Context Navigation

← Previous Revision
Next Revision →
Blame
Revision Log

MG_species.cxx

Visit:

Last change on this file was 19349, checked in by westram, 3 years ago
fix mnemonics: in 'Tree' menu: p: was used for 'Print ' + 'Compare topology…' o: 'Sync scrolling..' → 'Compare topology…' e: 'Beautify ' → 'Sync scrolling..' u: 'Mark duplicates' → 'Beautify ' k: now used for 'Mark duplicates' removed 'Select ' (also bound to button). T: used for 'Tree admin' now (was 'Select ') i: used for (genome-only) 'Relink to organisms' (was 'Tree admin') in 'Sequence' menu: S: was used for 'Split sequences' + 'Align Sequences'. l: now used for 'Align sequences'. in species transfer of merge tool. in properties menu of 'ARB gene map'. in properties menu of 'PROBE and SAI' (most changed).
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 53.9 KB

Line
1	// =============================================================== //
2	// //
3	// File : MG_species.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "merge.hxx"
12	#include "MG_adapt_ali.hxx"
13
14	#include <AW_rename.hxx>
15	#include <db_query.h>
16	#include <db_scanner.hxx>
17	#include <item_sel_list.h>
18
19	#include <xfergui.h>
20	#include <xferset.h>
21
22	#include <aw_awars.hxx>
23	#include <aw_msg.hxx>
24	#include <arb_progress.h>
25	#include <aw_root.hxx>
26	#include <aw_question.hxx>
27
28	#include <arb_str.h>
29	#include <arb_strbuf.h>
30	#include <arb_global_defs.h>
31
32
33	#define AWAR_SPECIES_SRC AWAR_MERGE_TMP_SRC "name"
34	#define AWAR_FIELD_SRC AWAR_MERGE_TMP_SRC "field"
35	#define AWAR_TAG_SRC AWAR_MERGE_TMP_SRC "tag"
36
37	#define AWAR_SPECIES_DST AWAR_MERGE_TMP_DST "name"
38	#define AWAR_FIELD_DST AWAR_MERGE_TMP_DST "field"
39	#define AWAR_TAG_DST AWAR_MERGE_TMP_DST "tag"
40
41	#define AWAR_TAG_DEL AWAR_MERGE_TMP "tagdel"
42	#define AWAR_APPEND AWAR_MERGE_TMP "append"
43
44	#define AWAR_SPECIES_XFER_TYPE AWAR_MERGE_SAV "xferType"
45	#define AWAR_SPECIES_XFER_SCOPE AWAR_MERGE_SAV "xferScope"
46	#define AWAR_SPECIES_XFER_FTS AWAR_MERGE_SAV "fts"
47
48	static DbScanner *scanner_src = NULp;
49	static DbScanner *scanner_dst = NULp;
50
51	enum SpeciesXferType {
52	SXT_WHOLE_SPECIES,
53	SXT_SINGLE_FIELD, // (skips alignment data)
54	SXT_USING_FTS, // field transfer set
55	SXT_USING_FTS_SKIP_ALI, // field transfer set (skips alignment data)
56	};
57
58	enum SpeciesXferScope {
59	SXS_SELECTED_SPECIES,
60	SXS_LISTED_SPECIES,
61	};
62
63	const char *MG_left_AWAR_SPECIES_NAME() { return AWAR_SPECIES_SRC; }
64
65	void MG_create_species_awars(AW_root *aw_root, AW_default aw_def) {
66	aw_root->awar_string(AWAR_SPECIES_SRC, "", aw_def);
67	aw_root->awar_string(AWAR_SPECIES_DST, "", aw_def);
68
69	aw_root->awar_string(AWAR_FIELD_SRC, NO_FIELD_SELECTED, aw_def);
70	aw_root->awar_string(AWAR_FIELD_DST, NO_FIELD_SELECTED, aw_def);
71
72	aw_root->awar_int(AWAR_APPEND, 0, aw_def);
73
74	aw_root->awar_int(AWAR_SPECIES_XFER_TYPE, SXT_WHOLE_SPECIES, aw_def);
75	aw_root->awar_int(AWAR_SPECIES_XFER_SCOPE, SXS_LISTED_SPECIES, aw_def);
76
77	aw_root->awar_string(AWAR_SPECIES_XFER_FTS, "", aw_def);
78	}
79
80	static void MG_map_species(AW_root *aw_root, DbSel db) {
81	GBDATA *gb_main = get_gb_main(db);
82	const char *awar_name = db == SRC_DB ? AWAR_SPECIES_SRC : AWAR_SPECIES_DST;
83	DbScanner *scanner = db == SRC_DB ? scanner_src : scanner_dst;
84
85	GB_transaction ta(gb_main);
86	char *selected_species = aw_root->awar(awar_name)->read_string();
87	GBDATA *gb_species = GBT_find_species(gb_main, selected_species);
88	if (gb_species) {
89	scanner->Map(gb_species, awar_name); // @@@ why is awar_name passed here? (normally a changekey-path is used)
90	// @@@ undocumented feature in DbScanner or bug?
91	}
92	free(selected_species);
93	}
94
95	static GB_ERROR MG_transfer_fields_info(char *fieldname = NULp) {
96	GBDATA *gb_key_data = GB_search(GLOBAL_gb_src, CHANGE_KEY_PATH, GB_CREATE_CONTAINER);
97	GB_ERROR error = NULp;
98
99	if (!gb_key_data) error = GB_await_error();
100	else {
101	if (!GB_search(GLOBAL_gb_dst, CHANGE_KEY_PATH, GB_CREATE_CONTAINER)) error = GB_await_error();
102	else {
103	for (GBDATA *gb_key = GB_entry(gb_key_data, CHANGEKEY);
104	gb_key && !error;
105	gb_key = GB_nextEntry(gb_key))
106	{
107	GBDATA *gb_key_name = GB_entry(gb_key, CHANGEKEY_NAME);
108	if (gb_key_name) {
109	GBDATA *gb_key_type = GB_entry(gb_key, CHANGEKEY_TYPE);
110	if (gb_key_type) {
111	char *name = GB_read_string(gb_key_name);
112
113	if (!fieldname \|\| strcmp(fieldname, name) == 0) {
114	error = GBT_add_new_species_changekey(GLOBAL_gb_dst, name, GB_TYPES(GB_read_int(gb_key_type)));
115	}
116	free(name);
117	}
118	}
119	}
120	}
121	}
122	return error;
123	}
124
125	static GB_ERROR MG_transfer_one_species(AW_root *aw_root, MG_remaps& remap,
126	GBDATA gb_src_species, GBDATA gb_dst_species_data,
127	bool src_is_genome, bool dst_is_genome,
128	GB_HASH source_organism_hash, GB_HASH dest_species_hash,
129	GB_HASH *error_suppressor)
130	{
131	// copies species 'gb_src_species' from source to destination DB.
