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TreeCallbacks.cxx

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Last change on this file was 19206, checked in by westram, 2 years ago
reintegrates 'ali' into 'trunk' adds: log:branches/ali@19183:19205
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 37.6 KB

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1	// =============================================================== //
2	// //
3	// File : TreeCallbacks.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "TreeCallbacks.hxx"
12
13	#include <aw_color_groups.hxx>
14	#include <aw_awars.hxx>
15	#include <aw_advice.hxx>
16	#include <aw_msg.hxx>
17	#include <aw_root.hxx>
18	#include <arb_strbuf.h>
19	#include <mode_text.h>
20
21	#include <cctype>
22	#include <gb_aci.h>
23
24	using namespace AW;
25
26	// AISC_MKPT_PROMOTE:#ifndef TREEDISPLAY_HXX
27	// AISC_MKPT_PROMOTE:#include <TreeDisplay.hxx>
28	// AISC_MKPT_PROMOTE:#endif
29
30	void nt_mode_event(UNFIXED, TREE_canvas *ntw, AWT_COMMAND_MODE mode) {
31	const char *text;
32
33	switch (mode) {
34	case AWT_MODE_ZOOM: text = MODE_TEXT_STANDARD_ZOOMMODE(); break;
35	case AWT_MODE_EMPTY: text = MODE_TEXT_PLACEHOLDER(); break;
36
37	case AWT_MODE_SELECT: text = MODE_TEXT_1BUTTON("SELECT", "select species or open/close group"); break;
38	case AWT_MODE_INFO: text = MODE_TEXT_1BUTTON("INFO", "click for info"); break;
39	case AWT_MODE_WWW: text = MODE_TEXT_1BUTTON("WEB", "Launch node dependent URL (see <Properties/WWW...>)"); break;
40
41	case AWT_MODE_SWAP: text= MODE_TEXT_2BUTTONS("SWAP", "swap child branches", "flip whole subtree"); break;
42	case AWT_MODE_MARK: text= MODE_TEXT_2BUTTONS("MARK", "mark subtree", "unmark subtree"); break;
43	case AWT_MODE_GROUP: text= MODE_TEXT_2BUTTONS("GROUP", "fold/unfold group", "create/rename/destroy group"); break;
44	case AWT_MODE_NNI: text= MODE_TEXT_2BUTTONS("OPTI(NNI)", "once", "repeated"); break;
45	case AWT_MODE_KERNINGHAN: text= MODE_TEXT_2BUTTONS("OPTI(KL)", "once", "repeated"); break;
46	case AWT_MODE_OPTIMIZE: text= MODE_TEXT_2BUTTONS("OPTI(NNI&KL)", "once", "repeated"); break;
47	case AWT_MODE_SETROOT: text= MODE_TEXT_2BUTTONS("REROOT", "set root to clicked branch", "search optimal root"); break;
48
49	case AWT_MODE_ROTATE: text = MODE_TEXT_1BUTTON_KEYS("ROTATE", "drag branch to rotate", KEYINFO_ABORT_AND_RESET); break;
50	case AWT_MODE_SPREAD: text = MODE_TEXT_1BUTTON_KEYS("SPREAD", "drag branch to spread subtree", KEYINFO_ABORT_AND_RESET); break;
51
52	case AWT_MODE_LENGTH: text = MODE_TEXT_2BUTTONS_KEYS("LENGTH", "drag branch/ruler", "use discrete lengths", KEYINFO_ABORT_AND_RESET); break;
53	case AWT_MODE_MULTIFURC: text = MODE_TEXT_2BUTTONS_KEYS("MULTIFURC", "drag branch", "use discrete lengths", KEYINFO_ABORT_AND_RESET); break;
54	case AWT_MODE_LINE: text = MODE_TEXT_2BUTTONS_KEYS("LINE", "drag branch/ruler", "whole subtree", KEYINFO_ABORT_AND_RESET); break;
55	case AWT_MODE_MOVE: text = MODE_TEXT_2BUTTONS_KEYS("MOVE", "drag branch/ruler", "move groupinfo only", KEYINFO_ABORT); break;
56	case AWT_MODE_LZOOM: text = MODE_TEXT_2BUTTONS_KEYS("LOGICAL ZOOM", "show only subtree", "go up one step", KEYINFO_RESET); break;
57
58	default: text = no_mode_text_defined(); break;
59	}
60
61	td_assert(strlen(text) < AWAR_FOOTER_MAX_LEN); // text too long!
62
63	ntw->awr->awar(AWAR_FOOTER)->write_string(text);
64	ntw->set_mode(mode);
65	}
66
67	// ---------------------------------------
68	// Basic mark/unmark callbacks :
69
70	#define MARK_MODE_LOWER_BITS (1\|2)
71	#define MARK_MODE_UPPER_BITS (4\|8\|16)
72
73	#define COUNTING_MARKED(mode) (((mode)&MARK_MODE_LOWER_BITS) == 3)
74
75	static void show_count(GBDATA *gb_main, int mark_mode, int tree_mode, long count) {
76	// tree_mode: 0=none, 1=intree, 2=!intree
77	if (COUNTING_MARKED(mark_mode)) { // if counting
78	GBS_strstruct buf(200);
79
80	switch (count) {
81	case 0: buf.cat("There are NO"); break;
82	case 1: buf.cat("There is 1"); break;
83	default: buf.nprintf(100, "There are %li", count); break;
84	}
85
86	buf.cat(" marked");
87	switch (mark_mode&MARK_MODE_UPPER_BITS) {
88	case 0: // all sequences
89	buf.cat(" species");
90	break;
91	case 4: // full sequences only
92	buf.cat(" full-sequence species");
93	break;
94	case 8: // partial sequences only
95	buf.cat(" partial-sequence species");
96	break;
97	case 16: { // species with data in alignment only
98	char *ali = GBT_get_default_alignment(gb_main);
99	gb_assert(ali); // no caller calls 'show_count' in that case!
