1 | #include "phylo.hxx" |
---|
2 | #include "phwin.hxx" |
---|
3 | #include "PH_display.hxx" |
---|
4 | |
---|
5 | #include <awt_sel_boxes.hxx> |
---|
6 | #include <aw_preset.hxx> |
---|
7 | |
---|
8 | #include <awt.hxx> |
---|
9 | |
---|
10 | #include <cstdlib> |
---|
11 | #include <cstring> |
---|
12 | #include <iostream> |
---|
13 | |
---|
14 | using namespace std; |
---|
15 | |
---|
16 | extern void ph_view_matrix_cb(AW_window *); |
---|
17 | extern void ph_view_species_cb(AW_window *,AW_CL,AW_CL); |
---|
18 | extern void ph_view_filter_cb(AW_window *,AW_CL,AW_CL); |
---|
19 | extern void ph_calculate_matrix_cb(AW_window *,AW_CL,AW_CL); |
---|
20 | extern void PH_create_save_matrix_window(AW_root *,char *); |
---|
21 | extern void display_status(AW_window *,AW_CL,AW_CL); |
---|
22 | |
---|
23 | AW_HEADER_MAIN |
---|
24 | AW_window *create_tree_window(AW_root *aw_root); |
---|
25 | |
---|
26 | GBDATA *GLOBAL_gb_main; // global gb_main for arb_phylo |
---|
27 | char **filter_text; |
---|
28 | |
---|
29 | GB_ERROR ph_check_initialized() { |
---|
30 | if (!PHDATA::ROOT) return "Please select alignment and press DONE"; |
---|
31 | return 0; |
---|
32 | } |
---|
33 | |
---|
34 | void create_filter_text() |
---|
35 | { |
---|
36 | filter_text = (char **) calloc(FILTER_MODES,sizeof (char *)); |
---|
37 | for(int i=0;i<FILTER_MODES;i++) filter_text[i] = new char[100]; |
---|
38 | |
---|
39 | strcpy(filter_text[DONT_COUNT], "don't count (ignore) "); |
---|
40 | strcpy(filter_text[SKIP_COLUMN_IF_MAX], "if occurs most often => forget whole column "); |
---|
41 | strcpy(filter_text[SKIP_COLUMN_IF_OCCUR], "if occurs => forget whole column "); |
---|
42 | strcpy(filter_text[COUNT_DONT_USE_MAX], "count, but do NOT use as maximum "); |
---|
43 | strcpy(filter_text[TREAT_AS_UPPERCASE], "treat as uppercase character "); |
---|
44 | strcpy(filter_text[TREAT_AS_REGULAR], "treat as regular character "); |
---|
45 | } |
---|
46 | |
---|
47 | void startup_sequence_cb(AW_window *aww,AW_CL cd1, AW_CL cl_aww) |
---|
48 | { |
---|
49 | PHDATA *phd; |
---|
50 | char *use,*load_what; |
---|
51 | AW_root *aw_root; |
---|
52 | |
---|
53 | if(aww) aww->hide(); |
---|
54 | aw_root=(AW_root *) cd1; |
---|
55 | // loading database |
---|
56 | GB_push_transaction(GLOBAL_gb_main); |
---|
57 | if(GBT_get_alignment_len(GLOBAL_gb_main,aw_root->awar("phyl/alignment")->read_string())<1) { |
---|
58 | aw_root->awar("phyl/alignment")->write_string(GBT_get_default_alignment(GLOBAL_gb_main)); |
---|
59 | } |
---|
60 | GB_pop_transaction(GLOBAL_gb_main); |
---|
61 | |
---|
62 | use = aw_root->awar("phyl/alignment")->read_string(); |
---|
63 | load_what = aw_root->awar("phyl/which_species")->read_string(); // all, marked ... |
---|
64 | phd=new PHDATA(aw_root); |
---|
65 | GB_set_cache_size(GLOBAL_gb_main, PH_DB_CACHE_SIZE); |
---|
66 | phd->load(use); |
---|
67 | phd->ROOT = phd; |
---|
68 | long len = PHDATA::ROOT->get_seq_len(); |
---|
69 | aw_root->awar("phyl/filter/stopcol")->write_int(len ); |
---|
