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graph_aligner_gui.cxx

Revision 8696, 22.3 KB (checked in by westram, 3 weeks ago)
merge from saiali [8634:8695] unalign center (blockop) modify SAI range (using ACI/SRT) align ranges defined by SAI refactorings block ops selection lists

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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 <servercntrl.h>
24	#include <PT_com.h>
25	#include <client.h>
26	#include <arbdbt.h>
27	#include <arb_strbuf.h>
28
29	#include <sys/types.h>
30	#include <sys/wait.h>
31
32	#include <unistd.h>
33
34	#include <string>
35	#include <sstream>
36	#include <iostream>
37	#include <vector>
38
39
40	using std::cerr;
41	using std::cout;
42	using std::endl;
43
44	#define GA_AWAR_ROOT "sina/"
45	#define GA_AWAR_CMD GA_AWAR_ROOT "command"
46	#define GA_AWAR_TGT GA_AWAR_ROOT "target"
47	#define GA_AWAR_SAI GA_AWAR_ROOT "sai"
48	#define GA_AWAR_ALIGNMENT GA_AWAR_ROOT "alignment"
49	#define GA_AWAR_PROTECTION GA_AWAR_ROOT "protection"
50	#define GA_AWAR_TURN_CHECK GA_AWAR_ROOT "turncheck"
51	#define GA_AWAR_LOGLEVEL GA_AWAR_ROOT "loglevel"
52	#define GA_AWAR_REALIGN GA_AWAR_ROOT "realign"
53	#define GA_AWAR_PTLOAD GA_AWAR_ROOT "ptload"
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, "none", db1);
89	root->awar_int(GA_AWAR_PROTECTION, 0, db1);
90	root->awar_string(GA_AWAR_LOGLEVEL, "3", db1); // @@@ change to int?
91	root->awar_int(GA_AWAR_TURN_CHECK, 1, db1);
92	root->awar_int(GA_AWAR_REALIGN, 1, db1);
93	root->awar_int(GA_AWAR_PTLOAD, 0, db1);
94	root->awar_int(GA_AWAR_COPYMARKREF, 0, db1);
95	root->awar_float(GA_AWAR_GAP_PEN, 5.0, db1);
96	root->awar_float(GA_AWAR_GAP_EXT, 2.0, db1);
97	root->awar_float(GA_AWAR_MATCH_SCORE, 2.0, db1);
98	root->awar_float(GA_AWAR_MISMATCH_SCORE, -1.0, db1);
99	root->awar_int(GA_AWAR_ADVANCED, 0, db1);
100	root->awar_int(GA_AWAR_FS_MIN, 40, db1);
101	root->awar_int(GA_AWAR_FS_MAX, 40, db1);
102	root->awar_float(GA_AWAR_FS_MSC, .7, db1);
103	root->awar_int(GA_AWAR_MIN_FULL, 1, db1);
104	root->awar_int(GA_AWAR_FULL_MINLEN, 1400, db1);
105	root->awar_string(GA_AWAR_OVERHANG, "attach", db1);
106	root->awar_int(GA_AWAR_THREADS, 1, db1);
107	root->awar_int(GA_AWAR_QSIZE, 1, db1);
108	root->awar_int(GA_AWAR_KMER_LEN, 10, db1);
109	root->awar_int(GA_AWAR_KMER_MM, 0, db1);
110	root->awar_int(GA_AWAR_MIN_LEN, 150, db1);
111	root->awar_float(GA_AWAR_WEIGHT, 1, db1);
112	root->awar_string(GA_AWAR_INSERT, "shift", db1);
113	root->awar_string(GA_AWAR_LOWERCASE, "none", db1);
114	root->awar_string(GA_AWAR_AUTOFILTER, "none", db1);
115	root->awar_int(GA_AWAR_KMER_NOREL, 0, db1);
116	root->awar_int(GA_AWAR_KMER_NOFAST, 0, db1);
117	root->awar_int(GA_AWAR_SHOW_DIST, 0, db1);
118	root->awar_int(GA_AWAR_SHOW_DIFF, 0, db1);
119	root->awar_int(GA_AWAR_COLOR, 1, db1);
120	root->awar_int(GA_AWAR_GENE_START, 0, db1);
121	root->awar_int(GA_AWAR_GENE_END, 0, db1);
122	root->awar_int(GA_AWAR_FS_COVER_GENE, 1, db1);
123	}
124
125	AW_active sina_mask(AW_root *root) {
126	const char *sinaName = root->awar(GA_AWAR_CMD)->read_char_pntr();