100	buf.nprintf(100, " species with data in '%s'", ali);
101	free(ali);
102	break;
103	}
104	default:
105	td_assert(0); // illegal mode
106	break;
107	}
108	switch (tree_mode) {
109	case 0: // all species
110	break;
111	case 1: // tree member
112	buf.cat(" inside the tree");
113	break;
114	case 2: // tree non-members
115	buf.cat(" outside the tree");
116	break;
117	}
118	buf.put('.');
119
120	if ((mark_mode&MARK_MODE_UPPER_BITS) == 0 && tree_mode == 0) { // traditional count all marked
121	static bool hintShown = false;
122	if (!hintShown) {
123	buf.cat("\n(The number of species is displayed in the top area as well)");
124	hintShown = true;
125	}
126	}
127
128	aw_message(buf.get_data());
129	}
130	}
131
132	static bool species_has_alignment(GBDATA gb_species, void cd_use) {
133	return GBT_find_sequence(gb_species, (const char*)cd_use);
134	}
135
136	static bool sequence_is_partial(GBDATA gb_species, void cd_partial) {
137	long wanted = (long)cd_partial;
138	td_assert(wanted == 0 \|\| wanted == 1);
139	bool partial = GBT_is_partial(gb_species, 0, false);
140
141	return partial == wanted;
142	}
143
144	void NT_mark_all_cb(UNFIXED, TREE_canvas *ntw, int mark_mode) {
145	// Bits 0 and 1 of mark_mode:
146	//
147	// mark_mode&3 == 0 -> unmark
148	// mark_mode&3 == 1 -> mark
149	// mark_mode&3 == 2 -> toggle mark
150	// mark_mode&3 == 3 -> count marked
151	//
152	// Bits 2 .. 4 of mark_mode:
153	//
154	// mark_mode&12 == 4 -> affect only full sequences
155	// mark_mode&12 == 8 -> affect only partial sequences
156	// mark_mode&12 == 16 -> affect only species with data in current alignment
157	// else -> affect all sequences
158
159	AWT_auto_refresh allowed_on(ntw);
160	GB_transaction ta(ntw->gb_main);
161
162	GB_ERROR error = NULp;
163	long count = 0;
164	switch (mark_mode&MARK_MODE_UPPER_BITS) {
165	case 0: // all sequences
166	count = GBT_mark_all(ntw->gb_main, mark_mode&MARK_MODE_LOWER_BITS);
167	break;
168	case 4: // full sequences only
169	count = GBT_mark_all_that(ntw->gb_main, mark_mode&MARK_MODE_LOWER_BITS, sequence_is_partial, (void*)NULp);
170	break;
171	case 8: // partial sequences only
172	count = GBT_mark_all_that(ntw->gb_main, mark_mode&MARK_MODE_LOWER_BITS, sequence_is_partial, (void*)1);
173	break;
174	case 16: { // species with data in alignment only
175	char *ali = GBT_get_default_alignment(ntw->gb_main);
176	if (!ali) {
177	error = GB_await_error();
178	}
179	else {
180	count = GBT_mark_all_that(ntw->gb_main, mark_mode&MARK_MODE_LOWER_BITS, species_has_alignment, (void*)ali);
181	free(ali);
182	}
183	break;
184	}
185	default:
186	td_assert(0); // illegal mode
187	break;
188	}
189
190	if (error) {
191	aw_message(error);
192	}
193	else if (COUNTING_MARKED(mark_mode)) {
194	show_count(ntw->gb_main, mark_mode, 0, count);
195	}
196	else {
197	ntw->request_structure_update(); // includes refresh etc
198	}
199	}
200
201	static void mark_tree_cb(UNFIXED, TREE_canvas *ntw, int mark_mode) {
202	GB_transaction ta(ntw->gb_main);
203	AWT_auto_refresh allowed_on(ntw);
204	AWT_graphic_tree *gtree = AWT_TREE(ntw);
205	AP_tree *tree_root = gtree->get_root_node();
206
207	GB_ERROR error = NULp;
208	long count = 0;
209	switch (mark_mode&MARK_MODE_UPPER_BITS) {
210	case 0: // all sequences
211	count = gtree->mark_species_in_tree(tree_root, mark_mode&MARK_MODE_LOWER_BITS);
212	break;
213	case 4: // full sequences only
214	count = gtree->mark_species_in_tree_that(tree_root, mark_mode&MARK_MODE_LOWER_BITS, sequence_is_partial, (void*)NULp);
215	break;
216	case 8: // partial sequences only
217	count = gtree->mark_species_in_tree_that(tree_root, mark_mode&MARK_MODE_LOWER_BITS, sequence_is_partial, (void*)1);
218	break;
219	case 16: { // species with data in alignment only
220	char *ali = GBT_get_default_alignment(ntw->gb_main);
221	if (!ali) {
222	error = GB_await_error();
223	}
224	else {
225	count = gtree->mark_species_in_tree_that(tree_root, mark_mode&MARK_MODE_LOWER_BITS, species_has_alignment, (void*)ali);
226	free(ali);
227	}
228	break;
229	}
230	default:
231	td_assert(0); // illegal mode
232	break;
233	}
234
235	if (error) {
236	aw_message(error);
237	}
238	else if (COUNTING_MARKED(mark_mode)) {
239	show_count(ntw->gb_main, mark_mode, 1, count);
240	}
241	else {
242	ntw->request_structure_update(); // includes refresh etc
243	}
244	}
245
246	struct mark_nontree_cb_data {
247	int mark_mode_upper_bits;
248	char *ali; // current alignment (only if mark_mode_upper_bits == 16)
249	GB_HASH *hash;
250	};
251
252	static bool are_not_in_tree(GBDATA gb_species, void cb_data) {
253	struct mark_nontree_cb_data data = (mark_nontree_cb_data)cb_data;
254	bool mark_me = false;
255
256	if (GBS_read_hash(data->hash, GBT_get_name_or_description(gb_species)) == (long)gb_species) { // species is not in tree!
