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source: tags/ms_r16q3/SL/DB_UI/ui_species.cxx

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Last change on this file was 15176, checked in by westram, 8 years ago
reintegrates 'fixres' into 'trunk' fixes #715 adds: log:branches/fixres@15127:15175
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 60.5 KB

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1	// =============================================================== //
2	// //
3	// File : ui_species.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "dbui.h"
12
13	#include <awt_sel_boxes.hxx>
14	#include <arb_strbuf.h>
15	#include <cmath>
16	#include <probe_gui.hxx>
17	#include <arb_defs.h>
18	#include <awtc_next_neighbours.hxx>
19	#include <db_scanner.hxx>
20	#include <db_query.h>
21	#include <AW_rename.hxx>
22	#include <aw_awar_defs.hxx>
23	#include <aw_awar.hxx>
24	#include <aw_root.hxx>
25	#include <aw_msg.hxx>
26	#include <aw_question.hxx>
27	#include <algorithm>
28	#include <arb_progress.h>
29	#include <item_sel_list.h>
30	#include <map>
31	#include <info_window.h>
32	#include <awt_config_manager.hxx>
33
34	using namespace DBUI;
35	using namespace QUERY;
36
37	#define ui_assert(cond) arb_assert(cond)
38
39	#define AWAR_SPECIES_DEST "tmp/adspec/dest"
40
41	// awars shared between different itemtypes:
42	#define AWAR_FIELD_REORDER_ORDER "tmp/adreorder/order"
43
44	// separate awars for different itemtypes:
45	#define AWAR_FIELD_REORDER_SOURCE_TMPL "tmp/adreorder/%s/source"
46	#define AWAR_FIELD_REORDER_DEST_TMPL "tmp/adreorder/%s/dest"
47	#define AWAR_FIELD_CREATE_NAME_TMPL "tmp/adfield/%s/name"
48	#define AWAR_FIELD_CREATE_TYPE_TMPL "tmp/adfield/%s/type"
49	#define AWAR_FIELD_DELETE_TMPL "tmp/adfield/%s/source"
50	#define AWAR_FIELD_CONVERT_SOURCE_TMPL "tmp/adconvert/%s/source"
51	#define AWAR_FIELD_CONVERT_TYPE_TMPL "tmp/adconvert/%s/type"
52
53	// next neighbours of listed and selected:
54	// more defined in ../../AWTC/awtc_next_neighbours.hxx@AWAR_NN_BASE
55	#define AWAR_NN_COMPLEMENT AWAR_NN_BASE "complement"
56	#define AWAR_NN_RANGE_START AWAR_NN_BASE "range_start"
57	#define AWAR_NN_RANGE_END AWAR_NN_BASE "range_end"
58	#define AWAR_NN_MIN_SCORE AWAR_NN_BASE "min_scored"
59	#define AWAR_NN_MAX_HITS AWAR_NN_BASE "max_hits"
60
61	// next neighbours of selected only:
62	#define AWAR_NN_BASE_SELECTED AWAR_NN_BASE "selected/"
63	#define AWAR_NN_SELECTED_HIT_COUNT "tmp/" AWAR_NN_BASE_SELECTED "hit_count"
64	#define AWAR_NN_SELECTED_AUTO_SEARCH "tmp/" AWAR_NN_BASE_SELECTED "auto_search"
65	#define AWAR_NN_SELECTED_AUTO_MARK "tmp/" AWAR_NN_BASE_SELECTED "auto_mark"
66
67	// next neighbours of listed only:
68	#define AWAR_NN_BASE_LISTED AWAR_NN_BASE "listed/"
69	#define AWAR_NN_LISTED_DEST_FIELD AWAR_NN_BASE_LISTED "dest_field"
70	#define AWAR_NN_LISTED_SCORED_ENTRIES AWAR_NN_BASE_LISTED "scored_entries"
71
72	enum ReorderMode {
73	// real orders
74	ORDER_ALPHA,
75	ORDER_TYPE,
76	ORDER_FREQ,
77
78	// special modes
79	RIGHT_BEHIND_LEFT,
80	REVERSE_ORDER,
81	};
82
83	void DBUI::create_dbui_awars(AW_root *aw_root) {
84	aw_root->awar_string(AWAR_SPECIES_DEST, "", AW_ROOT_DEFAULT);
85	aw_root->awar_int (AWAR_FIELD_REORDER_ORDER, ORDER_ALPHA, AW_ROOT_DEFAULT);
86	}
87
88	inline const char itemAwar(const char name_template, ItemSelector& itype) {
89	return GBS_global_string(name_template, itype.item_name);
90	}
91	static void init_itemspecific_DBUI_awars(AW_root *aw_root, ItemSelector& itype) {
92	static bool initialized[QUERY_ITEM_TYPES] = { false };
93
94	if (!initialized[itype.type]) {
95	aw_root->awar_string(itemAwar(AWAR_FIELD_REORDER_SOURCE_TMPL, itype), "", AW_ROOT_DEFAULT);
96	aw_root->awar_string(itemAwar(AWAR_FIELD_REORDER_DEST_TMPL, itype), "", AW_ROOT_DEFAULT);
97	aw_root->awar_string(itemAwar(AWAR_FIELD_CREATE_NAME_TMPL, itype), "", AW_ROOT_DEFAULT);
98	aw_root->awar_int (itemAwar(AWAR_FIELD_CREATE_TYPE_TMPL, itype), GB_STRING, AW_ROOT_DEFAULT);
99	aw_root->awar_string(itemAwar(AWAR_FIELD_DELETE_TMPL, itype), "", AW_ROOT_DEFAULT);
100	aw_root->awar_string(itemAwar(AWAR_FIELD_CONVERT_SOURCE_TMPL, itype), "", AW_ROOT_DEFAULT);
101	aw_root->awar_int (itemAwar(AWAR_FIELD_CONVERT_TYPE_TMPL, itype), GB_STRING, AW_ROOT_DEFAULT);
102
103	initialized[itype.type] = true;
104	}
105	}
106
107	static void move_species_to_extended(AW_window aww, GBDATA gb_main) {
108	char *source = aww->get_root()->awar(AWAR_SPECIES_NAME)->read_string();
109	GB_ERROR error = GB_begin_transaction(gb_main);
110
111	if (!error) {
112	GBDATA *gb_sai_data = GBT_get_SAI_data(gb_main);
113	if (!gb_sai_data) error = GB_await_error();
114	else {
115	GBDATA *gb_species = GBT_find_species(gb_main, source);
116	GBDATA *gb_dest = GBT_find_SAI_rel_SAI_data(gb_sai_data, source);
117
118	if (gb_dest) error = GBS_global_string("SAI '%s' already exists", source);
119	else if (gb_species) {
120	gb_dest = GB_create_container(gb_sai_data, "extended");
121	if (!gb_dest) error = GB_await_error();
122	else {
123	error = GB_copy(gb_dest, gb_species);
124	if (!error) {
125	error = GB_delete(gb_species);
126	if (!error) aww->get_root()->awar(AWAR_SPECIES_NAME)->write_string("");
127	}
128	}
129	}
130	else error = "Please select a species";
131	}
132	}
133	GB_end_transaction_show_error(gb_main, error, aw_message);
134	free(source);
135	}
136
137
138	static void species_create_cb(AW_window aww, GBDATA gb_main) {
139	char *dest = aww->get_root()->awar(AWAR_SPECIES_DEST)->read_string();
140	if (dest[0]) {
141	GB_ERROR error = GB_begin_transaction(gb_main);
142	if (!error) {
143	GBDATA *gb_species_data = GBT_get_species_data(gb_main);
144	if (!gb_species_data) error = GB_await_error();
145	else {
146	GBDATA *gb_dest = GBT_find_species_rel_species_data(gb_species_data, dest);
147
148	if (gb_dest) error = GBS_global_string("Species '%s' already exists", dest);
149	else {
150	gb_dest = GBT_find_or_create_species_rel_species_data(gb_species_data, dest);
151	if (!gb_dest) error = GB_await_error();
152	else aww->get_root()->awar(AWAR_SPECIES_NAME)->write_string(dest);
153	}
154	}
155	}
156	GB_end_transaction_show_error(gb_main, error, aw_message);
157	}
158	else {
159	aw_message("Please enter a name for the new species");
160	}
161	free(dest);
162	}
163
164	static AW_window create_species_create_window(AW_root root, GBDATA *gb_main) {
165	AW_window_simple *aws = new AW_window_simple;
166
167	aws->init(root, "CREATE_SPECIES", "SPECIES CREATE");
168	aws->load_xfig("ad_al_si.fig");
169
170	aws->at("close");
171	aws->callback(AW_POPDOWN);
172	aws->create_button("CLOSE", "Close", "C");
173
174	aws->at("label");
175	aws->create_autosize_button(0, "Please enter the name\nof the new species");
176
177	aws->at("input");
178	aws->create_input_field(AWAR_SPECIES_DEST, 15);
179
180	aws->at("ok");
181	aws->callback(makeWindowCallback(species_create_cb, gb_main));
182	aws->create_button("GO", "Go", "G");
183
184	return aws;
185	}
186
187	static GBDATA expect_species_selected(AW_root aw_root, GBDATA gb_main, char *give_name = 0) {
188	GB_transaction ta(gb_main);
189	char *name = aw_root->awar(AWAR_SPECIES_NAME)->read_string();