70 | aw_root->awar("phyl/filter/startcol")->set_minmax(0,len); |
---|
71 | aw_root->awar("phyl/filter/stopcol")->set_minmax(0,len); |
---|
72 | |
---|
73 | ((AW_window*)cl_aww)->activate(); // pop up main window |
---|
74 | ph_view_species_cb(0,0,0); |
---|
75 | } |
---|
76 | |
---|
77 | ATTRIBUTED(__ATTR__NORETURN, static void ph_exit(AW_window *aw_window, PH_root *ph_root)) |
---|
78 | { |
---|
79 | AWUSE(aw_window); |
---|
80 | GBDATA *gb_main = ph_root->gb_main; |
---|
81 | if (gb_main) { |
---|
82 | aw_window->get_root()->unlink_awars_from_DB(gb_main); |
---|
83 | #if defined(DEBUG) |
---|
84 | AWT_browser_forget_db(gb_main); |
---|
85 | #endif // DEBUG |
---|
86 | GB_close(gb_main); |
---|
87 | } |
---|
88 | exit(0); |
---|
89 | } |
---|
90 | |
---|
91 | |
---|
92 | void expose_callb(AW_window *aw,AW_CL cd1,AW_CL cd2) |
---|
93 | { |
---|
94 | AWUSE(aw);AWUSE(cd1);AWUSE(cd2); |
---|
95 | |
---|
96 | if(PH_display::ph_display->displayed()!=NONE) |
---|
97 | { |
---|
98 | PH_display::ph_display->clear_window(); |
---|
99 | PH_display::ph_display->display(); |
---|
100 | } |
---|
101 | else // startup |
---|
102 | { |
---|
103 | //startup_sequence_cb(0,aw->get_root()); |
---|
104 | } |
---|
105 | } // expose_callb |
---|
106 | |
---|
107 | |
---|
108 | void resize_callb(AW_window *aw,AW_CL cd1,AW_CL cd2) |
---|
109 | { |
---|
110 | AWUSE(aw);AWUSE(cd1);AWUSE(cd2); |
---|
111 | if(PH_display::ph_display) |
---|
112 | { |
---|
113 | PH_display::ph_display->resized(); |
---|
114 | PH_display::ph_display->display(); |
---|
115 | } |
---|
116 | } |
---|
117 | // total_cells_horiz=PHDATA::ROOT->get_seq_len(); |
---|
118 | // { if(PHDATA::ROOT->markerline[x]>=0.0) |
---|
119 | |
---|
120 | static GB_ERROR PH_create_ml_multiline_SAI(GB_CSTR sai_name, int nr, GBDATA **gb_sai_ptr) { |
---|
121 | GBDATA *gb_sai = GBT_find_or_create_SAI(GLOBAL_gb_main, sai_name); |
---|
122 | GBDATA *gbd, *gb2; |
---|
123 | GB_ERROR error = ph_check_initialized(); |
---|
124 | |
---|
125 | if (!error) { |
---|
126 | for (gbd = GB_child(gb_sai); gbd; gbd = gb2) { |
---|
127 | gb2 = GB_nextChild(gbd); |
---|
128 | |
---|
129 | const char *key = GB_read_key_pntr(gbd); |
---|
130 | if (!strcmp(key,"name")) continue; |
---|
131 | if (!strncmp(key,"ali_",4)) continue; |
---|
132 | |
---|
133 | error = GB_delete(gbd); |
---|
134 | if (error) break; |
---|
135 | } |
---|
136 | } |
---|
137 | |
---|
138 | if (!error) { |
---|
139 | GBDATA *gb_ali = GB_search(gb_sai,PHDATA::ROOT->use,GB_FIND); |
---|
140 | if (gb_ali) { |
---|
141 | for (gbd = GB_child(gb_ali); gbd; gbd = gb2) { |
---|
142 | gb2 = GB_nextChild(gbd); |
---|
143 | |
---|
144 | const char *key = GB_read_key_pntr(gbd); |
---|
145 | if (!strcmp(key,"data")) continue; |
---|
146 | if (!strcmp(key,"_TYPE")) continue; |
---|
147 | |
---|
148 | error = GB_delete(gbd); |
---|
149 | if (error) break; |
---|
150 | } |
---|
151 | } |
---|
152 | } |
---|
153 | |
---|
154 | GBDATA *gb_data = 0, *gb_TYPE = 0; |
---|
155 | |
---|
156 | if (!error) { |