132	//
133	// 'source_organism_hash' may be NULp, otherwise it's used to search for source organisms (when merging from genome DB)
134	// 'dest_species_hash' may be NULp, otherwise created species is stored there
135
136	mg_assert(gb_src_species);
137
138	GB_ERROR error = NULp;
139	const char *src_name = GBT_get_name(gb_src_species);
140	bool transfer_fields = false;
141
142	if (!src_name) {
143	error = "refused to transfer unnamed species";
144	}
145	else {
146	if (src_is_genome) {
147	if (dst_is_genome) { // genome -> genome
148	if (GEN_is_pseudo_gene_species(gb_src_species)) {
149	const char *origin = GEN_origin_organism(gb_src_species);
150	GBDATA *dest_organism = dest_species_hash
151	? (GBDATA*)GBS_read_hash(dest_species_hash, origin)
152	: GEN_find_organism(GLOBAL_gb_dst, origin);
153
154	if (dest_organism) transfer_fields = true;
155	else {
156	error = GBS_global_string("Destination DB does not contain '%s's origin-organism '%s'",
157	src_name, origin);
158	}
159	}
160	// else: merge organism ok
161	}
162	else { // genome -> non-genome
163	if (GEN_is_pseudo_gene_species(gb_src_species)) transfer_fields = true;
164	else {
165	error = GBS_global_string("You can't merge organisms (%s) into a non-genome DB.\n"
166	"Only pseudo-species are possible", src_name);
167	}
168	}
169	}
170	else {
171	if (dst_is_genome) { // non-genome -> genome
172	error = GBS_global_string("You can't merge non-genome species (%s) into a genome DB", src_name);
173	}
174	// else: non-genome -> non-genome ok
175	}
176	}
177
178	GBDATA *gb_dst_species = NULp;
179	if (!error) {
180	gb_dst_species = dest_species_hash
181	? (GBDATA*)GBS_read_hash(dest_species_hash, src_name)
182	: GBT_find_species_rel_species_data(gb_dst_species_data, src_name);
183
184	if (gb_dst_species) error = GB_delete(gb_dst_species);
185	}
186	if (!error) {
187	gb_dst_species = GB_create_container(gb_dst_species_data, "species");
188	if (!gb_dst_species) error = GB_await_error();
189	}
190	if (!error) error = GB_copy_dropProtectMarksAndTempstate(gb_dst_species, gb_src_species);
191	if (!error && transfer_fields) {
192	mg_assert(src_is_genome);
193	error = MG_export_fields(aw_root, gb_src_species, gb_dst_species, error_suppressor, source_organism_hash);
194	}
195	if (!error) GB_write_flag(gb_dst_species, 1);
196	if (!error) error = MG_adaptAllCopiedAlignments(remap, gb_src_species, gb_dst_species);
197	if (!error && dest_species_hash) GBS_write_hash(dest_species_hash, src_name, (long)gb_dst_species);
198
199	return error;
200	}
201
202	static const char get_reference_species_names(AW_root awr) {
203	return awr->awar(AWAR_REMAP_SPECIES_LIST)->read_char_pntr();
204	}
205	static bool adaption_enabled(AW_root *awr) {
206	return awr->awar(AWAR_REMAP_ENABLE)->read_int() != 0;
207	}
208
209	static void mg_transfer_selected_species(AW_window *aww) {
210	if (MG_copy_and_check_alignments() != 0) return;
211
212	AW_root *aw_root = aww->get_root();
213	char *src_name = aw_root->awar(AWAR_SPECIES_SRC)->read_string();
214	GB_ERROR error = NULp;
215
216	if (!src_name \|\| !src_name[0]) {
217	error = "Please select a species in the left list";
218	}
219	else {
220	arb_progress progress("Transferring selected species");
221
222	error = GB_begin_transaction(GLOBAL_gb_src);
223	if (!error) error = GB_begin_transaction(GLOBAL_gb_dst);
224
225	if (!error) {
226	MG_remaps rm(GLOBAL_gb_src, GLOBAL_gb_dst, adaption_enabled(aw_root), get_reference_species_names(aw_root));
227
228	GBDATA *gb_src_species_data = GBT_get_species_data(GLOBAL_gb_src);
229	GBDATA *gb_dst_species_data = GBT_get_species_data(GLOBAL_gb_dst);
230
231	bool src_is_genome = GEN_is_genome_db(GLOBAL_gb_src, -1);
232	bool dst_is_genome = GEN_is_genome_db(GLOBAL_gb_dst, -1);
233
234	GBDATA *gb_src_species = GBT_find_species_rel_species_data(gb_src_species_data, src_name);
235	if (!gb_src_species) {
236	error = GBS_global_string("Could not find species '%s' in source database", src_name);
237	}
238	else {
239	error = MG_transfer_one_species(aw_root, rm,
240	gb_src_species, gb_dst_species_data,
241	src_is_genome, dst_is_genome,
242	NULp, NULp,
243	NULp);
244	}
245	}
246
247	if (!error) error = MG_transfer_fields_info();
248
249	error = GB_end_transaction(GLOBAL_gb_src, error);
250	error = GB_end_transaction(GLOBAL_gb_dst, error);
251	}
252
253	if (error) aw_message(error);
254	}
255
256	static void mg_transfer_listed_species(AW_window *aww) {
257	if (MG_copy_and_check_alignments() != 0) return;
258
259	GB_ERROR error = NULp;
260	GB_begin_transaction(GLOBAL_gb_src);
261	GB_begin_transaction(GLOBAL_gb_dst);
262
263	bool src_is_genome = GEN_is_genome_db(GLOBAL_gb_src, -1);
264	bool dst_is_genome = GEN_is_genome_db(GLOBAL_gb_dst, -1);
265
266	GB_HASH *error_suppressor = GBS_create_hash(50, GB_IGNORE_CASE);
267	GB_HASH *dest_species_hash = GBT_create_species_hash(GLOBAL_gb_dst);
268	GB_HASH *source_organism_hash = src_is_genome ? GBT_create_organism_hash(GLOBAL_gb_src) : NULp;
269
270	AW_root *aw_root = aww->get_root();
271	MG_remaps rm(GLOBAL_gb_src, GLOBAL_gb_dst, adaption_enabled(aw_root), get_reference_species_names(aw_root));
272
273	GBDATA *gb_src_species;
274	arb_progress progress("Transferring listed species", mg_count_queried(GLOBAL_gb_src));
275
276	for (gb_src_species = GBT_first_species(GLOBAL_gb_src);
277	gb_src_species;
278	gb_src_species = GBT_next_species(gb_src_species))
279	{
280	if (IS_QUERIED_SPECIES(gb_src_species)) {
281	GBDATA *gb_dst_species_data = GBT_get_species_data(GLOBAL_gb_dst);
282
283	error = MG_transfer_one_species(aw_root, rm,
284	gb_src_species, gb_dst_species_data,
285	src_is_genome, dst_is_genome,
286	source_organism_hash, dest_species_hash,
287	error_suppressor);
288
289	progress.inc_and_check_user_abort(error);
290	}
291	}
292
293	GBS_free_hash(dest_species_hash);
294	if (source_organism_hash) GBS_free_hash(source_organism_hash);
295	GBS_free_hash(error_suppressor);
296
297	if (!error) error = MG_transfer_fields_info();
298
299	error = GB_end_transaction(GLOBAL_gb_src, error);
300	GB_end_transaction_show_error(GLOBAL_gb_dst, error, aw_message);
301	}
302
303	static GB_ERROR transfer_single_field(GBDATA const gb_src_species, GBDATA const gb_dst_species, const char const field, GBDATA const gb_src_field, const bool append, const bool transfer_of_alignment, const MG_remaps& rm) {
304	GBDATA *gb_dst_field = GB_search(gb_dst_species, field, GB_FIND);
305	GB_TYPES src_type = GB_read_type(gb_src_field);
306	GB_TYPES dst_type = gb_dst_field ? GB_read_type(gb_dst_field) : src_type;
307
308	bool use_copy = true;
309	GB_ERROR error = NULp;
310
311	if (append) {
312	if (src_type != GB_STRING \|\| dst_type != GB_STRING) {
313	error = "You can use 'Append data' with text fields only!";
314	}
315	else if (gb_dst_field) { // append possible (otherwise use_copy!)
