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source: branches/port5/PROBE_DESIGN/probe_design.cxx

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Last change on this file was 8215, checked in by westram, 14 years ago
guard truncated probe match against misunderstandings increase match limit to 1M (should do until 6.0)
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 81.1 KB

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1	#include <stdio.h>
2	#include <stdlib.h>
3	#include <memory.h>
4	// #include <malloc.h>
5	#include <string.h>
6	#include <ctype.h>
7
8	#include <arbdb.h>
9	#include <arbdbt.h>
10
11	#include <aw_root.hxx>
12	#include <aw_device.hxx>
13	#include <aw_window.hxx>
14	#include <aw_awars.hxx>
15	#include <aw_preset.hxx>
16	#include <awt.hxx>
17	#include <awt_iupac.hxx>
18
19	#include <awt_canvas.hxx>
20	#include <awt_tree.hxx>
21	#include <awt_dtree.hxx>
22	#include <awt_tree_cb.hxx>
23	#include <awt_config_manager.hxx>
24	#include <awt_canvas.hxx>
25	#include <awt_sel_boxes.hxx>
26
27	#include <PT_com.h>
28	#include <client.h>
29	#include <servercntrl.h>
30	#include <probe_design.hxx>
31
32	#include <GEN.hxx>
33	#include "SaiProbeVisualization.hxx"
34	#include "probe_match_parser.hxx"
35
36	void NT_group_not_marked_cb(void dummy, AWT_canvas ntw); // real prototype is in awt_tree_cb.hxx
37
38	// general awars
39
40	#define AWAR_PROBE_CREATE_GENE_SERVER "tmp/probe_admin/gene_server" // whether to create a gene pt server
41
42	// probe match awars
43
44	// #define AWAR_PD_MATCH_ITEM AWAR_SPECIES_NAME
45	#define AWAR_PD_SELECTED_MATCH "tmp/probe_design/match"
46	#define AWAR_PD_MATCH_RESOLVE "tmp/probe_design/match_resolve" // for IUPAC resolution
47
48	#define AWAR_PD_MATCH_SORTBY "probe_match/sort_by" // weighted mismatches
49	#define AWAR_PD_MATCH_COMPLEMENT "probe_match/complement" // check reverse complement too
50	#define AWAR_PD_MATCH_MARKHITS "probe_match/mark_hits" // mark hitten species in database
51	#define AWAR_PD_MATCH_WRITE2TMP "probe_match/write_2_tmp" // write result to field tmp
52	#define AWAR_PD_MATCH_AUTOMATCH "probe_match/auto_match" // auto match probes when target string changes
53
54	#define AWAR_PD_MATCH_CLIPHITS "probe_match/clip_hits"
55	#define AWAR_PD_MATCH_NHITS "tmp/probe_match/nhits" // display the 'number of hits'
56
57	// probe design awars
58
59	#define AWAR_PD_DESIGN_CLIPRESULT "probe_design/CLIPRESULT" // 'length of output' (how many probes will get designed)
60	#define AWAR_PD_DESIGN_MISHIT "probe_design/MISHIT" // 'non group hits'
61	#define AWAR_PD_DESIGN_MAXBOND "probe_design/MAXBOND" // max hairpinbonds ?
62	#define AWAR_PD_DESIGN_MINTARGETS "probe_design/MINTARGETS" // 'min. group hits (%)'
63
64	#define AWAR_PD_DESIGN_PROBELENGTH "probe_design/PROBELENGTH" // length of probe
65	#define AWAR_PD_DESIGN_MIN_TEMP "probe_design/MINTEMP" // temperature (min)
66	#define AWAR_PD_DESIGN_MAX_TEMP "probe_design/MAXTEMP" // temperature (max)
67	#define AWAR_PD_DESIGN_MIN_GC "probe_design/MINGC" // GC content (min)
68	#define AWAR_PD_DESIGN_MAX_GC "probe_design/MAXGC" // GC content (max)
69	#define AWAR_PD_DESIGN_MIN_ECOLIPOS "probe_design/MINPOS" // ecolipos (min)
70	#define AWAR_PD_DESIGN_MAX_ECOLIPOS "probe_design/MAXPOS" // ecolipos (max)
71
72	#define AWAR_PD_DESIGN_GENE "probe_design/gene" // generate probes for genes ?
73
74	// probe design/match (expert window)
75	#define AWAR_PD_DESIGN_EXP_BONDS "probe_design/bonds/pos" // prefix for bonds
76	#define AWAR_PD_DESIGN_EXP_SPLIT "probe_design/SPLIT"
77	#define AWAR_PD_DESIGN_EXP_DTEDGE "probe_design/DTEDGE"
78	#define AWAR_PD_DESIGN_EXP_DT "probe_design/DT"
79
80	// ----------------------------------------
81
82	saiProbeData *g_spd = 0;
83
84	extern GBDATA GLOBAL_gb_main; / must exist */
85
86	struct gl_struct {
87	aisc_com *link;
88	T_PT_LOCS locs;
89	T_PT_MAIN com;
90	AW_window_simple *pd_design;
91	AW_selection_list *pd_design_id;
92	} pd_gl;
93
94	struct probe_match_event_para {
95	AW_window *aww;
96	AW_CL sel_id;
97	bool disable;
98	};
99	static probe_match_event_para auto_match_cb_settings = { 0, 0, true };
100	void probe_match_event(AW_window *aww, AW_CL cl_selection_id, AW_CL cl_count_ptr); // prototype
101
102	static void auto_match_cb(AW_root *root) {
103	if (!auto_match_cb_settings.disable) {
104	char *ts = root->awar(AWAR_TARGET_STRING)->read_string();
105	if (strlen(ts) > 0) {
106	probe_match_event(auto_match_cb_settings.aww, auto_match_cb_settings.sel_id, 0);
107	}
108	free(ts);
109	}
110	}
111
112	static const char *auto_match_sensitive_awars[] = {
113	AWAR_TARGET_STRING,
114	AWAR_PT_SERVER,
115	AWAR_PD_MATCH_COMPLEMENT,
116	AWAR_MAX_MISMATCHES,
117	AWAR_PD_MATCH_SORTBY,
118	0
119	};
120
121	static void auto_match_changed(AW_root *root) {
122	static bool callback_active = false;
123	int autoMatch = root->awar(AWAR_PD_MATCH_AUTOMATCH)->read_int();
124
125	if (autoMatch) {
126	if (!callback_active) {
127	for (int i = 0; auto_match_sensitive_awars[i]; ++i) {
128	root->awar(auto_match_sensitive_awars[i])->add_callback(auto_match_cb);
129	}
130	}
131	}
132	else {
133	if (callback_active) {
134	for (int i = 0; auto_match_sensitive_awars[i]; ++i) {
135	root->awar(auto_match_sensitive_awars[i])->remove_callback(auto_match_cb);
136	}
137	}
138	}
139	callback_active = bool(autoMatch);
140	}
141
142	static void enable_auto_match_cb(AW_root root, AW_window aww, AW_CL cl_sel_id) {
143	if (cl_sel_id == 0 && // small enable (w/o selection list)
144	auto_match_cb_settings.aww != 0) return; // is only done when not enabled yet
145
146	auto_match_cb_settings.aww = aww;
147	auto_match_cb_settings.sel_id = cl_sel_id;
148	auto_match_cb_settings.disable = false;
149	auto_match_changed(root);
150	}
151
152	static void popup_match_window_cb(AW_window *aww) {
153	AW_root *root = aww->get_root();
154	AW_window *match_window = create_probe_match_window(root, 0);
155	match_window->activate();
156	root->awar(AWAR_TARGET_STRING)->touch(); // force re-match
157	}
158
159	// --------------------------------------------------------------------------------
160
161	static void popup_probe_design_result_window(AW_window *aww)
162	{
163	if (!pd_gl.pd_design) {
164	AW_root *root = aww->get_root();
165
166	pd_gl.pd_design = new AW_window_simple;
167	pd_gl.pd_design->init(root, "PD_RESULT", "PD RESULT");
168	pd_gl.pd_design->load_xfig("pd_reslt.fig");
169
170	pd_gl.pd_design->at("close");
171	pd_gl.pd_design->callback((AW_CB0)AW_POPDOWN);
172	pd_gl.pd_design->create_button("CLOSE", "CLOSE", "C");
173
174	pd_gl.pd_design->at("help");
175	pd_gl.pd_design->callback(AW_POPUP_HELP, (AW_CL)"probedesignresult.hlp");
176	pd_gl.pd_design->create_button("HELP", "HELP", "H");
177
178	pd_gl.pd_design->at("auto");
179	pd_gl.pd_design->label("Auto match");
180	pd_gl.pd_design->create_toggle(AWAR_PD_MATCH_AUTOMATCH );
181
182	enable_auto_match_cb(root, pd_gl.pd_design, 0);
183
184	pd_gl.pd_design->at( "result" );
185	pd_gl.pd_design_id = pd_gl.pd_design->create_selection_list( AWAR_TARGET_STRING, NULL, "", 40, 5 );
186	pd_gl.pd_design->set_selection_list_suffix(pd_gl.pd_design_id, "prb");
187
188	pd_gl.pd_design->clear_selection_list(pd_gl.pd_design_id);
189	pd_gl.pd_design->insert_default_selection( pd_gl.pd_design_id, "No probes designed yet", "" );
190
191	pd_gl.pd_design->at("save");
192	pd_gl.pd_design->callback( AW_POPUP, (AW_CL)create_save_box_for_selection_lists, (AW_CL)pd_gl.pd_design_id );
193	pd_gl.pd_design->create_button("SAVE", "SAVE", "S");
194
195	pd_gl.pd_design->at("print");
196	pd_gl.pd_design->callback( create_print_box_for_selection_lists, (AW_CL)pd_gl.pd_design_id );
197	pd_gl.pd_design->create_button("PRINT", "PRINT", "P");
198
199	pd_gl.pd_design->at("match");
200	pd_gl.pd_design->callback( popup_match_window_cb);
201	pd_gl.pd_design->create_button("MATCH", "MATCH", "M");
202	}
203	pd_gl.pd_design->activate();
204	}
205
206	int init_local_com_struct()
207	{
208	const char *user = GB_getenvUSER();
209
210	if( aisc_create(pd_gl.link, PT_MAIN, pd_gl.com,
211	MAIN_LOCS, PT_LOCS, &pd_gl.locs,
212	LOCS_USER, user,
213	NULL)){
214	return 1;
215	}
216	return 0;
217	}
218
219	static const char PD_probe_pt_look_for_server(AW_root root, GB_ERROR& error) {
220	// return PT server info string (see GBS_read_arb_tcp for details)
221	// or NULL (in this case 'error' is set)
222
223	const char *result = 0;
224	char choice[256];
225
226	sprintf(choice, "ARB_PT_SERVER%li", root->awar(AWAR_PT_SERVER)->read_int());
227	error = arb_look_and_start_server(AISC_MAGIC_NUMBER, choice, GLOBAL_gb_main);
228	if (!error) {
229	result = GBS_read_arb_tcp(choice);
230	if (!result) error = GB_await_error();
231	}
232	pd_assert(!!result != !!error);
233	return result;
234	}
235
236	static GB_ERROR species_requires(GBDATA gb_species, const char whats_required) {
237	return GBS_global_string("Species '%s' needs %s", GBT_read_name(gb_species), whats_required);
238	}
239
240	static GB_ERROR gene_requires(GBDATA gb_gene, const char whats_required) {
241	GBDATA *gb_species = GB_get_grandfather(gb_gene);
242	pd_assert(gb_species);
243	return GBS_global_string("Gene '%s' of organism '%s' needs %s", GBT_read_name(gb_gene), GBT_read_name(gb_species), whats_required);
244	}
245
