED4_MostRecentWinContext() : most_recent(0) {
1542	if (!ED4_WinContext::have_context()) {
1543	most_recent = new ED4_LocalWinContext(ED4_ROOT->get_most_recently_used_window());
1544	}
1545	}
1546	~ED4_MostRecentWinContext() {
1547	delete most_recent;
1548	}
1549	};
1550
1551	inline void ED4_root::announce_deletion(ED4_base *object) {
1552	if (object->is_terminal()) {
1553	ED4_terminal *term = object->to_terminal();
1554	for (ED4_window *win = first_window; win; win = win->next) {
1555	ED4_LocalWinContext uses(win);
1556	win->announce_deletion(term);
1557	}
1558	}
1559	}
1560
1561	// ------------------------
1562	// manager classes
1563	//
1564	// All manager classes only differ in their static properties.
1565	// This kind of construction was chosen for using a minimum of RAM
1566
1567	class ED4_main_manager : public ED4_manager { // derived from a Noncopyable
1568	// first in hierarchy
1569
1570	E4B_AVOID_UNNEEDED_CASTS(main_manager);
1571
1572	// these terminals are redrawn after refresh (with increase clipping area)
1573	// to revert text from middle area drawn into top area:
1574	ED4_terminal *top_middle_line;
1575	ED4_terminal *top_middle_spacer;
1576
1577	public:
1578	ED4_main_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1579
1580	void set_top_middle_spacer_terminal(ED4_terminal *top_middle_spacer_) { top_middle_spacer = top_middle_spacer_; }
1581	void set_top_middle_line_terminal(ED4_terminal *top_middle_line_) { top_middle_line = top_middle_line_; }
1582
1583	ED4_terminal *get_top_middle_spacer_terminal() const { return top_middle_spacer; }
1584	ED4_terminal *get_top_middle_line_terminal() const { return top_middle_line; }
1585
1586	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1587
1588	void Show(bool refresh_all, bool is_cleared) OVERRIDE;
1589	void resize_requested_children() OVERRIDE;
1590
1591	void clear_whole_background();
1592	};
1593
1594	struct ED4_device_manager : public ED4_manager {
1595	E4B_AVOID_UNNEEDED_CASTS(device_manager);
1596	ED4_device_manager (const char id, AW_pos width, AW_pos height, ED4_manager parent);
1597	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1598	};
1599
1600	struct ED4_area_manager : public ED4_manager {
1601	E4B_AVOID_UNNEEDED_CASTS(area_manager);
1602	ED4_area_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1603	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1604
1605	ED4_multi_species_manager *get_multi_species_manager() const {
1606	return get_defined_level(LEV_MULTI_SPECIES)->to_multi_species_manager();
1607	}
1608	};
1609
1610	class ED4_multi_species_manager : public ED4_manager {
1611	E4B_AVOID_UNNEEDED_CASTS(multi_species_manager);
1612
1613	int species; // # of species (-1 == unknown)
1614	int selected_species; // # of selected species (-1 == unknown)
1615
1616	void set_species_counters(int no_of_species, int no_of_selected);
1617	#ifdef DEBUG
1618	void count_species(int speciesPtr, int selectedPtr) const;
1619	#endif
1620	void update_species_counters();
1621
1622	public:
1623	ED4_multi_species_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1624
1625	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1626
1627	void update_requested_children() OVERRIDE;
1628	void delete_requested_children() OVERRIDE;
1629
1630	int count_visible_children(); // is called by a multi_species_manager
1631
1632	ED4_species_manager *get_consensus_manager() const; // returns the consensus-manager or NULL
1633	ED4_species_name_terminal *get_consensus_name_terminal() const; // returns the consensus-name-terminal or NULL
1634
1635	// functions concerned with selection
1636	int get_no_of_selected_species();
1637	int get_no_of_species();
1638
1639	void update_group_id();
1640
1641	void invalidate_species_counters();
1642	int has_valid_counters() const { return species != -1 && selected_species!=-1; }
1643	bool all_are_selected() const { e4_assert(has_valid_counters()); return species == selected_species; }
1644
1645	void select_all(bool only_species);
1646	void deselect_all_species_and_SAI();
1647	void invert_selection_of_all_species();
1648	void marked_species_select(bool select);
1649	void selected_species_mark(bool mark);
1650
1651	void toggle_selected_species();
1652	};
1653
1654	class ED4_abstract_group_manager : public ED4_manager {
1655	E4B_AVOID_UNNEEDED_CASTS(abstract_group_manager);
1656	protected:
1657	BaseFrequencies my_table; // table concerning Consensusfunction
1658
1659	public:
1660	ED4_abstract_group_manager(const ED4_objspec& spec_, const char id, AW_pos width, AW_pos height, ED4_manager parent);