316	char *src_val = GB_read_string(gb_src_field);
317	char *dst_val = GB_read_string(gb_dst_field);
318
319	if (!src_val \|\| !dst_val) error = GB_await_error();
320	else {
321	if (!GBS_find_string(dst_val, src_val, 0)) { // do not append if dst_val contains src_val
322	error = GB_write_string(gb_dst_field, GBS_global_string("%s %s", dst_val, src_val));
323	if (!error) GB_write_flag(gb_dst_species, 1);
324	}
325	}
326
327	free(src_val);
328	free(dst_val);
329
330	use_copy = false;
331	}
332	}
333
334	if (!error && use_copy) {
335	if (dst_type != src_type) error = "type mismatch"; // abort early (previously failed in call to MG_transfer_fields_info below)
336	if (!error && src_type == GB_DB && gb_dst_field) {
337	// if type is container -> delete before copy
338	// (otherwise it would generate a mix of both containers; if wanted provide optionally)
339	error = GB_delete(gb_dst_field);
340	gb_dst_field = NULp; // trigger recreation+copy
341	}
342	if (!error && !gb_dst_field) { // create missing target field (otherwise simply overwrite)
343	gb_dst_field = GB_search(gb_dst_species, field, src_type);
344	if (!gb_dst_field) error = GB_await_error(); // failed to create?
345	}
346	if (!error) error = GB_copy_dropProtectMarksAndTempstate(gb_dst_field, gb_src_field); // [Note: if transfer_of_alignment -> copies 'data' field of one alignment]
347	if (!error && transfer_of_alignment) error = MG_adaptAllCopiedAlignments(rm, gb_src_species, gb_dst_species); // [Note: adapts all copied alignments, if adapt toggle is checked]
348	if (!error) GB_write_flag(gb_dst_species, 1);
349	}
350	return error;
351	}
352
353	inline bool fieldContainsAlignment(const char *field) {
354	return GBS_string_matches(field, "ali_*", GB_MIND_CASE);
355	}
356
357	static void transfer_field_of_listed_cb(AW_window *aww) {
358	if (MG_copy_and_check_alignments() != 0) return;
359
360	AW_root *aw_root = aww->get_root();
361	char *field = aw_root->awar(AWAR_FIELD_SRC)->read_string();
362	const bool append = aw_root->awar(AWAR_APPEND)->read_int();
363	GB_ERROR error = NULp;
364
365	if (strcmp(field, NO_FIELD_SELECTED) == 0) {
366	error = "Please select the field you like to transfer";
367	}
368	else if (strcmp(field, "name") == 0) {
369	error = "Transferring the 'name' field is forbidden";
370	}
371	else {
372	const bool transfer_of_alignment = fieldContainsAlignment(field);
373
374	if (transfer_of_alignment && append) {
375	error = "Appending alignment data is not permitted\n"
376	"(please refer to ARB_NT/Sequence/Concatenate.. to do so)";
377	}
378	else {
379	error = GB_begin_transaction(GLOBAL_gb_src);
380	if (!error) error = GB_begin_transaction(GLOBAL_gb_dst);
381
382	if (!error) {
383	arb_progress progress("Transferring fields of listed", mg_count_queried(GLOBAL_gb_src));
384
385	MG_remaps rm(GLOBAL_gb_src, GLOBAL_gb_dst, adaption_enabled(aw_root), get_reference_species_names(aw_root)); // @@@ unused if transfer_of_alignment == false
386
387	GBDATA *gb_dest_species_data = GBT_get_species_data(GLOBAL_gb_dst);
388	if (!gb_dest_species_data) error = GB_await_error();
389
390	for (GBDATA *gb_src_species = GBT_first_species(GLOBAL_gb_src);
391	gb_src_species && !error;
392	gb_src_species = GBT_next_species(gb_src_species))
393	{
394	if (IS_QUERIED_SPECIES(gb_src_species)) {
395	const char *src_name = GBT_get_name(gb_src_species);
396	if (src_name) {
397	GBDATA *gb_dst_species = GB_find_string(gb_dest_species_data, "name", src_name, GB_IGNORE_CASE, SEARCH_GRANDCHILD);
398
399	if (!gb_dst_species) {
400	gb_dst_species = GB_create_container(gb_dest_species_data, "species");
401	if (!gb_dst_species) error = GB_await_error();
402	else error = GBT_write_string(gb_dst_species, "name", src_name);
403	}
404	else {
405	gb_dst_species = GB_get_father(gb_dst_species);
406	}
407
408	if (!error) {
409	// @@@ DRY vs inner part of body of transfer_field_of_selected_cb .@DRY_TRANSFER_FIELD
410	GBDATA *gb_src_field = GB_search(gb_src_species, field, GB_FIND);
411
412	if (gb_src_field) {
413	error = transfer_single_field(gb_src_species, gb_dst_species, field, gb_src_field, append, transfer_of_alignment, rm);
414	}
415	}
416	if (error) error = GBS_global_string("%s (species=%s)", error, src_name); // mention name of species in error message
417	}
418	else {
419	error = "refusing to transfer from unnamed species";
420	}
421
422	progress.inc_and_check_user_abort(error);
423	}
424	}
425	}
426
427	if (!error) error = MG_transfer_fields_info(field);
428
429	error = GB_end_transaction(GLOBAL_gb_src, error);
430	error = GB_end_transaction(GLOBAL_gb_dst, error);
431	}
432	}
433
434	if (error) aw_message(error);
435	free(field);
436	}
437
438	static void transfer_field_of_selected_cb(AW_window *aww) {
439	if (MG_copy_and_check_alignments() != 0) return;
440
441	AW_root *aw_root = aww->get_root();
442	char *field = aw_root->awar(AWAR_FIELD_SRC)->read_string();
443	const bool append = false; // @@@ provide via GUI?