257	switch (data->mark_mode_upper_bits) {
258	case 0: // all sequences
259	mark_me = true;
260	break;
261	case 4: // full sequences only
262	mark_me = sequence_is_partial(gb_species, (void*)NULp);
263	break;
264	case 8: // partial sequences only
265	mark_me = sequence_is_partial(gb_species, (void*)1);
266	break;
267	case 16: // species with data in alignment only
268	mark_me = species_has_alignment(gb_species, data->ali);
269	break;
270	default:
271	td_assert(0); // illegal mode
272	break;
273	}
274	}
275
276	return mark_me;
277	}
278
279	static void mark_nontree_cb(UNFIXED, TREE_canvas *ntw, int mark_mode) {
280	AWT_graphic_tree *gtree = AWT_TREE(ntw);
281	GB_transaction ta(ntw->gb_main);
282	struct mark_nontree_cb_data cd;
283	AWT_auto_refresh allowed_on(ntw);
284
285	if ((mark_mode&MARK_MODE_LOWER_BITS) == 0) { // unmark is much faster
286	cd.hash = GBT_create_marked_species_hash(ntw->gb_main); // because it only hashes marked species
287	}
288	else {
289	cd.hash = GBT_create_species_hash(ntw->gb_main); // for mark we have to hash ALL species
290	}
291
292	NT_remove_species_in_tree_from_hash(gtree->get_root_node(), cd.hash);
293
294	cd.mark_mode_upper_bits = mark_mode&MARK_MODE_UPPER_BITS;
295
296	GB_ERROR error = NULp;
297	if (cd.mark_mode_upper_bits == 16) {
298	cd.ali = GBT_get_default_alignment(ntw->gb_main);
299	if (!cd.ali) error = GB_await_error();
300	}
301	else {
302	cd.ali = NULp;
303	}
304
305	long count = 0;
306	if (!error) {
307	count = GBT_mark_all_that(ntw->gb_main, mark_mode&MARK_MODE_LOWER_BITS, are_not_in_tree, (void*)&cd);
308	}
309	free(cd.ali);
310
311	if (error) {
312	aw_message(error);
313	}
314	else if (COUNTING_MARKED(mark_mode)) {
315	show_count(ntw->gb_main, mark_mode, 2, count);
316	}
317	else {
318	ntw->request_refresh(); // does only affect display of NDS list (if tree shown -> never changes; i.e. no structure update needed)
319	}
320	}
321
322	static char create_mark_menu_entry(const char attrib, const char *entry_template) {
323	char *entry = NULp;
324	if (attrib) {
325	bool append = attrib[0] == '-'; // if attrib starts with '-' then append (otherwise prepend)
326	if (append) ++attrib; // skip '-'
327
328	if (append) {
329	char *spaced_attrib = GBS_global_string_copy(" %s", attrib);
330	entry = GBS_global_string_copy(entry_template, "", spaced_attrib);
331	free(spaced_attrib);
332	}
333	else {
334	char *spaced_attrib = GBS_global_string_copy("%s ", attrib);
335	entry = GBS_global_string_copy(entry_template, spaced_attrib, "");
336
337	if (islower(entry[0])) entry[0] = toupper(entry[0]); // Caps prepended lowercase 'attrib'
338
339	free(spaced_attrib);
340	}
341	}
342	else {
343	entry = GBS_global_string_copy(entry_template, "", "");
344	}
345	return entry;
346	}
347	static char create_mark_menu_id(const char attrib, const char *id_suffix) {
348	char *id = NULp;
349	if (attrib) {
350	id = GBS_global_string_copy("%s_%s", attrib[0] == '-' ? attrib+1 : attrib, id_suffix);
351	}
352	else {
353	id = strdup(id_suffix);
354	}
355	return id;
356	}
357
358	static void insert_mark_topic(AW_window_menu_modes awm, AW_active mask, const char attrib, const char id_suffix, const char entry_template,
359	const char hotkey, const char helpfile, const WindowCallback& wcb)
360	{
361	char *entry = create_mark_menu_entry(attrib, entry_template);
362	char *id = create_mark_menu_id(attrib, id_suffix);
363
364	awm->insert_menu_topic(id, entry, hotkey, helpfile, mask, wcb);
365
366	free(id);
367	free(entry);
368	}
369
370	static void insert_mark_topics(AW_window_menu_modes awm, AW_active mask, TREE_canvas ntw, int affect, const char *attrib) {
371	td_assert(affect == (affect&MARK_MODE_UPPER_BITS)); // only bits 2 .. 4 are allowed
372
373	insert_mark_topic(awm, mask, attrib, "count_marked","Count marks of all %sSpecies%s", "C", "sp_mark.hlp", makeWindowCallback(NT_mark_all_cb, ntw, 3+affect));
374	awm->sep______________();
375	insert_mark_topic(awm, mask, attrib, "mark_all", "Mark all %sSpecies%s", "M", "sp_mark.hlp", makeWindowCallback(NT_mark_all_cb, ntw, 1+affect));
376	insert_mark_topic(awm, mask, attrib, "unmark_all", "Unmark all %sSpecies%s", "U", "sp_mark.hlp", makeWindowCallback(NT_mark_all_cb, ntw, 0+affect));