190	GBDATA *gb_species = GBT_find_species(gb_main, name);
191
192	if (!gb_species) {
193	if (name && name[0]) aw_message(GBS_global_string("Species '%s' does not exist.", name));
194	else aw_message("Please select a species first");
195	}
196
197	if (give_name) *give_name = name;
198	else free(name);
199
200	return gb_species;
201	}
202
203	static void species_copy_cb(AW_window aww, GBDATA gb_main) {
204	AW_root *aw_root = aww->get_root();
205	char *name;
206	GBDATA *gb_species = expect_species_selected(aw_root, gb_main, &name);
207
208	if (gb_species) {
209	GB_transaction ta(gb_main);
210	GBDATA *gb_species_data = GB_get_father(gb_species);
211	UniqueNameDetector und(gb_species_data);
212	GB_ERROR error = 0;
213	char *copy_name = AWTC_makeUniqueShortName(GBS_global_string("c%s", name), und);
214
215	if (!copy_name) error = GB_await_error();
216	else {
217	GBDATA *gb_new_species = GB_create_container(gb_species_data, "species");
218
219	if (!gb_new_species) error = GB_await_error();
220	else {
221	error = GB_copy(gb_new_species, gb_species);
222	if (!error) {
223	error = GBT_write_string(gb_new_species, "name", copy_name);
224	if (!error) aw_root->awar(AWAR_SPECIES_NAME)->write_string(copy_name); // set focus
225	}
226	}
227
228	free(copy_name);
229	}
230	if (error) {
231	error = ta.close(error);
232	aw_message(error);
233	}
234	}
235	}
236
237	static void species_rename_cb(AW_window aww, GBDATA gb_main) {
238	AW_root *aw_root = aww->get_root();
239	GBDATA *gb_species = expect_species_selected(aw_root, gb_main);
240	if (gb_species) {
241	GB_transaction ta(gb_main);
242	GBDATA *gb_full_name = GB_search(gb_species, "full_name", GB_STRING);
243	const char *full_name = gb_full_name ? GB_read_char_pntr(gb_full_name) : "";
244	char *new_full_name = aw_input("Enter new 'full_name' of species:", full_name);
245
246	if (new_full_name) {
247	GB_ERROR error = 0;
248
249	if (strcmp(full_name, new_full_name) != 0) {
250	error = GB_write_string(gb_full_name, new_full_name);
251	}
252	if (!error) {
253	bool recreateID = ARB_in_expert_mode(aw_root) && // never re-create ID in novice mode
254	aw_ask_sure("recreate_name_field",
255	"Regenerate species identifier ('name')?\n"
256	"(only do this if you know what you're doing)");
257	if (recreateID) {
258	arb_progress progress("Regenerating species ID", 1);
259	error = AWTC_recreate_name(gb_species);
260	if (!error) aw_root->awar(AWAR_SPECIES_NAME)->write_string(GBT_read_name(gb_species)); // set focus
261	}
262	}
263
264	if (error) {
265	error = ta.close(error);
266	aw_message(error);
267	}
268	}
269	}
270	}
271
272	static void species_delete_cb(AW_window aww, GBDATA gb_main) {
273	AW_root *aw_root = aww->get_root();
274	char *name;
275	GBDATA *gb_species = expect_species_selected(aw_root, gb_main, &name);
276	GB_ERROR error = 0;
277
278	if (!gb_species) {
279	error = "Please select a species first";
280	}
281	else if (aw_ask_sure("info_delete_species", GBS_global_string("Are you sure to delete the species '%s'?", name))) {
282	GB_transaction ta(gb_main);
283	error = GB_delete(gb_species);
284	error = ta.close(error);
285	if (!error) aw_root->awar(AWAR_SPECIES_NAME)->write_string("");
286	}
287
288	if (error) aw_message(error);
289	free(name);
290	}
291
292	static long count_field_occurrance(BoundItemSel bsel, const char field_name) {
293	QUERY_RANGE RANGE = QUERY_ALL_ITEMS;
294	long count = 0;
295	ItemSelector& sel = bsel->selector;
296
297	for (GBDATA *gb_container = sel.get_first_item_container(bsel->gb_main, NULL, RANGE);
298	gb_container;
299	gb_container = sel.get_next_item_container(gb_container, RANGE))
300	{
301	for (GBDATA *gb_item = sel.get_first_item(gb_container, RANGE);
302	gb_item;
303	gb_item = sel.get_next_item(gb_item, RANGE))
304	{
305	GBDATA *gb_field = GB_entry(gb_item, field_name);
306	if (gb_field) ++count;
307	}
308	}
309	return count;
310	}
311
312	class KeySorter : virtual Noncopyable {
313	int key_count;
314	GBDATA **key;
315
316	int field_count; // = key_count - container_count
317
318	bool order_changed;
319
320	// helper variables for sorting
321	static GB_HASH *order_hash;
322	static BoundItemSel *bitem_selector;
323	static arb_progress *sort_progress;
324
325	bool legal_pos(int p) { return p >= 0 && p<key_count; }
326	bool legal_field_pos(int p) const { return p >= 0 && p<field_count; }
327	bool legal_field_pos(int p1, int p2) const { return legal_field_pos(p1) && legal_field_pos(p2); }
328
329	void swap(int p1, int p2) {
330	ui_assert(legal_pos(p1));
331	ui_assert(legal_pos(p2));
332
333	GBDATA *k = key[p1];
334	key[p1] = key[p2];
335	key[p2] = k;
336
337	order_changed = true;
338	}
339
340	const char *field_name(int p) const {
341	GBDATA *gb_key_name = GB_entry(key[p], "key_name");
342	if (gb_key_name) return GB_read_char_pntr(gb_key_name);
343	return NULL;
344	}
345	GB_TYPES field_type(int p) const {
346	GBDATA *gb_key_type = GB_entry(key[p], "key_type");
347	if (gb_key_type) return GB_TYPES(GB_read_int(gb_key_type));
348	return GB_NONE;
349	}
350	int field_freq(int p) const {
351	const char *name = field_name(p);
352	if (!order_hash) order_hash = GBS_create_hash(key_count, GB_IGNORE_CASE);
353
354	long freq = GBS_read_hash(order_hash, name);
355	if (!freq) {
356	freq = 1+count_field_occurrance(bitem_selector, name);
357	GBS_write_hash(order_hash, name, freq);
358	if (sort_progress) sort_progress->inc();
359	}
360	return freq;
361	}
362
363	int compare(int p1, int p2, ReorderMode mode) {
364	switch (mode) {
365	case RIGHT_BEHIND_LEFT:
366	case REVERSE_ORDER:
367	ui_assert(0); // illegal ReorderMode
368	break;
369
370	case ORDER_TYPE: return field_type(p2)-field_type(p1);
371	case ORDER_ALPHA: return strcasecmp(field_name(p1), field_name(p2));
372	case ORDER_FREQ: return field_freq(p2)-field_freq(p1);
373	}
374	return p2-p1; // keep order
375	}
376
377	public:
378	KeySorter(GBDATA *gb_key_data) {
379	key_count = 0;
380	field_count = 0;
381	key = NULL;
382
383	for (GBDATA *gb_key = GB_child(gb_key_data); gb_key; gb_key = GB_nextChild(gb_key)) {
384	key_count++;
385	}
386
387	if (key_count) {
388	ARB_alloc(key, key_count);
389
390	int container_count = 0;
391	for (GBDATA *gb_key = GB_child(gb_key_data); gb_key; gb_key = GB_nextChild(gb_key)) {
392	GBDATA *gb_type = GB_entry(gb_key, CHANGEKEY_TYPE);
393	GB_TYPES type = GB_TYPES(GB_read_int(gb_type));
394
395	if (type == GB_DB) { // move containers behind fields
396	key[key_count-1-container_count++] = gb_key;
397	}
398	else {
399	key[field_count++] = gb_key;
400	}
401	}
402	ui_assert((container_count+field_count) == key_count);
403	reverse_order(field_count, key_count-1); // of containers
404	}
405	order_changed = false;
406	}
407	~KeySorter() {
408	ui_assert(!order_changed); // order changed but not written
409	free(key);
410	}
411
412	int get_field_count() const { return field_count; }
413
414	void bubble_sort(int p1, int p2, ReorderMode mode, BoundItemSel *selector) {
415	if (p1>p2) std::swap(p1, p2);
416	if (legal_field_pos(p1, p2)) {
417	if (mode == ORDER_FREQ) {
418	sort_progress = new arb_progress("Calculating field frequencies", p2-p1+1);
419	}
420	bitem_selector = selector;