444	GB_ERROR error = NULp;
445
446	if (strcmp(field, NO_FIELD_SELECTED) == 0) {
447	error = "Please select the field you like to transfer";
448	}
449	else if (strcmp(field, "name") == 0) {
450	error = "Transferring the 'name' field is forbidden";
451	}
452	else {
453	const bool transfer_of_alignment = fieldContainsAlignment(field);
454
455	if (transfer_of_alignment && append) { // @@@ append always false (see above)
456	error = "Appending alignment data is not permitted\n"
457	"(please refer to ARB_NT/Sequence/Concatenate.. to do so)";
458	}
459	else {
460	error = GB_begin_transaction(GLOBAL_gb_src);
461	if (!error) error = GB_begin_transaction(GLOBAL_gb_dst);
462
463	if (!error) {
464	arb_progress progress("Cross copy field");
465
466	MG_remaps rm(GLOBAL_gb_src, GLOBAL_gb_dst, adaption_enabled(aw_root), get_reference_species_names(aw_root)); // @@@ unused if transfer_of_alignment == false
467
468	GBDATA *gb_src_species;
469	GBDATA *gb_dst_species;
470	{
471	char *src_name = aw_root->awar(AWAR_SPECIES_SRC)->read_string();
472	char *dst_name = aw_root->awar(AWAR_SPECIES_DST)->read_string();
473
474	gb_src_species = GBT_find_species(GLOBAL_gb_src, src_name);
475	gb_dst_species = GBT_find_species(GLOBAL_gb_dst, dst_name);
476
477	free(dst_name);
478	free(src_name);
479	}
480
481	if (!gb_src_species) error = "Please select a species in left hitlist";
482	if (!gb_dst_species) error = "Please select a species in right hitlist";
483
484	if (!error) {
485	// @@@ DRY vs loop-body of transfer_field_of_listed_cb .@DRY_TRANSFER_FIELD
486	GBDATA *gb_src_field = GB_search(gb_src_species, field, GB_FIND);
487	if (!gb_src_field) error = GBS_global_string("Source species has no field '%s'", field);
488
489	if (!error) {
490	error = transfer_single_field(gb_src_species, gb_dst_species, field, gb_src_field, append, transfer_of_alignment, rm);
491	}
492	}
493	}
494	if (!error) error = MG_transfer_fields_info(field);
495
496	error = GB_end_transaction(GLOBAL_gb_src, error);
497	error = GB_end_transaction(GLOBAL_gb_dst, error);
498	}
499	}
500
501	if (error) aw_message(error);
502
503	free(field);
504	}
505
506	static void popup_single_field_transfer_window(AW_root *aw_root, SpeciesXferScope scope) {
507	static AW_window *aww[2] = { NULp, NULp };
508
509	if (!aww[scope]) {
510	GB_transaction ta(GLOBAL_gb_src);
511	AW_window_simple *aws = new AW_window_simple;
512
513	bool listed = scope == SXS_LISTED_SPECIES;
514	mg_assert(implicated(!listed, scope == SXS_SELECTED_SPECIES));
515
516	if (listed) aws->init(aw_root, "MERGE_XFER_FIELD_OF_LISTED", "Transfer field of listed");
517	else aws->init(aw_root, "MERGE_XFER_SINGLE_FIELD", "Transfer field of selected");
518
519	aws->load_xfig("merge/mg_transfield.fig");
520	aws->button_length(10);
521
522	aws->callback(AW_POPDOWN);
523	aws->at("close");
524	aws->create_button("CLOSE", "CLOSE", "C");
525
526	aws->at("help");
527	aws->callback(makeHelpCallback(listed ? "mg_xfer_field_of_listed.hlp" : "mg_xfer_field_of_sel.hlp"));
528	aws->create_button("HELP", "HELP");
529
530	if (listed) {
531	aws->at("append");
532	aws->label("Append data?");
533	aws->create_toggle(AWAR_APPEND);
534	}
535
536	long typeFilter = listed ? FIELD_FILTER_ANY_FIELD : FIELD_UNFILTERED;
537	create_itemfield_selection_button(aws, FieldSelDef(AWAR_FIELD_SRC, GLOBAL_gb_src, SPECIES_get_selector(), typeFilter, "source/target field"), "scandb");
538
539	aws->at("go");
540	aws->callback(listed ? transfer_field_of_listed_cb : transfer_field_of_selected_cb);
541	aws->create_button("GO", "GO");
542
543	aww[scope] = aws;
544	}
545	aww[scope]->activate();
546	}
547
548	static void MG_merge_tagged_field_cb(AW_window *aww) {
549	GB_transaction ta_merge(GLOBAL_gb_src);
550	GB_ERROR error = GB_begin_transaction(GLOBAL_gb_dst);
551
552	if (!error) {
553	AW_root *awr = aww->get_root();
554
555	char *src_field = awr->awar(AWAR_FIELD_SRC)->read_string();
556	char *dst_field = awr->awar(AWAR_FIELD_DST)->read_string();
557
558	if (strcmp(src_field, NO_FIELD_SELECTED) == 0 \|\|
559	strcmp(dst_field, NO_FIELD_SELECTED) == 0)
560	{
561	error = "Please select source- and target-fields.";
562	}
563
564	if (!error) {
565	char *src_tag = awr->awar(AWAR_TAG_SRC)->read_string();
566	char *dst_tag = awr->awar(AWAR_TAG_DST)->read_string();
567	char *del_tag = awr->awar(AWAR_TAG_DEL)->read_string();
568
569	arb_progress progress("Merging tagged fields", mg_count_queried(GLOBAL_gb_src));
570
571	GBDATA *gb_dest_species_data = GBT_get_species_data(GLOBAL_gb_dst);
572	if (!gb_dest_species_data) error = GB_await_error();
573	else {
574	for (GBDATA *gb_src_species = GBT_first_species(GLOBAL_gb_src);
575	gb_src_species && !error;
576	gb_src_species = GBT_next_species(gb_src_species))
577	{
578	if (IS_QUERIED_SPECIES(gb_src_species)) {
579	char *name = GBT_read_string(gb_src_species, "name");
580	if (!name) error = GB_await_error();
581	else {
582	GBDATA *gb_dst_species = GBT_find_or_create_species_rel_species_data(gb_dest_species_data, name, true);
583	if (!gb_dst_species) error = GB_await_error();
584	else {
585	char *src_val = GBT_readOrCreate_string(gb_src_species, src_field, "");
586	char *dst_val = GBT_readOrCreate_string(gb_dst_species, dst_field, "");
587
588	if (!src_val \|\| !dst_val) error = GB_await_error();
589	else {
590	char *sum = GBS_merge_tagged_strings(src_val, src_tag, del_tag,
591	dst_val, dst_tag, del_tag);
592
593	if (!sum) error = GB_await_error();
594	else error = GBT_write_string(gb_dst_species, dst_field, sum);
595	free(sum);
596	}
597	free(dst_val);
598	free(src_val);
599	}
600	}
601	free(name);
602	progress.inc_and_check_user_abort(error);
603	}
604	}
605	}
606
607	if (error) progress.done();
608
609	free(del_tag);
610	free(dst_tag);
611	free(src_tag);
612	}
613	free(dst_field);
614	free(src_field);
615	}
616	GB_end_transaction_show_error(GLOBAL_gb_dst, error, aw_message);
617	}
618
619	static AW_window create_mg_merge_tagged_fields_window(AW_root aw_root) {
620	static AW_window_simple *aws = NULp;
621	if (aws) return aws;
622
623	GB_transaction ta(GLOBAL_gb_src);
624
625	aw_root->awar_string(AWAR_TAG_SRC, "S");
626	aw_root->awar_string(AWAR_TAG_DST, "D");
627