377	insert_mark_topic(awm, mask, attrib, "swap_marked", "Invert marks of all %sSpecies%s", "I", "sp_mark.hlp", makeWindowCallback(NT_mark_all_cb, ntw, 2+affect));
378	awm->sep______________();
379
380	char *label = create_mark_menu_entry(attrib, "%sSpecies%s in Tree");
381
382	awm->insert_sub_menu(label, "T");
383	insert_mark_topic(awm, mask, attrib, "count_marked_tree","Count marks of %sSpecies%s in Tree", "C", "sp_mark.hlp", makeWindowCallback(mark_tree_cb, ntw, 3+affect));
384	awm->sep______________();
385	insert_mark_topic(awm, mask, attrib, "mark_tree", "Mark %sSpecies%s in Tree", "M", "sp_mark.hlp", makeWindowCallback(mark_tree_cb, ntw, 1+affect));
386	insert_mark_topic(awm, mask, attrib, "unmark_tree", "Unmark %sSpecies%s in Tree", "U", "sp_mark.hlp", makeWindowCallback(mark_tree_cb, ntw, 0+affect));
387	insert_mark_topic(awm, mask, attrib, "swap_marked_tree", "Invert marks of %sSpecies%s in Tree", "I", "sp_mark.hlp", makeWindowCallback(mark_tree_cb, ntw, 2+affect));
388	awm->close_sub_menu();
389
390	freeset(label, create_mark_menu_entry(attrib, "%sSpecies%s NOT in Tree"));
391
392	awm->insert_sub_menu(label, "N");
393	insert_mark_topic(awm, mask, attrib, "count_marked_nontree","Count marks of %sSpecies%s NOT in Tree", "C", "sp_mark.hlp", makeWindowCallback(mark_nontree_cb, ntw, 3+affect));
394	awm->sep______________();
395	insert_mark_topic(awm, mask, attrib, "mark_nontree", "Mark %sSpecies%s NOT in Tree", "M", "sp_mark.hlp", makeWindowCallback(mark_nontree_cb, ntw, 1+affect));
396	insert_mark_topic(awm, mask, attrib, "unmark_nontree", "Unmark %sSpecies%s NOT in Tree", "U", "sp_mark.hlp", makeWindowCallback(mark_nontree_cb, ntw, 0+affect));
397	insert_mark_topic(awm, mask, attrib, "swap_marked_nontree", "Invert marks of %sSpecies%s NOT in Tree", "I", "sp_mark.hlp", makeWindowCallback(mark_nontree_cb, ntw, 2+affect));
398	awm->close_sub_menu();
399
400	free(label);
401	}
402
403	void NT_insert_mark_submenus(AW_window_menu_modes awm, TREE_canvas ntw, int insert_as_submenu) {
404	if (insert_as_submenu) {
405	awm->insert_sub_menu("Mark species", "M");
406	}
407
408	{
409	insert_mark_topics(awm, AWM_ALL, ntw, 0, NULp);
410	awm->sep______________();
411
412	awm->insert_sub_menu("Complete sequences", "o");
413	insert_mark_topics(awm, AWM_EXP, ntw, 4, "complete");
414	awm->close_sub_menu();
415
416	awm->insert_sub_menu("Partial sequences", "P");
417	insert_mark_topics(awm, AWM_EXP, ntw, 8, "partial");
418	awm->close_sub_menu();
419
420	awm->insert_sub_menu("Current Alignment", "A");
421	insert_mark_topics(awm, AWM_EXP, ntw, 16, "-with data");
422	awm->close_sub_menu();
423	}
424
425	if (insert_as_submenu) {
426	awm->close_sub_menu();
427	}
428	}
429
430	// ----------------------------------------
431	// Automated collapse/expand tree
432
433	static void group_and_refold_tree(TREE_canvas *ntw, CollapseMode mode, int color_group) {
434	GB_transaction ta(ntw->gb_main);
435	AWT_auto_refresh allowed_on(ntw);
436	AWT_graphic_tree *agt = AWT_TREE(ntw);
437	AP_tree *root_node = agt->get_root_node();
438
439	agt->group_tree(root_node, mode, color_group);
440
441	agt->fast_sync_changed_folding(root_node);
442	}
443
444	static void collapse_all_cb (UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, COLLAPSE_ALL, 0); }
445	static void collapse_terminal_cb(UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, COLLAPSE_TERMINAL, 0); }
446	static void expand_unmarked_cb (UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, EXPAND_UNMARKED, 0); }
447	static void expand_all_cb (UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, EXPAND_ALL, 0); }
448	void NT_expand_marked_cb (UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, EXPAND_MARKED, 0); }
449	static void expand_zombies_cb (UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, EXPAND_ZOMBIES, 0); }
450
451	static void expand_color_cb(UNFIXED, TREE_canvas *ntw, int colornum) { group_and_refold_tree(ntw, EXPAND_COLOR, colornum); }
452
453	static void insert_color_collapse_submenu(AW_window_menu_modes awm, TREE_canvas ntree_canvas) {
454	const int MAXLABEL = 31;