421	while (p1<p2) {
422	bool changed = false;
423
424	int i = p2;
425	while (i>p1) {
426	if (compare(i-1, i, mode)>0) {
427	swap(i-1, i);
428	changed = true;
429	}
430	--i;
431	}
432	if (!changed) break;
433	++p1;
434	}
435	if (order_hash) {
436	GBS_free_hash(order_hash);
437	order_hash = NULL;
438	}
439	if (sort_progress) {
440	delete sort_progress;
441	sort_progress = NULL;
442	}
443	}
444	}
445	void reverse_order(int p1, int p2) {
446	if (p1>p2) std::swap(p1, p2);
447	if (legal_field_pos(p1, p2)) while (p1<p2) swap(p1++, p2--);
448	}
449
450	int index_of(GBDATA *gb_key) {
451	int i;
452	for (i = 0; i<key_count; i++) {
453	if (gb_key == key[i]) break;
454	}
455	if (i == key_count) {
456	ui_assert(0);
457	i = -1;
458	}
459	return i;
460	}
461
462	void move_to(int to_move, int wanted_position) {
463	if (legal_field_pos(to_move, wanted_position)) {
464	while (to_move<wanted_position) {
465	swap(to_move, to_move+1);
466	to_move++;
467	}
468	while (to_move>wanted_position) {
469	swap(to_move, to_move-1);
470	to_move--;
471	}
472	}
473	}
474
475	__ATTR__USERESULT GB_ERROR save_changes() {
476	GB_ERROR warning = NULL;
477	if (order_changed) {
478	if (key_count) {
479	GBDATA *gb_main = GB_get_root(key[0]);
480	warning = GB_resort_data_base(gb_main, key, key_count);
481	}
482	order_changed = false;
483	}
484	return warning;
485	}
486	};
487
488	GB_HASH *KeySorter::order_hash = NULL;
489	BoundItemSel *KeySorter::bitem_selector = NULL;
490	arb_progress *KeySorter::sort_progress = NULL;
491
492	static void reorder_keys(AW_window aws, ReorderMode mode, Itemfield_Selection sel_left, Itemfield_Selection *sel_right) {
493	ItemSelector& selector = sel_left->get_selector();
494	ui_assert(&selector == &sel_right->get_selector());
495
496	int left_index = sel_left->get_sellist()->get_index_of_selected();
497	int right_index = sel_right->get_sellist()->get_index_of_selected();
498
499	GB_ERROR warning = 0;
500
501	GBDATA *gb_main = sel_left->get_gb_main();
502	AW_root *awr = aws->get_root();
503
504	init_itemspecific_DBUI_awars(awr, selector);
505
506	GB_begin_transaction(gb_main);
507
508	GBDATA *gb_left_field = GBT_get_changekey(gb_main, awr->awar(itemAwar(AWAR_FIELD_REORDER_SOURCE_TMPL, selector))->read_char_pntr(), selector.change_key_path);
509	GBDATA *gb_right_field = GBT_get_changekey(gb_main, awr->awar(itemAwar(AWAR_FIELD_REORDER_DEST_TMPL, selector))->read_char_pntr(), selector.change_key_path);
510
511	if (!gb_left_field \|\| !gb_right_field \|\| gb_left_field == gb_right_field) {
512	warning = "Please select different fields in both list";
513	}
514	else {
515	GBDATA *gb_key_data = GB_search(gb_main, selector.change_key_path, GB_CREATE_CONTAINER);
516	KeySorter sorter(gb_key_data);
517
518	int left_key_idx = sorter.index_of(gb_left_field);
519	int right_key_idx = sorter.index_of(gb_right_field);
520
521	switch (mode) {
522	case RIGHT_BEHIND_LEFT:
523	sorter.move_to(right_key_idx, left_key_idx+(left_key_idx<right_key_idx));
524	if (right_index>left_index) { left_index++; right_index++; } // make it simple to move several consecutive keys
525	break;
526	case REVERSE_ORDER:
527	sorter.reverse_order(left_key_idx, right_key_idx);
528	std::swap(left_index, right_index);
529	break;
530	default: {
531	BoundItemSel bis(gb_main, selector);
532	sorter.bubble_sort(left_key_idx, right_key_idx, mode, &bis);
533	break;
534	}
535	}
536
537	warning = sorter.save_changes();
538	}
539	GB_commit_transaction(gb_main);
540
541	if (warning) {
542	aw_message(warning);
543	}
544	else {
545	sel_left->get_sellist()->select_element_at(left_index);
546	sel_right->get_sellist()->select_element_at(right_index);
547	}
548	}
549
550	static void reorder_right_behind_left(AW_window aws, Itemfield_Selection selleft, Itemfield_Selection *selright) { reorder_keys(aws, RIGHT_BEHIND_LEFT, selleft, selright); }
551	static void reverse_key_order (AW_window aws, Itemfield_Selection selleft, Itemfield_Selection *selright) { reorder_keys(aws, REVERSE_ORDER, selleft, selright); }
552
553	static void sort_keys(AW_window aws, Itemfield_Selection selleft, Itemfield_Selection *selright) {
554	ReorderMode mode = ReorderMode(aws->get_root()->awar(AWAR_FIELD_REORDER_ORDER)->read_int());
555	reorder_keys(aws, mode, selleft, selright);
556	}
557
558	static void reorder_up_down(AW_window aws, Itemfield_Selection sel_right, int dir) {
559	GBDATA *gb_main = sel_right->get_gb_main();
560
561	GB_begin_transaction(gb_main);
562	ItemSelector& selector = sel_right->get_selector();
563	int list_index = sel_right->get_sellist()->get_index_of_selected();
564
565	const char *field_name = aws->get_root()->awar(itemAwar(AWAR_FIELD_REORDER_DEST_TMPL, selector))->read_char_pntr();
566	GBDATA *gb_field = GBT_get_changekey(gb_main, field_name, selector.change_key_path);
567	GB_ERROR warning = 0;
568
569	if (!gb_field) {
570	warning = "Please select the item to move in the right box";
571	}
572	else {
573	GBDATA *gb_key_data = GB_search(gb_main, selector.change_key_path, GB_CREATE_CONTAINER);
574	KeySorter sorter(gb_key_data);
575
576	int curr_index = sorter.index_of(gb_field);
577	int dest_index = -1;
578	if (abs(dir) == 1) {
579	dest_index = curr_index+dir;
580	list_index = -1;
581	}
582	else {
583	dest_index = dir<0 ? 0 : sorter.get_field_count()-1;
584	}
585
586	sorter.move_to(curr_index, dest_index);
587	warning = sorter.save_changes();
588
589	}
590
591	GB_commit_transaction(gb_main);
592	if (list_index >= 0) sel_right->get_sellist()->select_element_at(list_index);
593	if (warning) aw_message(warning);
594	}
595
596	AW_window DBUI::create_fields_reorder_window(AW_root root, BoundItemSel *bound_selector) {
597	ItemSelector& selector = bound_selector->selector;
598
599	static AW_window_simple *awsa[QUERY_ITEM_TYPES];
600	if (!awsa[selector.type]) {
601	AW_window_simple *aws = new AW_window_simple;
602	awsa[selector.type] = aws;
603
604	init_itemspecific_DBUI_awars(root, selector);
605	init_itemType_specific_window(root, aws, selector, "REORDER_FIELDS", "Reorder %s fields");
606	aws->load_xfig("ad_kreo.fig");
607
608	aws->at("close");
609	aws->callback(AW_POPDOWN);
610	aws->create_button("CLOSE", "Close", "C");
611
612	aws->at("help");
613	const char *HELPFILE = "spaf_reorder.hlp";
614	aws->callback(makeHelpCallback(HELPFILE));
615	aws->create_button("HELP", "Help", "H");
616
617	Itemfield_Selection *sel1 = create_itemfield_selection_list(aws, FieldSelDef(itemAwar(AWAR_FIELD_REORDER_SOURCE_TMPL, selector), bound_selector->gb_main, selector, FIELD_UNFILTERED), "source");
618	Itemfield_Selection *sel2 = create_itemfield_selection_list(aws, FieldSelDef(itemAwar(AWAR_FIELD_REORDER_DEST_TMPL, selector), bound_selector->gb_main, selector, FIELD_UNFILTERED), "dest");
619
620	aws->button_length(8);
621
622	aws->at("sort");
623	aws->callback(makeWindowCallback(sort_keys, sel1, sel2));
624	aws->help_text(HELPFILE);
625	aws->create_button("SORT", "Sort by");
626
627	aws->at("sorttype");
628	aws->create_option_menu(AWAR_FIELD_REORDER_ORDER, true);
629	aws->insert_option("name", "a", ORDER_ALPHA);
630	aws->insert_option("type", "t", ORDER_TYPE);