---|
157 | gb_data = GBT_add_data(gb_sai,PHDATA::ROOT->use,"data",GB_STRING); |
---|
158 | if (!gb_data) error = GB_await_error(); |
---|
159 | } |
---|
160 | |
---|
161 | if (!error) { |
---|
162 | gb_TYPE = GBT_add_data(gb_sai,PHDATA::ROOT->use,"_TYPE",GB_STRING); |
---|
163 | if (!gb_TYPE) error = GB_await_error(); |
---|
164 | } |
---|
165 | |
---|
166 | if (!error && !PHDATA::ROOT->markerline) { |
---|
167 | error = "Nothing calculated yet"; |
---|
168 | } |
---|
169 | |
---|
170 | if (!error) { |
---|
171 | char *full_save_name = 0; |
---|
172 | FILE *saveResults = 0; |
---|
173 | if (nr == 2) { |
---|
174 | char *save_name = GB_unique_filename("conservationProfile", "gnu"); |
---|
175 | saveResults = GB_fopen_tempfile(save_name, "w+", &full_save_name); |
---|
176 | GB_remove_on_exit(full_save_name); |
---|
177 | free(save_name); |
---|
178 | |
---|
179 | if (!saveResults) error = GB_await_error(); |
---|
180 | } |
---|
181 | |
---|
182 | if (!error) { |
---|
183 | AW_window *main_win = PH_used_windows::windowList->phylo_main_window; |
---|
184 | long minhom = main_win->get_root()->awar("phyl/filter/minhom")->read_int(); |
---|
185 | long maxhom = main_win->get_root()->awar("phyl/filter/maxhom")->read_int(); |
---|
186 | long startcol = main_win->get_root()->awar("phyl/filter/startcol")->read_int(); |
---|
187 | long stopcol = main_win->get_root()->awar("phyl/filter/stopcol")->read_int(); |
---|
188 | float *markerline = PHDATA::ROOT->markerline; |
---|
189 | long len = PHDATA::ROOT->get_seq_len(); |
---|
190 | |
---|
191 | char *data = (char *)calloc(sizeof(char),(int)len+1); |
---|
192 | int cnt = 0; |
---|
193 | |
---|
194 | |
---|
195 | for (int x=0;x<len;x++) { |
---|
196 | char c; |
---|
197 | |
---|
198 | if (x<startcol || x>stopcol) { |
---|
199 | c = '.'; |
---|
200 | } |
---|
201 | else { |
---|
202 | float ml = markerline[x]; |
---|
203 | if (nr==2 && ml>0.0) { |
---|
204 | ph_assert(saveResults); |
---|
205 | fprintf(saveResults, "%i\t%.2f\n", cnt, ml); |
---|
206 | cnt++; |
---|
207 | } |
---|
208 | |
---|
209 | if (ml>=0.0 && ml>=minhom && ml<=maxhom) { |
---|
210 | int digit = -1; |
---|
211 | switch (nr) { |
---|
212 | case 0: // hundred |
---|
213 | if (ml>=100.0) digit = 1; |
---|
214 | break; |
---|
215 | case 1: // ten |
---|
216 | if (ml>=10.0) digit = int(ml/10); |
---|
217 | break; |
---|
218 | case 2: // one |
---|
219 | digit = int(ml); |
---|
220 | break; |
---|
221 | default: |
---|
222 | gb_assert(0); |
---|
223 | break; |
---|
224 | } |
---|
225 | |
---|
226 | if (digit<0) c = '-'; |
---|
227 | else c = '0' + digit%10; |
---|
228 | } |
---|
229 | else { |
---|
230 | c = '-'; |
---|
231 | } |
---|
232 | } |
---|
233 | |
---|
234 | data[x] = c; |
---|
235 | } |
---|
236 | data[len] = 0; |
---|
237 | |
---|
238 | if (saveResults) { |
---|
239 | fclose(saveResults); |
---|
240 | fprintf(stderr, "Note: Frequencies as well saved to '%s'\n", full_save_name); |
---|
241 | } |
---|
242 | |
---|
243 | error = GB_write_string(gb_data, data); |