1661
1662	DECLARE_DUMP_FOR_BASECLASS(ED4_abstract_group_manager, ED4_manager);
1663
1664	BaseFrequencies& table() { return my_table; }
1665	const BaseFrequencies& table() const { return my_table; }
1666
1667	ED4_multi_species_manager *get_multi_species_manager() const {
1668	return get_defined_level(LEV_MULTI_SPECIES)->to_multi_species_manager();
1669	}
1670
1671	char *build_consensus_string(PosRange range) const { return table().build_consensus_string(range, ED4_ROOT->get_consensus_params()); }
1672	char build_consensus_string(int cons_length = NULL) const {
1673	if (cons_length) *cons_length = table().size();
1674	return table().build_consensus_string(ED4_ROOT->get_consensus_params());
1675	}
1676	};
1677
1678	struct ED4_group_manager : public ED4_abstract_group_manager {
1679	E4B_AVOID_UNNEEDED_CASTS(group_manager);
1680	ED4_group_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1681	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_group_manager);
1682	void reinit_char_table();
1683
1684	void fold();
1685	void unfold();
1686	void toggle_folding();
1687	};
1688
1689	enum ED4_remap_mode {
1690	ED4_RM_NONE, // no remapping (normal mode)
1691	ED4_RM_SHOW_ABOVE, // Show all positions, where xxx% of all edited sequences have any base
1692	ED4_RM_MAX_ALIGN, // ------------------------- any edited sequence has a base
1693	ED4_RM_MAX_EDIT, // like ED4_RM_MAX_ALIGN, but bases are pushed OVER remapped gaps (not INTO)
1694	ED4_RM_DYNAMIC_GAPS, // gaps shown as spaces (more gaps => more spaces)
1695
1696	ED4_RM_MODES
1697
1698	};
1699
1700	class ED4_remap : virtual Noncopyable {
1701
1702	ED4_remap_mode mode;
1703	int show_above_percent; // used only for ED4_RM_SHOW_ABOVE
1704
1705	size_t sequence_table_len; // allocated size of sequence_to_screen_tab
1706	size_t screen_table_len; // allocated size of screen_to_sequence_tab
1707
1708	size_t sequence_len; // size of recently compiled part of sequence_to_screen_tab
1709	size_t screen_len; // size of recently compiled part of screen_to_sequence_tab
1710
1711	int *screen_to_sequence_tab;
1712	int *sequence_to_screen_tab; // <0 means position is not mapped (last displayed sequence position); 0 may be mapped or not; see is_shown() below
1713
1714	int changed; // remap-table changed at last compile
1715	int update_needed; // remapping should be recompiled
1716
1717	inline void set_sequence_to_screen(int pos, int newVal);
1718
1719	public:
1720
1721	ED4_remap();
1722	~ED4_remap();
1723
1724	int screen_to_sequence(int screen_pos) const;
1725
1726	int sequence_to_screen_PLAIN(int sequence_pos) const {
1727	e4_assert(sequence_pos>=0 && size_t(sequence_pos)<=sequence_len);
1728	return sequence_to_screen_tab[sequence_pos];
1729	}
1730	int shown_sequence_to_screen(int sequence_pos) const {
1731	// as well works for sequence_pos == MAXSEQUENCECHARACTERLENGTH
1732	int screen_pos = sequence_to_screen_PLAIN(sequence_pos);
1733	e4_assert(screen_pos >= 0); // sequence_pos expected to be visible (i.e. not folded away)
1734	return screen_pos;
1735	}
1736
1737	int clipped_sequence_to_screen_PLAIN(int sequence_pos) const;
1738	int sequence_to_screen(int sequence_pos) const;
1739
1740	PosRange sequence_to_screen(PosRange range) const {
1741	e4_assert(!range.is_empty());
1742	return PosRange(sequence_to_screen(range.start()), sequence_to_screen(range.end()));
1743	}
1744	PosRange screen_to_sequence(PosRange range) const {
1745	e4_assert(!range.is_empty());
1746	if (range.is_unlimited()) return PosRange::from(screen_to_sequence(range.start()));
1747	return PosRange(screen_to_sequence(range.start()), screen_to_sequence(range.end()));
1748	}
1749
1750	size_t get_max_screen_pos() const { return screen_len-1; }
1751
1752	void adjacent_screen_positions(int seq_pos, int& screen_pos_left, int& screen_pos_right);
1753
1754	ED4_remap_mode get_mode() const { return mode; }
1755	void set_mode(ED4_remap_mode Mode, int above_percent) {
1756	if (Mode<0 \|\| Mode>=ED4_RM_MODES) {
1757	Mode = ED4_RM_NONE;
1758	}
1759	if (mode!=Mode) {
1760	mode = Mode;
1761	update_needed = 1;
1762	}
1763
1764	if (show_above_percent!=above_percent) {
1765	show_above_percent = above_percent;
1766	if (mode==ED4_RM_SHOW_ABOVE) {
1767	update_needed = 1;
1768	}
1769	}
1770	}
1771
1772	void mark_compile_needed(); // recompile if mode != none
1773	void mark_compile_needed_force(); // always recompile
1774	int compile_needed() const { return update_needed; }
1775
1776	GB_ERROR compile(ED4_root_group_manager *gm);
1777	int was_changed() const { return changed; } // mapping changed by last compile ?