455	const int MAXENTRY = AW_COLOR_GROUP_NAME_LEN+10;
456
457	td_assert(ntree_canvas);
458
459	awm->insert_sub_menu("Expand color ...", "o");
460
461	char label_buf[MAXLABEL+1];
462	char entry_buf[MAXENTRY+1];
463	char hotkey[] = "x";
464	const char *hotkeys = "AN1234567890BC"+1;
465
466	for (int i = -1; i <= AW_COLOR_GROUPS; ++i) {
467	hotkey[0] = hotkeys[i];
468	if (hotkey[0] == ' ') hotkey[0] = 0;
469
470	if (i) {
471	if (i<0) {
472	strcpy(label_buf, "tree_group_not_any_color");
473	strcpy(entry_buf, "Any color group");
474	}
475	else {
476	sprintf(label_buf, "tree_group_not_color_%i", i);
477
478	char *color_group_name = AW_get_color_group_name(awm->get_root(), i);
479	size_t len = strlen(color_group_name);
480	if (len>AW_COLOR_GROUP_NAME_LEN) {
481	color_group_name[AW_COLOR_GROUP_NAME_LEN] = 0; // truncate overlong colorgroup names
482	}
483	sprintf(entry_buf, "%s group '%s'", hotkey, color_group_name);
484	free(color_group_name);
485	}
486	}
487	else {
488	strcpy(label_buf, "tree_group_not_no_color");
489	strcpy(entry_buf, "No color group");
490	}
491
492	awm->insert_menu_topic(awm->local_id(label_buf), entry_buf, hotkey, "tree_group.hlp", AWM_ALL, makeWindowCallback(expand_color_cb, ntree_canvas, i));
493	}
494
495	awm->close_sub_menu();
496	}
497
498	void NT_insert_collapse_submenu(AW_window_menu_modes awm, TREE_canvas ntw) {
499	awm->insert_sub_menu("Collapse/expand groups", "d");
500	{
501	const char *grouphelp = "tree_group.hlp";
502	awm->insert_menu_topic(awm->local_id("tree_group_all"), "Collapse all", "C", grouphelp, AWM_ALL, makeWindowCallback(collapse_all_cb, ntw));
503	awm->insert_menu_topic(awm->local_id("tree_group_term_groups"), "Collapse terminal", "t", grouphelp, AWM_ALL, makeWindowCallback(collapse_terminal_cb, ntw));
504	awm->sep______________();
505	awm->insert_menu_topic(awm->local_id("tree_ungroup_all"), "Expand all", "E", grouphelp, AWM_ALL, makeWindowCallback(expand_all_cb, ntw));
506	awm->insert_menu_topic(awm->local_id("tree_group_not_marked"), "Expand marked", "m", grouphelp, AWM_ALL, makeWindowCallback(NT_expand_marked_cb, ntw));
507	awm->insert_menu_topic(awm->local_id("tree_ungroup_unmarked"), "Expand unmarked", "u", grouphelp, AWM_ALL, makeWindowCallback(expand_unmarked_cb, ntw));
508	awm->insert_menu_topic(awm->local_id("tree_ungroup_zombies"), "Expand zombies", "z", grouphelp, AWM_ALL, makeWindowCallback(expand_zombies_cb, ntw));
509	awm->sep______________();
510	insert_color_collapse_submenu(awm, ntw);
511	}
512	awm->close_sub_menu();
513	}
514
515	// ------------------------
516	// tree sorting :
517
518	GB_ERROR NT_with_displayed_tree_do(TREE_canvas ntw, bool (displayed_tree_cb)(TreeNode *tree, GB_ERROR& error)) {
519	// 'displayed_tree_cb' has to return true if tree was changed and needs to be saved
520
521	GB_transaction ta(ntw->gb_main);
522	AWT_auto_refresh allowed_on(ntw);
523
524	GB_ERROR error = NULp;
525	if (displayed_tree_cb(AWT_TREE(ntw)->get_root_node(), error)) {
526	ntw->request_save_and_zoom_reset();
527	}
528	return error;
529	}
530
531	void NT_resort_tree_cb(UNFIXED, TREE_canvas *ntw, TreeOrder order) {
532	GB_transaction ta(ntw->gb_main);
533	AWT_auto_refresh allowed_on(ntw);
534
535	AWT_TREE(ntw)->reorderTree(order);
536	ntw->request_save_and_zoom_reset();
537	}
538
539	void NT_reset_lzoom_cb(UNFIXED, TREE_canvas *ntw) {
540	GB_transaction ta(ntw->gb_main);
541	AWT_auto_refresh allowed_on(ntw);
542	AWT_graphic_tree *agt = AWT_TREE(ntw);
543
544	agt->set_logical_root_to(agt->get_root_node());
545	ntw->request_zoom_reset();
546	}
547
548	void NT_reset_pzoom_cb(UNFIXED, TREE_canvas *ntw) {
549	GB_transaction ta(ntw->gb_main);
550	AWT_auto_refresh allowed_on(ntw);
551	ntw->request_zoom_reset();
552	}
553
554	void NT_set_tree_style(UNFIXED, TREE_canvas *ntw, AP_tree_display_style style) {
555	{
556	AWT_auto_refresh allowed_on(ntw);
557	AWT_TREE(ntw)->set_tree_style(style, ntw);
558	ntw->request_zoom_reset();
559	}
560	TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_STYLE);
561	}
562
563	void NT_reinit_treetype(UNFIXED, TREE_canvas *ntw) {
564	NT_set_tree_style(NULp, ntw, AWT_TREE(ntw)->get_tree_style());
565	}
566