---|
244 | if (!error) { |
---|
245 | const char *buffer = GBS_global_string("FMX: Filter by Maximum Frequency: " |
---|
246 | "Start %li; Stop %li; Minhom %li%%; Maxhom %li%%", |
---|
247 | startcol, stopcol, minhom, maxhom); |
---|
248 | error = GB_write_string(gb_TYPE, buffer); |
---|
249 | } |
---|
250 | free(data); |
---|
251 | } |
---|
252 | free(full_save_name); |
---|
253 | } |
---|
254 | |
---|
255 | if (!error) *gb_sai_ptr = gb_sai; |
---|
256 | return error; |
---|
257 | } |
---|
258 | |
---|
259 | void PH_save_ml_multiline_cb(AW_window *aww) { |
---|
260 | GB_begin_transaction(GLOBAL_gb_main); |
---|
261 | GB_ERROR error = 0; |
---|
262 | char *fname = aww->get_root()->awar("tmp/phylo/markerlinename")->read_string(); |
---|
263 | int fname_len = strlen(fname); |
---|
264 | { |
---|
265 | char *digit_appended = (char*)malloc(fname_len+2); |
---|
266 | memcpy(digit_appended, fname, fname_len); |
---|
267 | strcpy(digit_appended+fname_len, "0"); |
---|
268 | |
---|
269 | freeset(fname, digit_appended); |
---|
270 | } |
---|
271 | GBDATA *gb_sai[3]; |
---|
272 | int i; |
---|
273 | for (i=0; !error && i<3; i++) { |
---|
274 | fname[fname_len] = '0'+i; |
---|
275 | error = PH_create_ml_multiline_SAI(fname, i, &gb_sai[i]); |
---|
276 | } |
---|
277 | |
---|
278 | delete fname; |
---|
279 | |
---|
280 | if (error) { |
---|
281 | GB_abort_transaction(GLOBAL_gb_main); |
---|
282 | aw_message(error); |
---|
283 | }else{ |
---|
284 | GB_commit_transaction(GLOBAL_gb_main); |
---|
285 | } |
---|
286 | } |
---|
287 | |
---|
288 | void PH_save_ml_cb(AW_window *aww) { |
---|
289 | GB_begin_transaction(GLOBAL_gb_main); |
---|
290 | GB_ERROR error = 0; |
---|
291 | |
---|
292 | char *fname = aww->get_root()->awar("tmp/phylo/markerlinename")->read_string(); |
---|
293 | GBDATA *gb_sai = GBT_find_or_create_SAI(GLOBAL_gb_main,fname); |
---|
294 | GBDATA *gbd,*gb2; |
---|
295 | |
---|
296 | error = ph_check_initialized(); |
---|
297 | |
---|
298 | if (!error) { |
---|
299 | for (gbd = GB_child(gb_sai); gbd; gbd = gb2) { |
---|
300 | gb2 = GB_nextChild(gbd); |
---|
301 | |
---|
302 | const char *key = GB_read_key_pntr(gbd); |
---|
303 | if (!strcmp(key,"name")) continue; |
---|
304 | if (!strncmp(key,"ali_",4)) continue; |
---|
305 | |
---|
306 | error = GB_delete(gbd); |
---|
307 | if (error) break; |
---|
308 | } |
---|
309 | } |
---|
310 | |
---|
311 | if (!error) { |
---|
312 | GBDATA *gb_ali = GB_search(gb_sai,PHDATA::ROOT->use,GB_FIND); |
---|
313 | if (gb_ali) { |
---|
314 | for (gbd = GB_child(gb_ali); gbd; gbd = gb2) { |
---|
315 | gb2 = GB_nextChild(gbd); |
---|
316 | |
---|
317 | const char *key = GB_read_key_pntr(gbd); |
---|
318 | if (!strcmp(key,"bits")) continue; |
---|
319 | if (!strcmp(key,"_TYPE")) continue; |
---|
320 | |
---|
321 | error = GB_delete(gbd); |
---|
322 | if (error) break; |
---|
323 | } |
---|
324 | } |
---|
325 | } |
---|
326 | |
---|
327 | GBDATA *gb_bits = 0, *gb_TYPE = 0; |
---|
328 | |
---|
329 | if (!error) { |
---|