631	aws->insert_option("frequency", "f", ORDER_FREQ);
632	aws->update_option_menu();
633
634	aws->at("leftright");
635	aws->callback(makeWindowCallback(reorder_right_behind_left, sel1, sel2));
636	aws->help_text(HELPFILE);
637	aws->create_autosize_button("MOVE_RIGHT_BEHIND_LEFT", "Move right\nbehind left");
638
639	aws->at("reverse");
640	aws->callback(makeWindowCallback(reverse_key_order, sel1, sel2));
641	aws->help_text(HELPFILE);
642	aws->create_autosize_button("REVERSE", "Reverse");
643
644	aws->button_length(6);
645	struct {
646	const char *tag;
647	const char *macro;
648	int dir;
649	} reorder[4] = {
650	{ "Top", "MOVE_TOP_RIGHT", -2 },
651	{ "Up", "MOVE_UP_RIGHT", -1 },
652	{ "Down", "MOVE_DOWN_RIGHT", +1 },
653	{ "Bottom", "MOVE_BOT_RIGHT", +2 },
654	};
655
656	for (int i = 0; i<4; ++i) {
657	aws->at(reorder[i].tag);
658	aws->callback(makeWindowCallback(reorder_up_down, sel2, reorder[i].dir));
659	aws->help_text(HELPFILE);
660	aws->create_button(reorder[i].macro, reorder[i].tag);
661	}
662	}
663
664	return awsa[selector.type];
665	}
666
667	static void hide_field_cb(AW_window aws, Itemfield_Selection item_sel, int hide) {
668	GBDATA *gb_main = item_sel->get_gb_main();
669	GB_ERROR error = GB_begin_transaction(gb_main);
670
671	if (!error) {
672	ItemSelector& selector = item_sel->get_selector();
673	char *source = aws->get_root()->awar(itemAwar(AWAR_FIELD_DELETE_TMPL, selector))->read_string();
674	GBDATA *gb_source = GBT_get_changekey(gb_main, source, selector.change_key_path);
675
676	if (!gb_source) error = "Please select the field you want to (un)hide";
677	else error = GBT_write_int(gb_source, CHANGEKEY_HIDDEN, hide);
678
679	free(source);
680	}
681	GB_end_transaction_show_error(gb_main, error, aw_message);
682	if (!error) item_sel->get_sellist()->move_selection(1);
683	}
684
685	static void field_delete_cb(AW_window aws, Itemfield_Selection item_sel) {
686	GBDATA *gb_main = item_sel->get_gb_main();
687	GB_ERROR error = GB_begin_transaction(gb_main);
688
689	if (!error) {
690	ItemSelector& selector = item_sel->get_selector();
691	char *source = aws->get_root()->awar(itemAwar(AWAR_FIELD_DELETE_TMPL, selector))->read_string();
692	AW_selection_list *sellist = item_sel->get_sellist();
693	int curr_index = sellist->get_index_of_selected();
694	GBDATA *gb_source = GBT_get_changekey(gb_main, source, selector.change_key_path);
695
696	if (!gb_source) error = "Please select the field you want to delete";
697	else error = GB_delete(gb_source);
698
699	for (GBDATA *gb_item_container = selector.get_first_item_container(gb_main, aws->get_root(), QUERY_ALL_ITEMS);
700	!error && gb_item_container;
701	gb_item_container = selector.get_next_item_container(gb_item_container, QUERY_ALL_ITEMS))
702	{
703	for (GBDATA * gb_item = selector.get_first_item(gb_item_container, QUERY_ALL_ITEMS);
704	!error && gb_item;
705	gb_item = selector.get_next_item(gb_item, QUERY_ALL_ITEMS))
706	{
707	GBDATA *gbd = GB_search(gb_item, source, GB_FIND);
708
709	if (gbd) {
710	error = GB_delete(gbd);
711	if (!error) {
712	// item has disappeared, this selects the next one:
713	sellist->select_element_at(curr_index);
714	}
715	}
716	}
717	}
718
719	free(source);
720	}
721
722	GB_end_transaction_show_error(gb_main, error, aw_message);
723	}
724
725
726	AW_window DBUI::create_field_delete_window(AW_root root, BoundItemSel *bound_selector) {
727	ItemSelector& selector = bound_selector->selector;
728
729	static AW_window_simple *awsa[QUERY_ITEM_TYPES];
730	if (!awsa[selector.type]) {
731	AW_window_simple *aws = new AW_window_simple;
732	awsa[selector.type] = aws;
733
734	init_itemspecific_DBUI_awars(root, selector);
735	init_itemType_specific_window(root, aws, selector, "DELETE_FIELD", "Delete %s field");
736	aws->load_xfig("ad_delof.fig");
737	aws->button_length(6);
738
739	aws->at("close"); aws->callback(AW_POPDOWN);
740	aws->create_button("CLOSE", "Close", "C");
741
742	aws->at("help"); aws->callback(makeHelpCallback("spaf_delete.hlp"));
743	aws->create_button("HELP", "Help", "H");
744
745	Itemfield_Selection *item_sel = create_itemfield_selection_list(aws, FieldSelDef(itemAwar(AWAR_FIELD_DELETE_TMPL, selector), bound_selector->gb_main, selector, FIELD_UNFILTERED, "field", SF_HIDDEN), "source");
746
747	aws->button_length(13);
748	aws->at("hide");
749	aws->callback(makeWindowCallback(hide_field_cb, item_sel, 1));
750	aws->create_button("HIDE_FIELD", "Hide field", "H");
751
752	aws->at("unhide");
753	aws->callback(makeWindowCallback(hide_field_cb, item_sel, 0));
754	aws->create_button("UNHIDE_FIELD", "Unhide field", "U");
755
756	aws->at("delf");
757	aws->callback(makeWindowCallback(field_delete_cb, item_sel));
758	aws->create_button("DELETE_FIELD", "Delete field\n(data deleted)", "C");
759	}
760
761	return awsa[selector.type];
762	}
763
764	static void field_create_cb(AW_window aws, BoundItemSel bound_selector) {
765	ItemSelector& selector = bound_selector->selector;
766
767	GB_push_transaction(bound_selector->gb_main);
768	char *name = aws->get_root()->awar(itemAwar(AWAR_FIELD_CREATE_NAME_TMPL, selector))->read_string();
769	GB_ERROR error = GB_check_key(name);
770	GB_ERROR error2 = GB_check_hkey(name);
771	if (error && !error2) {
772	aw_message("Warning: Your key contain a '/' character,\n"
773	" that means it is a hierarchical key");
774	error = 0;
775	}
776
777	int type = (int)aws->get_root()->awar(itemAwar(AWAR_FIELD_CREATE_TYPE_TMPL, selector))->read_int();
778
779	if (!error) error = GBT_add_new_changekey_to_keypath(bound_selector->gb_main, name, type, selector.change_key_path);
780	aws->hide_or_notify(error);
781	free(name);
782	GB_pop_transaction(bound_selector->gb_main);
783	}
784
785	inline void insert_fieldtype_toggles(AW_window *aws) {
786	aws->insert_toggle("Ascii text", "s", (int)GB_STRING);
787	aws->insert_toggle("Rounded numerical", "i", (int)GB_INT);
788	aws->insert_toggle("Floating-point n.", "F", (int)GB_FLOAT);
789	aws->insert_toggle("Bitmask (0/1)", "B", (int)GB_BITS);
790	aws->insert_toggle("Link", "L", (int)GB_LINK);
791	// keep in sync with ../ITEMS/item_sel_list.cxx@FIELD_TYPE_DESCRIPTIONS
792	}
793
794	AW_window DBUI::create_field_create_window(AW_root root, BoundItemSel *bound_selector) {
795	ItemSelector& selector = bound_selector->selector;
796
797	static AW_window_simple *awsa[QUERY_ITEM_TYPES];
798	if (awsa[selector.type]) return awsa[selector.type];
799
800	AW_window_simple *aws = new AW_window_simple;
801	awsa[selector.type] = aws;
802
803	init_itemspecific_DBUI_awars(root, selector);
804	init_itemType_specific_window(root, aws, selector, "CREATE_FIELD", "Create new %s field");
805	aws->load_xfig("ad_fcrea.fig");
806
807	aws->at("close");
808	aws->callback(AW_POPDOWN);
809	aws->create_button("CLOSE", "Close", "C");
810
811	aws->at("input");
812	aws->label("FIELD NAME");
813	aws->create_input_field(itemAwar(AWAR_FIELD_CREATE_NAME_TMPL, selector), 15);
814
815	aws->at("type");
816	aws->create_toggle_field(itemAwar(AWAR_FIELD_CREATE_TYPE_TMPL, selector), "FIELD TYPE", "F");
817	insert_fieldtype_toggles(aws);
818	aws->update_toggle_field();
819
820	aws->at("ok");