127	char *sina = GB_executable(sinaName);
128	const char *fail_reason = 0;
129
130	if (sina) {
131	int exitstatus = system(GBS_global_string("%s --has-cli-vers ARB5.99", sina));
132	exitstatus = WEXITSTATUS(exitstatus);
133
134	switch (exitstatus) {
135	case EXIT_SUCCESS:
136	break;
137
138	case EXIT_FAILURE:
139	fail_reason = "Incompatible SINA and ARB versions";
140	break;
141
142	case 127: // libs missing
143	default: // unexpected
144	fail_reason = GBS_global_string("Could execute SINA binary '%s' (exitstatus was %i)",
145	sinaName, exitstatus);
146	break;
147	}
148	free(sina);
149	}
150	else {
151	fail_reason = GBS_global_string("%s not found", sinaName);
152	}
153
154	if (fail_reason) {
155	fprintf(stderr,
156	"Note: SINA (SILVA Aligner) disabled (Reason: %s)\n"
157	" Visit http://www.ribocon.com/sina/ for more information.\n",
158	fail_reason);
159	}
160
161	return fail_reason ? AWM_DISABLED : AWM_ALL;
162	}
163
164	inline const char *stream2static(const std::stringstream& str) {
165	return GBS_global_string("%s", str.str().c_str());
166	}
167
168	static void sina_start(AW_window *window, AW_CL cl_AlignDataAccess) {
169	cerr << "Starting SINA..." << endl;
170
171	// make string from pt server selection
172	AW_root *root = window->get_root();
173	int pt = root->awar(AWAR_PT_SERVER)->read_int();
174
175	std::stringstream ptnam;
176	ptnam << "ARB_PT_SERVER" << pt;
177
178	const char *pt_server = GBS_read_arb_tcp(ptnam.str().c_str());
179	GB_ERROR gb_error = NULL;
180
181	if (!pt_server) gb_error = "Unable to find definition for chosen PT-server";
182	else {
183	const char *pt_db = pt_server + strlen(pt_server) + 1;
184	pt_db += strlen(pt_db)+3;
185
186	// start pt server if necessary
187	gb_error = arb_look_and_start_server(AISC_MAGIC_NUMBER, ptnam.str().c_str());
188	if (gb_error) {
189	std::stringstream tmp;
190	tmp << "Cannot contact PT server. Aborting" << endl
191	<< " ID: \"" << tmp.str().c_str()
192	<< "\" PORT: \"" << pt_server
193	<< "\" DB: \"" << pt_db << endl
194	<< "\" GBERROR: \"" << gb_error << "\"" << endl;
195	gb_error = stream2static(tmp);
196	}
197	else {
198	// create temporary file
199	char* tmpfile;
200	FILE* tmpfile_F;
201	{
202	char* tmpfile_tpl = GB_unique_filename("sina_select", "tmp");
203	tmpfile_F = GB_fopen_tempfile(tmpfile_tpl, "w", &tmpfile);
204	free(tmpfile_tpl);
205	}
206
207	if (!tmpfile_F) {
208	std::stringstream tmp;
209	tmp << "Error: Unable to create temporary file \"" << tmpfile << "\"!";
210	gb_error = stream2static(tmp);
211	}
212	else {
213	GB_remove_on_exit(tmpfile);
214
215	std::vector<std::string> spec_names;
216	switch (root->awar(GA_AWAR_TGT)->read_int()) {
217	case 0: { // current
218	char *spec_name = root->awar(AWAR_SPECIES_NAME)->read_string();
219	if (spec_name) {
220	fwrite(spec_name, strlen(spec_name), 1, tmpfile_F);
221	fwrite("\n", 1, 1, tmpfile_F);
222	}
223	else {
224	gb_error = "Unable to get name of currently active species";
225	}
226	free(spec_name);
227	break;
228	}
229	case 1: { // selected
230	const AlignDataAccess data_access = (const AlignDataAccess )cl_AlignDataAccess;