330 | gb_bits = GBT_add_data(gb_sai,PHDATA::ROOT->use,"bits",GB_BITS); |
---|
331 | if (!gb_bits) error = GB_await_error(); |
---|
332 | } |
---|
333 | |
---|
334 | if (!error) { |
---|
335 | gb_TYPE = GBT_add_data(gb_sai,PHDATA::ROOT->use,"_TYPE",GB_STRING); |
---|
336 | if (!gb_TYPE) error = GB_await_error(); |
---|
337 | } |
---|
338 | |
---|
339 | if (!error && !PHDATA::ROOT->markerline) { |
---|
340 | error = "Nothing calculated yet"; |
---|
341 | } |
---|
342 | |
---|
343 | if (!error) { |
---|
344 | AW_window *main_win = PH_used_windows::windowList->phylo_main_window; |
---|
345 | long minhom = main_win->get_root()->awar("phyl/filter/minhom")->read_int(); |
---|
346 | long maxhom = main_win->get_root()->awar("phyl/filter/maxhom")->read_int(); |
---|
347 | long startcol = main_win->get_root()->awar("phyl/filter/startcol")->read_int(); |
---|
348 | long stopcol = main_win->get_root()->awar("phyl/filter/stopcol")->read_int(); |
---|
349 | long len = PHDATA::ROOT->get_seq_len(); |
---|
350 | char *bits = (char *)calloc(sizeof(char),(int)len+1); |
---|
351 | int x; |
---|
352 | float *markerline = PHDATA::ROOT->markerline; |
---|
353 | |
---|
354 | for (x=0;x<len;x++) { |
---|
355 | int bit; |
---|
356 | |
---|
357 | if (x < startcol || x>stopcol) { |
---|
358 | bit = 0; |
---|
359 | } |
---|
360 | else { |
---|
361 | float ml = markerline[x]; |
---|
362 | |
---|
363 | if (ml>=0.0 && ml>=minhom && ml<=maxhom) bit = 1; |
---|
364 | else bit = 0; |
---|
365 | |
---|
366 | } |
---|
367 | bits[x] = '0'+bit; |
---|
368 | } |
---|
369 | |
---|
370 | GB_write_bits(gb_bits,bits,len, "0"); |
---|
371 | char buffer[1024]; |
---|
372 | sprintf(buffer,"FMX: Filter by Maximum Frequency: " |
---|
373 | "Start %li; Stop %li; Minhom %li%%; Maxhom %li%%", |
---|
374 | startcol, stopcol, minhom, maxhom); |
---|
375 | |
---|
376 | GB_write_string(gb_TYPE,buffer); |
---|
377 | |
---|
378 | free(bits); |
---|
379 | } |
---|
380 | free(fname); |
---|
381 | |
---|
382 | if (error) { |
---|
383 | GB_abort_transaction(GLOBAL_gb_main); |
---|
384 | aw_message(error); |
---|
385 | }else{ |
---|
386 | GB_commit_transaction(GLOBAL_gb_main); |
---|
387 | } |
---|
388 | } |
---|
389 | |
---|
390 | |
---|
391 | AW_window *PH_save_markerline(AW_root *root, AW_CL cl_multi_line) |
---|
392 | { |
---|
393 | int multi_line = int(cl_multi_line); // ==1 -> save three SAI's usable as column percentage |
---|
394 | |
---|
395 | root->awar_string("tmp/phylo/markerlinename","markerline",AW_ROOT_DEFAULT); |
---|
396 | |
---|
397 | AW_window_simple *aws = new AW_window_simple; |
---|
398 | |
---|
399 | if (multi_line) { |
---|
400 | aws->init( root, "EXPORT_FREQUENCY_LINES", "Export Frequency Lines"); |
---|
401 | } |
---|
402 | else { |
---|
403 | aws->init( root, "EXPORT_MARKER_LINE", "Export Marker Line"); |
---|
404 | } |
---|
405 | |
---|
406 | aws->load_xfig("phylo/save_markerline.fig"); |
---|
407 | |
---|
408 | aws->callback( AW_POPDOWN); |
---|
409 | aws->at("close"); |
---|
410 | aws->create_button("CLOSE","CLOSE","C"); |