821	aws->callback(makeWindowCallback(field_create_cb, bound_selector));
822	aws->create_button("CREATE", "Create", "C");
823
824	return aws;
825	}
826
827	#if defined(WARN_TODO)
828	#warning GBT_convert_changekey currently only works for species fields, make it work with genes/exp/... as well (use selector)
829	#endif
830
831	static void field_convert_commit_cb(AW_window aws, BoundItemSel bound_selector) {
832	AW_root *root = aws->get_root();
833	GBDATA *gb_main = bound_selector->gb_main;
834
835	GB_push_transaction(gb_main);
836	ItemSelector& selector = bound_selector->selector;
837	GB_ERROR error = GBT_convert_changekey(gb_main,
838	root->awar(itemAwar(AWAR_FIELD_CONVERT_SOURCE_TMPL, selector))->read_char_pntr(),
839	(GB_TYPES)root->awar(itemAwar(AWAR_FIELD_CONVERT_TYPE_TMPL, selector))->read_int());
840
841	GB_end_transaction_show_error(gb_main, error, aw_message);
842	}
843
844	static void field_convert_update_typesel_cb(AW_root root, BoundItemSel bound_selector) {
845	ItemSelector& selector = bound_selector->selector;
846	int type;
847	{
848	GBDATA *gb_main = bound_selector->gb_main;
849	GB_transaction ta(gb_main);
850
851	type = GBT_get_type_of_changekey(gb_main,
852	root->awar(itemAwar(AWAR_FIELD_CONVERT_SOURCE_TMPL, selector))->read_char_pntr(),
853	selector.change_key_path);
854	}
855
856	root->awar(itemAwar(AWAR_FIELD_CONVERT_TYPE_TMPL, selector))->write_int(type);
857	}
858
859	static AW_window create_field_convert_window(AW_root root, BoundItemSel *bound_selector) {
860	ItemSelector& selector = bound_selector->selector;
861
862	static AW_window_simple *awsa[QUERY_ITEM_TYPES];
863	if (awsa[selector.type]) return awsa[selector.type];
864
865	AW_window_simple *aws = new AW_window_simple;
866	awsa[selector.type] = aws;
867
868	init_itemspecific_DBUI_awars(root, selector);
869	init_itemType_specific_window(root, aws, selector, "CONVERT_FIELD", "Convert %s field");
870	aws->load_xfig("ad_conv.fig");
871
872	aws->at("close");
873	aws->callback(AW_POPDOWN);
874	aws->create_button("CLOSE", "Close", "C");
875
876	aws->at("help");
877	aws->callback(makeHelpCallback("spaf_convert.hlp"));
878	aws->create_button("HELP", "Help", "H");
879
880	const char *awarname_field = itemAwar(AWAR_FIELD_CONVERT_SOURCE_TMPL, selector);
881	root->awar(awarname_field)->add_callback(makeRootCallback(field_convert_update_typesel_cb, bound_selector));
882	create_itemfield_selection_list(aws, FieldSelDef(awarname_field, bound_selector->gb_main, selector, FIELD_FILTER_STRING_READABLE, "field", SF_SHOW_TYPE), "source");
883
884	aws->at("typesel");
885	aws->create_toggle_field(itemAwar(AWAR_FIELD_CONVERT_TYPE_TMPL, selector), NULL, "F");
886	insert_fieldtype_toggles(aws);
887	aws->update_toggle_field();
888
889	aws->at("convert");
890	aws->callback(makeWindowCallback(field_convert_commit_cb, bound_selector));
891	aws->create_button("CONVERT", "Convert", "T");
892
893	return aws;
894	}
895
896	void DBUI::insert_field_admin_menuitems(AW_window aws, GBDATA gb_main) {
897	static BoundItemSel *bis = new BoundItemSel(gb_main, SPECIES_get_selector());
898	ui_assert(bis->gb_main == gb_main);
899
900	aws->insert_menu_topic(aws->local_id("spec_reorder_fields"), "Reorder fields ...", "R", "spaf_reorder.hlp", AWM_ALL, makeCreateWindowCallback(create_fields_reorder_window, bis));
901	aws->insert_menu_topic(aws->local_id("spec_delete_field"), "Delete/Hide fields ...", "D", "spaf_delete.hlp", AWM_EXP, makeCreateWindowCallback(create_field_delete_window, bis));
902	aws->insert_menu_topic(aws->local_id("spec_create_field"), "Create fields ...", "C", "spaf_create.hlp", AWM_ALL, makeCreateWindowCallback(create_field_create_window, bis));
903	aws->insert_menu_topic(aws->local_id("spec_convert_field"), "Convert fields ...", "t", "spaf_convert.hlp", AWM_EXP, makeCreateWindowCallback(create_field_convert_window, bis));
904	aws->sep______________();
905	aws->insert_menu_topic("spec_unhide_fields", "Show all hidden fields", "S", "scandb.hlp", AWM_ALL, makeWindowCallback(species_field_selection_list_unhide_all_cb, gb_main));
906	aws->insert_menu_topic("spec_refresh_fields", "Refresh fields", "f", "scandb.hlp", AWM_ALL, makeWindowCallback(species_field_selection_list_update_cb, gb_main));
907	}
908
909	inline int get_and_fix_range_from_awar(AW_awar *awar) {
910	const char *input = awar->read_char_pntr();
911	int bpos = atoi(input);
912	int ipos;
913
914	if (bpos>0) {
915	awar->write_string(GBS_global_string("%i", bpos));
916	ipos = bio2info(bpos);
917	}
918	else {
919	ipos = -1;
920	awar->write_string("");
921	}
922	return ipos;
923	}
924
925	class NN_GlobalData {
926	DbQuery *query;
927	AW_selection_list *resultList; // result list from create_next_neighbours_selected_window()
928
929	public:
930	NN_GlobalData() : query(0), resultList(0) {}
931
932	void set_query(DbQuery *new_query) {
933	if (new_query != query) {
934	ui_assert(!query); // need redesign b4 changing query works
935	query = new_query;
936	}
937	}
938	void set_result_list(AW_selection_list *new_resultList) {
939	if (new_resultList != resultList) {
940	ui_assert(!resultList); // need redesign b4 changing query works
941	resultList = new_resultList;
942	}
943	}
944
945	DbQuery *get_query() const { ui_assert(query); return query; }
946
947	AW_selection_list *get_result_list() const { ui_assert(resultList); return resultList; }
948	GBDATA *get_gb_main() const { return query_get_gb_main(get_query()); }
949	};
950	static NN_GlobalData NN_GLOBAL;
951
952	static PosRange get_nn_range_from_awars(AW_root *aw_root) {
953	int start = get_and_fix_range_from_awar(aw_root->awar(AWAR_NN_RANGE_START));
954	int end = get_and_fix_range_from_awar(aw_root->awar(AWAR_NN_RANGE_END));
955
956	return PosRange(start, end);
957	}
958
959	inline char read_sequence_region(GBDATA gb_data, const PosRange& range) {
960	return range.dup_corresponding_part(GB_read_char_pntr(gb_data), GB_read_count(gb_data));
961	}
962
963	static void awtc_nn_search_all_listed(AW_window *aww) {
964	DbQuery *query = NN_GLOBAL.get_query();
965	GBDATA *gb_main = query_get_gb_main(query);
966
967	ui_assert(get_queried_itemtype(query).type == QUERY_ITEM_SPECIES);
968
969	GB_begin_transaction(gb_main);
970
971	long queriedCount = count_queried_items(query, QUERY_ALL_ITEMS);
972	GB_ERROR error = queriedCount ? NULL : "No species listed in query";
973	const char *dest_field = NULL;
974	AW_root *aw_root = aww->get_root();
975
976	if (!error) {
977	dest_field = prepare_and_get_selected_itemfield(aw_root, AWAR_NN_LISTED_DEST_FIELD, gb_main, get_queried_itemtype(query));
978	error = dest_field ? NULL : GB_await_error();
979	}
980
981	if (!error) {
982	arb_progress progress("Searching next neighbours", queriedCount);
983	progress.auto_subtitles("Species");
984
985	int pts = aw_root->awar(AWAR_PROBE_ADMIN_PT_SERVER)->read_int();
986	char *ali_name = aw_root->awar(AWAR_DEFAULT_ALIGNMENT)->read_string();
987	int oligo_len = aw_root->awar(AWAR_NN_OLIGO_LEN)->read_int();
988	int mismatches = aw_root->awar(AWAR_NN_MISMATCHES)->read_int();
989	bool fast_mode = aw_root->awar(AWAR_NN_FAST_MODE)->read_int();
990	bool rel_matches = aw_root->awar(AWAR_NN_REL_MATCHES)->read_int();
991	int wanted_entries = aw_root->awar(AWAR_NN_MAX_HITS)->read_int();
992	bool scored_entries = aw_root->awar(AWAR_NN_LISTED_SCORED_ENTRIES)->read_int();
993	float min_score = aw_root->awar(AWAR_NN_MIN_SCORE)->read_float();
994
995	FF_complement compl_mode = static_cast<FF_complement>(aw_root->awar(AWAR_NN_COMPLEMENT)->read_int());
996	RelativeScoreScaling rel_scaling = static_cast<RelativeScoreScaling>(aw_root->awar(AWAR_NN_REL_SCALING)->read_int());
997
998	PosRange org_range = get_nn_range_from_awars(aw_root);
999
1000	for (GBDATA *gb_species = GBT_first_species(gb_main);
1001	!error && gb_species;
1002	gb_species = GBT_next_species(gb_species))
1003	{
1004	if (!IS_QUERIED(gb_species, query)) continue;
1005	GBDATA *gb_data = GBT_find_sequence(gb_species, ali_name);
1006	if (gb_data) {
1007	PosRange range = org_range; // modified by read_sequence_region
1008	char *sequence = read_sequence_region(gb_data, range);
1009	PT_FamilyFinder ff(gb_main, pts, oligo_len, mismatches, fast_mode, rel_matches, rel_scaling);
1010
1011	ff.restrict_2_region(range);
1012
1013	error = ff.searchFamily(sequence, compl_mode, wanted_entries, min_score);
1014	if (!error) {
1015	const FamilyList *fm = ff.getFamilyList();
1016
1017	GBS_strstruct *value = NULL;
1018	while (fm) {
1019	const char *thisValue = 0;
1020	if (rel_matches) {
1021	ui_assert((fm->rel_matches*100) >= min_score); // filtered by ptserver
1022	thisValue = scored_entries
1023	? GBS_global_string("%.1f%%:%s", fm->rel_matches*100, fm->name)
1024	: fm->name;
1025	}
1026	else {
1027	ui_assert(fm->matches >= min_score); // filtered by ptserver
1028	thisValue = scored_entries
1029	? GBS_global_string("%li:%s", fm->matches, fm->name)
1030	: fm->name;
1031	}
1032
1033	if (thisValue) {
1034	if (value == NULL) { // first entry
1035	value = GBS_stropen(1000);
1036	}
1037	else {
1038	GBS_chrcat(value, ';');
1039	}
1040	GBS_strcat(value, thisValue);
1041	}
1042
1043	fm = fm->next;
1044	}
1045
1046	if (value) {
1047	ui_assert(GBT_get_type_of_changekey(gb_main, dest_field, CHANGE_KEY_PATH) == GB_STRING);
1048	GBDATA *gb_dest = GB_search(gb_species, dest_field, GB_STRING);
1049	error = GB_write_string(gb_dest, GBS_mempntr(value));
1050	GBS_strforget(value);
1051	}
1052	else {
1053	GBDATA *gb_dest = GB_search(gb_species, dest_field, GB_FIND);
1054	if (gb_dest) error = GB_delete(gb_dest);
1055	}
1056	}
1057	free(sequence);
1058	}
1059	progress.inc_and_check_user_abort(error);
1060	}
1061	free(ali_name);
1062	}
1063	GB_end_transaction_show_error(gb_main, error, aw_message);
1064	}
1065
1066	static void awtc_mark_hits(AW_window *) {
1067	AW_selection_list *resultList = NN_GLOBAL.get_result_list();
1068	GB_HASH *list_hash = resultList->to_hash(false);
1069	GBDATA *gb_main = NN_GLOBAL.get_gb_main();
1070
1071	GB_transaction ta(gb_main);
1072	for (GBDATA *gb_species = GBT_first_species(gb_main);
1073	gb_species;
1074	gb_species = GBT_next_species(gb_species))
1075	{
1076	int hit = GBS_read_hash(list_hash, GBT_get_name(gb_species));
1077	GB_write_flag(gb_species, hit);
1078	}
1079	}
1080
1081	static void awtc_nn_search(AW_window *) {
1082	AW_root *aw_root = AW_root::SINGLETON;
1083	GBDATA *gb_main = NN_GLOBAL.get_gb_main();
1084	GB_ERROR error = 0;
1085	PosRange range = get_nn_range_from_awars(aw_root);
1086	char *sequence = 0;
1087	{
1088	GB_transaction ta(gb_main);
1089
1090	char *sel_species = aw_root->awar(AWAR_SPECIES_NAME)->read_string();
1091	GBDATA *gb_species = GBT_find_species(gb_main, sel_species);
1092
1093	if (!gb_species) {
1094	error = "Select a species first";
1095	}
1096	else {
1097	char *ali_name = aw_root->awar(AWAR_DEFAULT_ALIGNMENT)->read_string();
1098	GBDATA *gb_data = GBT_find_sequence(gb_species, ali_name);
1099
1100	if (gb_data) {
1101	sequence = read_sequence_region(gb_data, range);
1102	}
1103	else {
1104	error = GBS_global_string("Species '%s' has no sequence '%s'", sel_species, ali_name);
1105	}
1106	free(ali_name);
1107	}
1108	free(sel_species);
1109	}
1110
1111	int pts = aw_root->awar(AWAR_PROBE_ADMIN_PT_SERVER)->read_int();
1112	int oligo_len = aw_root->awar(AWAR_NN_OLIGO_LEN)->read_int();
1113	int mismatches = aw_root->awar(AWAR_NN_MISMATCHES)->read_int();
1114	bool fast_mode = aw_root->awar(AWAR_NN_FAST_MODE)->read_int();
1115	bool rel_matches = aw_root->awar(AWAR_NN_REL_MATCHES)->read_int();
1116	float min_score = aw_root->awar(AWAR_NN_MIN_SCORE)->read_float();
1117
1118	RelativeScoreScaling rel_scaling = static_cast<RelativeScoreScaling>(aw_root->awar(AWAR_NN_REL_SCALING)->read_int());
1119
1120	PT_FamilyFinder ff(gb_main, pts, oligo_len, mismatches, fast_mode, rel_matches, rel_scaling);
1121
1122	ff.restrict_2_region(range);
1123
1124	int max_hits = 0; // max wanted hits
1125
1126	if (!error) {
1127	FF_complement compl_mode = static_cast<FF_complement>(aw_root->awar(AWAR_NN_COMPLEMENT)->read_int());
1128	max_hits = aw_root->awar(AWAR_NN_MAX_HITS)->read_int();
1129
1130	error = ff.searchFamily(sequence, compl_mode, max_hits, min_score);
1131	}
1132
1133	// update result list
1134	{
1135	AW_selection_list* sel = NN_GLOBAL.get_result_list();
1136	sel->clear();
1137
1138	int hits = 0;
1139	if (error) {
1140	aw_message(error);
1141	sel->insert_default("<Error>", "");
1142	}
1143	else {
1144	int count = 1;
1145	int shownHits = max_hits>0 ? max_hits : ff.getRealHits();
1146	int numWidth = log(shownHits)/log(10)+1;
1147
1148	for (const FamilyList *fm = ff.getFamilyList(); fm; fm = fm->next) {
1149	const char *dis;
1150	if (rel_matches) {
1151	dis = GBS_global_string("#%0i %-12s Rel.hits: %5.1f%%", numWidth, count, fm->name, fm->rel_matches100);
1152	}
1153	else {
1154	dis = GBS_global_string("#%0*i %-12s Hits: %4li", numWidth, count, fm->name, fm->matches);
1155	}
1156
1157	sel->insert(dis, fm->name);
1158	count++;
1159	}
1160
1161	sel->insert_default(ff.hits_were_truncated() ? "<List truncated>" : "<No more hits>", "");
1162	hits = ff.getRealHits();
1163	}
1164	aw_root->awar(AWAR_NN_SELECTED_HIT_COUNT)->write_int(hits);
1165	if (aw_root->awar(AWAR_NN_SELECTED_AUTO_MARK)->read_int()) {
1166	awtc_mark_hits(NULL);
1167	aw_root->awar(AWAR_TREE_REFRESH)->touch();
1168	}
1169	sel->update();
1170	}
1171
1172	free(sequence);
1173	}
1174
1175	static void awtc_move_hits(AW_window *aww) {
1176	AW_root *aw_root = aww->get_root();
1177	char *current_species = aw_root->awar(AWAR_SPECIES_NAME)->read_string();
1178
1179	if (!current_species) current_species = strdup("<unknown>");
1180
1181	char *hit_description = GBS_global_string_copy("<neighbour of %s: %%s>", current_species);
1182
1183	copy_selection_list_2_query_box(NN_GLOBAL.get_query(), NN_GLOBAL.get_result_list(), hit_description);
1184
1185	free(hit_description);
1186	free(current_species);
1187	}
1188
1189	static bool autosearch_triggered = false;
1190	static unsigned nn_perform_delayed_autosearch_cb(AW_root*) {
1191	awtc_nn_search(NULL);
1192	autosearch_triggered = false;
1193	return 0;
1194	}
1195	static void nn_trigger_delayed_autosearch_cb(AW_root *awr) {
1196	// automatic search is triggered delayed to make sure
1197	// dependencies between involved awars have propagated.