246	GB_ERROR pd_get_the_names(bytestring &bs, bytestring &checksum) {
247	GBS_strstruct *names = GBS_stropen(1024);
248	GBS_strstruct *checksums = GBS_stropen(1024);
249	GB_ERROR error = 0;
250
251	GB_begin_transaction(GLOBAL_gb_main);
252
253	char *use = GBT_get_default_alignment(GLOBAL_gb_main);
254
255	for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL_gb_main); gb_species; gb_species = GBT_next_marked_species(gb_species)) {
256	GBDATA *gb_name = GB_entry(gb_species, "name");
257	if (!gb_name) { error = species_requires(gb_species, "name"); break; }
258
259	GBDATA *gb_data = GBT_read_sequence(gb_species, use);
260	if (!gb_data) { error = species_requires(gb_species, GBS_global_string("data in '%s'", use)); break; }
261
262	GBS_intcat(checksums, GBS_checksum(GB_read_char_pntr(gb_data), 1, ".-"));
263	GBS_strcat(names, GB_read_char_pntr(gb_name));
264	GBS_chrcat(checksums, '#');
265	GBS_chrcat(names, '#');
266	}
267
268	GBS_str_cut_tail(names, 1); // remove trailing '#'
269	GBS_str_cut_tail(checksums, 1); // remove trailing '#'
270
271	free(use);
272
273	bs.data = GBS_strclose(names);
274	bs.size = strlen(bs.data)+1;
275
276	checksum.data = GBS_strclose(checksums);
277	checksum.size = strlen(checksum.data)+1;
278
279	GB_commit_transaction(GLOBAL_gb_main);
280
281	return error;
282	}
283
284	GB_ERROR pd_get_the_gene_names(bytestring &bs, bytestring &checksum){
285	GBS_strstruct *names = GBS_stropen(1024);
286	GBS_strstruct *checksums = GBS_stropen(1024);
287	GB_ERROR error = 0;
288
289	GB_begin_transaction(GLOBAL_gb_main);
290	const char *use = GENOM_ALIGNMENT; // gene pt server is always build on 'ali_genom'
291
292	for (GBDATA *gb_species = GEN_first_organism(GLOBAL_gb_main); gb_species && !error; gb_species = GEN_next_organism(gb_species)) {
293	const char *sequence = 0;
294	const char *species_name = 0;
295	{
296	GBDATA *gb_data = GBT_read_sequence(gb_species, use);
297	if (!gb_data) { error = species_requires(gb_species, GBS_global_string("data in '%s'", use)); break; }
298	sequence = GB_read_char_pntr(gb_data);
299
300	GBDATA *gb_name = GB_search(gb_species, "name", GB_FIND);
301	if (!gb_name) { error = species_requires(gb_species, "name"); break; }
302	species_name = GB_read_char_pntr(gb_name);
303	}
304
305	for (GBDATA *gb_gene = GEN_first_marked_gene(gb_species); gb_gene && !error; gb_gene = GEN_next_marked_gene(gb_gene)) {
306	const char *gene_name = 0;
307	{
308	GBDATA *gb_gene_name = GB_entry(gb_gene, "name");
309	if (!gb_gene_name) { error = gene_requires(gb_gene, "name"); break; }
310	gene_name = GB_read_char_pntr(gb_gene_name);
311	}
312
313	{
314	char *gene_seq = GBT_read_gene_sequence(gb_gene, GB_FALSE, 0);
315	if (!gene_seq) error = GB_await_error();
316	else {
317	long CheckSum = GBS_checksum(gene_seq, 1, ".-");
318	const char *id = GBS_global_string("%s/%s", species_name, gene_name);
319
320	GBS_intcat(checksums, CheckSum);
321	GBS_strcat(names, id);
322	GBS_chrcat(checksums, '#');
323	GBS_chrcat(names, '#');
324
325	free(gene_seq);
326	}
327	}
328	}
329	}
330
331	GBS_str_cut_tail(names, 1); // remove trailing '#'
332	GBS_str_cut_tail(checksums, 1); // remove trailing '#'
333
334	if (error) {
335	GBS_strforget(names);
336	GBS_strforget(checksums);
337	}
338	else {
339	bs.size = GBS_memoffset(names)+1;
340	bs.data = GBS_strclose(names);
341
342	checksum.size = GBS_memoffset(checksums)+1;
343	checksum.data = GBS_strclose(checksums);
344	}
345	error = GB_end_transaction(GLOBAL_gb_main, error);
346	return error;
347	}
348
349	int probe_design_send_data(AW_root *root, T_PT_PDC pdc)
350	{
351	int i;
352	char buffer[256];
353	if (aisc_put(pd_gl.link, PT_PDC, pdc,
354	PDC_DTEDGE, (double)root->awar(AWAR_PD_DESIGN_EXP_DTEDGE)->read_float()*100.0,
355	PDC_DT, (double)root->awar(AWAR_PD_DESIGN_EXP_DT)->read_float()*100.0,
356	PDC_SPLIT, (double)root->awar(AWAR_PD_DESIGN_EXP_SPLIT)->read_float(),
357	PDC_CLIPRESULT, root->awar(AWAR_PD_DESIGN_CLIPRESULT)->read_int(),
358	NULL)) return 1;
359	for (i=0;i<16;i++) {
360	sprintf(buffer,AWAR_PD_DESIGN_EXP_BONDS "%i",i);
361	if (aisc_put(pd_gl.link,PT_PDC, pdc,
362	PT_INDEX, i,
363	PDC_BONDVAL, (double)root->awar(buffer)->read_float(),
364	NULL) ) return 1;
365	}
366	#if 0
367	T_PT_SPECIALS specials;
368	for (i=0;i<PROBE_DESIGN_EXCEPTION_MAX;i++){
369	char pdcmode[256],pdcll[256],pdcl[256],pdcc[256],pdcr[256],pdcrr[256];
370
371	sprintf(pdcmode,"probe_design/exceptions/nr%i/MODE",i);
372	if (root->awar(pdcmode)->read_int()<0) break;
373	sprintf(pdcll,"probe_design/exceptions/nr%i/LLEFT",i);
374	sprintf(pdcl,"probe_design/exceptions/nr%i/LEFT",i);
375	sprintf(pdcc,"probe_design/exceptions/nr%i/CENTER",i);
376	sprintf(pdcr,"probe_design/exceptions/nr%i/RIGHT",i);
377	sprintf(pdcrr,"probe_design/exceptions/nr%i/RRIGHT",i);
378	if (aisc_create(pd_gl.link,PT_PDC, pdc,
379	PDC_SPECIALS, PT_SPECIALS, &specials,
380	SPECIALS_MODE, root->awar(pdcmode)->read_int(),
381	SPECIALS_LLEFT, (double)root->awar(pdcll)->read_float(),
382	SPECIALS_LEFT, (double)root->awar(pdcl)->read_float(),
383	SPECIALS_CENTER, (double)root->awar(pdcc)->read_float(),
384	SPECIALS_RIGHT, (double)root->awar(pdcr)->read_float(),
385	SPECIALS_RRIGHT, (double)root->awar(pdcrr)->read_float(),
386	NULL)) return 1;
387	}
388	#endif
389	return 0;
390	}
391
392	void probe_design_event(AW_window *aww)
393	{
394	AW_root *root = aww->get_root();
395	T_PT_PDC pdc;
396	T_PT_TPROBE tprobe;
397	bytestring bs;
398	bytestring check;
399	char *match_info;
400	GB_ERROR error = 0;
401
402	aw_openstatus("Probe Design");
403	aw_status("Search a free running server");
404
405	{
406	const char *servername = PD_probe_pt_look_for_server(root, error);
407	if (servername) {
408	pd_gl.link = (aisc_com *)aisc_open(servername, &pd_gl.com,AISC_MAGIC_NUMBER);
409	if (!pd_gl.link) error = "can't contact PT server";
410	}
411	}
412
413	if (!error && init_local_com_struct()) {
414	error = "Cannot contact to probe server: Connection Refused";
415	}
416
417	bool design_gene_probes = root->awar(AWAR_PD_DESIGN_GENE)->read_int();
418	if (design_gene_probes) {
419	GB_transaction ta(GLOBAL_gb_main);
420	if (!GEN_is_genome_db(GLOBAL_gb_main, -1)) design_gene_probes = false;
421	}
422
423	if (!error){
424	if (design_gene_probes) { // design probes for genes
425	error = pd_get_the_gene_names(bs,check);
426	}
427	else {
428	error = pd_get_the_names(bs,check);
429	}
430	}
431
432	if (error){
433	aw_message (error);
434	aw_closestatus();
435	return;
436	}
437
438	aw_status("Start probe design (Cannot be stopped)");
439
440	aisc_create(pd_gl.link,PT_LOCS, pd_gl.locs,
441	LOCS_PROBE_DESIGN_CONFIG, PT_PDC, &pdc,
442	PDC_PROBELENGTH, root->awar(AWAR_PD_DESIGN_PROBELENGTH)->read_int(),
443	PDC_MINTEMP, (double)root->awar(AWAR_PD_DESIGN_MIN_TEMP)->read_float(),
444	PDC_MAXTEMP, (double)root->awar(AWAR_PD_DESIGN_MAX_TEMP)->read_float(),
445	PDC_MINGC, (double)root->awar(AWAR_PD_DESIGN_MIN_GC)->read_float()/100.0,
446	PDC_MAXGC, (double)root->awar(AWAR_PD_DESIGN_MAX_GC)->read_float()/100.0,
447	PDC_MAXBOND, (double)root->awar(AWAR_PD_DESIGN_MAXBOND)->read_int(),
448	NULL);
449	aisc_put(pd_gl.link,PT_PDC, pdc,
450	PDC_MINPOS, root->awar(AWAR_PD_DESIGN_MIN_ECOLIPOS)->read_int(),
451	PDC_MAXPOS, root->awar(AWAR_PD_DESIGN_MAX_ECOLIPOS)->read_int(),
452	PDC_MISHIT, root->awar(AWAR_PD_DESIGN_MISHIT)->read_int(),
453	PDC_MINTARGETS, (double)root->awar(AWAR_PD_DESIGN_MINTARGETS)->read_float()/100.0,
454	NULL);
455
456	if (probe_design_send_data(root,pdc)) {
457	aw_message ("Connection to PT_SERVER lost (1)");
458	aw_closestatus();
459	return;
460	}
461
462	aisc_put(pd_gl.link,PT_PDC, pdc,
463	PDC_NAMES, &bs,
464	PDC_CHECKSUMS, &check,
465	NULL);
466
467
468	/* Get the unknown names */
469	bytestring unknown_names;
470	if (aisc_get(pd_gl.link,PT_PDC, pdc,
471	PDC_UNKNOWN_NAMES, &unknown_names,
472	NULL)){
473	aw_message ("Connection to PT_SERVER lost (1)");
474	aw_closestatus();
475	return;
476	}
477
478	char *unames = unknown_names.data;
479	bool abort = false;
480
481	if (unknown_names.size>1) {
482	if (design_gene_probes) { // updating sequences of missing genes is not possible with gene PT server
483	aw_message(GBS_global_string("Your PT server is not up to date or wrongly chosen.\n"
484	"The following genes are new to it: %s\n"
485	"You'll have to re-build the PT server.", unames));
486	abort = true;
487	}
488	else if (aw_question(GBS_global_string("Your PT server is not up to date or wrongly chosen\n"
489	" The following names are new to it:\n"
490	" %s\n"
491	" This version allows you to quickly add the unknown sequences\n"
492	" to the pt_server\n",
493	unames),
494	"Add and Continue,Abort"))
495	{
496	abort = true;
497	}
498	else {
499	GB_transaction dummy(GLOBAL_gb_main);
500
501	char *h;
502	char *ali_name = GBT_get_default_alignment(GLOBAL_gb_main);
503
504	for (; unames && !abort; unames = h) {
505	h = strchr(unames,'#');
506	if (h) *(h++) = 0;
507	GBDATA *gb_species = GBT_find_species(GLOBAL_gb_main,unames);
508	if (!gb_species) {
509	aw_message(GBS_global_string("Species '%s' not found", unames));
510	abort = true;
511	}
512	else {
513	GBDATA *data = GBT_read_sequence(gb_species,ali_name);
514	if (!data) {
515	aw_message( GB_export_errorf("Species '%s' has no sequence belonging to alignment '%s'", unames, ali_name));
516	abort = true;