1778
1779	int is_shown(int seq_pos) const {
1780	int scr_pos = sequence_to_screen_PLAIN(seq_pos);
1781	if (scr_pos<0) return false;
1782	if (scr_pos>0) return true;
1783
1784	int seq_pos2 = screen_to_sequence_tab[0];
1785	return seq_pos == seq_pos2;
1786	}
1787
1788	ExplicitRange clip_screen_range(PosRange screen_range) const { return ExplicitRange(screen_range, screen_len-1); }
1789	};
1790
1791	class ED4_root_group_manager : public ED4_abstract_group_manager {
1792	E4B_AVOID_UNNEEDED_CASTS(root_group_manager);
1793	ED4_remap my_remap;
1794	public:
1795	ED4_root_group_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1796
1797	bool update_remap(); // 'true' if mapping has changed
1798
1799	const ED4_remap *remap() const { return &my_remap; }
1800	ED4_remap *remap() { return &my_remap; }
1801
1802	void Show(bool refresh_all, bool is_cleared) OVERRIDE;
1803	void resize_requested_children() OVERRIDE;
1804
1805	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_group_manager);
1806	};
1807
1808	class ED4_species_manager : public ED4_manager {
1809	E4B_AVOID_UNNEEDED_CASTS(species_manager);
1810
1811	ED4_cb_list<ED4_species_manager, ED4_species_managerCallback> changed_cbs; // called when sequence changes
1812
1813	ED4_species_type type;
1814	bool selected;
1815
1816	public:
1817	ED4_species_manager(ED4_species_type type_, const char id, AW_pos width, AW_pos height, ED4_manager parent);
1818	~ED4_species_manager() OVERRIDE;
1819
1820	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1821
1822	ED4_species_type get_type() const { return type; }
1823
1824	bool is_selected() const { return selected; }
1825	void set_selected(bool select) {
1826	// e4_assert(type != ED4_SP_CONSENSUS); // it's not allowed to select a consensus // @@@ happens atm when moving a group
1827	selected = select;
1828	}
1829
1830	bool setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfold_groups, ED4_CursorJumpType jump_type);
1831
1832	void add_sequence_changed_cb(const ED4_species_managerCallback& cb) { changed_cbs.add_cb(cb); }
1833	void remove_sequence_changed_cb(const ED4_species_managerCallback& cb) { changed_cbs.remove_cb(cb); }
1834	void do_callbacks() { changed_cbs.call(this); }
1835
1836	ED4_species_name_terminal *get_name_terminal() const { return member(0)->to_species_name_terminal(); }
1837	};
1838
1839	inline ED4_species_manager *ED4_base::containing_species_manager() const {
1840	ED4_base *sman = get_parent(LEV_SPECIES);
1841	return sman ? sman->to_species_manager() : NULL;
1842	}
1843
1844	inline bool ED4_base::is_consensus_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_CONSENSUS; }
1845	inline bool ED4_base::is_SAI_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_SAI; }
1846	inline bool ED4_base::is_species_seq_manager() const { return is_species_manager() && to_species_manager()->get_type() == ED4_SP_SPECIES; }
1847
1848	inline ED4_species_type ED4_base::get_species_type() const {
1849	ED4_species_manager *sman = containing_species_manager();
1850	return sman ? sman->get_type() : ED4_SP_NONE;
1851	}
1852
1853	inline bool ED4_base::inside_consensus_manager() const { return get_species_type() == ED4_SP_CONSENSUS; }
1854	inline bool ED4_base::inside_SAI_manager() const { return get_species_type() == ED4_SP_SAI; }
1855	inline bool ED4_base::inside_species_seq_manager() const { return get_species_type() == ED4_SP_SPECIES; }
1856
1857	inline bool ED4_base::is_consensus_terminal() const { return is_sequence_terminal() && inside_consensus_manager(); }
1858	inline bool ED4_base::is_SAI_terminal() const { return is_sequence_terminal() && inside_SAI_manager(); }
1859	inline bool ED4_base::is_species_seq_terminal() const { return is_sequence_terminal() && inside_species_seq_manager(); }
1860
1861	inline bool ED4_cursor::in_species_seq_terminal() const { return owner_of_cursor && owner_of_cursor->is_species_seq_terminal(); }
1862	inline bool ED4_cursor::in_consensus_terminal() const { return owner_of_cursor && owner_of_cursor->is_consensus_terminal(); }