231	GB_begin_transaction(GLOBAL_gb_main);
232	int num_selected = 0;
233	for (GBDATA *gb_spec = data_access->get_first_selected_species(&num_selected);
234	gb_spec;
235	gb_spec = data_access->get_next_selected_species())
236	{
237	GBDATA *gbd_name = GB_find(gb_spec, "name", SEARCH_CHILD);
238	if (gbd_name) {
239	const char *str = GB_read_char_pntr(gbd_name);
240	fwrite(str, strlen(str), 1, tmpfile_F);
241	fwrite("\n", 1, 1, tmpfile_F);
242	}
243	}
244	GB_commit_transaction(GLOBAL_gb_main);
245	break;
246	}
247	case 2: { // marked
248	GB_begin_transaction(GLOBAL_gb_main);
249	for (GBDATA *gb_spec = GBT_first_marked_species(GLOBAL_gb_main);
250	gb_spec; gb_spec = GBT_next_marked_species(gb_spec)) {
251	GBDATA *gbd_name = GB_find(gb_spec, "name", SEARCH_CHILD);
252	if (gbd_name) {
253	const char *str = GB_read_char_pntr(gbd_name);
254	fwrite(str, strlen(str), 1, tmpfile_F);
255	fwrite("\n", 1, 1, tmpfile_F);
256	}
257	}
258	GB_commit_transaction(GLOBAL_gb_main);
259	break;
260	}
261	}
262	fclose(tmpfile_F);
263
264	if (!gb_error) {
265	// build command line
266	GBS_strstruct *cl = GBS_stropen(2000);
267
268	GBS_strcat(cl, root->awar(GA_AWAR_CMD)->read_char_pntr());
269	GBS_strcat(cl, " -i :");
270	GBS_strcat(cl, " --ptdb "); GBS_strcat(cl, root->awar(GA_AWAR_PTLOAD)->read_int() ? pt_db : ":");
271	GBS_strcat(cl, " --ptport "); GBS_strcat(cl, pt_server);
272	GBS_strcat(cl, " --turn "); GBS_strcat(cl, root->awar(GA_AWAR_TURN_CHECK)->read_int() ? "all" : "none");
273	GBS_strcat(cl, " --overhang "); GBS_strcat(cl, root->awar(GA_AWAR_OVERHANG)->read_char_pntr());
274	GBS_strcat(cl, " --filter "); GBS_strcat(cl, root->awar(GA_AWAR_SAI)->read_char_pntr());
275	GBS_strcat(cl, " --fs-min "); GBS_intcat(cl, root->awar(GA_AWAR_FS_MIN)->read_int());
276	GBS_strcat(cl, " --fs-msc "); GBS_floatcat(cl, root->awar(GA_AWAR_FS_MSC)->read_float());
277	GBS_strcat(cl, " --fs-max "); GBS_intcat(cl, root->awar(GA_AWAR_FS_MAX)->read_int());
278	GBS_strcat(cl, " --fs-req 1");
279	GBS_strcat(cl, " --fs-req-full "); GBS_intcat(cl, root->awar(GA_AWAR_MIN_FULL)->read_int());
280	GBS_strcat(cl, " --fs-full-len "); GBS_intcat(cl, root->awar(GA_AWAR_FULL_MINLEN)->read_int());
281	GBS_strcat(cl, " --fs-kmer-len "); GBS_intcat(cl, root->awar(GA_AWAR_KMER_LEN)->read_int());
282	GBS_strcat(cl, " --fs-kmer-mm "); GBS_intcat(cl, root->awar(GA_AWAR_KMER_MM)->read_int());
283	GBS_strcat(cl, " --fs-min-len "); GBS_intcat(cl, root->awar(GA_AWAR_MIN_LEN)->read_int());
284	GBS_strcat(cl, " --fs-weight "); GBS_intcat(cl, root->awar(GA_AWAR_WEIGHT)->read_float());
285	GBS_strcat(cl, " --pen-gap "); GBS_floatcat(cl, root->awar(GA_AWAR_GAP_PEN)->read_float());
286	GBS_strcat(cl, " --pen-gapext "); GBS_floatcat(cl, root->awar(GA_AWAR_GAP_EXT)->read_float());
287	GBS_strcat(cl, " --match-score "); GBS_floatcat(cl, root->awar(GA_AWAR_MATCH_SCORE)->read_float());
288	GBS_strcat(cl, " --mismatch-score "); GBS_floatcat(cl, root->awar(GA_AWAR_MISMATCH_SCORE)->read_float());
289	GBS_strcat(cl, " --prot-level "); GBS_intcat(cl, root->awar(GA_AWAR_PROTECTION)->read_int());