567	void NT_remove_leafs(UNFIXED, TREE_canvas *ntw, AWT_RemoveType mode) {
568	GB_transaction ta(ntw->gb_main);
569	AWT_auto_refresh allowed_on(ntw);
570
571	AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
572	if (root_node) {
573	AWT_TREE(ntw)->get_tree_root()->remove_leafs(mode);
574	ntw->request_save_and_zoom_reset();
575	}
576	else {
577	aw_message("Got no tree");
578	}
579	}
580
581	void NT_remove_bootstrap(UNFIXED, TREE_canvas *ntw) { // delete all bootstrap values
582	GB_transaction ta(ntw->gb_main);
583	AWT_auto_refresh allowed_on(ntw);
584
585	AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
586	if (root_node) {
587	root_node->remove_bootstrap();
588	ntw->request_save_and_zoom_reset();
589	}
590	else {
591	aw_message("Got no tree");
592	}
593	}
594
595	void NT_edit_bootstrap(UNFIXED, TREE_canvas *ntw) { // edit bootstrap values
596	GB_transaction ta(ntw->gb_main);
597	AWT_auto_refresh allowed_on(ntw);
598
599	AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
600	if (root_node) {
601	char *aci = aw_input("Enter ACI to apply to all branch remarks:");
602	if (aci) {
603	char *tree_name = ntw->get_awar_tree()->read_string();
604
605	GBL_env env(ntw->gb_main, tree_name);
606	GBL_call_env callEnv(NULp, env); // do not pass any species (will only be applied to inner branches)
607
608	GB_ERROR error = root_node->apply_aci_to_remarks(aci, callEnv);
609	ntw->request_save_and_zoom_reset();
610
611	error = ta.close(error);
612	if (error) aw_message(error);
613
614	free(tree_name);
615	}
616	}
617	else {
618	aw_message("Got no tree");
619	}
620	}
621
622	void NT_reset_branchlengths(UNFIXED, TREE_canvas *ntw) { // set all branchlengths to tree_defaults::LENGTH
623	GB_transaction ta(ntw->gb_main);
624	AWT_auto_refresh allowed_on(ntw);
625
626	AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
627	if (root_node) {
628	root_node->reset_branchlengths();
629	ntw->request_save_and_zoom_reset();
630	}
631	else {
632	aw_message("Got no tree");
633	}
634	}
635
636	void NT_multifurcate_tree(TREE_canvas *ntw, const TreeNode::multifurc_limits& below) {
637	GB_transaction ta(ntw->gb_main);
638	AWT_auto_refresh allowed_on(ntw);
639
640	TreeNode *tree = AWT_TREE(ntw)->get_root_node();
641	if (tree) {
642	tree->multifurcate_whole_tree(below);
643	ntw->request_save_and_zoom_reset();
644	}
645	else {
646	aw_message("Got no tree");
647	}
648	}
649
650	void NT_move_boot_branch(UNFIXED, TREE_canvas *ntw, int direction) { // copy branchlengths to bootstraps (or vice versa)
651	GB_transaction ta(ntw->gb_main);
652	AWT_auto_refresh allowed_on(ntw);
653
654	AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
655	if (root_node) {
656	if (direction == 0) root_node->bootstrap2branchlen();
657	else root_node->branchlen2bootstrap();
658
659	ntw->request_save_and_zoom_reset();
660
661	char *adviceText = GBS_global_string_copy("Please note, that you just overwrote your existing %s.",
662	direction ? "bootstrap values" : "branchlengths");
663	AW_advice(adviceText, AW_ADVICE_TOGGLE_AND_HELP, NULp, "tbl_boot2len.hlp");
664	free(adviceText);
665	}
666	else {
667	aw_message("Got no tree");
668	}
669	}
670
671	void NT_scale_tree(UNFIXED, TREE_canvas *ntw) { // scale branchlengths
672	char *answer = aw_input("Enter scale factor", "Scale branchlengths by factor:", "100");
673	if (answer) {
674	double factor = atof(answer);
675	AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
676
677	if (root_node) {
678	GB_transaction ta(ntw->gb_main);
679	AWT_auto_refresh allowed_on(ntw);
680	root_node->scale_branchlengths(factor);
681	ntw->request_save_and_zoom_reset();
682	}
683	else {
684	aw_message("Got no tree");
685	}
686	free(answer);
687	}
688	}
689
690	inline AP_tree common_ancestor(AP_tree t1, AP_tree *t2) {
691	return DOWNCAST(AP_tree*, t1->ancestor_common_with(t2));
692	}
693
694	void NT_jump_cb(UNFIXED, TREE_canvas *ntw, AP_tree_jump_type jumpType) {
695	if (jumpType == AP_DONT_JUMP) return;
696
697	AW_window *aww = ntw->aww;
698	AWT_graphic_tree *gtree = AWT_TREE(ntw);
699
700	GB_transaction ta(ntw->gb_main);
701	AWT_auto_refresh allowed_on(ntw);
702
703	AW_root *aw_root = aww->get_root();
704	const char *name = aw_root->awar(AWAR_SPECIES_NAME)->read_char_pntr();