628	aw_root->awar_string(AWAR_TAG_DEL, "S*");
629
630	aws = new AW_window_simple;
631	aws->init(aw_root, "MERGE_TAGGED_FIELD", "Merge tagged field");
632	aws->load_xfig("merge/mg_mergetaggedfield.fig");
633	aws->button_length(13);
634
635	aws->callback(AW_POPDOWN);
636	aws->at("close");
637	aws->create_button("CLOSE", "CLOSE", "C");
638
639	aws->at("go");
640	aws->callback(MG_merge_tagged_field_cb);
641	aws->create_button("GO", "GO");
642
643	aws->at("help");
644	aws->callback(makeHelpCallback("mergetaggedfield.hlp"));
645	aws->create_button("HELP", "HELP");
646
647	aws->at("tag1"); aws->create_input_field(AWAR_TAG_SRC, 5);
648	aws->at("tag2"); aws->create_input_field(AWAR_TAG_DST, 5);
649
650	aws->at("del1"); aws->create_input_field(AWAR_TAG_DEL, 5);
651
652	create_itemfield_selection_button(aws, FieldSelDef(AWAR_FIELD_SRC, GLOBAL_gb_src, SPECIES_get_selector(), FIELD_FILTER_STRING, "source-field"), "fields1");
653	create_itemfield_selection_button(aws, FieldSelDef(AWAR_FIELD_DST, GLOBAL_gb_dst, SPECIES_get_selector(), FIELD_FILTER_STRING, "target-field"), "fields2");
654
655	return aws;
656	}
657
658	static GB_ERROR MG_equal_alignments(bool autoselect_equal_alignment_name) {
659	//! Make the alignment names equal
660	ConstStrArray S_alignment_names;
661	ConstStrArray D_alignment_names;
662	GBT_get_alignment_names(S_alignment_names, GLOBAL_gb_src);
663	GBT_get_alignment_names(D_alignment_names, GLOBAL_gb_dst);
664
665	GB_ERROR error = NULp;
666	if (!S_alignment_names[0]) {
667	error = GB_export_error("No source sequences found");
668	}
669	else {
670	char *src_type = GBT_get_alignment_type_string(GLOBAL_gb_src, S_alignment_names[0]);
671	const char *dest = NULp;
672
673	for (int d = D_alignment_names.size()-1; d>0; --d) {
674	char *dst_type = GBT_get_alignment_type_string(GLOBAL_gb_dst, D_alignment_names[d]);
675	if (strcmp(src_type, dst_type) != 0) D_alignment_names.remove(d--);
676	free(dst_type);
677	}
678
679	int d = D_alignment_names.size();
680	switch (d) {
681	case 0:
682	error = GB_export_errorf("Cannot find a target alignment with a type of '%s'\n"
683	"You should create one first or select a different alignment type\n"
684	"during sequence import", src_type);
685	break;
686	case 1:
687	dest = D_alignment_names[0];
688	break;
689
690	default:
691	if (autoselect_equal_alignment_name) {
692	for (int i = 0; i<d; ++i) {
693	if (ARB_stricmp(S_alignment_names[0], D_alignment_names[i]) == 0) {
694	dest = D_alignment_names[i];
695	break;
696	}
697	}
698	}
699
700	if (!dest) {
701	GBS_strstruct buttonstr(100);
702
703	for (int i=0; i<d; i++) {
704	buttonstr.cat(D_alignment_names[i]);
705	buttonstr.put(',');
706	}
707	buttonstr.cat("ABORT");
708
709	int aliid = aw_question(NULp,
710	"There are more than one possible alignment targets\n"
711	"Choose one destination alignment or ABORT",
712	buttonstr.get_data());
713
714	if (aliid >= d) {
715	error = "Operation Aborted";
716	break;
717	}
718	dest = D_alignment_names[aliid];
719	}
720	break;
721	}
722	if (!error && dest && strcmp(S_alignment_names[0], dest) != 0) {
723	error = GBT_rename_alignment(GLOBAL_gb_src, S_alignment_names[0], dest);
724	if (error) {
725	error = GBS_global_string("Failed to rename alignment '%s' to '%s' (Reason: %s)",
726	S_alignment_names[0], dest, error);
727	}
728	else {
729	error = GBT_add_alignment_changekeys(GLOBAL_gb_src, dest);
730	}
731	}
732	free(src_type);
733	}
734
735	return error;
736	}
737
738	GB_ERROR MERGE_sequences_simple(AW_root *awr) {
739	//! Merge the sequences of two databases
740
741	static char *s_name = NULp;
742
743	GB_HASH *D_species_hash = NULp;
744
745	GB_topSecurityLevel srcUnsecured(GLOBAL_gb_src);
746	GB_topSecurityLevel dstUnsecured(GLOBAL_gb_dst);
747	GB_transaction taSrc(GLOBAL_gb_src);
748	GB_transaction taDst(GLOBAL_gb_dst);
749
750	GB_ERROR error = MG_equal_alignments(true);
751	if (!error) {
752	GBDATA *S_species_data = GBT_get_species_data(GLOBAL_gb_src);
753	GBDATA *D_species_data = GBT_get_species_data(GLOBAL_gb_dst);
754
755	freenull(s_name);
756
757	{
758	long S_species_count = GB_number_of_subentries(S_species_data);
759	long D_species_count = GB_number_of_subentries(D_species_data);
760
761	// create hash containing all species from gb_dst,
762	// but sized to hold all species from both DBs:
763	D_species_hash = GBT_create_species_hash_sized(GLOBAL_gb_dst, S_species_count+D_species_count);
764	}
765
766	bool overwriteall = false;
767	bool autorenameall = false;
768
769	for (GBDATA *S_species = GB_entry(S_species_data, "species"); S_species; S_species = GB_nextEntry(S_species)) {
770	GBDATA *S_name = GB_search(S_species, "name", GB_STRING);
771
772	freeset(s_name, GB_read_string(S_name));
773
774	int count = 1;
775	bool retry;
776	do {
777	retry = false;
778	count++;
779
780	GBDATA D_species = (GBDATA)GBS_read_hash(D_species_hash, s_name);
781	if (D_species) {
782	if (overwriteall) {
783	error = GB_delete(D_species);
784	}
785	else if (autorenameall) {
786	GB_ERROR dummy;
787	char *newname = AWTC_create_numbered_suffix(D_species_hash, s_name, dummy);
788
789	mg_assert(newname);
790	freeset(s_name, newname);
791	}
792	else {
793	switch (aw_question("merge_existing_species",
794	GBS_global_string("Warning: There is an ID conflict for species '%s'\n"
795	" You may:\n"
796	" - Overwrite existing species\n"
797	" - Overwrite all species with ID conflicts\n"
798	" - Not import species\n"
799	" - Enter ID for imported species\n"
800	" - Automatically create unique species IDs (append .NUM)\n"
801	" - Abort everything", s_name),
802	"overwrite, overwrite all, don't import, create ID, auto-create IDs, abort")) {
803	case 1:
804	overwriteall = true;
805	FALLTHROUGH;
806	case 0:
807	GB_delete(D_species);
808	break;
809
810	case 2:
811	continue;
812
813	case 3: {
814	GB_ERROR warning; // duplicated species warning (does not apply here)
815	char *autoname = AWTC_create_numbered_suffix(D_species_hash, s_name, warning);
816
817	if (!autoname) autoname = ARB_strdup(s_name);
818	freeset(s_name, aw_input("Species ID", "Enter new species ID", autoname));
819	free(autoname);
820	retry = true;
821	break;
822	}
823	case 4:
824	autorenameall = true;
825	retry = true;
826	break;
827