290	GBS_strcat(cl, " --select-file "); GBS_strcat(cl, tmpfile);
291	GBS_strcat(cl, " --insertion "); GBS_strcat(cl, root->awar(GA_AWAR_INSERT)->read_char_pntr());
292	GBS_strcat(cl, " --lowercase "); GBS_strcat(cl, root->awar(GA_AWAR_LOWERCASE)->read_char_pntr());
293	GBS_strcat(cl, " --auto-filter-field "); GBS_strcat(cl, root->awar(GA_AWAR_AUTOFILTER)->read_char_pntr());
294	GBS_strcat(cl, " --gene-start "); GBS_intcat(cl, root->awar(GA_AWAR_GENE_START)->read_int());
295	GBS_strcat(cl, " --gene-end "); GBS_intcat(cl, root->awar(GA_AWAR_GENE_END)->read_int());
296	GBS_strcat(cl, " --fs-cover-gene ");GBS_intcat(cl, root->awar(GA_AWAR_FS_COVER_GENE)->read_int());
297
298
299	if (root->awar(GA_AWAR_KMER_NOREL)->read_int()) GBS_strcat(cl, " --fs-kmer-norel ");
300	if (root->awar(GA_AWAR_KMER_NOFAST)->read_int()) GBS_strcat(cl, " --fs-kmer-no-fast ");
301	if (root->awar(GA_AWAR_SHOW_DIST)->read_int()) GBS_strcat(cl, " --show-dist ");
302	if (root->awar(GA_AWAR_SHOW_DIFF)->read_int()) GBS_strcat(cl, " --show-diff ");
303	if (root->awar(GA_AWAR_COLOR)->read_int()) GBS_strcat(cl, " --color");
304	if (root->awar(GA_AWAR_REALIGN)->read_int()) GBS_strcat(cl, " --realign");
305
306	gb_error = GB_xcmd(GBS_mempntr(cl), true, false);
307	GBS_strforget(cl);
308	}
309
310	if (!gb_error) aw_message("SINA finished aligning.");
311	}
312	free(tmpfile);
313	}
314	}
315
316	aw_message_if(gb_error);
317	}
318
319
320
321	static char* filter_sai(GBDATA *gb_extended, AW_CL) {
322	char *result = 0;
323	GBDATA *gbd = GB_search(gb_extended, "ali_16s/_TYPE", GB_FIND);
324	if (gbd) {
325	const char* type = GB_read_char_pntr(gbd);
326	if (type && strncmp("PV", type, 2) == 0) {
327	gbd = GB_find(gb_extended, "name", SEARCH_CHILD);
328	result = GB_read_string(gbd);
329	}
330	}
331	return result;
332	}
333
334	static AW_window_simple* new_sina_simple(AW_root *root, AW_CL cl_AlignDataAccess, bool adv) {
335	int closex, closey, startx, starty, winx, winy;
336	const int hgap = 10;
337	AW_window_simple *aws = new AW_window_simple;
338
339	aws->init(root, "SINA", "SINA (SILVA Incremental Aligner)");
340
341	aws->button_length(12);
342	aws->at(10, 10);
343	aws->auto_space(5, 5);
344
345	aws->callback(AW_POPDOWN);
346	aws->create_button("CLOSE", "CLOSE", "O");
347	aws->get_at_position(&closex, &closey);
348
349	aws->at_shift(10, 0);
350	aws->callback(show_sina_window, cl_AlignDataAccess, 0);
351	aws->label_length(0);
352	aws->label("Show advanced options");
353	aws->create_toggle(GA_AWAR_ADVANCED);
354
355	aws->at_newline();
356	aws->at_shift(0, hgap);
357	aws->label_length(15);
358	aws->create_toggle_field(GA_AWAR_TGT, "Align what?", "A");
359	aws->insert_toggle("Current Species:", "C", 0);
360	aws->insert_toggle("Selected Species", "S", 1);
361	aws->insert_default_toggle("Marked Species", "M", 2);
362	aws->update_toggle_field();
363
364	aws->at_shift(0, 3);
365	aws->create_input_field(AWAR_SPECIES_NAME, 20);
366
367	aws->at_newline();
368	aws->at_shift(0, hgap);
369	aws->button_length(24);
370	aws->label("PT Server:");
371	awt_create_selection_list_on_pt_servers(aws, AWAR_PT_SERVER, true);