---|
411 | |
---|
412 | aws->callback( AW_POPUP_HELP,(AW_CL)"ph_export_markerline.hlp"); |
---|
413 | aws->at("help"); |
---|
414 | aws->create_button("HELP","HELP","H"); |
---|
415 | |
---|
416 | aws->at("name"); |
---|
417 | aws->create_input_field("tmp/phylo/markerlinename"); |
---|
418 | |
---|
419 | aws->at("box"); |
---|
420 | awt_create_selection_list_on_extendeds(GLOBAL_gb_main,aws,"tmp/phylo/markerlinename"); |
---|
421 | |
---|
422 | aws->at("save"); |
---|
423 | if (multi_line) aws->callback(PH_save_ml_multiline_cb); |
---|
424 | else aws->callback(PH_save_ml_cb); |
---|
425 | aws->create_button("EXPORT","EXPORT","E"); |
---|
426 | |
---|
427 | return aws; |
---|
428 | } |
---|
429 | |
---|
430 | AW_window *create_phyl_main_window(AW_root *aw_root,PH_root *ph_root,AWT_graphic * awd) |
---|
431 | { |
---|
432 | AWUSE(awd); |
---|
433 | AW_window_menu_modes *awm = new AW_window_menu_modes(); |
---|
434 | awm->init(aw_root,"ARB_PHYLO", "ARB_PHYLO", 830,630); |
---|
435 | |
---|
436 | // create menues and menu inserts with callbacks |
---|
437 | // |
---|
438 | |
---|
439 | AW_gc_manager gcmiddle = AW_manage_GC( awm, |
---|
440 | awm->get_device (AW_MIDDLE_AREA), |
---|
441 | PH_GC_0, PH_GC_0_DRAG, AW_GCM_DATA_AREA, |
---|
442 | resize_callb, 0,0, |
---|
443 | false, // no color groups |
---|
444 | "#CC9AF8", |
---|
445 | "#SEQUENCE$#000000", |
---|
446 | "#MARKER$#FF0000", |
---|
447 | "NOT_MARKER$#A270C0", |
---|
448 | NULL); |
---|
449 | AW_gc_manager gcbottom = AW_manage_GC( awm, |
---|
450 | awm->get_device (AW_BOTTOM_AREA), |
---|
451 | PH_GC_0, PH_GC_0_DRAG, AW_GCM_WINDOW_AREA, |
---|
452 | resize_callb, 0,0, |
---|
453 | false, // no color groups |
---|
454 | "pink", |
---|
455 | "#FOOTER",NULL); |
---|
456 | |
---|
457 | GBUSE(gcbottom); |
---|
458 | |
---|
459 | #if defined(DEBUG) |
---|
460 | AWT_create_debug_menu(awm); |
---|
461 | #endif // DEBUG |
---|
462 | |
---|
463 | // File menu |
---|
464 | awm->create_menu("File","F"); |
---|
465 | awm->insert_menu_topic("export_filter", "Export Filter", "E", "ph_export_markerline.hlp", AWM_ALL, (AW_CB)AW_POPUP, (AW_CL)PH_save_markerline, 0); |
---|
466 | awm->insert_menu_topic("export_freq", "Export Frequencies", "F", "ph_export_markerline.hlp", AWM_ALL, (AW_CB)AW_POPUP, (AW_CL)PH_save_markerline, 1); |
---|
467 | awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, (AW_CB)ph_exit, (AW_CL)ph_root, 0); |
---|
468 | |
---|
469 | // Calculate menu |
---|
470 | awm->create_menu("Calculate","C" ); |
---|
471 | awm->insert_menu_topic("calc_column_filter", "Column Filter", "F", "no help", AWM_ALL, (AW_CB2)ph_view_filter_cb, (AW_CL)0, (AW_CL)0); |
---|
472 | |
---|
473 | // Config menu |
---|
474 | awm->create_menu("Config","o"); |
---|
475 | awm->insert_menu_topic("config_column_filter", "Column Filter", "F", "no help", AWM_ALL, AW_POPUP, (AW_CL)PH_create_filter_window, 0); |
---|
476 | |
---|
477 | // Properties menu |
---|
478 | awm->create_menu("Properties","P"); |
---|