705	GBDATA *gb_group = gtree->get_selected_group().get_group_data();
706
707	char *msg = NULp;
708	bool verboose = jumpType & AP_JUMP_BE_VERBOOSE;
709
710	if (name[0] \|\| gb_group) {
711	AP_tree *found = NULp;
712	bool is_tree = is_tree_style(gtree->get_tree_style());
713	bool jump_to_group = gb_group && is_tree; // @@@ prefer group atm
714
715	if (is_tree) {
716	if (gtree && gtree->get_logical_root()) {
717	if (jump_to_group) {
718	found = gtree->locate_selected_group(gtree->get_logical_root());
719	td_assert(found && found->is_clade());
720	}
721	else {
722	found = gtree->get_logical_root()->findLeafNamed(name);
723	}
724
725	if (!found && gtree->is_logically_zoomed()) {
726	if (jump_to_group) {
727	found = gtree->locate_selected_group(gtree->get_root_node());
728	}
729	else {
730	found = gtree->get_root_node()->findLeafNamed(name);
731	}
732
733	if (found) { // species/group is invisible because it is outside logically zoomed tree
734	if (jumpType & AP_JUMP_LOGICAL_UNZOOM) {
735	gtree->set_logical_root_to(common_ancestor(found, gtree->get_logical_root()));
736	ntw->request_resize();
737	}
738	else {
739	if (verboose) {
740	if (jump_to_group) {
741	msg = GBS_global_string_copy("Group '%s' is outside logical zoomed subtree", gtree->get_selected_group().get_name());
742	}
743	else {
744	msg = GBS_global_string_copy("Species '%s' is outside logical zoomed subtree", name);
745	}
746	}
747
748	found = NULp;
749	}
750	}
751	}
752
753	if (found && !(jumpType&AP_JUMP_AUTO_UNFOLD) && found->is_inside_folded_group()) {
754	found = NULp; // => just undo auto-unfolding
755	}
756	gtree->auto_unfold(found);
757	}
758	}
759
760	if (found \|\| !is_tree) {
761	bool is_IRS = gtree->get_tree_style() == AP_TREE_IRS;
762	bool repeat = is_IRS;
763	bool do_jump = true;
764
765	ntw->sync_DB_model_and_view(false); // sync w/o refresh
766
767	while (do_jump) {
768	do_jump = false;
769
770	AW_device_size *device = aww->get_size_device(AW_MIDDLE_AREA);
771	device->set_filter(AW_SIZE\|AW_SIZE_UNSCALED);
772	device->reset();
773	ntw->init_device(device);
774	ntw->gfx->show(device);
775
776	const AW_screen_area& screen = device->get_area_size();
777
778	const Position& cursor = jump_to_group ? gtree->get_group_cursor() : gtree->get_cursor();
779	if (are_distinct(Origin, cursor)) {
780	Position S = device->transform(cursor);
781
782	int scroll_x = 0;
783	int scroll_y = 0;
784
785	bool do_vcenter = jumpType & AP_JUMP_FORCE_VCENTER;
786	bool do_hcenter = jumpType & AP_JUMP_FORCE_HCENTER;
787
788	if (!do_vcenter) {
789	if (is_IRS) {
790	// attempt to center IRS tree vertically often fails (too complicated to predict)
791	// => force into center-half of screen to reduce error rate
792	int border = screen.b/10;
793	do_vcenter = S.ypos()<border \|\| S.ypos()>(screen.b-border);
794	}
795	else {
796	do_vcenter = S.ypos()<0.0 \|\| S.ypos()>screen.b; // center if outside viewport
797	}
798	}
799
800	if (do_vcenter) {
801	scroll_y = (int)(S.ypos() - screen.b*(is_IRS ? .6 : .5)); // position a bit below vertical center for IRS tree
802
803	if (!scroll_y && (jumpType & AP_JUMP_ALLOW_HCENTER)) { // allow horizontal centering if vertical has no effect
804	do_hcenter = true;
805	}
806	}
807
808	if (do_hcenter) {
809	scroll_x = (int) (S.xpos() - screen.r * (is_tree ? .5 : .02));
810	}
811	else { // keep visible
812	if (S.xpos()<0.0) {
813	double relPos = 0;
814	switch (gtree->get_tree_style()) {
815	case AP_TREE_NORMAL:
816	case AP_TREE_IRS: relPos = .1; break;
817	case AP_TREE_RADIAL: relPos = .5; break;
818	case AP_LIST_NDS:
819	case AP_LIST_SIMPLE: relPos = .02; break;
820	}
821	scroll_x = (int)(S.xpos() - screen.r * relPos);
822	}
823	else if (S.xpos()>screen.r) {
824	scroll_x = (int)(S.xpos() - screen.r * .5);
825	}
826	}
827
828	if (scroll_x \|\| scroll_y) ntw->scroll(scroll_x, scroll_y);
829	if (repeat) {
830	// reposition jump in IRS tree (reduces jump failure rate)
831	repeat = false;
832	do_jump = true;
833	}
834	}
835	else {
836	td_assert(!is_tree); // jumped-to position should have been found
837	if (verboose) msg = GBS_global_string_copy("Species '%s' is no member of this list", name);
838	}