372
373	aws->at_newline();
374	aws->label_length(0);
375	aws->create_option_menu(GA_AWAR_OVERHANG, "Overhang placement");
376	aws->insert_option("keep attached", 0, "attach");
377	aws->insert_option("move to edge", 0, "edge");
378	aws->insert_option("remove", 0, "remove");
379	aws->update_option_menu();
380
381	aws->at_newline();
382	aws->create_option_menu(GA_AWAR_INSERT, "Handling of unmappable insertions", "I");
383	aws->insert_option("Shift surrounding bases", 0, "shift");
384	aws->insert_option("Forbid during DP alignment", 0, "forbid");
385	aws->insert_option("Delete bases", 0, "remove");
386	aws->update_option_menu();
387
388	aws->at_newline();
389	aws->create_option_menu(GA_AWAR_LOWERCASE, "Character Case","C");
390	aws->insert_option("Do not modify", 0, "original");
391	aws->insert_option("Show unaligned bases as lower case", 0, "unaligned");
392	aws->insert_option("Uppercase all", 0, "none");
393	aws->update_option_menu();
394
395	aws->at_newline();
396	aws->label("Family conservation weight (0-1)");
397	aws->create_input_field(GA_AWAR_WEIGHT, 3);
398
399	aws->at_newline();
400	aws->label("Size of full-length sequences");
401	aws->create_input_field(GA_AWAR_FULL_MINLEN, 5);
402
403	if (adv) {
404	aws->at_newline();
405	aws->at_shift(0, hgap);
406
407	aws->at_newline();
408
409	aws->label("Pos. Var.:");
410	awt_create_SAI_selection_button(GLOBAL_gb_main, aws, GA_AWAR_SAI, filter_sai, 0);
411
412	aws->at_newline();
413	aws->label("Field used for automatic filter selection");
414	aws->create_input_field(GA_AWAR_AUTOFILTER, 20);
415
416	aws->label("Turn check");
417	aws->create_toggle(GA_AWAR_TURN_CHECK);
418
419	aws->at_newline();
420	aws->label("Realign");
421	aws->create_toggle(GA_AWAR_REALIGN);
422
423	aws->at_newline();
424	aws->label("Load reference sequences from PT-Server");
425	aws->create_toggle(GA_AWAR_PTLOAD);
426
427	/*
428	aws->at_newline();
429	aws->label("(Copy and) mark sequences used as reference");
430	aws->create_toggle(GA_AWAR_COPYMARKREF);
431	*/
432
433	aws->at_newline();
434	aws->at_shift(0, hgap);
435	aws->label_length(0);
436
437	aws->label("Gap insertion/extension penalties");
438	aws->create_input_field(GA_AWAR_GAP_PEN, 5);
439	aws->create_input_field(GA_AWAR_GAP_EXT, 5);
440
441	aws->at_newline();
442	aws->label("Match score");
443	aws->create_input_field(GA_AWAR_MATCH_SCORE, 3);
444	aws->label("Mismatch score");
445	aws->create_input_field(GA_AWAR_MISMATCH_SCORE, 3);
446
447	aws->at_newline();
448	aws->label("Family search min/min_score/max");
449	aws->create_input_field(GA_AWAR_FS_MIN, 3);
450	aws->create_input_field(GA_AWAR_FS_MSC, 3);
451	aws->create_input_field(GA_AWAR_FS_MAX, 3);
452
453	aws->at_newline();
454	aws->label("Minimal number of full length sequences");
455	aws->create_input_field(GA_AWAR_MIN_FULL, 3);
456
457	aws->at_newline();
458	aws->label("Family search oligo length / mismatches");
459	aws->create_input_field(GA_AWAR_KMER_LEN, 3);
460	aws->create_input_field(GA_AWAR_KMER_MM, 3);
461
462	aws->at_newline();
463	aws->label("Minimal reference sequence length");