479 | awm->insert_menu_topic("props_menu", "Menu: Colors and Fonts ...", "M", "props_frame.hlp", AWM_ALL, AW_POPUP,(AW_CL)AW_preset_window, 0) ; |
---|
480 | awm->insert_menu_topic("props_data", "Data: Colors and Fonts ...", "D", "ph_props_data.hlp", AWM_ALL, AW_POPUP,(AW_CL)AW_create_gc_window, (AW_CL)gcmiddle ); |
---|
481 | awm->insert_menu_topic("save_props", "Save Properties (in ~/.arb_prop/phylo.arb)", "S", "savedef.hlp", AWM_ALL, (AW_CB)AW_save_defaults, 0, 0) ; |
---|
482 | |
---|
483 | |
---|
484 | // set window areas |
---|
485 | awm->set_info_area_height( 30 ); |
---|
486 | awm->at(5,2); |
---|
487 | awm->auto_space(5,-2); |
---|
488 | |
---|
489 | awm->callback( (AW_CB1)ph_exit ,(AW_CL)ph_root); |
---|
490 | awm->button_length(0); |
---|
491 | awm->help_text("quit.hlp"); |
---|
492 | awm->create_button("QUIT","QUIT"); |
---|
493 | |
---|
494 | awm->callback(AW_POPUP_HELP,(AW_CL)"phylo.hlp"); |
---|
495 | awm->button_length(0); |
---|
496 | awm->create_button("HELP","HELP","H"); |
---|
497 | |
---|
498 | |
---|
499 | awm->set_bottom_area_height( 120 ); |
---|
500 | |
---|
501 | awm->set_expose_callback(AW_MIDDLE_AREA, expose_callb, (AW_CL)awm, 0); |
---|
502 | awm->set_resize_callback(AW_MIDDLE_AREA, resize_callb, (AW_CL)awm, 0); |
---|
503 | awm->set_expose_callback(AW_BOTTOM_AREA, display_status, (AW_CL)aw_root, 0); |
---|
504 | awm->set_resize_callback(AW_BOTTOM_AREA, display_status, (AW_CL)aw_root, 0); |
---|
505 | |
---|
506 | return (AW_window *)awm; |
---|
507 | } |
---|
508 | |
---|
509 | |
---|
510 | AW_window *create_select_alignment_window(AW_root *aw_root, AW_CL cl_aww) |
---|
511 | { |
---|
512 | AW_window_simple *aws = new AW_window_simple; |
---|
513 | |
---|
514 | aws->init( aw_root,"SELECT_ALIGNMENT", "SELECT ALIGNMENT"); |
---|
515 | aws->load_xfig("phylo/select_ali.fig"); |
---|
516 | aws->button_length(10); |
---|
517 | |
---|
518 | aws->at("done"); |
---|
519 | aws->callback(startup_sequence_cb,(AW_CL) aw_root, cl_aww); |
---|
520 | aws->create_button("DONE","DONE","D"); |
---|
521 | |
---|
522 | aws->at("which_alignment"); |
---|
523 | awt_create_selection_list_on_ad(GLOBAL_gb_main,(AW_window *)aws,"phyl/alignment","*="); |
---|
524 | return (AW_window *) aws; |
---|
525 | } |
---|
526 | |
---|
527 | |
---|
528 | |
---|
529 | PH_used_windows::PH_used_windows(void) |
---|
530 | { |
---|
531 | memset((char *) this,0,sizeof(PH_used_windows)); |
---|
532 | } |
---|
533 | |
---|
534 | // initialize 'globals' |
---|
535 | PH_used_windows *PH_used_windows::windowList = 0; |
---|
536 | PH_display *PH_display::ph_display=0; |
---|
537 | PHDATA *PHDATA::ROOT = 0; |
---|
538 | |
---|
539 | |
---|
540 | int |
---|
541 | main(int argc, char **argv) |
---|
542 | { |
---|
543 | if (argc > 2 || (argc == 2 && strcmp(argv[1], "--help") == 0)) { |
---|
544 | fprintf(stderr, "Usage: arb_phylo [database]\n"); |
---|
545 | return EXIT_FAILURE; |
---|
546 | } |
---|
547 | |
---|
548 | PH_root *ph_root; |
---|
549 | AW_root *aw_root; |
---|
550 | char **alignment_names; |