1863	inline bool ED4_cursor::in_SAI_terminal() const { return owner_of_cursor && owner_of_cursor->is_SAI_terminal(); }
1864
1865
1866	struct ED4_multi_sequence_manager : public ED4_manager {
1867	E4B_AVOID_UNNEEDED_CASTS(multi_sequence_manager);
1868	ED4_multi_sequence_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1869	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1870	};
1871
1872	struct ED4_sequence_manager : public ED4_manager {
1873	E4B_AVOID_UNNEEDED_CASTS(sequence_manager);
1874	ED4_sequence_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1875	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1876	};
1877
1878	struct ED4_multi_name_manager : public ED4_manager {
1879	E4B_AVOID_UNNEEDED_CASTS(multi_name_manager);
1880	// member of ED4_species_manager (contains ED4_name_manager for name and info)
1881	ED4_multi_name_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1882	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1883	};
1884
1885
1886	struct ED4_name_manager : public ED4_manager {
1887	E4B_AVOID_UNNEEDED_CASTS(name_manager);
1888	// member of ED4_multi_name_manager (contains speciesname or other info concerning the species)
1889	ED4_name_manager(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1890	DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager);
1891	};
1892
1893
1894	// -------------------------
1895	// terminal classes
1896
1897
1898	struct ED4_tree_terminal : public ED4_terminal {
1899	E4B_AVOID_UNNEEDED_CASTS(tree_terminal);
1900
1901	void draw() OVERRIDE;
1902
1903	ED4_tree_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1904
1905	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
1906	};
1907
1908	struct ED4_bracket_terminal : public ED4_terminal {
1909	E4B_AVOID_UNNEEDED_CASTS(bracket_terminal);
1910
1911	void draw() OVERRIDE;
1912
1913	void toggle_folding();
1914
1915	ED4_bracket_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1916
1917	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
1918	};
1919
1920	struct ED4_text_terminal : public ED4_terminal {
1921	E4B_AVOID_UNNEEDED_CASTS(text_terminal);
1922
1923	// functions concerning graphic output
1924	void draw() OVERRIDE;
1925
1926	virtual int get_length() const = 0;
1927	void deleted_from_database() OVERRIDE;
1928
1929	ED4_text_terminal(const ED4_objspec& spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
1930	~ED4_text_terminal() OVERRIDE {}
1931
1932	DECLARE_DUMP_FOR_BASECLASS(ED4_text_terminal, ED4_terminal);
1933	};
1934
1935	class ED4_abstract_sequence_terminal : public ED4_text_terminal { // derived from a Noncopyable
1936
1937	PosRange pixel2index(PosRange pixel_range);
1938
1939	E4B_AVOID_UNNEEDED_CASTS(abstract_sequence_terminal);
1940	public:
1941	char *species_name; // @@@ wrong place (may be member of ED4_sequence_manager)
1942
1943
1944	ED4_abstract_sequence_terminal(const ED4_objspec& spec_, const char id, AW_pos width, AW_pos height, ED4_manager parent);
1945	~ED4_abstract_sequence_terminal() OVERRIDE;
1946
1947	virtual GB_alignment_type GetAliType() = 0;
1948	int get_length() const OVERRIDE { int len; resolve_pointer_to_char_pntr(&len); return len; }
1949
1950	ED4_species_name_terminal *corresponding_species_name_terminal() const {
1951	return get_parent(LEV_SPECIES)->search_spec_child_rek(LEV_SPECIES_NAME)->to_species_name_terminal();
1952	}
1953	PosRange calc_interval_displayed_in_rectangle(AW_screen_area *area_rect);
1954	PosRange calc_update_interval();
1955
1956	DECLARE_DUMP_FOR_BASECLASS(ED4_abstract_sequence_terminal, ED4_text_terminal);
1957	};
1958
1959	class ED4_orf_terminal : public ED4_abstract_sequence_terminal { // derived from a Noncopyable
1960	// NOTE: ED4_orf_terminal is a separate terminal class used to display Open Reading Frames (ORFs)
1961	// for the corresponding gene (DNA) sequence. It is used in ProteinViewer Module and should not be
1962	// used for drawing aminoacid sequence alone as in protein alignment. Aminoacid sequences are
1963	// handled by the standard "ED4_sequence_terminal" class.