464	aws->create_input_field(GA_AWAR_MIN_LEN, 5);
465
466	aws->at_newline();
467	aws->label("Alignment bounds: start");
468	aws->create_input_field(GA_AWAR_GENE_START, 6);
469	aws->label("end");
470	aws->create_input_field(GA_AWAR_GENE_END, 6);
471
472	aws->at_newline();
473	aws->label("Number of references required to touch bounds");
474	aws->create_input_field(GA_AWAR_FS_COVER_GENE, 3);
475
476	aws->at_newline();
477	aws->label("Disable fast search");
478	aws->create_toggle(GA_AWAR_KMER_NOFAST);
479
480	aws->at_newline();
481	aws->label("Score search results by absolute oligo match count");
482	aws->create_toggle(GA_AWAR_KMER_NOREL);
483
484	aws->at_newline();
485	aws->label("SINA command");
486	aws->create_input_field(GA_AWAR_CMD, 20);
487
488	aws->at_shift(0, hgap);
489	}
490
491	aws->at_newline();
492	aws->at_shift(0, hgap);
493
494	aws->label_length(17);
495	aws->create_option_menu(GA_AWAR_PROTECTION, "Protection Level", "P");
496	aws->insert_option("0", 0, 0);
497	aws->insert_option("1", 0, 1);
498	aws->insert_option("2", 0, 2);
499	aws->insert_option("3", 0, 3);
500	aws->insert_option("4", 0, 4);
501	aws->insert_option("5", 0, 5);
502	aws->insert_option("6", 0, 6);
503	aws->update_option_menu();
504
505	/*
506	aws->at_newline();
507	aws->create_option_menu(GA_AWAR_LOGLEVEL, "Logging level", "L");
508	aws->insert_option("silent", 0, "1");
509	aws->insert_option("quiet", 0, "2");
510	aws->insert_default_option("normal", 0, "3");
511	aws->insert_option("verbose", 0, "4");
512	aws->insert_option("debug", 0, "5");
513	aws->insert_option("debug more", 0, "6");
514	aws->update_option_menu();
515	*/
516
517	aws->at_newline();
518	aws->label("Show changed sections of alignment");
519	aws->create_toggle(GA_AWAR_SHOW_DIFF);
520	aws->label("color bases");
521	aws->create_toggle(GA_AWAR_COLOR);
522
523	aws->at_newline();
524	aws->label("Show statistics");
525	aws->create_toggle(GA_AWAR_SHOW_DIST);
526
527	aws->get_window_size(winx, winy);
528	aws->get_at_position(&startx, &starty);
529
530	aws->button_length(12);
531
532	aws->at(winx-closex+5, closey);
533	aws->callback(AW_POPUP_HELP, (AW_CL) "sina_main.hlp");
534	aws->create_button("HELP", "HELP");
535
536	aws->at(winx-closex+5, starty);
537	aws->callback(sina_start, cl_AlignDataAccess);
538	aws->highlight();
539	aws->create_button("Start", "Start", "S");
540
541	return aws;
542	}
543
544	void show_sina_window(AW_window *aw, AW_CL cl_AlignDataAccess, AW_CL) {
545	static AW_window_simple *ga_aws = 0;
546	static AW_window_simple *ga_aws_adv = 0;
547
548	AW_root *root = aw->get_root();
549	if (root->awar(GA_AWAR_ADVANCED)->read_int()) {
550	if (!ga_aws_adv) ga_aws_adv = new_sina_simple(root, cl_AlignDataAccess, true);
551	ga_aws_adv->show();
552	if (ga_aws) ga_aws->hide();
553	}
554	else {
555	if (!ga_aws) ga_aws = new_sina_simple(root, cl_AlignDataAccess, false);
556	ga_aws->show();
557	if (ga_aws_adv) ga_aws_adv->hide();
558	}
559	}

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root/trunk/EDIT4/graph_aligner_gui.cxx

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