828	case 5:
829	error = "Operation aborted";
830	break;
831	}
832	}
833	}
834	} while (retry);
835
836	if (!error) {
837	GBDATA *D_species = GB_create_container(D_species_data, "species");
838	if (!D_species) error = GB_await_error();
839	else {
840	error = GB_copy_dropMarksAndTempstate(D_species, S_species);
841
842	if (!error) {
843	GB_write_flag(D_species, 1); // mark species
844	GB_raise_user_flag(D_species, GB_USERFLAG_QUERY); // put in search&query hitlist
845	error = GBT_write_string(D_species, "name", s_name);
846	}
847	}
848
849	GBS_write_hash(D_species_hash, s_name, (long)D_species);
850	}
851
852	if (error) break;
853	}
854	}
855
856	if (D_species_hash) GBS_free_hash(D_species_hash);
857
858	if (!error) error = MG_transfer_fields_info();
859	if (!error) awr->awar(AWAR_SPECIES_NAME)->write_string(s_name);
860
861	error = taSrc.close(error);
862	error = taDst.close(error);
863
864	aw_message_if(error);
865	return error;
866	}
867
868	// -----------------------------
869	// MG_species_selector
870
871	static void mg_select_species1(GBDATA, AW_root aw_root, const char *item_name) {
872	aw_root->awar(AWAR_SPECIES_SRC)->write_string(item_name);
873	}
874	static void mg_select_species2(GBDATA, AW_root aw_root, const char *item_name) {
875	aw_root->awar(AWAR_SPECIES_DST)->write_string(item_name);
876	}
877
878	static GBDATA mg_get_first_species_data1(GBDATA, AW_root*, QUERY_RANGE) {
879	return GBT_get_species_data(GLOBAL_gb_src);
880	}
881	static GBDATA mg_get_first_species_data2(GBDATA, AW_root*, QUERY_RANGE) {
882	return GBT_get_species_data(GLOBAL_gb_dst);
883	}
884
885	static GBDATA mg_get_selected_species1(GBDATA, AW_root *aw_root) {
886	GB_transaction ta(GLOBAL_gb_src);
887	const char *species_name = aw_root->awar(AWAR_SPECIES_SRC)->read_char_pntr();
888	return species_name[0] ? GBT_find_species(GLOBAL_gb_src, species_name) : NULp;
889	}
890	static GBDATA mg_get_selected_species2(GBDATA, AW_root *aw_root) {
891	GB_transaction ta(GLOBAL_gb_dst);
892	const char *species_name = aw_root->awar(AWAR_SPECIES_DST)->read_char_pntr();
893	return species_name[0] ? GBT_find_species(GLOBAL_gb_dst, species_name) : NULp;
894	}
895
896	static MutableItemSelector MG_species_selector[2];
897
898	static void mg_initialize_species_selectors() {
899	static bool initialized = false;
900	if (!initialized) {
901	MG_species_selector[0] = MG_species_selector[1] = SPECIES_get_selector();
902
903	for (int s = 0; s <= 1; ++s) {
904	MutableItemSelector& sel = MG_species_selector[s];
905
906	sel.update_item_awars = s ? mg_select_species2 : mg_select_species1;
907	sel.get_first_item_container = s ? mg_get_first_species_data2 : mg_get_first_species_data1;
908	sel.get_selected_item = s ? mg_get_selected_species2 : mg_get_selected_species1;
909	}
910
911	initialized = true;
912	}
913	}
914
915	class ScopedTransporter { // @@@ later also use for old merge types (SXT_WHOLE_SPECIES + SXT_SINGLE_FIELD)
916	static QUERY::DbQuery *query2update;
917
918	GBDATA expect_selected_species(GBDATA gb_main, const char awarname_selected, const char species_role, const char *listLocation, GB_ERROR& error, bool acceptNone) {
919	GBDATA *gb_species = NULp;
920	if (!error) {
921	const char *species_name = AW_root::SINGLETON->awar(awarname_selected)->read_char_pntr();
922	if (species_name[0]) {
923	gb_species = GBT_expect_species(gb_main, species_name);
924	if (!gb_species) {
925	error = GBS_global_string("%s (selected in %s hitlist)", GB_await_error(), listLocation);
926	}
927	}
928	else {
929	if (!acceptNone) {
930	error = GBS_global_string("Please select a %s species in %s hitlist", species_role, listLocation);
931	}
932	}
933	}
934
935	mg_assert(implicated(!acceptNone, contradicted(error, gb_species)));
936	mg_assert(!(error && gb_species));
937
938	return gb_species;
939	}
940
941	GB_ERROR transferExistingOrNew(GBDATA gb_src_item, GBDATA gb_dst_item_container) {
942	GB_ERROR error = NULp;
943	const char *name = GBT_get_name(gb_src_item);
944
945	if (!name) {
946	error = "unnamed item";
947	}
948	else {
949	GBDATA *gb_dst_item = GBT_find_species_rel_species_data(gb_dst_item_container, name);
950	if (gb_dst_item) { // found existing species
951	error = transferOne(gb_src_item, gb_dst_item, NULp); // use it as target
952	}
953	else { // not found
954	if (GB_have_error()) { // due to error
955	error = GB_await_error();
956	}
957	else { // otherwise create new species
958	error = transferOne(gb_src_item, NULp, gb_dst_item_container);
959	}
960	}
961	}
962	return error;
963	}
964
965	protected:
966	static void markTarget(GBDATA *gb_dst_item) {
967	mg_assert(GB_is_ancestor_of(GLOBAL_gb_dst, gb_dst_item)); // only modify userflag of destination(!) database
968
969	GB_write_flag(gb_dst_item, 1); // mark species
970	GB_raise_user_flag(gb_dst_item, GB_USERFLAG_QUERY); // put in search&query (destination) hitlist
971	}
972
973	public:
974	virtual ~ScopedTransporter() {}
975
976	static void set_query_to_update(QUERY::DbQuery *query) { query2update = query; }
977
978	virtual GB_ERROR transferOne(GBDATA gb_src_item, GBDATA gb_dst_item, GBDATA *gb_dst_item_container) = 0;
979	/*! transfer one species (used when transferring selected/listed species)
980	* @param gb_src_item source of transfer
981	* @param gb_dst_item target of transfer (if not NULp)
982	* @param gb_dst_item_container transfer target will be created inside this container (if gb_dst_item == NULp)
983	*/
984
985	GB_ERROR transferAllIn(SpeciesXferScope scope, const char *progressTitle) {
986	GB_ERROR error = GB_begin_transaction(GLOBAL_gb_src);
987	error = GB_begin_transaction(GLOBAL_gb_dst);
988
989	{
990	unsigned long scopeSize = 0;
991	switch (scope) {
992	case SXS_SELECTED_SPECIES: scopeSize = 1; break;
993	case SXS_LISTED_SPECIES: scopeSize = mg_count_queried(GLOBAL_gb_src); break;
994	}
995
996	arb_progress progress(progressTitle, scopeSize);
997
998	GBDATA *gb_dst_species_container = GBT_get_species_data(GLOBAL_gb_dst);
999	if (!error) {
1000	switch (scope) {
1001	case SXS_SELECTED_SPECIES: {
1002	GBDATA *gb_src_species = expect_selected_species(GLOBAL_gb_src, AWAR_SPECIES_SRC, "source", "left", error, false);