1964
1965	char *aaSequence;
1966	size_t aaSeqLen;
1967	char *aaColor;
1968	int aaStartPos;
1969	int aaStrandType;
1970
1971	void draw() OVERRIDE;
1972	E4B_AVOID_UNNEEDED_CASTS(orf_terminal);
1973	public:
1974	ED4_orf_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
1975	~ED4_orf_terminal() OVERRIDE;
1976
1977	GB_alignment_type GetAliType() OVERRIDE;
1978
1979	void SET_aaSeqFlags (int startPos, int strandType) { aaStartPos = startPos; aaStrandType = strandType; }
1980	void SET_aaSequence(const char *aaSeq) { freedup(aaSequence, aaSeq); aaSeqLen = strlen(aaSequence); }
1981	void SET_aaColor(const char *aaSeq) { freedup(aaColor, aaSeq); }
1982
1983	int GET_aaStartPos () { return aaStartPos; }
1984	int GET_aaStrandType () { return aaStrandType; }
1985
1986	DECLARE_DUMP_FOR_LEAFCLASS(ED4_abstract_sequence_terminal);
1987	};
1988
1989	class ED4_sequence_terminal : public ED4_abstract_sequence_terminal { // derived from a Noncopyable
1990	mutable ED4_SearchResults searchResults;
1991	bool shall_display_secstruct_info; // helix or protstruct
1992
1993	void draw() OVERRIDE;
1994
1995	E4B_AVOID_UNNEEDED_CASTS(sequence_terminal);
1996
1997	public:
1998
1999	AP_tree *st_ml_node;
2000
2001	ED4_sequence_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent, bool shall_display_secstruct_info_);
2002
2003	GB_alignment_type GetAliType() OVERRIDE;
2004
2005	void deleted_from_database() OVERRIDE;
2006	int get_length() const OVERRIDE { return ED4_abstract_sequence_terminal::get_length(); }
2007
2008	virtual char get_sequence_copy(int str_len = 0) const { return resolve_pointer_to_string_copy(str_len); }
2009
2010	void set_secstruct_display(bool show) { shall_display_secstruct_info = show; }
2011
2012	ED4_SearchResults& results() const { return searchResults; }
2013
2014	ED4_columnStat_terminal *corresponding_columnStat_terminal() const {
2015	ED4_base *col_term = get_parent(LEV_MULTI_SEQUENCE)->search_spec_child_rek(LEV_COL_STAT);
2016	return col_term ? col_term->to_columnStat_terminal() : 0;
2017	}
2018
2019	DECLARE_DUMP_FOR_MIDCLASS(ED4_sequence_terminal,ED4_abstract_sequence_terminal);
2020	};
2021
2022	class ED4_columnStat_terminal : public ED4_text_terminal { // derived from a Noncopyable
2023	char *likelihood[4]; // likelihood-array for each base (ACGU) [length of array = alignment_length]
2024	int latest_update;
2025
2026	static double threshold;
2027
2028	int update_likelihood();
2029
2030	E4B_AVOID_UNNEEDED_CASTS(columnStat_terminal);
2031
2032	public:
2033	// functions concerning graphic output
2034	void draw() OVERRIDE;
2035	int get_length() const OVERRIDE { return corresponding_sequence_terminal()->get_length(); }
2036
2037	static int threshold_is_set();
2038	static void set_threshold(double aThreshold);
2039	static double get_threshold() { return threshold; }
2040
2041	ED4_sequence_terminal *corresponding_sequence_terminal() const { return get_parent(LEV_MULTI_SEQUENCE)->search_spec_child_rek(LEV_SEQUENCE_STRING)->to_sequence_terminal(); }
2042
2043	ED4_columnStat_terminal(GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
2044	~ED4_columnStat_terminal() OVERRIDE;
2045
2046	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2047	};
2048
2049	class ED4_species_name_terminal : public ED4_text_terminal { // derived from a Noncopyable
2050	E4B_AVOID_UNNEEDED_CASTS(species_name_terminal);
2051	bool set_dynamic_size() OVERRIDE;
2052
2053	public:
2054	ED4_species_name_terminal(GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
2055	~ED4_species_name_terminal() OVERRIDE { delete selection_info; }
2056
2057
2058	ED4_selection_entry *selection_info; // Info about i.e. Position
2059	bool dragged;
2060
2061	GB_CSTR get_displayed_text() const;
2062	int get_length() const OVERRIDE { return strlen(get_displayed_text()); }
2063
2064	ED4_sequence_terminal *corresponding_sequence_terminal() const {
2065	ED4_base *seq_term = get_parent(LEV_SPECIES)->search_spec_child_rek(LEV_SEQUENCE_STRING);