---|
551 | GB_ERROR error = 0; |
---|
552 | AW_default aw_default; |
---|
553 | PH_used_windows *puw = new PH_used_windows; |
---|
554 | PH_display *phd = new PH_display; |
---|
555 | int num_alignments; |
---|
556 | const char *db_server = (argc == 2 ? argv[1] : ":"); |
---|
557 | |
---|
558 | aw_initstatus(); |
---|
559 | aw_root = new AW_root; |
---|
560 | aw_default = aw_root->open_default(".arb_prop/phylo.arb"); |
---|
561 | aw_root->init_variables(aw_default); |
---|
562 | aw_root->init_root("ARB_PHYLO", false); |
---|
563 | |
---|
564 | if (argc == 2) { |
---|
565 | db_server = argv[1]; |
---|
566 | } |
---|
567 | ph_root = new PH_root; |
---|
568 | if ((error = ph_root->open(db_server))) { // initializes global 'GLOBAL_gb_main' |
---|
569 | aw_message(error); |
---|
570 | exit(-1); |
---|
571 | } |
---|
572 | |
---|
573 | // create arb_phylo awars : |
---|
574 | PH_create_filter_variables(aw_root, aw_default); |
---|
575 | PH_create_matrix_variables(aw_root, aw_default); |
---|
576 | ARB_init_global_awars(aw_root, aw_default, GLOBAL_gb_main); |
---|
577 | #if defined(DEBUG) |
---|
578 | AWT_create_db_browser_awars(aw_root, aw_default); |
---|
579 | #endif // DEBUG |
---|
580 | |
---|
581 | #if defined(DEBUG) |
---|
582 | AWT_announce_db_to_browser(GLOBAL_gb_main, GBS_global_string("ARB-database (%s)", db_server)); |
---|
583 | #endif // DEBUG |
---|
584 | |
---|
585 | create_filter_text(); |
---|
586 | |
---|
587 | // create main window : |
---|
588 | |
---|
589 | puw->phylo_main_window = create_phyl_main_window(aw_root, ph_root, 0); |
---|
590 | puw->windowList = puw; |
---|
591 | |
---|
592 | // exposing the main window is now done from inside startup_sequence_cb() |
---|
593 | // (otherwise it crashes during resize because the resize callback gets |
---|
594 | // called before startup_sequence_cb initialized the necessary data) |
---|
595 | // |
---|
596 | // puw->phylo_main_window->show(); |
---|
597 | |
---|
598 | phd->ph_display = phd; |
---|
599 | |
---|
600 | //loading database |
---|
601 | GB_push_transaction(GLOBAL_gb_main); |
---|
602 | alignment_names = GBT_get_alignment_names(GLOBAL_gb_main); |
---|
603 | |
---|
604 | for (num_alignments = 0; alignment_names[num_alignments] != 0; num_alignments++) ; |
---|
605 | if (num_alignments > 1) { |
---|
606 | AW_window *sel_ali_aww = create_select_alignment_window(aw_root, (AW_CL)puw->phylo_main_window); |
---|
607 | sel_ali_aww->show(); |
---|
608 | } |
---|
609 | else { |
---|
610 | aw_root->awar("phyl/alignment")->write_string( alignment_names[0]); |
---|
611 | startup_sequence_cb(0, (AW_CL)aw_root, (AW_CL)puw->phylo_main_window); |
---|
612 | } |
---|
613 | GBT_free_names(alignment_names); |
---|
614 | GB_pop_transaction(GLOBAL_gb_main); |
---|
615 | |
---|
616 | aw_root->main_loop(); |
---|
617 | return EXIT_SUCCESS; |
---|
618 | } |
---|
619 | |
---|
620 | |
---|
621 | |
---|
622 | void AD_map_viewer(GBDATA *dummy,AD_MAP_VIEWER_TYPE) |
---|
623 | { |
---|
624 | AWUSE(dummy); |
---|
625 | } |
---|