1003	GBDATA *gb_dst_species = expect_selected_species(GLOBAL_gb_dst, AWAR_SPECIES_DST, "target", "right", error, true);
1004
1005	if (!error) {
1006	if (gb_dst_species) { // source and target explicitely selected
1007	error = transferOne(gb_src_species, gb_dst_species, NULp);
1008	}
1009	else {
1010	error = transferExistingOrNew(gb_src_species, gb_dst_species_container);
1011	}
1012	progress.inc_and_check_user_abort(error);
1013	}
1014	break;
1015	}
1016
1017	case SXS_LISTED_SPECIES: {
1018	for (GBDATA *gb_src_species = GBT_first_species(GLOBAL_gb_src);
1019	gb_src_species && !error;
1020	gb_src_species = GBT_next_species(gb_src_species))
1021	{
1022	if (IS_QUERIED_SPECIES(gb_src_species)) {
1023	error = transferExistingOrNew(gb_src_species, gb_dst_species_container);
1024	if (error) { // mention name of species in error message:
1025	error = GBS_global_string("%s (species=%s)", error, GBT_get_name_or_description(gb_src_species));
1026	}
1027	progress.inc_and_check_user_abort(error);
1028	}
1029	}
1030	break;
1031	}
1032	}
1033	}
1034
1035	if (error) progress.done();
1036	}
1037	error = GB_end_transaction(GLOBAL_gb_src, error);
1038	error = GB_end_transaction(GLOBAL_gb_dst, error);
1039
1040	if (!error && query2update) DbQuery_update_list(query2update); // no need to update in case of error
1041
1042	return error;
1043	}
1044	};
1045
1046	QUERY::DbQuery *ScopedTransporter::query2update = NULp;
1047
1048	using namespace FieldTransfer;
1049
1050	typedef SmartPtr<MG_remaps> MG_remapsPtr;
1051
1052	class AdaptedAlignmentTransporter : public AlignmentTransporter {
1053	MG_remapsPtr remaps;
1054
1055	public:
1056	AdaptedAlignmentTransporter(MG_remapsPtr remaps_) : remaps(remaps_) {}
1057	bool shallCopyBefore() const OVERRIDE {
1058	return true; // ItemClonedByRuleSet::copyAlignments() shall be called b4 calling transport()
1059	}
1060	GB_ERROR transport(GBDATA gb_src_item, GBDATA gb_dst_item) const OVERRIDE {
1061	return MG_adaptAllCopiedAlignments(*remaps, gb_src_item, gb_dst_item);
1062	}
1063	};
1064
1065	struct DontTransportAlignment : public AlignmentTransporter {
1066	// this AlignmentTransporter simply does not transport anything
1067	bool shallCopyBefore() const OVERRIDE { return false; } // do not call copyAlignments() b4 calling transport()
1068	GB_ERROR transport(GBDATA , GBDATA ) const OVERRIDE { return NULp; } // do not transport alignment data
1069	};
1070
1071
1072
1073	class ViaFtsTransporter : public ScopedTransporter {
1074	RuleSetPtr fts;
1075	AlignmentTransporterPtr aliTransporter;
1076
1077	public:
1078	ViaFtsTransporter(RuleSetPtr fts_, AlignmentTransporterPtr transp) :
1079	fts(fts_),
1080	aliTransporter(transp)
1081	{}
1082	GB_ERROR transferOne(GBDATA gb_src_item, GBDATA gb_dst_item, GBDATA *gb_dst_item_container) OVERRIDE {
1083	mg_assert(fts.isSet());
1084	mg_assert(contradicted(gb_dst_item, gb_dst_item_container)); // exactly one of both shall be set
1085
1086	GB_ERROR error = NULp;
1087	GBDATA *gb_transferred = NULp;
1088	{
1089	ItemClonedByRuleSet transfer(gb_src_item, CLONE_ITEM_SPECIES, fts,
1090	gb_dst_item ? CLONE_INTO_EXISTING : REAL_CLONE,
1091	gb_dst_item ? gb_dst_item : gb_dst_item_container,
1092	&*aliTransporter);
1093
1094	if (transfer.has_error()) {
1095	error = transfer.get_error();
1096	}
1097	else {
1098	gb_transferred = transfer.get_clone();
1099	}
1100	}
1101
1102	mg_assert(contradicted(error, gb_transferred));
1103	if (!error) markTarget(gb_transferred);
1104
1105	return error;
1106	}
1107	};
1108
1109	static void mg_xfer_via_fts(AW_root *aw_root, SpeciesXferScope scope, bool xfer_seq_data) {
1110	if (MG_copy_and_check_alignments() != 0) return;
1111
1112	GB_ERROR error = NULp;
1113	const char *ftsname = XFER_getFullFTS(aw_root->awar(AWAR_SPECIES_XFER_FTS)->read_char_pntr());
1114
1115	if (!ftsname[0]) {
1116	error = "No FTS selected";
1117	}
1118	else {
1119	ErrorOrRuleSetPtr loaded = RuleSet::loadFrom(ftsname);
1120	if (loaded.hasError()) {
1121	ARB_ERROR lerror = loaded.getError();
1122	error = lerror.deliver();
1123	}
1124	else {
1125	AlignmentTransporterPtr transport_ali;
1126	if (xfer_seq_data) {
1127	MG_remapsPtr remaps;
1128	{
1129	GB_transaction ta_src(GLOBAL_gb_src);
1130	GB_transaction ta_dst(GLOBAL_gb_dst);
1131	remaps = new MG_remaps(GLOBAL_gb_src, GLOBAL_gb_dst, adaption_enabled(aw_root), get_reference_species_names(aw_root)); // @@@ use factory to make MG_remaps / MG_remapsPtr
1132	// @@@ can MG_remaps report error? (e.g. if wrong SAI/species specified as reference)
1133	}
1134
1135	transport_ali = new AdaptedAlignmentTransporter(remaps);
1136	}
1137	else {
1138	transport_ali = new DontTransportAlignment;
1139	}
1140
1141	ViaFtsTransporter transporter(loaded.getValue(), transport_ali);
1142	error = transporter.transferAllIn(scope, "Transfer using FTS");
1143	}
1144	}
1145	aw_message_if(error);
1146	}
1147
1148	struct MergeFieldScanner : public AvailableFieldScanner {
1149	void scanFields(StrArray& fields, FieldsToScan whatToScan) const OVERRIDE {
1150	if (whatToScan & SCAN_INPUT_FIELDS) {
1151	collectKeysRegisteredInDatabase(fields, GLOBAL_gb_src, SPECIES_get_selector(), true, false);
1152	}
1153	if (whatToScan & SCAN_OUTPUT_FIELDS) {
1154	collectKeysRegisteredInDatabase(fields, GLOBAL_gb_dst, SPECIES_get_selector(), true, false);
1155	}
1156	}
1157	};
1158
1159	static MergeFieldScanner fieldScanner;
1160
1161	static void MG_transfer_species(AW_window *aww) {
1162	AW_root *awr = aww->get_root();
1163
1164	SpeciesXferType type = SpeciesXferType (awr->awar(AWAR_SPECIES_XFER_TYPE) ->read_int());
1165	SpeciesXferScope scope = SpeciesXferScope(awr->awar(AWAR_SPECIES_XFER_SCOPE)->read_int());
1166
1167	switch (type) {
1168	case SXT_WHOLE_SPECIES:
1169	switch (scope) {
1170	case SXS_LISTED_SPECIES: mg_transfer_listed_species(aww); break;
1171	case SXS_SELECTED_SPECIES: mg_transfer_selected_species(aww); break;
1172	}
1173	break;
1174
1175	case SXT_SINGLE_FIELD:
1176	popup_single_field_transfer_window(awr, scope);
1177	break;
1178
1179	case SXT_USING_FTS:
1180	case SXT_USING_FTS_SKIP_ALI: {
1181	bool xfer_seq_data = (type == SXT_USING_FTS);
1182	mg_xfer_via_fts(awr, scope, xfer_seq_data);
1183	break;
1184	}
1185	}
1186	}
1187