517	}
518	else {
519	T_PT_SEQUENCE pts;
520	bytestring bs_seq;
521	bs_seq.data = (char*)GB_read_char_pntr(data);
522	bs_seq.size = GB_read_string_count(data)+1;
523	aisc_create(pd_gl.link, PT_PDC, pdc, PDC_SEQUENCE,
524	PT_SEQUENCE, &pts,
525	SEQUENCE_SEQUENCE, &bs_seq,
526	NULL);
527	}
528	}
529	}
530	}
531	free(unknown_names.data);
532	}
533
534	if (!abort) {
535	aisc_put(pd_gl.link,PT_PDC, pdc,
536	PDC_GO,0,
537	NULL);
538
539	aw_status("Read the results from the server");
540	{
541	char *locs_error = 0;
542	if (aisc_get( pd_gl.link, PT_LOCS, pd_gl.locs, LOCS_ERROR, &locs_error, NULL)) {
543	aw_message ("Connection to PT_SERVER lost (1)");
544	abort = true;
545	}
546	else if (*locs_error) {
547	aw_message(locs_error);
548	abort = true;
549	}
550	else {
551	free(locs_error);
552	}
553	}
554	}
555
556	if (!abort) {
557	aisc_get( pd_gl.link, PT_PDC, pdc,
558	PDC_TPROBE, &tprobe,
559	NULL);
560
561	popup_probe_design_result_window(aww);
562	pd_gl.pd_design->clear_selection_list(pd_gl.pd_design_id);
563
564	if (tprobe) {
565	aisc_get( pd_gl.link, PT_TPROBE, tprobe,
566	TPROBE_INFO_HEADER, &match_info,
567	NULL);
568	char *s = strtok(match_info,"\n");
569	while (s) {
570	pd_gl.pd_design->insert_selection( pd_gl.pd_design_id, s, "" );
571	s = strtok(0,"\n");
572	}
573	free(match_info);
574	}else{
575	pd_gl.pd_design->insert_selection( pd_gl.pd_design_id, "There are no results", "" );
576	}
577
578	//#define TEST_PD
579	#if defined(TEST_PD)
580	int my_TPROBE_KEY;
581	char *my_TPROBE_KEYSTRING;
582	int my_TPROBE_CNT;
583	int my_TPROBE_PARENT;
584	int my_TPROBE_LAST;
585	char *my_TPROBE_IDENT;
586	char *my_TPROBE_SEQUENCE;
587	double my_TPROBE_QUALITY;
588	int my_TPROBE_GROUPSIZE;
589	int my_TPROBE_HAIRPIN;
590	int my_TPROBE_WHAIRPIN;
591	// int my_TPROBE_PERC;
592	double my_TPROBE_TEMPERATURE;
593	int my_TPROBE_MISHIT;
594	int my_TPROBE_APOS;
595	int my_TPROBE_ECOLI_POS;
596
597	#endif // TEST_PD
598
599	while ( tprobe ){
600	long tprobe_next;
601	if (aisc_get( pd_gl.link, PT_TPROBE, tprobe,
602	TPROBE_NEXT, &tprobe_next,
603	TPROBE_INFO, &match_info,
604	#if defined(TEST_PD)
605	TPROBE_KEY, &my_TPROBE_KEY,
606	TPROBE_KEYSTRING, &my_TPROBE_KEYSTRING,
607	TPROBE_CNT, &my_TPROBE_CNT,
608	TPROBE_PARENT, &my_TPROBE_PARENT,
609	TPROBE_LAST, &my_TPROBE_LAST,
610	TPROBE_IDENT, &my_TPROBE_IDENT,
611	TPROBE_SEQUENCE, &my_TPROBE_SEQUENCE, // encoded probe sequence (2=A 3=C 4=G 5=U)
612	TPROBE_QUALITY, &my_TPROBE_QUALITY, // quality of probe ?
613	#endif // TEST_PD
614	NULL)) break;
615
616
617	#if defined(TEST_PD)
618	if (aisc_get( pd_gl.link, PT_TPROBE, tprobe,
619	TPROBE_GROUPSIZE, &my_TPROBE_GROUPSIZE, // groesse der Gruppe, die von Sonde getroffen wird?
620	TPROBE_HAIRPIN, &my_TPROBE_HAIRPIN,
621	TPROBE_WHAIRPIN, &my_TPROBE_WHAIRPIN,
622	// TPROBE_PERC, &my_TPROBE_PERC,
623	TPROBE_TEMPERATURE, &my_TPROBE_TEMPERATURE,
624	TPROBE_MISHIT, &my_TPROBE_MISHIT, // Treffer ausserhalb von Gruppe ?
625	TPROBE_APOS, &my_TPROBE_APOS, // Alignment-Position
626	TPROBE_ECOLI_POS, &my_TPROBE_ECOLI_POS,
627	NULL)) break;
628	#endif // TEST_PD
629	tprobe = tprobe_next;
630
631	char probe,space;
632	probe = strpbrk(match_info,"acgtuACGTU");
633	if (probe) space = strchr(probe,' ');
634	if (probe && space) {
635	space = 0; probe = strdup(probe);space=' ';
636	}else{
637	probe = strdup("");
638	}
639	pd_gl.pd_design->insert_selection( pd_gl.pd_design_id, match_info, probe );
640	free(probe);
641	free(match_info);
642	}
643	pd_gl.pd_design->insert_default_selection( pd_gl.pd_design_id, "default", "" );
644	pd_gl.pd_design->update_selection_list( pd_gl.pd_design_id );
645	}
646
647	aisc_close(pd_gl.link); pd_gl.link = 0;
648	aw_closestatus();
649	return;
650	}
651
652	static bool allow_probe_match_event = true;
653
654	void probe_match_event(AW_window *aww, AW_CL cl_selection_id, AW_CL cl_count_ptr)
655	{
656	if (allow_probe_match_event) {
657	AW_selection_list selection_id = (AW_selection_list)cl_selection_id;
658	int counter = (int)cl_count_ptr;
659	AW_root *root = aww->get_root();
660	T_PT_PDC pdc;
661	int show_status = 0;
662	int extras = 1; // mark species and write to temp fields,
663	GB_ERROR error = 0;
664
665	if (!GLOBAL_gb_main) {
666	error = "No database";
667	}
668
669	if (!error) {
670	const char *servername = PD_probe_pt_look_for_server(root, error);
671
672	if (!error) {
673	if (selection_id) {
674	aww->clear_selection_list(selection_id);
675	pd_assert(!counter);
676	show_status = 1;
677	}
678	else if (counter) {
679	extras = 0;
680	}
681
682	if (show_status) {
683	aw_openstatus("Probe Match");
684	aw_status("Open Connection");
685	}
686
687	pd_gl.link = (aisc_com *)aisc_open(servername, &pd_gl.com,AISC_MAGIC_NUMBER);
688	if (!pd_gl.link) error = "Cannot contact PT-server";
689	}
690	}
691
692	if (!error) {
693	if (show_status) aw_status("Initialize Server");
694	if (init_local_com_struct() ) error = "Cannot contact PT-server (2)";
695
696	if (!error) {
697	aisc_create(pd_gl.link,PT_LOCS, pd_gl.locs, LOCS_PROBE_DESIGN_CONFIG, PT_PDC, &pdc, NULL);
698	if (probe_design_send_data(root,pdc)) error = "Connection to PT_SERVER lost (2)";
699	}
700	}
701
702	char *probe = root->awar(AWAR_TARGET_STRING)->read_string();
703
704	if (!error) {
705	if (show_status) aw_status("Start Probe Match");
706
707	if (aisc_nput(pd_gl.link,PT_LOCS, pd_gl.locs,
708	LOCS_MATCH_REVERSED, root->awar(AWAR_PD_MATCH_COMPLEMENT)->read_int(),
709	LOCS_MATCH_SORT_BY, root->awar(AWAR_PD_MATCH_SORTBY)->read_int(),
710	LOCS_MATCH_COMPLEMENT, 0,
711	LOCS_MATCH_MAX_MISMATCHES, root->awar(AWAR_MAX_MISMATCHES)->read_int(),
712	LOCS_MATCH_MAX_SPECIES, root->awar(AWAR_PD_MATCH_CLIPHITS)->read_int(),
713	LOCS_SEARCHMATCH, probe,
714	NULL))
715	{
716	error = "Connection to PT_SERVER lost (2)";
717	}
718	else {
719	delete(g_spd); // delete previous probe data
720	g_spd = new saiProbeData;
721	transferProbeData(g_spd);
722
723	if (selection_id) {
724	g_spd->setProbeTarget(probe);
725	}
726	}
727	}
728
729	bytestring bs;
730	bs.data = 0;
731
732	long matches_truncated = 0;
733	if (!error) {
734	if (show_status) aw_status("Read the Results");
735
736	T_PT_MATCHLIST match_list;
737	long match_list_cnt = 0;
738	char *locs_error = 0;
739
740	if (aisc_get( pd_gl.link, PT_LOCS, pd_gl.locs,
741	LOCS_MATCH_LIST, &match_list,
742	LOCS_MATCH_LIST_CNT, &match_list_cnt,
743	LOCS_MATCH_STRING, &bs,
744	LOCS_MATCHES_TRUNCATED, &matches_truncated,
745	LOCS_ERROR, &locs_error,
746	NULL))
747	{
748	error = "Connection to PT_SERVER lost (3)";
749	}
750	else {
751	if (locs_error) {
752	if (*locs_error) error = GBS_global_string("%s", locs_error);
753	free(locs_error);
754	}
755	else {
756	error = "Missing status from server (connection aborted?)";
757	}
758	}
759
760	root->awar(AWAR_PD_MATCH_NHITS)->write_string(GBS_global_string(matches_truncated ? "[more than %li]" : "%li", match_list_cnt));
761	if (matches_truncated) {
762	aw_message("Too many matches, displaying a random digest.\n"
763	"ARB 6.0 will be able to configure the limit.");
764	}
765	}
766
767	long mcount = 0;
768	long unknown_species_count = 0;
769	long unknown_gene_count = 0;
770
771	if (!error) {
772	if (show_status) aw_status("Parse the Results");
773
774	char toksep[2] = { 1, 0 };
775	char *strtok_ptr = 0; // stores strtok position
776	const char *hinfo = strtok_r(bs.data,toksep, &strtok_ptr);
777
778	bool gene_flag = false;
779	ProbeMatchParser *parser = 0;
780	char result = (char)malloc(1024);
781
782
783	if (hinfo) {
784	g_spd->setHeadline(hinfo);
785	parser = new ProbeMatchParser(probe, hinfo);
786	error = parser->get_error();
787	if (!error) gene_flag = parser->is_gene_result();
788	}
789
790	if (selection_id) {
791	int width = 0;
792	if (parser && !error) width = parser->get_probe_region_offset()+2+10; // 2 cause headline is shorter and 10 for match prefix region
793
794	const char searched = GBS_global_string("%-s%s", width, "Searched for ", probe);
795	aww->insert_selection( selection_id, searched, probe );
796	if (hinfo) aww->insert_selection( selection_id, hinfo, "" );
797	}
798
799
800	// clear all marks and delete all 'tmp' entries
801
802	int mark = extras && (int)root->awar(AWAR_PD_MATCH_MARKHITS)->read_int();
803	int write_2_tmp = extras && (int)root->awar(AWAR_PD_MATCH_WRITE2TMP)->read_int();
804
805	GB_push_transaction(GLOBAL_gb_main);
806
807	GBDATA *gb_species_data = GB_search(GLOBAL_gb_main,"species_data",GB_CREATE_CONTAINER);
808	if (mark && !error) {
809	if (show_status) aw_status(gene_flag ? "Unmarking all species and genes" : "Unmarking all species");
810	for (GBDATA *gb_species = GBT_first_marked_species_rel_species_data(gb_species_data);
811	gb_species;
812	gb_species = GBT_next_marked_species(gb_species))
813	{
814	GB_write_flag(gb_species,0);
815	}
816
817	if (gene_flag) {
818	// unmark genes of ALL species
819	for (GBDATA *gb_species = GBT_first_species_rel_species_data(gb_species_data);
820	gb_species;
821	gb_species = GBT_next_species(gb_species))
822	{
823	GBDATA *genData = GEN_find_gene_data(gb_species);
824	if (genData) {
825	for (GBDATA *gb_gene = GEN_first_marked_gene(gb_species);
826	gb_gene;
827	gb_gene = GEN_next_marked_gene(gb_gene))
828	{
829	GB_write_flag(gb_gene,0);
830	}
831	}
832	}
833	}
834	}
835	if (write_2_tmp && !error) {
836	if (show_status) aw_status("Deleting old 'tmp' fields");
837	for (GBDATA *gb_species = GBT_first_species_rel_species_data(gb_species_data);
838	gb_species;
839	gb_species = GBT_next_species(gb_species) )
840	{
841	GBDATA *gb_tmp = GB_entry(gb_species,"tmp");
842	if (gb_tmp) GB_delete(gb_tmp);
843	if (gene_flag) {
844	for (GBDATA *gb_gene = GEN_first_gene(gb_species);
845	gb_gene;
846	gb_gene = GEN_next_gene(gb_species))
847	{
848	gb_tmp = GB_entry(gb_gene, "tmp");
849	if (gb_tmp) GB_delete(gb_tmp);
850	}
851	}
852	}
853	}
854
855	// read results from pt-server :
856
857	if (!error) {
858	if (show_status) aw_status("Parsing results..");
859
860	g_spd->probeSpecies.clear();
861	g_spd->probeSeq.clear();
862
863	if (gene_flag) {
864	if (!GEN_is_genome_db(GLOBAL_gb_main, -1)) {
865	error = "Wrong PT-Server chosen (selected one is built for genes)";
866	}
867	}
868	}
869
870	const char *match_name = 0;
871	while (hinfo && !error && (match_name = strtok_r(0,toksep, &strtok_ptr)) ) {
872	const char *match_info = strtok_r(0,toksep, &strtok_ptr);
873	if (!match_info) break;
874
875	pd_assert(parser);
876	ParsedProbeMatch ppm(match_info, *parser);
877	char *gene_str = 0;
878
879	if (gene_flag) {
880	gene_str = ppm.get_column_content("genename", true);
881
882	// #error change parse method for gene name
883	// // parse the gene name:
884	// int off = 0;
885	// while (match_info[off] == ' ') ++off; // search first non-space ( = start of species name)
886	// char *space1 = strchr(match_info+off, ' '); // space between species and gene name
887	// char *space2 = 0;
888	// if (space1) space2 = strchr(space1+1, ' '); // space after gene name
889	// if (space1 && space2) { // ok - parsing sucessful
890	// int len = space2-space1-1;
891	// // delete [] gene_str;
892	// gene_str = new char[len+1];
893	// memcpy(gene_str, space1+1, len);
894	// gene_str[len] = 0;
895	// }
896	// else {
897	// error = "cannot parse gene name from match result";
898	// }
899	}
900
901	if (!error) {
902	char flags[] = "xx";
903	GBDATA *gb_species = GBT_find_species_rel_species_data(gb_species_data, match_name);
904
905	if (gb_species) {
906	GBDATA *gb_gene = 0;
907	if (gene_flag && strncmp(gene_str,"intergene_", 10) != 0) { // real gene
908	gb_gene = GEN_find_gene(gb_species,gene_str);
909	if (!gb_gene) {
910	aw_message(GBS_global_string("Gene '%s' not found in organism '%s'", gene_str, match_name));
911	}
912	}
913
914	if (mark) {
915	GB_write_flag(gb_species, 1);
916	flags[0] = '*';
917	if (gb_gene) {
918	GB_write_flag(gb_gene, 1);
919	flags[1] = '*';
920	}
921	else {
922	flags[1] = '?'; // no gene
923	}
924	}
925	else {
926	flags[0] = " *"[GB_read_flag(gb_species)];
927	flags[1] = " *?"[gb_gene ? GB_read_flag(gb_gene) : 2];
928	}
929
930	if (write_2_tmp) {
931	GBDATA *gb_tmp = 0;
932	GB_ERROR error2 = 0;
933	{
934	GBDATA *gb_parent = gene_flag ? gb_gene : gb_species;
935	gb_tmp = GB_search(gb_parent, "tmp", GB_FIND);
936	if (gb_tmp) {
937	const char *name = "<unknown>";
938	GBDATA *gb_name = GB_search(gb_parent, "name", GB_FIND);
939	if (gb_name) name = GB_read_char_pntr(gb_name);
940	error2 = GBS_global_string("field 'tmp' already exists for %s '%s'", gene_flag ? "gene" : "species", name);
941	gb_tmp = 0; // don't overwrite
942	}
943	else {
944	gb_tmp = GB_search(gb_species, "tmp", GB_STRING);
945	}
946	}
947
948	if (!error2) {
949	pd_assert(gb_tmp);
950	error2 = GB_write_string(gb_tmp, match_info);
951	}
952
953	if (error2) aw_message(error2);
954	}
955	}
956	else {
957	flags[0] = flags[1] = '?'; // species does not exist
958	unknown_species_count++;
959	}
960
961
962	if (gene_flag) {
963	sprintf(result, "%s %s", flags, match_info+1); // both flags (skip 1 space from match info to keep alignment)
964	char *gene_match_name = new char[strlen(match_name) + strlen(gene_str)+2];
965	sprintf(gene_match_name,"%s/%s",match_name,gene_str);
966	if (selection_id) aww->insert_selection( selection_id, result, gene_match_name ); // @@@ wert fuer awar eintragen
967	}
968	else {
969	sprintf(result, "%c %s", flags[0], match_info); // only first flag ( = species related)
970	if (selection_id) aww->insert_selection( selection_id, result, match_name ); // @@@ wert fuer awar eintragen
971
972	if (selection_id) { // storing probe data into linked lists
973	g_spd->probeSeq.push_back(strdup(match_info));
974	g_spd->probeSpecies.push_back(strdup(match_name));
975	}
976	}
977	mcount++;
978	}
979
980	free(gene_str);
981	}
982
983	if (error) error = GBS_global_string("%s", error); // make static copy (error may be free'd by delete parser)
984	delete parser;
985	free(result);
986
987	GB_pop_transaction(GLOBAL_gb_main);
988	}
989
990	if (error) {
991	root->awar(AWAR_PD_MATCH_NHITS)->write_string("0"); // clear hits
992	aw_message(error);
993	}
994	else {
995	if (unknown_species_count>0) {
996	aw_message(GBS_global_string("%li matches hit unknown species -- PT-server is out-of-date or build upon a different database", unknown_species_count));
997	}
998	if (unknown_gene_count>0) {
999	aw_message(GBS_global_string("%li matches hit unknown genes -- PT-server is out-of-date or build upon a different database", unknown_gene_count));
1000	}
1001
1002	if (selection_id) { // if !selection_id then probe match window is not opened
1003	pd_assert(g_spd);
1004	root->awar(AWAR_SPV_DB_FIELD_NAME)->touch(); // force refresh of SAI/Probe window
1005	}
1006	}
1007
1008	if (counter) *counter = mcount;
1009
1010	aisc_close(pd_gl.link);
1011	pd_gl.link = 0;
1012
1013	if (selection_id) {
1014	const char *last_line = 0;
1015	if (error) last_line = GBS_global_string("**** Error: %s *****", error);
1016	else if (matches_truncated) last_line = "**** List is truncated *****";
1017	else last_line = "**** End of List *****";
1018
1019	aww->insert_default_selection( selection_id, last_line, "" );
1020
1021	if (show_status) aw_status("Formatting output");
1022	aww->update_selection_list( selection_id );
1023	}
1024
1025	if (show_status) aw_closestatus();
1026
1027	free(bs.data);
1028	free(probe);
1029
1030	allow_probe_match_event = false;
1031	root->awar(AWAR_TREE_REFRESH)->touch();
1032	allow_probe_match_event = true;
1033	}
1034
1035	return;
1036	}
1037
1038	void probe_match_all_event(AW_window *aww, AW_CL cl_iselection_id) {
1039	auto_match_cb_settings.disable = true;
1040
1041	AW_selection_list iselection_id = (AW_selection_list)cl_iselection_id;
1042	AW_root *root = aww->get_root();
1043	char *target_string = root->awar(AWAR_TARGET_STRING)->read_string();
1044
1045	aww->init_list_entry_iterator(iselection_id); // init
1046	aw_openstatus("Matching all resolved strings");
1047
1048	int string_count = aww->get_no_of_entries(iselection_id);
1049	int local_count = 0;
1050
1051	for (;;) {
1052	const char *entry = aww->get_list_entry_char_value();
1053	if (!entry) break;
1054
1055	double percent = local_count++/double(string_count);
1056	aw_status(GBS_global_string("Match string %i of %i", local_count, string_count));
1057	aw_status(percent);
1058
1059	root->awar(AWAR_TARGET_STRING)->write_string(entry); // probe match
1060	int counter = -1;
1061	probe_match_event(aww, AW_CL(0), AW_CL(&counter));
1062	if (counter==-1) break;
1063
1064	char *buffer = new char[strlen(entry)+10]; // write # of matched to list entries
1065	sprintf(buffer, "%5i %s", counter, entry);
1066	aww->set_list_entry_displayed(buffer);
1067	delete buffer;
1068
1069	aww->iterate_list_entry(1); // iterate
1070	}
1071
1072	aw_closestatus();
1073
1074	if (local_count) {
1075	aww->sort_selection_list(iselection_id, 1, 1);
1076	aww->update_selection_list(iselection_id);
1077	root->awar(AWAR_TARGET_STRING)->write_string(target_string);
1078	}
1079
1080	auto_match_cb_settings.disable = false;
1081	}
1082
1083	static void resolved_probe_chosen(AW_root *root) {
1084	char *string = root->awar(AWAR_PD_MATCH_RESOLVE)->read_string();
1085	root->awar(AWAR_TARGET_STRING)->write_string(string);
1086	}
1087
1088	static void selected_match_changed_cb(AW_root *root) {
1089	// this gets called when ever the selected probe match changes
1090	char *temp;
1091	char *selected_match = root->awar(AWAR_PD_SELECTED_MATCH)->read_string();
1092
1093	if (strchr(selected_match, '/')) { // "organism/gene"
1094	temp = strtok(selected_match,"/");
1095	root->awar(AWAR_SPECIES_NAME)->write_string(temp);
1096	temp = strtok(NULL," /\n");
1097	root->awar(AWAR_GENE_NAME)->write_string(temp);
1098	}
1099	else {
1100	root->awar(AWAR_SPECIES_NAME)->write_string(selected_match);
1101	}
1102
1103	{
1104	bool prev = allow_probe_match_event;
1105	allow_probe_match_event = false; // avoid recursion
1106	root->awar(AWAR_TARGET_STRING)->touch(); // forces editor to jump to probe match in gene
1107	allow_probe_match_event = prev;
1108	}
1109
1110	free(selected_match);
1111	}
1112
1113	void create_probe_design_variables(AW_root *root,AW_default db1, AW_default global)
1114	{
1115	char buffer[256]; memset(buffer,0,256);
1116	int i;
1117	pd_gl.pd_design = 0; /* design result window not created */
1118	root->awar_string(AWAR_SPECIES_NAME, "", db1);
1119	root->awar_string(AWAR_PD_SELECTED_MATCH, "", db1)->add_callback(selected_match_changed_cb);
1120	root->awar_float (AWAR_PD_DESIGN_EXP_DTEDGE, .5, db1);
1121	root->awar_float (AWAR_PD_DESIGN_EXP_DT, .5, db1);
1122
1123
1124	double default_bonds[16] = {
1125	0.0, 0.0, 0.5, 1.1,
1126	0.0, 0.0, 1.5, 0.0,
1127	0.5, 1.5, 0.4, 0.9,
1128	1.1, 0.0, 0.9, 0.0
1129	};
1130
1131	for (i=0;i<16;i++) {
1132	sprintf(buffer,AWAR_PD_DESIGN_EXP_BONDS "%i",i);
1133	root->awar_float( buffer, default_bonds[i], db1);
1134	root->awar(buffer)->set_minmax(0,3.0);
1135	}
1136	#if 0
1137	for (i=0;i<PROBE_DESIGN_EXCEPTION_MAX;i++){
1138	sprintf(buffer, "probe_design/exceptions/nr%i/MODE", i); root->awar_int (buffer, -1, db1);
1139	sprintf(buffer, "probe_design/exceptions/nr%i/LLEFT", i); root->awar_float(buffer, 0.0, db1);
1140	sprintf(buffer, "probe_design/exceptions/nr%i/LEFT", i); root->awar_float(buffer, 0.0, db1);
1141	sprintf(buffer, "probe_design/exceptions/nr%i/CENTER", i); root->awar_float(buffer, 0.0, db1);
1142	sprintf(buffer, "probe_design/exceptions/nr%i/RIGHT", i); root->awar_float(buffer, 0.0, db1);
1143	sprintf(buffer, "probe_design/exceptions/nr%i/RRIGHT", i); root->awar_float(buffer, 0.0, db1);
1144	}
1145	#endif
1146	root->awar_float(AWAR_PD_DESIGN_EXP_SPLIT, .5, db1);
1147	root->awar_float(AWAR_PD_DESIGN_EXP_DTEDGE, .5, db1);
1148	root->awar_float(AWAR_PD_DESIGN_EXP_DT, .5, db1);
1149
1150	root->awar_int (AWAR_PD_DESIGN_CLIPRESULT, 50, db1)->set_minmax(0, 1000 );
1151	root->awar_int (AWAR_PD_DESIGN_MISHIT, 0, db1)->set_minmax(0, 100000);
1152	root->awar_int (AWAR_PD_DESIGN_MAXBOND, 4, db1)->set_minmax(0, 20 );
1153	root->awar_float(AWAR_PD_DESIGN_MINTARGETS, 50.0, db1)->set_minmax(0, 100 );
1154
1155	root->awar_int (AWAR_PD_DESIGN_PROBELENGTH, 18, db1)->set_minmax(10, 100 );
1156	root->awar_float(AWAR_PD_DESIGN_MIN_TEMP, 50.0, db1)->set_minmax(0, 1000 );
1157	root->awar_float(AWAR_PD_DESIGN_MAX_TEMP, 100.0, db1)->set_minmax(0, 1000 );
1158	root->awar_float(AWAR_PD_DESIGN_MIN_GC, 50.0, db1)->set_minmax(0, 100 );
1159	root->awar_float(AWAR_PD_DESIGN_MAX_GC, 100.0, db1)->set_minmax(0, 100 );
1160	root->awar_int (AWAR_PD_DESIGN_MIN_ECOLIPOS, 0, db1)->set_minmax(0, 1000000);
1161	root->awar_int (AWAR_PD_DESIGN_MAX_ECOLIPOS, 100000, db1)->set_minmax(0, 1000000);
1162
1163	root->awar_int(AWAR_PT_SERVER, 0, db1);
1164	root->awar_int(AWAR_PD_DESIGN_GENE, 0, db1);
1165
1166	root->awar_int (AWAR_PD_MATCH_MARKHITS, 1, db1 );
1167	root->awar_int (AWAR_PD_MATCH_SORTBY, 0, db1 );
1168	root->awar_int (AWAR_PD_MATCH_WRITE2TMP, 0, db1 );
1169	root->awar_int (AWAR_PD_MATCH_COMPLEMENT, 0, db1 );
1170	root->awar_int (AWAR_MIN_MISMATCHES, 0, global);
1171	root->awar_int (AWAR_MAX_MISMATCHES, 0, global);
1172	root->awar_int (AWAR_PD_MATCH_CLIPHITS, 1000, db1 );
1173	root->awar_string(AWAR_TARGET_STRING, "", global);
1174	root->awar_string(AWAR_PD_MATCH_NHITS, 0, db1 );
1175	root->awar_int (AWAR_PD_MATCH_AUTOMATCH, 0, db1 )->add_callback(auto_match_changed);
1176
1177	root->awar_string(AWAR_PD_MATCH_RESOLVE, "", db1)->add_callback(resolved_probe_chosen);
1178	root->awar_string(AWAR_ITARGET_STRING, "", global);
1179
1180	root->awar_int (AWAR_PROBE_ADMIN_PT_SERVER, 0, db1 );
1181	root->awar_int (AWAR_PROBE_CREATE_GENE_SERVER, 0, db1 );
1182
1183	root->awar_string(AWAR_SPV_SAI_2_PROBE, "", global); // name of SAI selected in list
1184	root->awar_string(AWAR_SPV_DB_FIELD_NAME, "name", global); // name of displayed species field
1185	root->awar_int (AWAR_SPV_DB_FIELD_WIDTH, 10, global); // width of displayed species field
1186	root->awar_string(AWAR_SPV_ACI_COMMAND, "", global); // User defined or pre-defined ACI command to display
1187	root->awar_string(AWAR_SPV_SELECTED_PROBE, "", global); // For highlighting the selected PROBE
1188	}
1189
1190	AW_window create_probe_design_expert_window( AW_root root) {
1191	int i;
1192	char buffer[256];
1193	AW_window_simple *aws = new AW_window_simple;
1194	aws->init( root, "PD_EXPERT","PD-SPECIALS");
1195
1196	aws->load_xfig("pd_spec.fig");
1197	aws->label_length(30);
1198	aws->button_length(10);
1199
1200	aws->callback( (AW_CB0)AW_POPDOWN);
1201	aws->at("close");
1202	aws->create_button("CLOSE","CLOSE","C");
1203
1204	aws->callback( AW_POPUP_HELP, (AW_CL)"pd_spec_param.hlp");
1205	aws->at("help");
1206	aws->create_button("HELP","HELP","C");
1207
1208	aws->at("dt");
1209	aws->create_input_field(AWAR_PD_DESIGN_EXP_DT,6);
1210
1211	aws->at("dt_edge");
1212	aws->create_input_field(AWAR_PD_DESIGN_EXP_DTEDGE,6);
1213
1214	aws->at("split");
1215	aws->create_input_field(AWAR_PD_DESIGN_EXP_SPLIT,6);
1216
1217
1218	for (i=0;i<16;i++) {
1219	sprintf(buffer,"%i",i);
1220	aws->at(buffer);
1221	sprintf(buffer,AWAR_PD_DESIGN_EXP_BONDS "%i",i);
1222	aws->create_input_field(buffer,4);
1223	}
1224
1225	#if 0
1226	for (i=0;i<PROBE_DESIGN_EXCEPTION_MAX;i++) {
1227	sprintf(buffer,"m%i",i);
1228	aws->at(buffer);
1229	sprintf(buffer,"probe_design/exceptions/nr%i/MODE",i);
1230	aws->create_option_menu( buffer, NULL , "" );
1231	aws->insert_option( "don't use", "d", -1 );
1232	aws->insert_option( "don't split", "d", 0 );
1233	aws->insert_option( "split", "d", 1 );
1234	aws->update_option_menu();
1235
1236	sprintf(buffer,"ll%i",i);
1237	aws->at(buffer);
1238	sprintf(buffer,"probe_design/exceptions/nr%i/LLEFT",i);
1239	aws->create_input_field(buffer,4);
1240
1241	sprintf(buffer,"l%i",i);
1242	aws->at(buffer);
1243	sprintf(buffer,"probe_design/exceptions/nr%i/LEFT",i);
1244	aws->create_input_field(buffer,5);
1245
1246	sprintf(buffer,"c%i",i);
1247	aws->at(buffer);
1248	sprintf(buffer,"probe_design/exceptions/nr%i/CENTER",i);
1249	aws->create_input_field(buffer,5);
1250
1251	sprintf(buffer,"r%i",i);
1252	aws->at(buffer);
1253	sprintf(buffer,"probe_design/exceptions/nr%i/RIGHT",i);
1254	aws->create_input_field(buffer,5);
1255
1256	sprintf(buffer,"rr%i",i);
1257	aws->at(buffer);
1258	sprintf(buffer,"probe_design/exceptions/nr%i/RRIGHT",i);
1259	aws->create_input_field(buffer,5);
1260	}
1261	#endif
1262	return aws;
1263	}
1264
1265	static AWT_config_mapping_def probe_design_mapping_def[] = {
1266	{ AWAR_PD_DESIGN_CLIPRESULT, "clip" },
1267	{ AWAR_PD_DESIGN_MISHIT, "mishit" },
1268	{ AWAR_PD_DESIGN_MAXBOND, "maxbond" },
1269	{ AWAR_PD_DESIGN_MINTARGETS, "mintarget"},
1270	{ AWAR_PD_DESIGN_PROBELENGTH, "probelen" },
1271	{ AWAR_PD_DESIGN_MIN_TEMP, "mintemp" },
1272	{ AWAR_PD_DESIGN_MAX_TEMP, "maxtemp" },
1273	{ AWAR_PD_DESIGN_MIN_GC, "mingc" },
1274	{ AWAR_PD_DESIGN_MAX_GC, "maxgc" },
1275	{ AWAR_PD_DESIGN_MIN_ECOLIPOS, "minecoli" },
1276	{ AWAR_PD_DESIGN_MAX_ECOLIPOS, "maxecoli" },
1277	{ AWAR_PD_DESIGN_GENE, "gene" },
1278	{ AWAR_PD_DESIGN_EXP_SPLIT, "split" },
1279	{ AWAR_PD_DESIGN_EXP_DTEDGE, "dtedge" },
1280	{ AWAR_PD_DESIGN_EXP_DT, "dt" },
1281	{ 0, 0 }
1282	};
1283
1284	static void probe_design_init_config(AWT_config_definition& cdef) {
1285	cdef.add(probe_design_mapping_def);
1286	for (int i = 0; i<16; ++i) {
1287	cdef.add(GBS_global_string(AWAR_PD_DESIGN_EXP_BONDS "%i", i), "bond", i);
1288	}
1289	}
1290
1291	static char probe_design_store_config(AW_window aww, AW_CL, AW_CL) {
1292	AWT_config_definition cdef(aww->get_root());
1293	probe_design_init_config(cdef);
1294	return cdef.read();
1295	}
1296	static void probe_design_restore_config(AW_window aww, const char stored_string, AW_CL, AW_CL) {
1297	AWT_config_definition cdef(aww->get_root());
1298	probe_design_init_config(cdef);
1299	cdef.write(stored_string);
1300	}
1301
1302	void probe_design_save_default(AW_window *aw,AW_default aw_def)
1303	{
1304	AW_root *aw_root = aw->get_root();
1305	aw_root->save_default(aw_def,0);
1306	}
1307
1308
1309	AW_window create_probe_design_window( AW_root root, AW_CL cl_genome_db) {
1310	AW_window_simple *aws = new AW_window_simple;
1311	int is_genom_db = (int)cl_genome_db;
1312
1313	aws->init( root, "PROBE_DESIGN","PROBE DESIGN");
1314
1315	aws->load_xfig("pd_main.fig");
1316
1317	aws->callback( (AW_CB0)AW_POPDOWN);
1318	aws->at("close");
1319	aws->create_button("CLOSE","CLOSE","C");
1320
1321	aws->at("help");
1322	aws->callback(AW_POPUP_HELP,(AW_CL)"probedesign.hlp");
1323	aws->create_button("HELP","HELP","H");
1324
1325	aws->callback( probe_design_event);
1326	aws->at("design");
1327	aws->highlight();
1328	aws->create_button("GO","GO","G");
1329
1330	// aws->callback( (AW_CB1)AW_save_defaults, (int) def);
1331	// aws->at("save_default");
1332	// aws->create_button("SAVE DEFAULTS","S");
1333
1334	aws->callback(popup_probe_design_result_window);
1335	aws->at("result");
1336	aws->create_button("RESULT","RESULT","S");
1337
1338	// aws->callback( AW_POPUP, (AW_CL)create_probe_design_window, (int)def);
1339	// aws->at("open");
1340	// aws->create_button("REOPEN","REOPEN","S");
1341
1342	aws->callback( (AW_CB1)AW_POPUP,(AW_CL)create_probe_design_expert_window);
1343	aws->at("expert");
1344	aws->create_button("EXPERT","EXPERT","S");
1345
1346	aws->at( "pt_server" );
1347	aws->label("PT-Server:");
1348	awt_create_selection_list_on_pt_servers(aws,AWAR_PT_SERVER,true);
1349
1350	aws->at("lenout" ); aws->create_input_field(AWAR_PD_DESIGN_CLIPRESULT, 6);
1351	aws->at("mishit" ); aws->create_input_field(AWAR_PD_DESIGN_MISHIT, 6);
1352	aws->sens_mask(AWM_EXP);
1353	aws->at("maxbonds"); aws->create_input_field(AWAR_PD_DESIGN_MAXBOND, 6);
1354	aws->sens_mask(AWM_ALL);
1355	aws->at("minhits" ); aws->create_input_field(AWAR_PD_DESIGN_MINTARGETS, 6);
1356
1357	aws->at("minlen"); aws->create_input_field(AWAR_PD_DESIGN_PROBELENGTH, 5);
1358	aws->at("mint" ); aws->create_input_field(AWAR_PD_DESIGN_MIN_TEMP, 5);
1359	aws->at("maxt" ); aws->create_input_field(AWAR_PD_DESIGN_MAX_TEMP, 5);
1360	aws->at("mingc" ); aws->create_input_field(AWAR_PD_DESIGN_MIN_GC, 5);
1361	aws->at("maxgc" ); aws->create_input_field(AWAR_PD_DESIGN_MAX_GC, 5);
1362	aws->at("minpos"); aws->create_input_field(AWAR_PD_DESIGN_MIN_ECOLIPOS, 5);
1363	aws->at("maxpos"); aws->create_input_field(AWAR_PD_DESIGN_MAX_ECOLIPOS, 5);
1364
1365	if (is_genom_db) {
1366	aws->at("gene");
1367	aws->label("Gene probes?");
1368	aws->create_toggle(AWAR_PD_DESIGN_GENE);
1369	}
1370
1371	aws->at("save");
1372	AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "probe_design", probe_design_store_config, probe_design_restore_config, 0, 0);
1373
1374	return aws;
1375	}
1376
1377	void print_event( AW_window *aww, AW_CL selection_id, AW_CL name ) {
1378	char filename = (char )name;
1379	aww->save_selection_list( (AW_selection_list *)selection_id, filename );
1380	}
1381
1382	// -------------------------------------------------------------------
1383
1384
1385	inline void my_strupr(char *s) {
1386	pd_assert(s);
1387	for (int i=0; s[i]; i++) {
1388	s[i] = toupper(s[i]);
1389	}
1390	}
1391
1392	static GB_alignment_type ali_used_for_resolvement = GB_AT_UNKNOWN;
1393
1394	static void resolve_IUPAC_target_string(AW_root *, AW_CL cl_aww, AW_CL cl_selid) {
1395	AW_window aww = (AW_window)cl_aww;
1396	AW_selection_list selection_id = (AW_selection_list)cl_selid;
1397
1398	aww->clear_selection_list(selection_id);
1399
1400	if (ali_used_for_resolvement != GB_AT_RNA && ali_used_for_resolvement!=GB_AT_DNA) {
1401	aww->insert_default_selection(selection_id, "Wrong alignment type!", "");
1402	aww->update_selection_list(selection_id);
1403	return;
1404	}
1405
1406	int index = ali_used_for_resolvement==GB_AT_RNA ? 1 : 0;
1407	AW_root *root = aww->get_root();
1408	char *istring = root->awar(AWAR_ITARGET_STRING)->read_string();
1409	GB_ERROR err = 0;
1410
1411	if (istring && istring[0]) { // contains sth?
1412	my_strupr(istring);
1413
1414	int bases_to_resolve = 0;
1415	char *istr = istring;
1416	int istring_length = strlen(istring);
1417
1418	for (;;) {
1419	char i = *istr++;
1420	if (!i) break;
1421	if (i=='?') continue; // ignore '?'
1422
1423	int idx = i-'A';
1424	if (idx<0 \|\| idx>=26 \|\| AWT_iupac_code[idx][index].iupac==0) {
1425	err = GB_export_errorf("Illegal character '%c' in IUPAC-String", i);
1426	break;
1427	}
1428
1429	if (AWT_iupac_code[idx][index].count>1) {
1430	bases_to_resolve++;
1431	}
1432	}
1433
1434	if (!err) {
1435	int *offsets_to_resolve = new int[bases_to_resolve];
1436	int resolutions = 1;
1437	{
1438	istr = istring;
1439	int offset = 0;
1440	int offset_count = 0;
1441	for (;;) {
1442	char i = *istr++;
1443	if (!i) break;
1444
1445	if (i!='?') {
1446	int idx = AWT_iupac2index(i);
1447	pd_assert(AWT_iupac_code[idx][index].iupac);
1448
1449	if (AWT_iupac_code[idx][index].count>1) {
1450	offsets_to_resolve[offset_count++] = offset; // store string offsets of non-unique base-codes
1451	resolutions *= AWT_iupac_code[idx][index].count; // calc # of resolutions
1452	}
1453	}
1454	offset++;
1455	}
1456	}
1457
1458	int cont = 1;
1459	if (resolutions>5000) {
1460	const char *warning = GBS_global_string("Resolution of this string will result in %i single strings", resolutions);
1461	cont = aw_question(warning, "Abort,Continue");
1462	}
1463
1464	if (cont) { // continue with resolution?
1465	int *resolution_idx = new int[bases_to_resolve];
1466	int *resolution_max_idx = new int[bases_to_resolve];
1467	{
1468	int i;
1469	for (i=0; i<bases_to_resolve; i++) {
1470	resolution_idx[i] = 0;
1471	int idx = AWT_iupac2index(istring[offsets_to_resolve[i]]);
1472	resolution_max_idx[i] = AWT_iupac_code[idx][index].count-1;
1473	}
1474	}
1475
1476	char *buffer = new char[istring_length+1];
1477	int not_last = resolutions-1;
1478
1479	for (;;) {
1480	// create string according to resolution_idx[]:
1481	int i;
1482
1483	memcpy(buffer, istring, istring_length+1);
1484	for (i=0; i<bases_to_resolve; i++) {
1485	int off = offsets_to_resolve[i];
1486	int idx = AWT_iupac2index(istring[off]);
1487
1488	pd_assert(AWT_iupac_code[idx][index].iupac);
1489	buffer[off] = AWT_iupac_code[idx][index].iupac[resolution_idx[i]];
1490	}
1491
1492	/if (not_last) / aww->insert_selection (selection_id, buffer, buffer);
1493	/else aww->insert_default_selection(selection_id, buffer, buffer); /
1494	not_last--;
1495
1496	// permutatate indices:
1497	int nidx = bases_to_resolve-1;
1498	int done = 0;
1499	while (!done && nidx>=0) {
1500	if (resolution_idx[nidx]<resolution_max_idx[nidx]) {
1501	resolution_idx[nidx]++;
1502	done = 1;
1503	break;
1504	}
1505	nidx--;
1506	}
1507	if (!done) break; // we did all permutations!
1508
1509	nidx++; // do not touch latest incremented index
1510	while (nidx<bases_to_resolve) resolution_idx[nidx++] = 0; // zero all other indices
1511	}
1512
1513	delete buffer;
1514	delete resolution_max_idx;
1515	delete resolution_idx;
1516
1517	aww->insert_default_selection(selection_id, "", "");
1518	aww->update_selection_list(selection_id);
1519	}
1520
1521	delete offsets_to_resolve;
1522	}
1523	}
1524
1525	if (err) {
1526	aw_message(err);
1527	}
1528	}
1529
1530	enum ModMode { TS_MOD_CLEAR, TS_MOD_REV_COMPL, TS_MOD_COMPL };
1531
1532	static void modify_target_string(AW_window *aww, AW_CL cl_mod_mode) {
1533	ModMode mod_mode = ModMode(cl_mod_mode);
1534	AW_root *root = aww->get_root();
1535	char *target_string = root->awar(AWAR_TARGET_STRING)->read_string();
1536	GB_ERROR error = 0;
1537
1538	if (mod_mode == TS_MOD_CLEAR) target_string[0] = 0;
1539	else {
1540	GB_transaction dummy(GLOBAL_gb_main);
1541	GB_alignment_type ali_type = GBT_get_alignment_type(GLOBAL_gb_main, GBT_get_default_alignment(GLOBAL_gb_main));
1542	if (mod_mode == TS_MOD_REV_COMPL) {
1543	char T_or_U;
1544	error = GBT_determine_T_or_U(ali_type, &T_or_U, "reverse-complement");
1545	if (!error) GBT_reverseComplementNucSequence(target_string, strlen(target_string), T_or_U);
1546	}
1547	else if (mod_mode == TS_MOD_COMPL) {
1548	char T_or_U;
1549	error = GBT_determine_T_or_U(ali_type, &T_or_U, "complement");
1550	if (!error) freeset(target_string, GBT_complementNucSequence(target_string, strlen(target_string), T_or_U));
1551	}
1552	}
1553
1554	if (error) aw_message(error);
1555	else root->awar(AWAR_TARGET_STRING)->write_string(target_string);
1556	free(target_string);
1557	}
1558
1559	AW_window create_IUPAC_resolve_window(AW_root root) {
1560	AW_window_simple *aws = new AW_window_simple;
1561	aws->init( root, "PROBE_MATCH_RESOLVE_IUPAC","Resolve IUPAC for Probe Match");
1562	aws->load_xfig("pd_match_iupac.fig");
1563
1564	aws->callback( (AW_CB0)AW_POPDOWN);
1565	aws->at("close");
1566	aws->create_button("CLOSE","CLOSE","C");
1567
1568	aws->callback( AW_POPUP_HELP, (AW_CL)"pd_match_iupac.hlp");
1569	aws->at("help");
1570	aws->create_button("HELP","HELP","C");
1571
1572	AW_selection_list *iselection_id;
1573	aws->at( "iresult" );
1574	iselection_id = aws->create_selection_list( AWAR_PD_MATCH_RESOLVE, NULL, "", 32, 15 );
1575	aws->insert_default_selection( iselection_id, "---empty---", "" );
1576
1577	aws->at("istring");
1578	aws->create_input_field(AWAR_ITARGET_STRING,32);
1579
1580	// automatically resolve AWAR_ITARGET_STRING:
1581	{
1582	GB_transaction dummy(GLOBAL_gb_main);
1583	ali_used_for_resolvement = GBT_get_alignment_type(GLOBAL_gb_main, GBT_get_default_alignment(GLOBAL_gb_main));
1584	}
1585	root->awar(AWAR_ITARGET_STRING)->add_callback(resolve_IUPAC_target_string, AW_CL(aws), AW_CL(iselection_id));
1586
1587	aws->callback(probe_match_all_event, (AW_CL)iselection_id);
1588	aws->at("match_all");
1589	aws->create_button("MATCH_ALL", "MATCH ALL", "A");
1590
1591	return aws;
1592	}
1593
1594	static void popupSaiProbeMatchWindow(AW_window *aw) {
1595	static AW_window *aw_saiProbeMatch = 0;
1596
1597	if (!aw_saiProbeMatch) aw_saiProbeMatch = createSaiProbeMatchWindow(aw->get_root());
1598	if(g_spd) transferProbeData(g_spd); //transferring probe data to saiProbeMatch function
1599
1600	aw_saiProbeMatch->activate();
1601	}
1602
1603	AW_window create_probe_match_window( AW_root root,AW_default) {
1604	static AW_window_simple *aws = 0; // the one and only probe match window
1605	if (aws) return aws;
1606
1607	aws = new AW_window_simple;
1608
1609	aws->init( root, "PROBE_MATCH", "PROBE MATCH");
1610
1611	aws->load_xfig("pd_match.fig");
1612
1613	aws->callback( (AW_CB0)AW_POPDOWN);
1614	aws->at("close");
1615	aws->create_button("CLOSE","CLOSE","C");
1616
1617	aws->callback( AW_POPUP_HELP,(AW_CL)"probematch.hlp");
1618	aws->at("help");
1619	aws->create_button("HELP","HELP","H");
1620
1621	aws->at("string");
1622	aws->create_input_field(AWAR_TARGET_STRING,32);
1623
1624	AW_selection_list *selection_id;
1625	aws->at( "result" );
1626	selection_id = aws->create_selection_list( AWAR_PD_SELECTED_MATCH, NULL, "", 110, 15 );
1627	aws->insert_default_selection( selection_id, "**** No results yet *****", "" ); // if list is empty -> crashed if new species was selected in ARB_EDIT4
1628
1629	aws->callback( create_print_box_for_selection_lists, (AW_CL)selection_id );
1630	aws->at("print");
1631	aws->create_button("PRINT","PRINT","P");
1632
1633	aws->at("matchSai");
1634	aws->callback(popupSaiProbeMatchWindow);
1635	aws->create_button("MATCH_SAI","Match SAI","S");
1636
1637	aws->callback( (AW_CB1)AW_POPUP,(AW_CL)create_probe_design_expert_window);
1638	aws->at("expert");
1639	aws->create_button("EXPERT","EXPERT","X");
1640
1641	aws->at( "pt_server" );
1642	awt_create_selection_list_on_pt_servers(aws,AWAR_PT_SERVER,true);
1643
1644	aws->at( "complement" );
1645	aws->create_toggle( AWAR_PD_MATCH_COMPLEMENT );
1646
1647	aws->at( "mark" );
1648	aws->create_toggle( AWAR_PD_MATCH_MARKHITS );
1649
1650	aws->at( "weighted" );
1651	aws->create_toggle( AWAR_PD_MATCH_SORTBY );
1652
1653	aws->at( "mismatches" );
1654	aws->create_option_menu(AWAR_MAX_MISMATCHES, NULL , "" );
1655	aws->insert_default_option( "Search up to zero mismatches", "", 0 );
1656	for (int mm = 1; mm <= 20; ++mm) {
1657	aws->insert_option(GBS_global_string("Search up to %i mismatches", mm), "", mm);
1658	}
1659	aws->update_option_menu();
1660
1661	aws->at("tmp");
1662	aws->create_toggle( AWAR_PD_MATCH_WRITE2TMP );
1663
1664	aws->at("nhits");
1665	aws->create_button(0,AWAR_PD_MATCH_NHITS);
1666
1667	aws->callback(probe_match_event,(AW_CL)selection_id, (AW_CL)0);
1668	aws->at("match");
1669	aws->create_button("MATCH","MATCH","D");
1670
1671	aws->at("auto");
1672	aws->label("Auto");
1673	aws->create_toggle( AWAR_PD_MATCH_AUTOMATCH );
1674	enable_auto_match_cb(root, aws, (AW_CL)selection_id);
1675
1676	aws->callback(modify_target_string, (AW_CL)TS_MOD_CLEAR);
1677	aws->at("clear");
1678	aws->create_button("CLEAR","Clear","0");
1679
1680	aws->callback(modify_target_string, (AW_CL)TS_MOD_REV_COMPL);
1681	aws->at("revcompl");
1682	aws->create_button("REVCOMPL","RevCompl","R");
1683
1684	aws->callback(modify_target_string, (AW_CL)TS_MOD_COMPL);
1685	aws->at("compl");
1686	aws->create_button("COMPL","Compl","C");
1687
1688	aws->callback( (AW_CB1)AW_POPUP,(AW_CL)create_IUPAC_resolve_window);
1689	aws->at("iupac");
1690	aws->create_button("IUPAC","IUPAC","I");
1691
1692	return aws;
1693	}
1694
1695	void pd_start_pt_server(AW_window *aww)
1696	{
1697	AW_root *awr = aww->get_root();
1698	char pt_server[256];
1699	sprintf(pt_server,"ARB_PT_SERVER%li",awr->awar(AWAR_PROBE_ADMIN_PT_SERVER)->read_int());
1700	GB_ERROR error;
1701	aw_openstatus("Start a server");
1702	aw_status("Look for server or start one");
1703	error = arb_look_and_start_server(AISC_MAGIC_NUMBER,pt_server,GLOBAL_gb_main);
1704	if (error) {
1705	aw_message(error);
1706	}
1707	aw_closestatus();
1708	}
1709
1710	void pd_kill_pt_server(AW_window *aww, AW_CL kill_all)
1711	{
1712	if (aw_ask_sure(GBS_global_string("Are you sure to stop %s",
1713	kill_all ? "all servers" : "that server")))
1714	{
1715	long min = 0;
1716	long max = 0;
1717
1718	if (kill_all) {
1719	const char * const pt_servers = GBS_get_arb_tcp_entries("ARB_PT_SERVER");
1720	while (pt_servers[max]) max++;
1721	}
1722	else {
1723	min = max = aww->get_root()->awar(AWAR_PROBE_ADMIN_PT_SERVER)->read_int(); // selected server
1724	}
1725
1726	aw_openstatus("Stopping PT-servers..");
1727
1728	for (int i= min ; i <=max ; i++) {
1729	char *choice = GBS_ptserver_id_to_choice(i, 0);
1730	if (!choice) {
1731	aw_message(GB_await_error());
1732	break;
1733	}
1734
1735	aw_status(GBS_global_string("Trying to stop '%s'",choice));
1736
1737	const char *pt_server = GBS_global_string("ARB_PT_SERVER%i",i);
1738	GB_ERROR error = arb_look_and_kill_server(AISC_MAGIC_NUMBER, pt_server);
1739
1740	if (error) aw_message(GBS_global_string("Could not stop '%s' (Reason: %s)", choice, error));
1741	else aw_message(GBS_global_string("Stopped '%s'", choice));
1742
1743	free(choice);
1744	}
1745	aw_closestatus();
1746	}
1747	}
1748
1749	void pd_query_pt_server(AW_window *aww)
1750	{
1751	AW_root *awr = aww->get_root();
1752	char pt_server[256];
1753	sprintf(pt_server,"ARB_PT_SERVER%li",awr->awar(AWAR_PROBE_ADMIN_PT_SERVER)->read_int());
1754
1755	GBS_strstruct *strstruct = GBS_stropen(1024);
1756	GBS_strcat(strstruct, "echo Contents of directory ARBHOME/lib/pts:;echo;"
1757	"(cd $ARBHOME/lib/pts; ls -l);"
1758	"echo; echo Disk space for PT_server files:; echo;"
1759	"df $ARBHOME/lib/pts;");
1760	GBS_strcat(strstruct,"echo;echo 'Running ARB programs:';");
1761
1762	{
1763	const char *server = GBS_read_arb_tcp(pt_server);
1764	char *arb_who = prefixSSH(server, "$ARBHOME/bin/arb_who", 0);
1765	GBS_strcat(strstruct, arb_who);
1766	free(arb_who);
1767	}
1768
1769	char *sys = GBS_strclose(strstruct);
1770	GB_xcmd(sys,GB_TRUE, GB_FALSE);
1771	free(sys);
1772	}
1773
1774	static void pd_export_pt_server(AW_window *aww)
1775	{
1776	AW_root *awr = aww->get_root();
1777	GB_ERROR error = 0;
1778	char pt_server[256];
1779
1780	bool create_gene_server = awr->awar(AWAR_PROBE_CREATE_GENE_SERVER)->read_int();
1781	{
1782	GB_transaction ta(GLOBAL_gb_main);
1783	if (create_gene_server && !GEN_is_genome_db(GLOBAL_gb_main, -1)) create_gene_server = false;
1784
1785	// check alignment first
1786	if (create_gene_server) {
1787	GBDATA *gb_ali = GBT_get_alignment(GLOBAL_gb_main, GENOM_ALIGNMENT);
1788	if (!gb_ali) error = GB_await_error();
1789	}
1790	else { // normal pt server
1791	char *use = GBT_get_default_alignment(GLOBAL_gb_main);
1792	GB_alignment_type alitype = GBT_get_alignment_type(GLOBAL_gb_main, use);
1793	if (alitype == GB_AT_AA) error = "The PT-server does only support RNA/DNA sequence data";
1794	free(use);
1795	}
1796	}
1797
1798	long serverid = awr->awar(AWAR_PROBE_ADMIN_PT_SERVER)->read_int();
1799	sprintf(pt_server,"ARB_PT_SERVER%li", serverid);
1800
1801	if (!error &&
1802	aw_question("This function will send your currently loaded data as the new data to the pt_server !!!\n"
1803	"The server will need a long time (up to several hours) to analyse the data.\n"
1804	"Until the new server has analyzed all data, no server functions are available.\n\n"
1805	"Note 1: You must have the write permissions to do that ($ARBHOME/lib/pts/xxx))\n"
1806	"Note 2: The server will do the job in background,\n"
1807	" quitting this program won't affect the server",
1808	"Cancel,Do it"))
1809	{
1810	aw_openstatus("Updating PT-server");
1811	aw_status("Stopping PT-server");
1812	arb_look_and_kill_server(AISC_MAGIC_NUMBER,pt_server);
1813
1814	const char *ipPort = GBS_read_arb_tcp(pt_server);
1815	const char *file = GBS_scan_arb_tcp_param(ipPort, "-d");
1816
1817	GBS_add_ptserver_logentry(GBS_global_string("Started build of '%s'", file));
1818	{
1819	char *db_name = awr->awar(AWAR_DB_PATH)->read_string();
1820	GBS_add_ptserver_logentry(GBS_global_string("Exporting DB '%s'", db_name));
1821	free(db_name);
1822	}
1823
1824	aw_status("Exporting the database");
1825	{
1826	const char *mode = "bfm"; // save PT-server database with Fastload file
1827
1828	if (create_gene_server) {
1829	char temp_server_name = GBS_string_eval(file, ".arb=*_temp.arb", 0);
1830	error = GB_save_as(GLOBAL_gb_main, temp_server_name, mode);
1831
1832	if (!error) {
1833	// convert database (genes -> species)
1834	aw_status("Preparing DB for gene PT server");
1835	GBS_add_ptserver_logentry("Preparing DB for gene PT server");
1836	char *command = GBS_global_string_copy("$ARBHOME/bin/arb_gene_probe %s %s", temp_server_name, file);
1837	printf("Executing '%s'\n", command);
1838	int result = system(command);
1839	if (result != 0) {
1840	error = GBS_global_string("Couldn't convert database for gene pt server (arb_gene_probe failed, see console for reason)");
1841	}
1842	free(command);
1843	}
1844	free(temp_server_name);
1845	}
1846	else { // normal pt_server
1847	error = GB_save_as(GLOBAL_gb_main, file, mode);
1848	}
1849	}
1850
1851	if (!error) { // set pt-server database file to same permissions as pts directory
1852	char dir = const_cast<char>(strrchr(file,'/'));
1853	if (dir) {
1854	*dir = 0;
1855	long modi = GB_mode_of_file(file);
1856	*dir = '/';
1857	modi &= 0666;
1858	error = GB_set_mode_of_file(file,modi);
1859	}
1860	}
1861
1862	if (!error ) {
1863	aw_status("Start PT-server (builds in background)");
1864	error = arb_start_server(pt_server,GLOBAL_gb_main, 1);
1865	}
1866	aw_closestatus();
1867
1868	}
1869	if (error) aw_message(error);
1870	}
1871
1872	static void arb_tcp_dat_changed_cb(const char /path/, bool fileChanged, bool /editorTerminated*/) {
1873	#if defined(DEBUG) && 0
1874	printf("File '%s': changed=%i editorTerminated=%i\n", path, int(fileChanged), int(editorTerminated));
1875	#endif // DEBUG
1876	if (fileChanged) {
1877	awt_refresh_all_pt_server_selection_lists();
1878	}
1879	}
1880
1881	static void pd_edit_arb_tcp(AW_window *aww, AW_CL cl_gb_main) {
1882	GBDATA gb_main = (GBDATA)cl_gb_main;
1883	AWT_edit("$(ARBHOME)/lib/arb_tcp.dat", arb_tcp_dat_changed_cb, aww, gb_main);
1884	}
1885
1886	AW_window create_probe_admin_window( AW_root root, AW_CL cl_genome_db) {
1887	AW_window_simple *aws = new AW_window_simple;
1888	bool is_genom_db = (bool)cl_genome_db;
1889
1890	aws->init( root, "PT_SERVER_ADMIN", "PT_SERVER ADMIN");
1891
1892	aws->load_xfig("pd_admin.fig");
1893
1894
1895	aws->callback( AW_POPUP_HELP,(AW_CL)"probeadmin.hlp");
1896	aws->at("help");
1897	aws->create_button("HELP","HELP","H");
1898
1899	aws->callback( (AW_CB0)AW_POPDOWN);
1900	aws->at("close");
1901	aws->create_button("CLOSE","CLOSE","C");
1902
1903	aws->button_length(18);
1904
1905	aws->at( "pt_server" );
1906	awt_create_selection_list_on_pt_servers(aws, AWAR_PROBE_ADMIN_PT_SERVER, false);
1907
1908	aws->at( "start" );
1909	aws->callback(pd_start_pt_server);
1910	aws->create_button("START_SERVER","Start server");
1911
1912	aws->at( "kill" );
1913	aws->callback(pd_kill_pt_server,0);
1914	aws->create_button("KILL_SERVER","Stop server");
1915
1916	aws->at( "query" );
1917	aws->callback(pd_query_pt_server);
1918	aws->create_button("CHECK_SERVER","Check server");
1919
1920	aws->at( "kill_all" );
1921	aws->callback(pd_kill_pt_server,1);
1922	aws->create_button("KILL_ALL_SERVERS","Stop all servers");
1923
1924	aws->at( "edit" );
1925	aws->callback(pd_edit_arb_tcp, (AW_CL)GLOBAL_gb_main);
1926	aws->create_button("CREATE_TEMPLATE","Configure");
1927
1928	aws->at( "export" );
1929	aws->callback(pd_export_pt_server);
1930	aws->create_button("UPDATE_SERVER","Build server");
1931
1932	if (is_genom_db) {
1933	aws->at( "gene_server" );
1934	aws->label("Gene server?");
1935	aws->create_toggle(AWAR_PROBE_CREATE_GENE_SERVER);
1936	}
1937
1938	return aws;
1939	}
1940
1941	// --------------------------------------------------------------------------------
1942	// Probe group result visualization
1943
1944	#define AWAR_PG_SELECTED_RESULT "tmp/pg_result/selected"
1945
1946	static struct pg_global_struct {
1947	char *awar_pg_result_filename; // awar containing result filename
1948	AW_window_simple *pg_groups_window; // window showing groups
1949	AW_selection_list *selList; // list containing groups
1950	AW_root *aw_root;
1951	AWT_canvas *ntw; // canvas of main window
1952
1953	char *pg_filename; // database containing results (from one result file)
1954	GBDATA *pg_main; // root-handle of database
1955
1956	} pg_global;
1957
1958
1959
1960	static void pg_result_selected(AW_window /aww*/) {
1961
1962	AW_root *aw_root = pg_global.aw_root;
1963	long position = aw_root->awar(AWAR_PG_SELECTED_RESULT)->read_int();
1964
1965	if (position) { // ignore headline
1966	long i = 1;
1967
1968	GB_transaction dummy(pg_global.pg_main);
1969	GB_transaction dummy2(GLOBAL_gb_main);
1970
1971	GBT_mark_all(GLOBAL_gb_main, 0); // unmark all species
1972
1973	GBDATA *gb_species_data = GB_search(GLOBAL_gb_main, "species_data", GB_FIND);
1974	gb_assert(gb_species_data);
1975	GBDATA *pg_group = GB_search(pg_global.pg_main, "probe_groups/group", GB_FIND);
1976	long count = 0;
1977	long marked = 0;
1978	for (; pg_group; pg_group=GB_nextChild(pg_group),++i) {
1979	if (i==position) {
1980	GBDATA *pg_species = GB_search(pg_group, "species/name", GB_FIND);
1981	for (; pg_species; pg_species=GB_nextChild(pg_species),count++) {
1982	const char *name = GB_read_char_pntr(pg_species);
1983	GBDATA *gb_speciesname = GB_find_string(gb_species_data, "name", name, GB_IGNORE_CASE, down_2_level);
1984	if (gb_speciesname) {
1985	GBDATA *gb_species = GB_get_father(gb_speciesname);
1986	gb_assert(gb_species);
1987	GB_write_flag(gb_species, 1); // mark species
1988	if (!marked) { // select first species
1989	aw_root->awar(AWAR_SPECIES_NAME)->write_string(name);
1990	}
1991	marked++;
1992	}
1993	else {
1994	aw_message(GBS_global_string("No species '%s' in current DB", name));
1995	}
1996	}
1997	break;
1998	}
1999	}
2000
2001	if (marked!=count) {
2002	aw_message(GBS_global_string("%li species were in group - %li species marked in database", count, marked));
2003	}
2004
2005	NT_group_not_marked_cb(0, pg_global.ntw);
2006	}
2007	}
2008
2009
2010	// --------------------------------------------------------------------------------
2011	// static void create_probe_group_result_awars(AW_root *aw_root)
2012	// --------------------------------------------------------------------------------
2013	static void create_probe_group_result_awars(AW_root *aw_root) {
2014	aw_root->awar_int(AWAR_PG_SELECTED_RESULT, 0);
2015	}
2016
2017	// --------------------------------------------------------------------------------
2018	// static void create_probe_group_result_sel_box(AW_root aw_root, AW_window aws)
2019	// --------------------------------------------------------------------------------
2020	static void create_probe_group_result_sel_box(AW_root aw_root, AW_window aws) {
2021	char *file_name = aw_root->awar(pg_global.awar_pg_result_filename)->read_string();
2022
2023	AW_selection_list *selList = pg_global.selList;
2024
2025	static bool awars_created;
2026	if (!awars_created) {
2027	create_probe_group_result_awars(aw_root);
2028	awars_created = 1;
2029	}
2030	aw_root->awar(AWAR_PG_SELECTED_RESULT)->write_int(0); // reset to element #0
2031
2032	if (selList==0) {
2033	aws->at("box");
2034	aws->callback(pg_result_selected);
2035	selList = pg_global.selList = aws->create_selection_list(AWAR_PG_SELECTED_RESULT, 0, "", 2, 2);
2036	}
2037	else {
2038	aws->clear_selection_list(selList);
2039	}
2040
2041	GB_ERROR error = 0;
2042
2043	if (pg_global.pg_main) {
2044	GB_close(pg_global.pg_main);
2045	pg_global.pg_main = 0;
2046	freeset(pg_global.pg_filename, 0);
2047	}
2048
2049	pg_global.aw_root = aw_root;
2050	pg_global.pg_filename = strdup(file_name);
2051	pg_global.pg_main = GB_open(file_name, "r");
2052
2053	if (pg_global.pg_main) {
2054	const char *reason = 0;
2055	long i = 0;
2056	aws->insert_selection(selList, "members \| probes \| fitness \| quality \| mintarget \| mishit \| probelen \| birth", i++);
2057
2058	GB_transaction dummy(pg_global.pg_main);
2059	GBDATA *pg_group = GB_search(pg_global.pg_main, "probe_groups/group", GB_FIND);
2060	if (pg_group) {
2061	for (; pg_group; pg_group=GB_nextChild(pg_group),++i) {
2062
2063	double fitness=-1, quality=-1, min_targets=-1;
2064	int mishit=-1, probelength=-1, birth=-1;
2065	int member_count = 0;
2066	int probe_count = 0;
2067
2068	GBDATA *field;
2069
2070	field = GB_entry(pg_group, "fitness"); if (field) fitness = GB_read_float(field);
2071	field = GB_entry(pg_group, "quality"); if (field) quality = GB_read_float(field);
2072	field = GB_entry(pg_group, "min_targets"); if (field) min_targets = GB_read_float(field);
2073	field = GB_entry(pg_group, "mishit"); if (field) mishit = GB_read_int(field);
2074	field = GB_entry(pg_group, "probelength"); if (field) probelength = GB_read_int(field);
2075	field = GB_entry(pg_group, "birth"); if (field) birth = GB_read_int(field);
2076
2077	GBDATA *species = GB_search(pg_group, "species/name", GB_FIND);
2078	for (; species; species=GB_nextChild(species)) member_count++;
2079
2080	GBDATA *probe = GB_search(pg_group, "probes/data", GB_FIND);
2081	for (; probe; probe=GB_nextChild(probe)) probe_count++;
2082
2083	char entry[200];
2084
2085	sprintf(entry, "%7i \| %6i \| %7.5f \| %7.1f \| %9.2f \| %6i \| %8i \| %5i",
2086	member_count,
2087	probe_count,
2088	fitness,
2089	quality,
2090	min_targets,
2091	mishit,
2092	probelength,
2093	birth);
2094
2095	aws->insert_selection(selList, entry, i);
2096	}
2097	}
2098	else {
2099	reason = "probe_group/group - no such entry";
2100	}
2101
2102	if (reason) {
2103	error = GB_export_errorf("Error in database format (reason: %s)", reason);
2104	aws->insert_selection(selList, error, (long)0);
2105	}
2106
2107	aws->update_selection_list(selList);
2108	}
2109	else {
2110	error = GB_export_errorf("Can't open database '%s'", file_name);
2111	freeset(pg_global.pg_filename, 0);
2112	}
2113
2114	free(file_name);
2115
2116	if (error) {
2117	aw_message(error);
2118	}
2119	}
2120
2121	// --------------------------------------------------------------------------------
2122	// static void create_probe_group_groups_window(AW_window *aww)
2123	// --------------------------------------------------------------------------------
2124	static void create_probe_group_groups_window(AW_window *aww) {
2125	AW_root *aw_root = aww->get_root();
2126
2127	if (pg_global.pg_groups_window==0) { // window was not created yet
2128	AW_window_simple *aws = new AW_window_simple;
2129
2130	aws->init(aw_root, "PG_RESULT_SELECTION", "Probe group results");
2131	aws->load_xfig("pg_select.fig");
2132
2133	aws->at("close");
2134	aws->callback((AW_CB0)AW_POPDOWN);
2135	aws->create_button("CLOSE", "CLOSE","C");
2136
2137	aws->at("help");
2138	aws->callback(AW_POPUP_HELP,(AW_CL)"");
2139	aws->create_button("HELP","HELP");
2140
2141	create_probe_group_result_sel_box(aw_root, aws);
2142
2143	pg_global.pg_groups_window = aws;
2144	}
2145	else { // window already created -> refresh selection box
2146	create_probe_group_result_sel_box(aw_root, pg_global.pg_groups_window);
2147	}
2148
2149	pg_global.pg_groups_window->show();
2150	}
2151
2152	// --------------------------------------------------------------------------------
2153	// AW_window create_probe_group_result_window(AW_root awr, AW_default cl_AW_canvas_ntw)
2154	// --------------------------------------------------------------------------------
2155	AW_window create_probe_group_result_window(AW_root awr, AW_default cl_AW_canvas_ntw){
2156	freeset(pg_global.awar_pg_result_filename, 0);
2157	pg_global.ntw = (AWT_canvas*)cl_AW_canvas_ntw;
2158
2159	return awt_create_load_box(awr, "arb_probe_group result", "arb", &pg_global.awar_pg_result_filename,
2160	create_probe_group_groups_window,
2161	0);
2162	}
2163
2164

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