1198	if (!autosearch_triggered) { // ignore multiple triggers (happens when multiple awars change, e.g. when loading config)
1199	autosearch_triggered = true;
1200	awr->add_timed_callback(200, makeTimedCallback(nn_perform_delayed_autosearch_cb));
1201	}
1202	}
1203
1204	static void nn_auto_search_changed_cb(AW_root *awr) {
1205	int auto_search = awr->awar(AWAR_NN_SELECTED_AUTO_SEARCH)->read_int();
1206
1207	AW_awar *awar_sel_species = awr->awar(AWAR_SPECIES_NAME);
1208	if (auto_search) {
1209	awar_sel_species->add_callback(nn_trigger_delayed_autosearch_cb);
1210	nn_trigger_delayed_autosearch_cb(awr);
1211	}
1212	else {
1213	awar_sel_species->remove_callback(nn_trigger_delayed_autosearch_cb);
1214	}
1215	}
1216
1217	static AW_window *nn_of_sel_win = NULL;
1218	static void nn_searchRel_awar_changed_cb(AW_root *awr) {
1219	int auto_search = awr->awar(AWAR_NN_SELECTED_AUTO_SEARCH)->read_int();
1220	if (auto_search &&
1221	nn_of_sel_win && nn_of_sel_win->is_shown()) // do not trigger if window is not shown
1222	{
1223	nn_trigger_delayed_autosearch_cb(awr);
1224	}
1225	}
1226
1227	static void create_next_neighbours_vars(AW_root *aw_root) {
1228	static bool created = false;
1229
1230	if (!created) {
1231	RootCallback searchRel_awar_changed_cb = makeRootCallback(nn_searchRel_awar_changed_cb);
1232
1233	aw_root->awar_int(AWAR_PROBE_ADMIN_PT_SERVER)->add_callback(searchRel_awar_changed_cb);
1234	aw_root->awar_int(AWAR_NN_COMPLEMENT, FF_FORWARD)->add_callback(searchRel_awar_changed_cb);
1235
1236	aw_root->awar_string(AWAR_NN_RANGE_START, "")->add_callback(searchRel_awar_changed_cb);
1237	aw_root->awar_string(AWAR_NN_RANGE_END, "")->add_callback(searchRel_awar_changed_cb);
1238	aw_root->awar_int (AWAR_NN_MAX_HITS, 10)->set_minmax(0, 1000)->add_callback(searchRel_awar_changed_cb);;
1239	aw_root->awar_float (AWAR_NN_MIN_SCORE, 80)->set_minmax(0, 200)->add_callback(searchRel_awar_changed_cb);;
1240
1241	aw_root->awar_int(AWAR_NN_SELECTED_HIT_COUNT, 0);
1242	aw_root->awar_int(AWAR_NN_SELECTED_AUTO_SEARCH, 0)->add_callback(nn_auto_search_changed_cb);
1243	aw_root->awar_int(AWAR_NN_SELECTED_AUTO_MARK, 0);
1244
1245	aw_root->awar_string(AWAR_NN_LISTED_DEST_FIELD, "tmp");
1246	aw_root->awar_int (AWAR_NN_LISTED_SCORED_ENTRIES, 1);
1247
1248	AWTC_create_common_next_neighbour_vars(aw_root, searchRel_awar_changed_cb);
1249
1250	created = true;
1251	}
1252	}
1253
1254	static AWT_config_mapping_def next_neighbour_config_mapping[] = {
1255	// same as ../FAST_ALIGNER/fast_aligner.cxx@RELATIVES_CONFIG
1256	{ AWAR_NN_OLIGO_LEN, "oligolen" },
1257	{ AWAR_NN_MISMATCHES, "mismatches" },
1258	{ AWAR_NN_FAST_MODE, "fastmode" },
1259	{ AWAR_NN_REL_MATCHES, "relmatches" },
1260	{ AWAR_NN_REL_SCALING, "relscaling" },
1261
1262	{ AWAR_NN_COMPLEMENT, "complement" },
1263	{ AWAR_NN_RANGE_START, "rangestart" },
1264	{ AWAR_NN_RANGE_END, "rangeend" },
1265	{ AWAR_NN_MAX_HITS, "maxhits" },
1266	{ AWAR_NN_MIN_SCORE, "minscore" },
1267
1268	{ 0, 0}
1269	};
1270
1271	static void setup_next_neighbour_config(AWT_config_definition& cdef, bool for_listed) {
1272	// fields common for 'listed' and 'selected'
1273	cdef.add(next_neighbour_config_mapping);
1274
1275	if (for_listed) {
1276	cdef.add(AWAR_NN_LISTED_SCORED_ENTRIES, "addscore");
1277	}
1278	else {
1279	cdef.add(AWAR_NN_SELECTED_AUTO_SEARCH, "autosearch");
1280	cdef.add(AWAR_NN_SELECTED_AUTO_MARK, "automark");
1281	}
1282	}
1283
1284	static void create_common_next_neighbour_fields(AW_window *aws, bool for_listed) {
1285	aws->at("pt_server");
1286	awt_create_PTSERVER_selection_button(aws, AWAR_PROBE_ADMIN_PT_SERVER);
1287
1288	const int SCALER_LENGTH = 200;
1289
1290	aws->auto_space(5, 5);
1291	AWTC_create_common_next_neighbour_fields(aws, SCALER_LENGTH);
1292
1293
1294	aws->at("range");
1295	aws->create_input_field(AWAR_NN_RANGE_START, 6);
1296	aws->create_input_field(AWAR_NN_RANGE_END, 6);
1297
1298	aws->at("compl");
1299	aws->create_option_menu(AWAR_NN_COMPLEMENT, true);
1300	aws->insert_default_option("forward", "", FF_FORWARD);
1301	aws->insert_option ("reverse", "", FF_REVERSE);
1302	aws->insert_option ("complement", "", FF_COMPLEMENT);
1303	aws->insert_option ("reverse-complement", "", FF_REVERSE_COMPLEMENT);
1304	aws->insert_option ("fwd + rev-compl", "", FF_FORWARD\|FF_REVERSE_COMPLEMENT);
1305	aws->insert_option ("rev + compl", "", FF_REVERSE\|FF_COMPLEMENT);
1306	aws->insert_option ("any", "", FF_FORWARD\|FF_REVERSE\|FF_COMPLEMENT\|FF_REVERSE_COMPLEMENT);
1307	aws->update_option_menu();
1308
1309	aws->at("results");
1310	aws->create_input_field_with_scaler(AWAR_NN_MAX_HITS, 5, SCALER_LENGTH, AW_SCALER_EXP_LOWER);
1311
1312	aws->at("min_score");
1313	aws->create_input_field_with_scaler(AWAR_NN_MIN_SCORE, 5, SCALER_LENGTH, AW_SCALER_LINEAR);
1314
1315	aws->at("config");
1316	AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "next_neighbours", makeConfigSetupCallback(setup_next_neighbour_config, for_listed));
1317	}
1318
1319	static AW_window create_next_neighbours_listed_window(AW_root aw_root, DbQuery *query) {
1320	static AW_window_simple *aws = 0;
1321	NN_GLOBAL.set_query(query);
1322	if (!aws) {
1323	create_next_neighbours_vars(aw_root);
1324
1325	aws = new AW_window_simple;
1326	aws->init(aw_root, "SEARCH_NEXT_NEIGHBOURS_OF_LISTED", "Search Next Neighbours of Listed");
1327	aws->load_xfig("ad_spec_nnm.fig");
1328
1329	aws->at("close");
1330	aws->callback(AW_POPDOWN);
1331	aws->create_button("CLOSE", "Close", "C");
1332
1333	aws->at("help");
1334	aws->callback(makeHelpCallback("next_neighbours_listed.hlp"));
1335	aws->create_button("HELP", "Help", "H");
1336
1337	create_common_next_neighbour_fields(aws, true);
1338
1339	aws->at("add_score");
1340	aws->create_toggle(AWAR_NN_LISTED_SCORED_ENTRIES);
1341
1342	aws->at("field");
1343	create_itemfield_selection_button(aws, FieldSelDef(AWAR_NN_LISTED_DEST_FIELD, query_get_gb_main(query), SPECIES_get_selector(), FIELD_FILTER_STRING_WRITEABLE, "target field", SF_ALLOW_NEW), "field");
1344
1345	aws->at("go");
1346	aws->callback(awtc_nn_search_all_listed);
1347	aws->button_length(10);
1348	aws->create_button("WRITE_FIELDS", "GO");
1349	}
1350	return aws;
1351	}
1352
1353	static AW_window create_next_neighbours_selected_window(AW_root aw_root, DbQuery *query) {
1354	static AW_window_simple *aws = 0;
1355	NN_GLOBAL.set_query(query);
1356	if (!aws) {
1357	create_next_neighbours_vars(aw_root);
1358
1359	aws = new AW_window_simple;
1360	aws->init(aw_root, "SEARCH_NEXT_RELATIVE_OF_SELECTED", "Search Next Neighbours of Selected");
1361	aws->load_xfig("ad_spec_nn.fig");
1362
1363	aws->at("close");
1364	aws->callback(AW_POPDOWN);
1365	aws->create_button("CLOSE", "Close", "C");
1366
1367	aws->at("help");
1368	aws->callback(makeHelpCallback("next_neighbours.hlp"));
1369	aws->create_button("HELP", "Help", "H");
1370
1371	create_common_next_neighbour_fields(aws, false);
1372
1373	aws->button_length(10);
1374	aws->at("hit_count");
1375	aws->create_button(0, AWAR_NN_SELECTED_HIT_COUNT, 0, "+");
1376
1377	aws->at("hits");
1378	AW_selection_list *resultList = aws->create_selection_list(AWAR_SPECIES_NAME, false);
1379	NN_GLOBAL.set_result_list(resultList);
1380	resultList->insert_default("No hits found", "");
1381	resultList->update();
1382
1383	aws->at("go");
1384	aws->callback(awtc_nn_search);
1385	aws->create_button("SEARCH", "Search");
1386
1387	aws->at("auto_go");
1388	aws->label("Auto search on change");
1389	aws->create_toggle(AWAR_NN_SELECTED_AUTO_SEARCH);
1390
1391	aws->at("mark");
1392	aws->callback(awtc_mark_hits);
1393	aws->create_autosize_button("MARK_HITS", "Mark hits");
1394
1395	aws->at("auto_mark");
1396	aws->label("Auto");
1397	aws->create_toggle(AWAR_NN_SELECTED_AUTO_MARK);
1398
1399	aws->at("move");
1400	aws->callback(awtc_move_hits);
1401	aws->create_autosize_button("MOVE_TO_HITLIST", "Move to hitlist");
1402
1403	nn_of_sel_win = aws; // store current window (to disable auto search when this window was popped down)
1404	}
1405	return aws;
1406	}
1407
1408	// ---------------------------------------------
1409	// species/organism specific callbacks
1410
1411	static AW_window popup_new_speciesOrganismWindow(AW_root aw_root, GBDATA *gb_main, bool organismWindow, int detach_id);
1412
1413	static void popup_detached_speciesOrganismWindow(AW_window aw_parent, const InfoWindow infoWin) {
1414	const InfoWindow reusable = InfoWindowRegistry::infowin.find_reusable_of_same_type_as(infoWin);
1415	if (reusable) reusable->reuse();
1416	else { // create a new window if none is reusable
1417	popup_new_speciesOrganismWindow(aw_parent->get_root(),
1418	infoWin->get_gbmain(),
1419	infoWin->mapsOrganism(),
1420	InfoWindowRegistry::infowin.allocate_detach_id(*infoWin));
1421	}
1422	}
1423
1424	static AW_window popup_new_speciesOrganismWindow(AW_root aw_root, GBDATA *gb_main, bool organismWindow, int detach_id) { // INFO_WINDOW_CREATOR
1425	// if detach_id is MAIN_WINDOW -> create main window (not detached)
1426
1427	AW_window_simple_menu *aws = new AW_window_simple_menu;
1428	const ItemSelector& itemType = organismWindow ? ORGANISM_get_selector() : SPECIES_get_selector();
1429
1430	init_info_window(aw_root, aws, itemType, detach_id);
1431
1432	aws->load_xfig("ad_spec.fig");
1433
1434	aws->button_length(8);
1435
1436	aws->at("close");
1437	aws->callback(AW_POPDOWN);
1438	aws->create_button("CLOSE", "Close", "C");
1439
1440	aws->at("search");
1441	aws->callback(makeCreateWindowCallback(DBUI::create_species_query_window, gb_main));
1442	aws->create_autosize_button("SEARCH", "Search...", "S");
1443
1444	aws->at("help");
1445	aws->callback(makeHelpCallback(detach_id ? "sp_info_locked.hlp" : "sp_info.hlp")); // uses_hlp_res("sp_info_locked.hlp", "sp_info.hlp"); see ../../SOURCE_TOOLS/check_resources.pl@uses_hlp_res
1446	aws->create_button("HELP", "Help", "H");
1447
1448	DbScanner *scanner = create_db_scanner(gb_main, aws, "box", 0, "field", "enable", DB_VIEWER, "mark", itemType);
1449	const InfoWindow& infoWin = InfoWindowRegistry::infowin.registerInfoWindow(aws, scanner, detach_id);
1450
1451	if (infoWin.is_maininfo()) {
1452	if (organismWindow) aws->create_menu("ORGANISM", "O", AWM_ALL);
1453	else aws->create_menu("SPECIES", "S", AWM_ALL);
1454
1455	aws->insert_menu_topic("species_delete", "Delete", "D", "spa_delete.hlp", AWM_ALL, makeWindowCallback (species_delete_cb, gb_main));
1456	aws->insert_menu_topic("species_rename", "Rename", "R", "spa_rename.hlp", AWM_ALL, makeWindowCallback (species_rename_cb, gb_main));
1457	aws->insert_menu_topic("species_copy", "Copy", "y", "spa_copy.hlp", AWM_ALL, makeWindowCallback (species_copy_cb, gb_main));
1458	aws->insert_menu_topic(aws->local_id("species_create"), "Create", "C", "spa_create.hlp", AWM_ALL, makeCreateWindowCallback(create_species_create_window, gb_main));
1459	aws->sep______________();
1460	aws->insert_menu_topic("species_convert_2_sai", "Convert to SAI", "S", "sp_sp_2_ext.hlp", AWM_ALL, makeWindowCallback (move_species_to_extended, gb_main));
1461	}
1462
1463	aws->create_menu("FIELDS", "F", AWM_ALL);
1464	insert_field_admin_menuitems(aws, gb_main);
1465
1466	aws->at("detach");
1467	infoWin.add_detachOrGet_button(popup_detached_speciesOrganismWindow);
1468
1469	aws->show();
1470	infoWin.attach_selected_item();
1471	return aws;
1472	}
1473
1474	static void popup_speciesOrganismWindow(AW_root aw_root, GBDATA gb_main, bool organismWindow) {
1475	int windowIdx = (int)organismWindow;
1476
1477	static AW_window *AWS[2] = { 0, 0 };
1478	if (!AWS[windowIdx]) {
1479	AWS[windowIdx] = popup_new_speciesOrganismWindow(aw_root, gb_main, organismWindow, InfoWindow::MAIN_WINDOW);
1480	}
1481	else {
1482	AWS[windowIdx]->activate();
1483	}
1484	}
1485
1486	void DBUI::popup_species_info_window (AW_root aw_root, GBDATA gb_main) { popup_speciesOrganismWindow(aw_root, gb_main, false); }
1487	void DBUI::popup_organism_info_window(AW_root aw_root, GBDATA gb_main) { popup_speciesOrganismWindow(aw_root, gb_main, true); }
1488
1489	static DbQuery *GLOBAL_species_query = NULL; // @@@ fix design
1490
1491	void DBUI::unquery_all() {
1492	QUERY::unquery_all(0, GLOBAL_species_query);
1493	}
1494
1495	void DBUI::query_update_list() {
1496	DbQuery_update_list(GLOBAL_species_query);
1497	}
1498
1499	AW_window DBUI::create_species_query_window(AW_root aw_root, GBDATA *gb_main) {
1500	static AW_window_simple_menu *aws = 0;
1501	if (!aws) {
1502	aws = new AW_window_simple_menu;
1503	aws->init(aw_root, "SPECIES_QUERY", "SEARCH and QUERY");
1504	aws->create_menu("More functions", "f");
1505	aws->load_xfig("ad_query.fig");
1506
1507
1508	query_spec awtqs(SPECIES_get_selector());
1509
1510	awtqs.gb_main = gb_main;
1511	awtqs.species_name = AWAR_SPECIES_NAME;
1512	awtqs.tree_name = AWAR_TREE;
1513	awtqs.select_bit = GB_USERFLAG_QUERY;
1514	awtqs.use_menu = 1;
1515	awtqs.ere_pos_fig = "ere2";
1516	awtqs.by_pos_fig = "by2";
1517	awtqs.qbox_pos_fig = "qbox";
1518	awtqs.key_pos_fig = 0;
1519	awtqs.query_pos_fig = "content";
1520	awtqs.result_pos_fig = "result";
1521	awtqs.count_pos_fig = "count";
1522	awtqs.do_query_pos_fig = "doquery";
1523	awtqs.config_pos_fig = "doconfig";
1524	awtqs.do_mark_pos_fig = "domark";
1525	awtqs.do_unmark_pos_fig = "dounmark";
1526	awtqs.do_delete_pos_fig = "dodelete";
1527	awtqs.do_set_pos_fig = "doset";
1528	awtqs.do_refresh_pos_fig = "dorefresh";
1529	awtqs.open_parser_pos_fig = "openparser";
1530	awtqs.popup_info_window = popup_species_info_window;
1531
1532	DbQuery *query = create_query_box(aws, &awtqs, "spec");
1533	GLOBAL_species_query = query;
1534
1535	aws->create_menu("More search", "s");
1536	aws->insert_menu_topic("spec_search_equal_fields_within_db", "Search For Equal Fields and Mark Duplicates", "E", "search_duplicates.hlp", AWM_ALL, makeWindowCallback (search_duplicated_field_content, query, false));
1537	aws->insert_menu_topic("spec_search_equal_words_within_db", "Search For Equal Words Between Fields and Mark Duplicates", "W", "search_duplicates.hlp", AWM_ALL, makeWindowCallback (search_duplicated_field_content, query, true));
1538	aws->insert_menu_topic("spec_search_next_relativ_of_sel", "Search Next Relatives of SELECTED Species in PT_Server ...", "R", "next_neighbours.hlp", AWM_ALL, makeCreateWindowCallback(create_next_neighbours_selected_window, query));
1539	aws->insert_menu_topic("spec_search_next_relativ_of_listed", "Search Next Relatives of LISTED Species in PT_Server ...", "L", "next_neighbours_listed.hlp", AWM_ALL, makeCreateWindowCallback(create_next_neighbours_listed_window, query));
1540
1541	aws->button_length(7);
1542
1543	aws->at("close");
1544	aws->callback(AW_POPDOWN);
1545	aws->create_button("CLOSE", "Close", "C");
1546
1547	aws->at("help");
1548	aws->callback(makeHelpCallback("sp_search.hlp"));
1549	aws->create_button("HELP", "Help", "H");
1550	}
1551	return aws;
1552	}
1553
1554

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