1188	AW_window MG_create_merge_species_window(AW_root awr, bool dst_is_new) {
1189	GB_ERROR error = MG_expect_renamed();
1190	if (error) {
1191	aw_message(error);
1192	return NULp; // deny to open window before user has renamed species
1193	}
1194
1195	awr->awar_string(AWAR_REMAP_SPECIES_LIST, "ecoli", GLOBAL_gb_dst);
1196	awr->awar_int(AWAR_REMAP_ENABLE, 0, GLOBAL_gb_dst);
1197
1198	AW_window_simple_menu *aws = new AW_window_simple_menu;
1199	aws->init(awr, "MERGE_TRANSFER_SPECIES", "TRANSFER SPECIES");
1200	aws->load_xfig("merge/species.fig");
1201
1202	aws->at("close");
1203	aws->callback(AW_POPDOWN);
1204	aws->create_button("CLOSE", "CLOSE", "C");
1205
1206	aws->at("help");
1207	aws->callback(makeHelpCallback("mg_species.hlp"));
1208	aws->create_button("HELP", "HELP", "H");
1209
1210	mg_initialize_species_selectors();
1211
1212	{
1213	QUERY::query_spec awtqs(MG_species_selector[0]);
1214	aws->create_menu("Source-DB", "S");
1215
1216	awtqs.gb_main = GLOBAL_gb_src;
1217	awtqs.gb_ref = GLOBAL_gb_dst;
1218	awtqs.expect_hit_in_ref_list = false;
1219	awtqs.species_name = AWAR_SPECIES_SRC;
1220	awtqs.tree_name = NULp; // no selected tree here -> can't use tree related ACI commands without specifying a tree
1221	awtqs.select_bit = GB_USERFLAG_QUERY;
1222	awtqs.ere_pos_fig = "ere1";
1223	awtqs.by_pos_fig = "by1";
1224	awtqs.qbox_pos_fig = "qbox1";
1225	awtqs.key_pos_fig = NULp;
1226	awtqs.query_pos_fig = "content1";
1227	awtqs.result_pos_fig = "result1";
1228	awtqs.count_pos_fig = "count1";
1229	awtqs.do_query_pos_fig = "doquery1";
1230	awtqs.config_pos_fig = "doconfig1";
1231	awtqs.do_mark_pos_fig = NULp;
1232	awtqs.do_unmark_pos_fig = NULp;
1233	awtqs.do_delete_pos_fig = "dodelete1";
1234	awtqs.do_set_pos_fig = "doset1";
1235	awtqs.do_refresh_pos_fig = "dorefresh1";
1236	awtqs.open_parser_pos_fig = "openparser1";
1237	awtqs.use_menu = 1;
1238
1239	create_query_box(aws, &awtqs, "db1");
1240
1241	DbScanner *scanner = DbScanner::create(GLOBAL_gb_src, "merge_spec1", aws, "box1", NULp, NULp, DB_SCANNER, NULp, awtqs.get_queried_itemtype());
1242	scanner_src = scanner;
1243	aws->get_root()->awar(AWAR_SPECIES_SRC)->add_callback(makeRootCallback(MG_map_species, SRC_DB));
1244	}
1245	{
1246	QUERY::query_spec awtqs(MG_species_selector[1]);
1247	aws->create_menu("Target-DB", "T");
1248
1249	awtqs.gb_main = GLOBAL_gb_dst;
1250	awtqs.gb_ref = GLOBAL_gb_src;
1251	awtqs.expect_hit_in_ref_list = true;
1252	awtqs.species_name = AWAR_SPECIES_DST;
1253	awtqs.select_bit = GB_USERFLAG_QUERY;
1254	awtqs.ere_pos_fig = "ere2";
1255	awtqs.by_pos_fig = "by2";
1256	awtqs.qbox_pos_fig = "qbox2";
1257	awtqs.key_pos_fig = NULp;
1258	awtqs.query_pos_fig = "content2";
1259	awtqs.result_pos_fig = "result2";
1260	awtqs.count_pos_fig = "count2";
1261	awtqs.do_query_pos_fig = "doquery2";
1262	awtqs.config_pos_fig = "doconfig2";
1263	awtqs.do_mark_pos_fig = NULp;
1264	awtqs.do_unmark_pos_fig = NULp;
1265	awtqs.do_delete_pos_fig = "dodelete2";
1266	awtqs.do_set_pos_fig = "doset2";
1267	awtqs.do_refresh_pos_fig = "dorefresh2";
1268	awtqs.open_parser_pos_fig = "openparser2";
1269	awtqs.use_menu = 1;
1270
1271	ScopedTransporter::set_query_to_update(create_query_box(aws, &awtqs, "db2"));
1272
1273	DbScanner *scanner = DbScanner::create(GLOBAL_gb_dst, "merge_spec2", aws, "box2", NULp, NULp, DB_SCANNER, NULp, awtqs.get_queried_itemtype());
1274	scanner_dst = scanner;
1275	aws->get_root()->awar(AWAR_SPECIES_DST)->add_callback(makeRootCallback(MG_map_species, DST_DB));
1276	}
1277
1278	// ---------------------
1279	// middle area
1280
1281	// top icon
1282	aws->button_length(0);
1283	aws->at("icon");
1284	aws->callback(makeHelpCallback("mg_species.hlp"));
1285	aws->create_button("HELP_MERGE", "#merge/icon.xpm");
1286
1287	// adapt alignments
1288	{
1289	if (dst_is_new) {
1290	aws->sens_mask(AWM_DISABLED); // if dest DB is new = > adaption impossible
1291	awr->awar(AWAR_REMAP_ENABLE)->write_int(0); // disable adaption
1292	}
1293
1294	aws->at("adapt");
1295	aws->create_toggle(AWAR_REMAP_ENABLE);
1296
1297	aws->at("reference");
1298	aws->create_text_field(AWAR_REMAP_SPECIES_LIST);
1299
1300	aws->at("pres_sel");
1301	aws->callback(MG_create_preserves_selection_window);
1302	aws->create_autosize_button("SELECT", "SELECT", "S");
1303
1304	aws->sens_mask(AWM_ALL);
1305	}
1306
1307	// transfer options:
1308	aws->at("xferType");
1309	aws->create_option_menu(AWAR_SPECIES_XFER_TYPE);
1310	aws->insert_option("whole species", "w", SXT_WHOLE_SPECIES);
1311	aws->insert_option("single field", "s", SXT_SINGLE_FIELD);
1312	aws->insert_option("using FTS (with seq)", "F", SXT_USING_FTS);
1313	aws->insert_option("using FTS (w/o seq)", "o", SXT_USING_FTS_SKIP_ALI);
1314	aws->update_option_menu();
1315
1316	aws->at("fts");
1317	aws->callback(makeWindowCallback(XFER_select_RuleSet, AWAR_SPECIES_XFER_FTS, static_cast<AvailableFieldScanner*>(&fieldScanner)));
1318	aws->create_button("SELECT_FTS", AWAR_SPECIES_XFER_FTS);
1319
1320	aws->at("xferWhat");
1321	aws->create_option_menu(AWAR_SPECIES_XFER_SCOPE);
1322	aws->insert_option("listed species", "l", SXS_LISTED_SPECIES);
1323	aws->insert_option("selected species", "s", SXS_SELECTED_SPECIES);
1324	aws->update_option_menu();
1325
1326	{
1327	aws->shadow_width(3);
1328
1329	aws->at("transfer");
1330	aws->callback(MG_transfer_species);
1331	aws->create_button("TRANSFER", "Transfer species");
1332
1333	aws->shadow_width(1);
1334	}
1335
1336	aws->create_menu("Source->Target", "g");
1337	aws->insert_menu_topic("compare_field_of_listed", "Compare a field of listed species ...", "C", "checkfield.hlp", AWM_ALL, create_mg_check_fields_window);
1338	aws->insert_menu_topic("merge_field_of_listed_to_new_field", "Merge tagged field ...", "M", "mergetaggedfield.hlp", AWM_ALL, create_mg_merge_tagged_fields_window);
1339	aws->sep______________();
1340	aws->insert_menu_topic("def_gene_species_field_xfer", "Define field transfer for gene-species", "g", "gene_species_field_transfer.hlp", AWM_ALL, MG_gene_species_create_field_transfer_def_window);
1341
1342
1343	return aws;
1344	}
1345

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

Context Navigation

source: branches/lib/MERGE/MG_species.cxx

Download in other formats: