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source: tags/ms_r16q2/EDIT4/graph_aligner_gui.cxx

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Last change on this file was 14686, checked in by westram, 8 years ago
change datatypes used in awar-access (only changed simple cases)
File size: 24.2 KB

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1	// =============================================================== //
2	// //
3	// File : graph_aligner_gui.cxx //
4	// Purpose : //
5	// //
6	// Coded by Elmar Pruesse in October 2008 //
7	// Institute of Microbiology (Technical University Munich) //
8	// http://www.arb-home.de/ //
9	// //
10	// =============================================================== //
11
12	#include "graph_aligner_gui.hxx"
13
14	#include "ed4_defs.hxx"
15
16	// need to use AlignDataAccess defined here to get selected species
17	#include <fast_aligner.hxx>
18
19	#include <aw_awars.hxx>
20	#include <aw_msg.hxx>
21	#include <aw_root.hxx>
22	#include <awt_sel_boxes.hxx>
23	#include <awt_config_manager.hxx>
24	#include <servercntrl.h>
25	#include <PT_com.h>
26	#include <client.h>
27	#include <arbdbt.h>
28	#include <arb_strbuf.h>
29	#include <arb_misc.h>
30
31	#include <sys/types.h>
32	#include <sys/wait.h>
33
34	#include <unistd.h>
35
36	#include <string>
37	#include <sstream>
38	#include <iostream>
39	#include <vector>
40
41	using std::cerr;
42	using std::cout;
43	using std::endl;
44
45	#define GA_AWAR_ROOT "sina/"
46
47	#define GA_AWAR_CMD GA_AWAR_ROOT "command"
48	#define GA_AWAR_TGT GA_AWAR_ROOT "target"
49	#define GA_AWAR_SAI GA_AWAR_ROOT "sai"
50	#define GA_AWAR_ALIGNMENT GA_AWAR_ROOT "alignment"
51	#define GA_AWAR_PROTECTION GA_AWAR_ROOT "protection"
52	#define GA_AWAR_TURN_CHECK GA_AWAR_ROOT "turncheck"
53	#define GA_AWAR_REALIGN GA_AWAR_ROOT "realign"
54	#define GA_AWAR_COPYMARKREF GA_AWAR_ROOT "copymarkref"
55	#define GA_AWAR_MATCH_SCORE GA_AWAR_ROOT "match_score"
56	#define GA_AWAR_MISMATCH_SCORE GA_AWAR_ROOT "mismatch_score"
57	#define GA_AWAR_GAP_PEN GA_AWAR_ROOT "gap_pen"
58	#define GA_AWAR_GAP_EXT GA_AWAR_ROOT "gap_ext"
59	#define GA_AWAR_ADVANCED GA_AWAR_ROOT "advanced"
60	#define GA_AWAR_FS_MIN GA_AWAR_ROOT "fs_min"
61	#define GA_AWAR_FS_MAX GA_AWAR_ROOT "fs_max"
62	#define GA_AWAR_FS_MSC GA_AWAR_ROOT "fs_msc"
63	#define GA_AWAR_MIN_FULL GA_AWAR_ROOT "min_full"
64	#define GA_AWAR_FULL_MINLEN GA_AWAR_ROOT "full_minlen"
65	#define GA_AWAR_OVERHANG GA_AWAR_ROOT "overhang"
66	#define GA_AWAR_THREADS GA_AWAR_ROOT "threads"
67	#define GA_AWAR_QSIZE GA_AWAR_ROOT "qsize"
68	#define GA_AWAR_KMER_LEN GA_AWAR_ROOT "kmer_len"
69	#define GA_AWAR_KMER_MM GA_AWAR_ROOT "kmer_mm"
70	#define GA_AWAR_MIN_LEN GA_AWAR_ROOT "min_len"
71	#define GA_AWAR_WEIGHT GA_AWAR_ROOT "weight"
72	#define GA_AWAR_INSERT GA_AWAR_ROOT "insert"
73	#define GA_AWAR_LOWERCASE GA_AWAR_ROOT "lowercase"
74	#define GA_AWAR_AUTOFILTER GA_AWAR_ROOT "autofilter"
75	#define GA_AWAR_KMER_NOREL GA_AWAR_ROOT "kmer_norel"
76	#define GA_AWAR_KMER_NOFAST GA_AWAR_ROOT "kmer_nofast"
77	#define GA_AWAR_SHOW_DIST GA_AWAR_ROOT "show_dist"
78	#define GA_AWAR_SHOW_DIFF GA_AWAR_ROOT "show_diff"
79	#define GA_AWAR_COLOR GA_AWAR_ROOT "color"
80	#define GA_AWAR_GENE_START GA_AWAR_ROOT "gene_start"
81	#define GA_AWAR_GENE_END GA_AWAR_ROOT "gene_end"
82	#define GA_AWAR_FS_COVER_GENE GA_AWAR_ROOT "fs_cover_gene"
83
84	void create_sina_variables(AW_root *root, AW_default db1) {
85	root->awar_string(GA_AWAR_CMD, "sina", db1);
86	root->awar_int (GA_AWAR_TGT, 2, db1);
87	root->awar_int (AWAR_PT_SERVER, 0, db1);
88	root->awar_string(GA_AWAR_SAI, "", db1);
89	root->awar_int (GA_AWAR_PROTECTION, 0, db1);
90	root->awar_int (GA_AWAR_TURN_CHECK, 1, db1);
91	root->awar_int (GA_AWAR_REALIGN, 1, db1);
92	root->awar_int (GA_AWAR_COPYMARKREF, 0, db1);
93	root->awar_float (GA_AWAR_GAP_PEN, 5.0, db1);
94	root->awar_float (GA_AWAR_GAP_EXT, 2.0, db1);
95	root->awar_float (GA_AWAR_MATCH_SCORE, 2.0, db1);
96	root->awar_float (GA_AWAR_MISMATCH_SCORE, -1.0, db1);
97	root->awar_int (GA_AWAR_ADVANCED, 0, db1);
98	root->awar_int (GA_AWAR_FS_MIN, 40, db1);
99	root->awar_int (GA_AWAR_FS_MAX, 40, db1);
100	root->awar_float (GA_AWAR_FS_MSC, .7, db1);
101	root->awar_int (GA_AWAR_MIN_FULL, 1, db1);
102	root->awar_int (GA_AWAR_FULL_MINLEN, 1400, db1);
103	root->awar_string(GA_AWAR_OVERHANG, "attach", db1);
104	root->awar_int (GA_AWAR_THREADS, 1, db1);
105	root->awar_int (GA_AWAR_QSIZE, 1, db1);
106	root->awar_int (GA_AWAR_KMER_LEN, 10, db1);
107	root->awar_int (GA_AWAR_KMER_MM, 0, db1);
108	root->awar_int (GA_AWAR_MIN_LEN, 150, db1);
109	root->awar_float (GA_AWAR_WEIGHT, 1, db1);
110	root->awar_string(GA_AWAR_INSERT, "shift", db1);
111	root->awar_string(GA_AWAR_LOWERCASE, "none", db1);
112	root->awar_string(GA_AWAR_AUTOFILTER, "none", db1);
113	root->awar_int (GA_AWAR_KMER_NOREL, 0, db1);
114	root->awar_int (GA_AWAR_KMER_NOFAST, 0, db1);
115	root->awar_int (GA_AWAR_SHOW_DIST, 0, db1);
116	root->awar_int (GA_AWAR_SHOW_DIFF, 0, db1);
117	root->awar_int (GA_AWAR_COLOR, 1, db1);
118	root->awar_int (GA_AWAR_GENE_START, 0, db1);
119	root->awar_int (GA_AWAR_GENE_END, 0, db1);
120	root->awar_int (GA_AWAR_FS_COVER_GENE, 1, db1);
121	}
122
123	AW_active sina_mask(AW_root *root) {
124	const char *sinaName = root->awar(GA_AWAR_CMD)->read_char_pntr();
125	char *sina = ARB_executable(sinaName, GB_getenv("PATH"));
126	const char *fail_reason = 0;
127
128	if (sina) {
129	int exitstatus = system(GBS_global_string("%s --has-cli-vers ARB5.99", sina));
130	exitstatus = WEXITSTATUS(exitstatus);
131
132	switch (exitstatus) {
133	case EXIT_SUCCESS:
134	break;
135
136	case EXIT_FAILURE:
137	fail_reason = "Incompatible SINA and ARB versions";
138	break;
139
140	case 127: // libs missing
141	default: // unexpected
142	fail_reason = GBS_global_string("Could execute SINA binary '%s' (exitstatus was %i)",
143	sinaName, exitstatus);
144	break;
145	}
146	free(sina);
147	}
148	else {
149	fail_reason = GBS_global_string("%s not found", sinaName);
150	}
151
152	if (fail_reason) {
153	fprintf(stderr,
154	"Note: SINA (SILVA Aligner) disabled (Reason: %s)\n"
155	" Visit http://www.ribocon.com/sina/ for more information.\n",
156	fail_reason);
157	}
158
159	return fail_reason ? AWM_DISABLED : AWM_ALL;
160	}
161
162	inline const char *stream2static(const std::stringstream& str) {
163	return GBS_static_string(str.str().c_str());
164	}
165
166	inline const char empty_as_none(const char sainame) {
167	// see http://bugs.arb-home.de/ticket/519
168	if (sainame && !sainame[0]) sainame = "none";
169	return sainame;
170	}
171
172	static void sina_start(AW_window window, const AlignDataAccess data_access) {
173	cerr << "Starting SINA..." << endl;
174
175	// make string from pt server selection
176	AW_root *root = window->get_root();
177	int pt = root->awar(AWAR_PT_SERVER)->read_int();
178
179	std::stringstream ptnam;
180	ptnam << "ARB_PT_SERVER" << pt;
181
182	const char *pt_server = GBS_read_arb_tcp(ptnam.str().c_str());
183	GB_ERROR gb_error = NULL;
184
185	if (!pt_server) {
186	gb_error = GBS_global_string("Unable to find definition for chosen PT-server\n(Reason: %s)", GB_await_error());
187	}
188	else {
189	const char *pt_db = pt_server + strlen(pt_server) + 1;
190	pt_db += strlen(pt_db)+3;
191
192	// start pt server if necessary
193	gb_error = arb_look_and_start_server(AISC_MAGIC_NUMBER, ptnam.str().c_str());
194	if (gb_error) {
195	std::stringstream tmp;
196	tmp << "Cannot contact PT server. Aborting" << endl
197	<< " ID: \"" << tmp.str().c_str()
198	<< "\" PORT: \"" << pt_server
199	<< "\" DB: \"" << pt_db << endl
200	<< "\" GBERROR: \"" << gb_error << "\"" << endl;
201	gb_error = stream2static(tmp);
202	}
203	else {
204	// create temporary file
205	char* tmpfile;
206	FILE* tmpfile_F;
207	{
208	char* tmpfile_tpl = GB_unique_filename("sina_select", "tmp");
209	tmpfile_F = GB_fopen_tempfile(tmpfile_tpl, "w", &tmpfile);
210	free(tmpfile_tpl);
211	}
212
213	if (!tmpfile_F) {
214	std::stringstream tmp;
215	tmp << "Error: Unable to create temporary file \"" << tmpfile << "\"!";
216	gb_error = stream2static(tmp);
217	}
218	else {
219	GB_remove_on_exit(tmpfile);
220
221	std::vector<std::string> spec_names;
222	switch (root->awar(GA_AWAR_TGT)->read_int()) {
223	case 0: { // current
224	char *spec_name = root->awar(AWAR_SPECIES_NAME)->read_string();
225	if (spec_name) {
226	fwrite(spec_name, strlen(spec_name), 1, tmpfile_F);
227	fwrite("\n", 1, 1, tmpfile_F);
228	}
229	else {
230	gb_error = "Unable to get name of currently active species";
231	}
232	free(spec_name);
233	break;
234	}
235	case 1: { // selected
236	GB_begin_transaction(GLOBAL_gb_main);
237	int num_selected = 0;
238	for (GBDATA *gb_spec = data_access->get_first_selected_species(&num_selected);
239	gb_spec;
240	gb_spec = data_access->get_next_selected_species())
241	{
242	GBDATA *gbd_name = GB_find(gb_spec, "name", SEARCH_CHILD);
243	if (gbd_name) {
244	const char *str = GB_read_char_pntr(gbd_name);
245	fwrite(str, strlen(str), 1, tmpfile_F);
246	fwrite("\n", 1, 1, tmpfile_F);
247	}
248	}
249	GB_commit_transaction(GLOBAL_gb_main);
250	break;
251	}
252	case 2: { // marked
253	GB_begin_transaction(GLOBAL_gb_main);
254	for (GBDATA *gb_spec = GBT_first_marked_species(GLOBAL_gb_main);
255	gb_spec; gb_spec = GBT_next_marked_species(gb_spec)) {
256	GBDATA *gbd_name = GB_find(gb_spec, "name", SEARCH_CHILD);
257	if (gbd_name) {
258	const char *str = GB_read_char_pntr(gbd_name);
259	fwrite(str, strlen(str), 1, tmpfile_F);
260	fwrite("\n", 1, 1, tmpfile_F);
261	}
262	}
263	GB_commit_transaction(GLOBAL_gb_main);
264	break;
265	}
266	}
267	fclose(tmpfile_F);
268
269	if (!gb_error) {
270	// build command line
271	GBS_strstruct *cl = GBS_stropen(2000);
272
273	GBS_strcat(cl, root->awar(GA_AWAR_CMD)->read_char_pntr());
274	GBS_strcat(cl, " -i :");
275	GBS_strcat(cl, " --ptdb :");
276	GBS_strcat(cl, " --ptport "); GBS_strcat(cl, pt_server);
277	GBS_strcat(cl, " --turn "); GBS_strcat(cl, root->awar(GA_AWAR_TURN_CHECK)->read_int() ? "all" : "none");
278	GBS_strcat(cl, " --overhang "); GBS_strcat(cl, root->awar(GA_AWAR_OVERHANG)->read_char_pntr());
279	GBS_strcat(cl, " --filter "); GBS_strcat(cl, empty_as_none(root->awar(GA_AWAR_SAI)->read_char_pntr()));
280	GBS_strcat(cl, " --fs-min "); GBS_intcat(cl, root->awar(GA_AWAR_FS_MIN)->read_int());
281	GBS_strcat(cl, " --fs-msc "); GBS_floatcat(cl, root->awar(GA_AWAR_FS_MSC)->read_float());
282	GBS_strcat(cl, " --fs-max "); GBS_intcat(cl, root->awar(GA_AWAR_FS_MAX)->read_int());
283	GBS_strcat(cl, " --fs-req 1");
284	GBS_strcat(cl, " --fs-req-full "); GBS_intcat(cl, root->awar(GA_AWAR_MIN_FULL)->read_int());
285	GBS_strcat(cl, " --fs-full-len "); GBS_intcat(cl, root->awar(GA_AWAR_FULL_MINLEN)->read_int());
286	GBS_strcat(cl, " --fs-kmer-len "); GBS_intcat(cl, root->awar(GA_AWAR_KMER_LEN)->read_int());
287	GBS_strcat(cl, " --fs-kmer-mm "); GBS_intcat(cl, root->awar(GA_AWAR_KMER_MM)->read_int());
288	GBS_strcat(cl, " --fs-min-len "); GBS_intcat(cl, root->awar(GA_AWAR_MIN_LEN)->read_int());
289	GBS_strcat(cl, " --fs-weight "); GBS_intcat(cl, root->awar(GA_AWAR_WEIGHT)->read_float()); // @@@ possible type conflict?
290	GBS_strcat(cl, " --pen-gap "); GBS_floatcat(cl, root->awar(GA_AWAR_GAP_PEN)->read_float());
291	GBS_strcat(cl, " --pen-gapext "); GBS_floatcat(cl, root->awar(GA_AWAR_GAP_EXT)->read_float());
292	GBS_strcat(cl, " --match-score "); GBS_floatcat(cl, root->awar(GA_AWAR_MATCH_SCORE)->read_float());
293	GBS_strcat(cl, " --mismatch-score "); GBS_floatcat(cl, root->awar(GA_AWAR_MISMATCH_SCORE)->read_float());
294	GBS_strcat(cl, " --prot-level "); GBS_intcat(cl, root->awar(GA_AWAR_PROTECTION)->read_int());
295	GBS_strcat(cl, " --select-file "); GBS_strcat(cl, tmpfile);
296	GBS_strcat(cl, " --insertion "); GBS_strcat(cl, root->awar(GA_AWAR_INSERT)->read_char_pntr());
297	GBS_strcat(cl, " --lowercase "); GBS_strcat(cl, root->awar(GA_AWAR_LOWERCASE)->read_char_pntr());
298	GBS_strcat(cl, " --auto-filter-field "); GBS_strcat(cl, root->awar(GA_AWAR_AUTOFILTER)->read_char_pntr());
299	GBS_strcat(cl, " --gene-start "); GBS_intcat(cl, root->awar(GA_AWAR_GENE_START)->read_int());
300	GBS_strcat(cl, " --gene-end "); GBS_intcat(cl, root->awar(GA_AWAR_GENE_END)->read_int());
301	GBS_strcat(cl, " --fs-cover-gene ");GBS_intcat(cl, root->awar(GA_AWAR_FS_COVER_GENE)->read_int());
302
303
304	if (root->awar(GA_AWAR_KMER_NOREL)->read_int()) GBS_strcat(cl, " --fs-kmer-norel ");
305	if (root->awar(GA_AWAR_KMER_NOFAST)->read_int()) GBS_strcat(cl, " --fs-kmer-no-fast ");
306	if (root->awar(GA_AWAR_SHOW_DIST)->read_int()) GBS_strcat(cl, " --show-dist ");
307	if (root->awar(GA_AWAR_SHOW_DIFF)->read_int()) GBS_strcat(cl, " --show-diff ");
308	if (root->awar(GA_AWAR_COLOR)->read_int()) GBS_strcat(cl, " --color");
309	if (root->awar(GA_AWAR_REALIGN)->read_int()) GBS_strcat(cl, " --realign");
310
311	gb_error = GB_xcmd(GBS_mempntr(cl), true, false);
312	GBS_strforget(cl);
313	}
314
315	if (!gb_error) aw_message("SINA finished aligning.");
316	}
317	free(tmpfile);
318	}
319	}
320
321	aw_message_if(gb_error);
322	}
323
324
325
326	static char* filter_posvar_SAI_for_ali(GBDATA gb_extended, const char ali_name) {
327	char *result = 0;
328	char *typePath = GBS_global_string_copy("%s/_TYPE", ali_name);
329	GBDATA *gbd = GB_search(gb_extended, typePath, GB_FIND);
330	if (gbd) {
331	const char* type = GB_read_char_pntr(gbd);
332	if (type && strncmp("PV", type, 2) == 0) {
333	gbd = GB_find(gb_extended, "name", SEARCH_CHILD);
334	result = GB_read_string(gbd);
335	}
336	}
337	free(typePath);
338	return result;
339	}
340
341	static AWT_config_mapping_def sina_config_mapping[] = {
342	// both
343	{ GA_AWAR_TGT, "target" },
344	{ GA_AWAR_OVERHANG, "overhang" },
345	{ GA_AWAR_INSERT, "insertions" },
346	{ GA_AWAR_LOWERCASE, "lowercase" },
347	{ GA_AWAR_WEIGHT, "weight" },
348	{ GA_AWAR_FULL_MINLEN, "fullminlen" },
349
350	// advanced only
351	{ GA_AWAR_SAI, "sai" },
352	{ GA_AWAR_AUTOFILTER, "autofilter" },
353	{ GA_AWAR_TURN_CHECK, "turncheck" },
354	{ GA_AWAR_REALIGN, "realign" },
355	{ GA_AWAR_GAP_PEN, "gappen" },
356	{ GA_AWAR_GAP_EXT, "gapext" },
357	{ GA_AWAR_MATCH_SCORE, "matchscore" },
358	{ GA_AWAR_MISMATCH_SCORE, "mismatchscore" },
359	{ GA_AWAR_FS_MIN, "fs_min" },
360	{ GA_AWAR_FS_MSC, "fs_minscore" },
361	{ GA_AWAR_FS_MAX, "fs_min" },
362	{ GA_AWAR_MIN_FULL, "minfull" },
363	{ GA_AWAR_KMER_LEN, "kmerlen" },
364	{ GA_AWAR_KMER_MM, "kmermm" },
365	{ GA_AWAR_MIN_LEN, "refminlen" },
366	{ GA_AWAR_GENE_START, "genestart" },
367	{ GA_AWAR_GENE_END, "geneend" },
368	{ GA_AWAR_FS_COVER_GENE, "fs_covergene" },
369	{ GA_AWAR_KMER_NOFAST, "kmernofast" },
370	{ GA_AWAR_KMER_NOREL, "kmernorel" },
371
372	// both
373	{ GA_AWAR_SHOW_DIFF, "showdiff" },
374	{ GA_AWAR_COLOR, "color" },
375	{ GA_AWAR_SHOW_DIST, "showdist" },
376
377	{ 0, 0 }
378	};
379
380	static AW_window_simple* new_sina_simple(AW_root root, const AlignDataAccess alignData, bool adv) {
381	int closex, closey, startx, starty, winx, winy;
382	const int hgap = 10;
383	AW_window_simple *aws = new AW_window_simple;
384
385	aws->init(root, adv ? "XSINA" : "SINA", "SINA (SILVA Incremental Aligner)");
386
387	aws->button_length(12);
388	aws->at(10, 10);
389	aws->auto_space(5, 5);
390
391	aws->callback(AW_POPDOWN);
392	aws->create_button("CLOSE", "CLOSE", "O");
393	aws->get_at_position(&closex, &closey);
394
395	aws->at_shift(10, 0);
396	aws->label_length(0);
397	aws->label("Show advanced options");
398	aws->create_toggle(GA_AWAR_ADVANCED);
399
400	bool cbInstalled = false;
401	if (!cbInstalled) {
402	root->awar(GA_AWAR_ADVANCED)->add_callback(makeRootCallback(show_sina_window, alignData));
403	cbInstalled = true;
404	}
405
406	aws->at_newline();
407	aws->at_shift(0, hgap);
408	aws->label_length(15);
409	aws->create_toggle_field(GA_AWAR_TGT, "Align what?", "A");
410	aws->insert_toggle("Current Species:", "C", 0);
411	aws->insert_toggle("Selected Species", "S", 1);
412	aws->insert_default_toggle("Marked Species", "M", 2);
413	aws->update_toggle_field();
414
415	aws->at_shift(0, 3);
416	aws->create_input_field(AWAR_SPECIES_NAME, 20);
417
418	aws->at_newline();
419	aws->at_shift(0, hgap);
420	aws->button_length(24);
421	aws->label("PT Server:");
422	awt_create_PTSERVER_selection_button(aws, AWAR_PT_SERVER);
423
424	aws->at_newline();
425	aws->label_length(0);
426	aws->label("Overhang placement");
427	aws->create_option_menu(GA_AWAR_OVERHANG, true);
428	aws->insert_option("keep attached", 0, "attach");
429	aws->insert_option("move to edge", 0, "edge");
430	aws->insert_option("remove", 0, "remove");
431	aws->update_option_menu();
432
433	aws->at_newline();
434	aws->label("Handling of unmappable insertions");
435	aws->create_option_menu(GA_AWAR_INSERT, true);
436	aws->insert_option("Shift surrounding bases", 0, "shift");
437	aws->insert_option("Forbid during DP alignment", 0, "forbid");
438	aws->insert_option("Delete bases", 0, "remove");
439	aws->update_option_menu();
440
441	aws->at_newline();
442	aws->label("Character Case");
443	aws->create_option_menu(GA_AWAR_LOWERCASE, true);
444	aws->insert_option("Do not modify", 0, "original");
445	aws->insert_option("Show unaligned bases as lower case", 0, "unaligned");
446	aws->insert_option("Uppercase all", 0, "none");
447	aws->update_option_menu();
448
449	aws->at_newline();
450	aws->label("Family conservation weight (0-1)");
451	aws->create_input_field(GA_AWAR_WEIGHT, 3);
452
453	aws->at_newline();
454	aws->label("Size of full-length sequences");
455	aws->create_input_field(GA_AWAR_FULL_MINLEN, 5);
456
457	if (adv) {
458	aws->at_newline();
459	aws->at_shift(0, hgap);
460
461	aws->at_newline();
462
463	aws->label("Pos. Var.:");
464	awt_create_SAI_selection_button(GLOBAL_gb_main, aws, GA_AWAR_SAI, makeSaiSelectionlistFilterCallback(filter_posvar_SAI_for_ali, alignData->alignment_name.c_str()));
465
466	aws->at_newline();
467	aws->label("Field used for automatic filter selection");
468	aws->create_input_field(GA_AWAR_AUTOFILTER, 20);
469
470	aws->label("Turn check");
471	aws->create_toggle(GA_AWAR_TURN_CHECK);
472
473	aws->at_newline();
474	aws->label("Realign");
475	aws->create_toggle(GA_AWAR_REALIGN);
476
477	/*
478	aws->at_newline();
479	aws->label("(Copy and) mark sequences used as reference");
480	aws->create_toggle(GA_AWAR_COPYMARKREF);
481	*/
482
483	aws->at_newline();
484	aws->at_shift(0, hgap);
485	aws->label_length(0);
486
487	aws->label("Gap insertion/extension penalties");
488	aws->create_input_field(GA_AWAR_GAP_PEN, 5);
489	aws->create_input_field(GA_AWAR_GAP_EXT, 5);
490
491	aws->at_newline();
492	aws->label("Match score");
493	aws->create_input_field(GA_AWAR_MATCH_SCORE, 3);
494	aws->label("Mismatch score");
495	aws->create_input_field(GA_AWAR_MISMATCH_SCORE, 3);
496
497	aws->at_newline();
498	aws->label("Family search min/min_score/max");
499	aws->create_input_field(GA_AWAR_FS_MIN, 3);
500	aws->create_input_field(GA_AWAR_FS_MSC, 3);
501	aws->create_input_field(GA_AWAR_FS_MAX, 3);
502
503	aws->at_newline();
504	aws->label("Minimal number of full length sequences");
505	aws->create_input_field(GA_AWAR_MIN_FULL, 3);
506
507	aws->at_newline();
508	aws->label("Family search oligo length / mismatches");
509	aws->create_input_field(GA_AWAR_KMER_LEN, 3);
510	aws->create_input_field(GA_AWAR_KMER_MM, 3);
511
512	aws->at_newline();
513	aws->label("Minimal reference sequence length");
514	aws->create_input_field(GA_AWAR_MIN_LEN, 5);
515
516	aws->at_newline();
517	aws->label("Alignment bounds: start");
518	aws->create_input_field(GA_AWAR_GENE_START, 6);
519	aws->label("end");
520	aws->create_input_field(GA_AWAR_GENE_END, 6);
521
522	aws->at_newline();
523	aws->label("Number of references required to touch bounds");
524	aws->create_input_field(GA_AWAR_FS_COVER_GENE, 3);
525
526	aws->at_newline();
527	aws->label("Disable fast search");
528	aws->create_toggle(GA_AWAR_KMER_NOFAST);
529
530	aws->at_newline();
531	aws->label("Score search results by absolute oligo match count");
532	aws->create_toggle(GA_AWAR_KMER_NOREL);
533
534	aws->at_newline();
535	aws->label("SINA command");
536	aws->create_input_field(GA_AWAR_CMD, 20);
537
538	aws->at_shift(0, hgap);
539	}
540
541	aws->at_newline();
542	aws->at_shift(0, hgap);
543
544	aws->label_length(17);
545	aws->label("Protection Level");
546	aws->create_option_menu(GA_AWAR_PROTECTION, true);
547	aws->insert_option("0", 0, 0);
548	aws->insert_option("1", 0, 1);
549	aws->insert_option("2", 0, 2);
550	aws->insert_option("3", 0, 3);
551	aws->insert_option("4", 0, 4);
552	aws->insert_option("5", 0, 5);
553	aws->insert_option("6", 0, 6);
554	aws->update_option_menu();
555
556	aws->at_newline();
557	aws->label("Show changed sections of alignment");
558	aws->create_toggle(GA_AWAR_SHOW_DIFF);
559	aws->label("color bases");
560	aws->create_toggle(GA_AWAR_COLOR);
561
562	aws->at_newline();
563	aws->label("Show statistics");
564	aws->create_toggle(GA_AWAR_SHOW_DIST);
565
566	aws->get_window_size(winx, winy);
567	aws->get_at_position(&startx, &starty);
568
569	aws->button_length(12);
570
571	aws->at(winx-closex+5, closey);
572	aws->callback(makeHelpCallback("sina_main.hlp"));
573	aws->create_button("HELP", "HELP");
574
575	aws->at(winx-closex+5, starty);
576	aws->callback(makeWindowCallback(sina_start, alignData));
577	aws->highlight();
578	aws->create_button("Start", "Start", "S");
579
580	aws->at(winx-50, starty-50);
581	AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "sina", sina_config_mapping);
582
583	return aws;
584	}
585
586	void show_sina_window(UNFIXED, const AlignDataAccess *alignData) {
587	AW_root *root = AW_root::SINGLETON;
588
589	static AW_window_simple *ga_aws = new_sina_simple(root, alignData, false);
590	static AW_window_simple *ga_aws_adv = new_sina_simple(root, alignData, true);
591
592	if (root->awar(GA_AWAR_ADVANCED)->read_int()) {
593	ga_aws_adv->show();
594	ga_aws->hide();
595	}
596	else {
597	ga_aws->show();
598	ga_aws_adv->hide();
599	}
600	}
601

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