2066	return seq_term ? seq_term->to_sequence_terminal() : 0;
2067	}
2068
2069	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2070	};
2071
2072	class ED4_flag_header_terminal : public ED4_text_terminal { // derived from a Noncopyable
2073	// displays header of flags
2074
2075	E4B_AVOID_UNNEEDED_CASTS(flag_header_terminal);
2076	bool set_dynamic_size() OVERRIDE;
2077
2078	public:
2079	ED4_flag_header_terminal(GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent);
2080
2081	GB_CSTR get_displayed_text() const;
2082	int get_length() const OVERRIDE;
2083
2084	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2085	};
2086
2087	class ED4_sequence_info_terminal : public ED4_text_terminal {
2088	E4B_AVOID_UNNEEDED_CASTS(sequence_info_terminal);
2089	bool set_dynamic_size() OVERRIDE;
2090
2091	public:
2092	ED4_sequence_info_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
2093
2094	ED4_species_name_terminal *corresponding_species_name_terminal() const {
2095	return get_parent(LEV_SPECIES)->search_spec_child_rek(LEV_SPECIES_NAME)->to_species_name_terminal();
2096	}
2097
2098	void draw() OVERRIDE;
2099
2100	GBDATA *data() { return get_species_pointer(); } // DB-entry ("ali_xxx/data")
2101	const GBDATA *data() const { return get_species_pointer(); }
2102
2103	int get_length() const OVERRIDE { return 1+strlen(id); }
2104
2105	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2106	};
2107
2108	struct ED4_pure_text_terminal : public ED4_text_terminal {
2109	E4B_AVOID_UNNEEDED_CASTS(pure_text_terminal);
2110
2111	ED4_pure_text_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
2112
2113	int get_length() const OVERRIDE { int len; resolve_pointer_to_char_pntr(&len); return len; }
2114
2115	DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal);
2116	};
2117
2118	class ED4_consensus_sequence_terminal : public ED4_sequence_terminal { // derived from a Noncopyable
2119	E4B_AVOID_UNNEEDED_CASTS(consensus_sequence_terminal);
2120
2121	void draw() OVERRIDE;
2122	const ED4_abstract_group_manager *get_group_manager() const { return get_parent(LEV_GROUP)->to_group_manager(); }
2123	const BaseFrequencies& get_char_table() const { return get_group_manager()->table(); }
2124
2125	public:
2126	char *temp_cons_seq; // used for editing consensus (normally NULL)
2127
2128	ED4_consensus_sequence_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
2129	#if defined(ASSERTION_USED)
2130	virtual ~ED4_consensus_sequence_terminal() { e4_assert(!temp_cons_seq); }
2131	#endif
2132
2133	int get_length() const OVERRIDE;
2134	char get_sequence_copy(int str_len = 0) const OVERRIDE;
2135
2136	DECLARE_DUMP_FOR_LEAFCLASS(ED4_sequence_terminal);
2137	};
2138
2139	class ED4_spacer_terminal : public ED4_terminal {
2140	E4B_AVOID_UNNEEDED_CASTS(spacer_terminal);
2141	bool shallDraw; // true -> spacer is really drawn (otherwise it's only a placeholder)
2142
2143	bool set_dynamic_size() OVERRIDE;
2144
2145	public:
2146	void Show(bool refresh_all, bool is_cleared) OVERRIDE;
2147	void draw() OVERRIDE;
2148
2149	ED4_spacer_terminal(const char id, bool shallDraw_, AW_pos width, AW_pos height, ED4_manager parent);
2150
2151	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2152	};
2153
2154	class ED4_line_terminal : public ED4_terminal {
2155	E4B_AVOID_UNNEEDED_CASTS(line_terminal);
2156	bool set_dynamic_size() OVERRIDE;
2157
2158	public:
2159	void draw() OVERRIDE;
2160
2161	ED4_line_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
2162
2163	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2164	};
2165
2166	class ED4_flag_terminal : public ED4_terminal {
2167	E4B_AVOID_UNNEEDED_CASTS(flag_terminal);
2168	bool set_dynamic_size() OVERRIDE;
2169
2170	public:
2171	void draw() OVERRIDE;
2172
2173	ED4_flag_terminal(const char id, AW_pos width, AW_pos height, ED4_manager parent);
2174
2175	GBDATA *get_species() const { return get_parent(LEV_SPECIES)->get_species_pointer(); }
2176	void handle_left_click(const AW::Position& click);
2177
2178	DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal);
2179	};
2180
2181
2182	// ----------------------------------------------
2183	// inlines which need complete classdefs
2184
2185	inline void ED4_base::set_update() { // @@@ rename into request_update
2186	if (!update_info.update_requested) {
2187	update_info.update_requested = 1;
2188	if (parent) parent->update_requested_by_child();
2189	}
2190	}
2191
2192	inline void ED4_base::request_resize() {
2193	update_info.set_resize(1);
2194	if (parent) parent->resize_requested_by_child();
2195	}
2196
2197	void ED4_manager::resize_requested_by_child() {
2198	if (!update_info.resize) request_resize();
2199	}
2200
2201	inline bool ED4_terminal::setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfoldGroups, ED4_CursorJumpType jump_type) {
2202	ED4_species_manager *sm = get_parent(LEV_SPECIES)->to_species_manager();
2203	return sm->setCursorTo(cursor, seq_pos, unfoldGroups, jump_type);
2204	}
2205
2206	E4B_IMPL_CASTOP(area_manager); // to_area_manager
2207	E4B_IMPL_CASTOP(abstract_group_manager); // to_abstract_group_manager
2208	E4B_IMPL_CASTOP(bracket_terminal); // to_bracket_terminal
2209	E4B_IMPL_CASTOP(columnStat_terminal); // to_columnStat_terminal
2210	E4B_IMPL_CASTOP(consensus_sequence_terminal); // to_consensus_sequence_terminal
2211	E4B_IMPL_CASTOP(device_manager); // to_device_manager
2212	E4B_IMPL_CASTOP(group_manager); // to_group_manager
2213	E4B_IMPL_CASTOP(line_terminal); // to_line_terminal
2214	E4B_IMPL_CASTOP(manager); // to_manager
2215	E4B_IMPL_CASTOP(multi_name_manager); // to_multi_name_manager
2216	E4B_IMPL_CASTOP(multi_sequence_manager); // to_multi_sequence_manager
2217	E4B_IMPL_CASTOP(multi_species_manager); // to_multi_species_manager
2218	E4B_IMPL_CASTOP(name_manager); // to_name_manager
2219	E4B_IMPL_CASTOP(orf_terminal); // to_orf_terminal
2220	E4B_IMPL_CASTOP(pure_text_terminal); // to_pure_text_terminal
2221	E4B_IMPL_CASTOP(root_group_manager); // to_root_group_manager
2222	E4B_IMPL_CASTOP(sequence_info_terminal); // to_sequence_info_terminal
2223	E4B_IMPL_CASTOP(sequence_manager); // to_sequence_manager
2224	E4B_IMPL_CASTOP(sequence_terminal); // to_sequence_terminal
2225	E4B_IMPL_CASTOP(spacer_terminal); // to_spacer_terminal
2226	E4B_IMPL_CASTOP(species_manager); // to_species_manager
2227	E4B_IMPL_CASTOP(species_name_terminal); // to_species_name_terminal
2228	E4B_IMPL_CASTOP(terminal); // to_terminal
2229	E4B_IMPL_CASTOP(text_terminal); // to_text_terminal
2230	E4B_IMPL_CASTOP(flag_header_terminal); // to_flag_header_terminal
2231	E4B_IMPL_CASTOP(flag_terminal); // to_flag_terminal
2232
2233	inline ED4_device_manager *ED4_root::get_device_manager() {
2234	return main_manager->search_spec_child_rek(LEV_DEVICE)->to_device_manager();
2235	}
2236
2237
2238	inline ED4_species_name_terminal *ED4_multi_species_manager::get_consensus_name_terminal() const {
2239	ED4_species_manager *consensus_man = get_consensus_manager();
2240	return consensus_man ? consensus_man->get_name_terminal() : NULL;
2241	}
2242
2243	// ----------------------------------------
2244
2245	enum SpeciesCreationMode {
2246	CREATE_NEW_SPECIES,
2247	CREATE_FROM_CONSENSUS, // create new species from group consensus (of surrounding group)
2248	COPY_SPECIES, // copy current species
2249	};
2250
2251	#if defined(ASSERTION_USED)
2252	CONSTEXPR_RETURN inline bool valid(SpeciesCreationMode m) { return m>=CREATE_NEW_SPECIES && m<=COPY_SPECIES; }
2253	#endif
2254
2255	extern ST_ML *st_ml;
2256	struct AlignDataAccess;
2257
2258	// -------------------------------------------------
2259	// factory functions (hierarchy builders):
2260
2261	ED4_group_manager ED4_build_group_manager_start(ED4_manager group_parent,
2262	GB_CSTR group_name,
2263	int group_depth,
2264	bool is_folded,
2265	ED4_reference_terminals& refterms,