839	}
840	}
841
842	if (!found && is_tree && verboose && !msg) {
843	td_assert(!jump_to_group); // need special handling
844	msg = GBS_global_string_copy("Species '%s' is no member of this %s", name, gtree->get_tree_style() == AP_LIST_NDS ? "list" : "tree");
845	}
846
847	}
848	else { // select "no species" and "no group"
849	gtree->auto_unfold(NULp); // undo auto-unfolding
850	if (verboose) {
851	msg = strdup("Neither species nor group selected");
852	}
853	}
854
855	if (gtree) gtree->exports.request_refresh(); // always do refresh to show change of selected species
856
857	if (msg) {
858	td_assert(verboose);
859	aw_message(msg);
860	free(msg);
861	}
862	}
863
864	void TREE_auto_jump_cb(UNFIXED, TREE_canvas *ntw, AP_tree_jump_reason cause) {
865	/*! jump to species when tree/treemode/species changes
866	* @param cause reason why auto-jump was triggered
867	*/
868
869	AWT_auto_refresh allowed_on(ntw);
870
871	bool tree_change = cause == AP_JUMP_REASON_TREE \|\| cause == AP_JUMP_REASON_STYLE;
872
873	const char *awar_name = tree_change ? AWAR_DTREE_AUTO_JUMP_TREE : AWAR_DTREE_AUTO_JUMP;
874	AW_root *awr = ntw->aww->get_root();
875	AP_tree_jump_type jump_type = AP_tree_jump_type(awr->awar(awar_name)->read_int());
876
877	if (jump_type == AP_DONT_JUMP) {
878	ntw->request_refresh();
879	}
880	else {
881	bool auto_unfold = awr->awar(AWAR_DTREE_AUTO_UNFOLD)->read_int();
882	if (auto_unfold) jump_type = AP_tree_jump_type(jump_type\|AP_JUMP_AUTO_UNFOLD);
883	NT_jump_cb(NULp, ntw, jump_type);
884	}
885	}
886
887	void NT_reload_tree_event(AW_root , TREE_canvas ntw, bool unzoom_and_expose) {
888	GB_push_transaction(ntw->gb_main);
889
890	{
891	AWT_auto_refresh update(ntw);
892
893	AWT_graphic_tree *agt = ntw->get_graphic_tree();
894	AP_tree_root *troot = agt->get_tree_root();
895
896	if (!troot->get_gb_tree()) { // happens at initial startup (=first load) and after a shown tree gets renamed
897	// forget all about old tree
898	agt->forget_auto_unfolded();
899	agt->deselect_group();
900	}
901	else {
902	agt->auto_unfold(NULp); // undo auto-unfolding before tree-change (otherwise temp. unfolding remains saved in DB)
903	}
904	update.suppress_update_and_refresh(); // suppress update (speed)
905	}
906
907	char *tree_name = ntw->get_awar_tree()->read_string();
908	GB_ERROR error = ntw->gfx->load_from_DB(ntw->gb_main, tree_name);
909	if (error) {
910	aw_message(error);
911	}
912	else {
913	int zombies, duplicates;
914	DOWNCAST(AWT_graphic_tree*, ntw->gfx)->get_zombies_and_duplicates(zombies, duplicates);
915
916	if (zombies \|\| duplicates) {
917	const char *msg = NULp;
918	if (duplicates) {
919	if (zombies) msg = GBS_global_string("%i zombie%s and %i duplicate%s", zombies, plural(zombies), duplicates, plural(duplicates));
920	else msg = GBS_global_string("%i duplicate%s", duplicates, plural(duplicates));
921	}
922	else {
923	td_assert(zombies);
924	msg = GBS_global_string("%i zombie%s", zombies, plural(zombies));
925	}
926	aw_message(GBS_global_string("%s in '%s'", msg, tree_name));
927	}
928	}
929	free(tree_name);
930	if (unzoom_and_expose) {
931	AWT_auto_refresh allowed_on(ntw);
932	ntw->request_zoom_reset();
933	}
934	GB_pop_transaction(ntw->gb_main);
935	}
936
937	static void tree_recompute_cb(UNFIXED, AWT_canvas *ntw) {
938	AWT_auto_refresh allowed_on(ntw);
939	ntw->request_structure_update();
940	}
941
942	void TREE_GC_changed_cb(GcChange whatChanged, AWT_canvas *ntw) {
943	AWT_auto_refresh allowed_on(ntw);
944
945	if (whatChanged == GC_COLOR_GROUP_USE_CHANGED) {
946	tree_recompute_cb(NULp, ntw);
947	}
948	else {
949	AWT_GC_changed_cb(whatChanged, ntw);
950	}
951	}
952
953	void NT_remove_species_in_tree_from_hash(AP_tree tree, GB_HASH hash) {
954	if (!tree) return;
955	if (tree->is_leaf() && tree->name) {
956	GBS_write_hash(hash, tree->name, 0); // delete species in hash table
957	}
958	else {
959	NT_remove_species_in_tree_from_hash(tree->get_leftson(), hash);
960	NT_remove_species_in_tree_from_hash(tree->get_rightson(), hash);
961	}
962	}
963

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source: trunk/SL/TREEDISP/TreeCallbacks.cxx

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