2266	ED4_multi_species_manager*& multi_species_manager);
2267
2268	void ED4_build_group_manager_end(ED4_multi_species_manager *multi_species_manager);
2269
2270	// -------------------------------------
2271	// hierarchy access functions:
2272
2273	ED4_species_name_terminal ED4_find_species_name_terminal(const char species_name);
2274	ED4_species_name_terminal ED4_find_SAI_name_terminal(const char sai_name);
2275	ED4_species_name_terminal ED4_find_species_or_SAI_name_terminal(const char species_name);
2276
2277	ED4_multi_species_manager *ED4_find_MoreSequences_manager();
2278
2279	// --------------------------
2280	// other functions:
2281
2282	void ED4_new_editor_window(AW_window *aww);
2283	void ED4_with_all_edit_windows(void (cb)(ED4_window ));
2284
2285	void ED4_resize_all_extensions();
2286	void ED4_calc_terminal_extentions();
2287
2288	void ED4_input_cb(AW_window *aww);
2289	void ED4_remote_event(AW_event *faked_event);
2290	void ED4_motion_cb(AW_window *aww);
2291	void ED4_vertical_change_cb(AW_window *aww);
2292	void ED4_horizontal_change_cb(AW_window *aww);
2293	void ED4_scrollbar_change_cb(AW_window *aww);
2294	void ED4_trigger_instant_refresh();
2295	void ED4_request_relayout();
2296	void ED4_request_full_refresh();
2297	void ED4_request_full_instant_refresh();
2298
2299	void ED4_store_curpos(AW_window *aww);
2300	void ED4_restore_curpos(AW_window *aww);
2301	void ED4_clear_stored_curpos();
2302	void ED4_helix_jump_opposite(AW_window *aww);
2303	void ED4_jump_to_cursor_position(AW_window aww, const char awar_name, PositionType posType);
2304	void ED4_remote_set_cursor_cb(AW_root *awr);
2305	void ED4_change_cursor(AW_window *aww);
2306
2307	void ED4_set_iupac(AW_window aww, const char awar_name);
2308	void ED4_set_helixnr(AW_window aww, const char awar_name);
2309	void ed4_changesecurity(AW_root *root);
2310	void ed4_change_edit_mode(AW_root *root);
2311
2312	void ED4_jump_to_current_species(AW_window *);
2313	void ED4_get_and_jump_to_current(AW_window *);
2314	void ED4_get_and_jump_to_species(GB_CSTR species_name);
2315
2316	void ED4_get_marked_from_menu(AW_window *);
2317	void ED4_selected_species_changed_cb(AW_root *aw_root);
2318
2319	AW_window ED4_create_loadSAI_window(AW_root awr);
2320	void ED4_get_and_jump_to_selected_SAI(AW_window *aww);
2321	void ED4_selected_SAI_changed_cb(AW_root *aw_root);
2322
2323	void ED4_init_notFoundMessage();
2324	void ED4_finish_and_show_notFoundMessage();
2325
2326	const AlignDataAccess *ED4_get_aligner_data_access();
2327
2328	void ED4_popup_gc_window(AW_window awp, AW_gc_manager gcman);
2329	void ED4_no_dangerous_modes();
2330
2331	void group_species_cb(AW_window *aww, bool use_fields);
2332	AW_window ED4_create_group_species_by_field_window(AW_root aw_root);
2333
2334	AW_window ED4_create_loadConfiguration_window(AW_root awr);
2335	void ED4_reloadConfiguration(AW_window *aww);
2336	void ED4_saveConfiguration(AW_window *aww, bool hide_aww);
2337	AW_window ED4_create_saveConfigurationAs_window(AW_root awr);
2338
2339	ARB_ERROR rebuild_consensus(ED4_base *object);
2340
2341	void ED4_create_consensus_awars(AW_root *aw_root);
2342	AW_window ED4_create_consensus_definition_window(AW_root root);
2343	void ED4_consensus_definition_changed(AW_root*);
2344	void ED4_consensus_display_changed(AW_root *root);
2345
2346	AW_window ED4_create_editor_options_window(AW_root root);
2347	void ED4_compression_toggle_changed_cb(AW_root *root, bool hideChanged);
2348	void ED4_compression_changed_cb(AW_root *awr);
2349	void ED4_alignment_length_changed(GBDATA *gb_alignment_len, GB_CB_TYPE gbtype);
2350
2351	AW_window ED4_create_new_seq_window(AW_root root, SpeciesCreationMode creation_mode);
2352
2353	void ED4_quit_editor(AW_window *aww);
2354	void ED4_exit() __ATTR__NORETURN;
2355
2356
2357	#else
2358	#error ed4_class included twice
2359	#endif
2360

Note: See TracBrowser for help on using the repository browser.

Download in other formats: