1 | // ============================================================= // |
---|
2 | // // |
---|
3 | // File : ED4_main.cxx // |
---|
4 | // Purpose : // |
---|
5 | // // |
---|
6 | // Institute of Microbiology (Technical University Munich) // |
---|
7 | // http://www.arb-home.de/ // |
---|
8 | // // |
---|
9 | // ============================================================= // |
---|
10 | |
---|
11 | |
---|
12 | #include "ed4_class.hxx" |
---|
13 | #include "ed4_awars.hxx" |
---|
14 | #include "ed4_edit_string.hxx" |
---|
15 | #include "ed4_nds.hxx" |
---|
16 | #include "ed4_visualizeSAI.hxx" |
---|
17 | #include "ed4_ProteinViewer.hxx" |
---|
18 | #include "ed4_protein_2nd_structure.hxx" |
---|
19 | #include "ed4_dots.hxx" |
---|
20 | #include "ed4_detect_bad_ali.hxx" |
---|
21 | #include "ed4_naligner.hxx" |
---|
22 | #include "ed4_seq_colors.hxx" |
---|
23 | #include "graph_aligner_gui.hxx" |
---|
24 | #include <ed4_extern.hxx> |
---|
25 | |
---|
26 | #include <st_window.hxx> |
---|
27 | #include <gde.hxx> |
---|
28 | #include <AW_helix.hxx> |
---|
29 | #include <AP_pro_a_nucs.hxx> |
---|
30 | #include <ad_config.h> |
---|
31 | #include <awt_map_key.hxx> |
---|
32 | #include <awt.hxx> |
---|
33 | |
---|
34 | #include <aw_preset.hxx> |
---|
35 | #include <aw_awars.hxx> |
---|
36 | #include <aw_msg.hxx> |
---|
37 | #include <aw_root.hxx> |
---|
38 | #include <aw_advice.hxx> |
---|
39 | |
---|
40 | #include <arbdbt.h> |
---|
41 | |
---|
42 | #include <arb_defs.h> |
---|
43 | #include <arb_global_defs.h> |
---|
44 | #include <macros.hxx> |
---|
45 | #include <aw_question.hxx> |
---|
46 | |
---|
47 | AW_HEADER_MAIN |
---|
48 | |
---|
49 | ED4_root *ED4_ROOT = NULp; |
---|
50 | |
---|
51 | int TERMINAL_HEIGHT; |
---|
52 | |
---|
53 | int INFO_TERM_TEXT_YOFFSET; |
---|
54 | int SEQ_TERM_TEXT_YOFFSET; |
---|
55 | |
---|
56 | int MAXSEQUENCECHARACTERLENGTH; // greatest # of characters in a sequence string terminal |
---|
57 | int MAXNAME_WIDTH; |
---|
58 | int MAXINFO_WIDTH; |
---|
59 | int FLAG_WIDTH; |
---|
60 | |
---|
61 | long ED4_counter = 0; |
---|
62 | |
---|
63 | size_t not_found_counter; // nr of species which haven't been found |
---|
64 | GBS_strstruct *not_found_message; |
---|
65 | |
---|
66 | long max_seq_terminal_length; // global maximum of sequence terminal length |
---|
67 | ED4_EDITMODE awar_edit_mode; |
---|
68 | long awar_edit_rightward; |
---|
69 | bool DRAW; |
---|
70 | |
---|
71 | inline void replaceChars(char *s, char o, char n) { |
---|
72 | while (1) { |
---|
73 | char c = *s++; |
---|
74 | if (!c) { |
---|
75 | break; |
---|
76 | } |
---|
77 | if (c==o) { |
---|
78 | s[-1] = n; |
---|
79 | } |
---|
80 | } |
---|
81 | } |
---|
82 | |
---|
83 | inline void set_and_realloc_gde_array(uchar **&the_names, uchar **&the_sequences, long &allocated, long &numberspecies, long &maxalign, |
---|
84 | const char *name, int name_len, const char *seq, int seq_len) |
---|
85 | { |
---|
86 | if (allocated==numberspecies) { |
---|
87 | long new_allocated = (allocated*3)/2; |
---|
88 | |
---|
89 | ARB_recalloc(the_names, allocated, new_allocated); |
---|
90 | ARB_recalloc(the_sequences, allocated, new_allocated); |
---|
91 | allocated = new_allocated; |
---|
92 | } |
---|
93 | |
---|
94 | the_names[numberspecies] = (uchar*)ARB_strndup(name, name_len); |
---|
95 | the_sequences[numberspecies] = (uchar*)ARB_strndup(seq, seq_len); |
---|
96 | |
---|
97 | replaceChars((char*)the_names[numberspecies], ' ', '_'); |
---|
98 | |
---|
99 | if (seq_len>maxalign) { |
---|
100 | maxalign = seq_len; |
---|
101 | } |
---|
102 | |
---|
103 | numberspecies++; |
---|
104 | } |
---|
105 | |
---|
106 | static char *add_area_for_gde(ED4_area_manager *area_man, uchar **&the_names, uchar **&the_sequences, |
---|
107 | long &allocated, long &numberspecies, long &maxalign, |
---|
108 | int show_sequence, int show_SAI, int show_helix, int show_consensus, int show_remark) |
---|
109 | { |
---|
110 | ED4_terminal *terminal = area_man->get_first_terminal(); |
---|
111 | ED4_terminal *last = area_man->get_last_terminal(); |
---|
112 | |
---|
113 | for (; terminal;) { |
---|
114 | if (terminal->is_species_name_terminal()) { |
---|
115 | ED4_species_manager *species_manager = terminal->get_parent(LEV_SPECIES)->to_species_manager(); |
---|
116 | ED4_species_name_terminal *species_name = species_manager->search_spec_child_rek(LEV_SPECIES_NAME)->to_species_name_terminal(); |
---|
117 | int name_len; |
---|
118 | char *name = species_name->resolve_pointer_to_string_copy(&name_len); |
---|
119 | ED4_sequence_terminal *sequence_terminal; |
---|
120 | |
---|
121 | { |
---|
122 | ED4_base *sequence_term = species_manager->search_spec_child_rek(LEV_SEQUENCE_STRING); |
---|
123 | if (!sequence_term) goto end_of_loop; |
---|
124 | sequence_terminal = sequence_term->to_sequence_terminal(); |
---|
125 | } |
---|
126 | |
---|
127 | int show = -1; |
---|
128 | |
---|
129 | bool is_consensus = false; |
---|
130 | bool is_SAI = false; |
---|
131 | |
---|
132 | if (sequence_terminal->is_consensus_terminal()) { |
---|
133 | is_consensus = true; |
---|
134 | show = show_consensus; |
---|
135 | } |
---|
136 | else if (sequence_terminal->is_SAI_terminal()) { |
---|
137 | is_SAI = true; |
---|
138 | show = show_SAI; |
---|
139 | } |
---|
140 | else { |
---|
141 | show = show_sequence; |
---|
142 | } |
---|
143 | |
---|
144 | e4_assert(show!=-1); |
---|
145 | |
---|
146 | if (show) { |
---|
147 | int seq_len; |
---|
148 | char *seq = NULp; |
---|
149 | |
---|
150 | if (is_consensus) { |
---|
151 | ED4_group_manager *group_manager = sequence_terminal->get_parent(LEV_GROUP)->to_group_manager(); |
---|
152 | |
---|
153 | seq = group_manager->build_consensus_string(&seq_len); |
---|
154 | e4_assert(seq && strlen(seq) == size_t(seq_len)); |
---|
155 | |
---|
156 | ED4_group_manager *folded_group_man = sequence_terminal->is_in_folded_group(); |
---|
157 | |
---|
158 | if (folded_group_man) { // we are in a folded group |
---|
159 | if (folded_group_man==group_manager) { // we are the consensus of the folded group |
---|
160 | if (folded_group_man->is_in_folded_group()) { // a folded group inside a folded group -> do not show |
---|
161 | freenull(seq); |
---|
162 | } |
---|
163 | else { // group folded but consensus shown -> add '-' before name |
---|
164 | char *new_name = ARB_alloc<char>(name_len+2); |
---|
165 | |
---|
166 | sprintf(new_name, "-%s", name); |
---|
167 | freeset(name, new_name); |
---|
168 | name_len++; |
---|
169 | } |
---|
170 | } |
---|
171 | else { // we are really inside a folded group -> don't show |
---|
172 | freenull(seq); |
---|
173 | } |
---|
174 | } |
---|
175 | } |
---|
176 | else { // sequence |
---|
177 | if (!sequence_terminal->is_in_folded_group()) { |
---|
178 | seq = sequence_terminal->resolve_pointer_to_string_copy(&seq_len); |
---|
179 | } |
---|
180 | } |
---|
181 | |
---|
182 | if (seq) { |
---|
183 | set_and_realloc_gde_array(the_names, the_sequences, allocated, numberspecies, maxalign, name, name_len, seq, seq_len); |
---|
184 | if (show_helix && !is_SAI && ED4_ROOT->helix->size()) { |
---|
185 | char *helix = ED4_ROOT->helix->seq_2_helix(seq, '.'); |
---|
186 | set_and_realloc_gde_array(the_names, the_sequences, allocated, numberspecies, maxalign, name, name_len, helix, seq_len); |
---|
187 | free(helix); |
---|
188 | } |
---|
189 | if (show_remark && !is_consensus) { |
---|
190 | ED4_manager *ms_man = sequence_terminal->get_parent(LEV_MULTI_SEQUENCE); |
---|
191 | if (ms_man) { |
---|
192 | ED4_base *remark_name_term = ms_man->search_ID("remark"); |
---|
193 | if (remark_name_term) { |
---|
194 | ED4_base *remark_term = remark_name_term->get_next_terminal(); |
---|
195 | e4_assert(remark_term); |
---|
196 | |
---|
197 | int remark_len; |
---|
198 | char *remark = remark_term->resolve_pointer_to_string_copy(&remark_len); |
---|
199 | |
---|
200 | replaceChars(remark, ' ', '_'); |
---|
201 | set_and_realloc_gde_array(the_names, the_sequences, allocated, numberspecies, maxalign, name, name_len, remark, remark_len); |
---|
202 | free(remark); |
---|
203 | } |
---|
204 | } |
---|
205 | } |
---|
206 | free(seq); |
---|
207 | } |
---|
208 | } |
---|
209 | free(name); |
---|
210 | } |
---|
211 | end_of_loop : |
---|
212 | if (terminal==last) break; |
---|
213 | terminal = terminal->get_next_terminal(); |
---|
214 | } |
---|
215 | |
---|
216 | return NULp; |
---|
217 | } |
---|
218 | |
---|
219 | static char *ED4_create_sequences_for_gde(GBDATA **&the_species, uchar **&the_names, uchar **&the_sequences, long &numberspecies, long &maxalign) { |
---|
220 | int top = ED4_ROOT->aw_root->awar("gde/top_area")->read_int(); |
---|
221 | int tops = ED4_ROOT->aw_root->awar("gde/top_area_sai")->read_int(); |
---|
222 | int toph = ED4_ROOT->aw_root->awar("gde/top_area_helix")->read_int(); |
---|
223 | int topk = ED4_ROOT->aw_root->awar("gde/top_area_kons")->read_int(); |
---|
224 | int topr = ED4_ROOT->aw_root->awar("gde/top_area_remark")->read_int(); |
---|
225 | int middle = ED4_ROOT->aw_root->awar("gde/middle_area")->read_int(); |
---|
226 | int middles = ED4_ROOT->aw_root->awar("gde/middle_area_sai")->read_int(); |
---|
227 | int middleh = ED4_ROOT->aw_root->awar("gde/middle_area_helix")->read_int(); |
---|
228 | int middlek = ED4_ROOT->aw_root->awar("gde/middle_area_kons")->read_int(); |
---|
229 | int middler = ED4_ROOT->aw_root->awar("gde/middle_area_remark")->read_int(); |
---|
230 | |
---|
231 | numberspecies = 0; |
---|
232 | maxalign = 0; |
---|
233 | |
---|
234 | long allocated = 100; |
---|
235 | the_species = NULp; |
---|
236 | |
---|
237 | ARB_calloc(the_names, allocated); |
---|
238 | ARB_calloc(the_sequences, allocated); |
---|
239 | |
---|
240 | char *err = add_area_for_gde(ED4_ROOT->top_area_man, the_names, the_sequences, allocated, numberspecies, maxalign, top, tops, toph, topk, topr); |
---|
241 | if (!err) { |
---|
242 | err = add_area_for_gde(ED4_ROOT->middle_area_man, the_names, the_sequences, allocated, numberspecies, maxalign, middle, middles, middleh, middlek, middler); |
---|
243 | } |
---|
244 | |
---|
245 | if (allocated!=(numberspecies+1)) { |
---|
246 | ARB_recalloc(the_names, allocated, numberspecies+1); |
---|
247 | ARB_recalloc(the_sequences, allocated, numberspecies+1); |
---|
248 | } |
---|
249 | |
---|
250 | return err; |
---|
251 | } |
---|
252 | |
---|
253 | void ED4_setup_gaps_and_alitype(const char *gap_chars, GB_alignment_type alitype) { |
---|
254 | BaseFrequencies::setup(gap_chars, alitype); |
---|
255 | } |
---|
256 | |
---|
257 | static void ED4_gap_chars_changed(AW_root *root) { |
---|
258 | char *gap_chars = root->awar_string(ED4_AWAR_GAP_CHARS)->read_string(); |
---|
259 | ED4_setup_gaps_and_alitype(gap_chars, ED4_ROOT->alignment_type); |
---|
260 | free(gap_chars); |
---|
261 | } |
---|
262 | |
---|
263 | void ED4_with_all_edit_windows(void (*cb)(ED4_window *)) { |
---|
264 | for (ED4_window *win = ED4_ROOT->first_window; win; win = win->next) { |
---|
265 | ED4_LocalWinContext uses(win); |
---|
266 | cb(win); |
---|
267 | } |
---|
268 | } |
---|
269 | |
---|
270 | static void redraw_cursor(ED4_window *win) { win->cursor.redraw(); } |
---|
271 | static void ED4_edit_direction_changed(AW_root * /* awr */) { |
---|
272 | ED4_with_all_edit_windows(redraw_cursor); |
---|
273 | } |
---|
274 | |
---|
275 | static void ed4_bind_mainDB_awar_callbacks(AW_root *root) { |
---|
276 | // callbacks to main DB awars are bound later |
---|
277 | // (otherwise its easy to crash the editor by clicking around in ARB_NTREE during editor startup) |
---|
278 | |
---|
279 | root->awar(AWAR_SET_CURSOR_POSITION)->add_callback(ED4_remote_set_cursor_cb); |
---|
280 | root->awar(AWAR_SPECIES_NAME)->add_callback(ED4_selected_species_changed_cb); |
---|
281 | root->awar(AWAR_SAI_NAME)->add_callback(ED4_selected_SAI_changed_cb); |
---|
282 | } |
---|
283 | |
---|
284 | static void ed4_create_mainDB_awars(AW_root *root) { |
---|
285 | // WARNING: do not bind callbacks here -> do it in ed4_bind_mainDB_awar_callbacks() |
---|
286 | |
---|
287 | GBDATA *gb_main = ED4_ROOT->get_gb_main(); |
---|
288 | |
---|
289 | root->awar_int(AWAR_CURSOR_POSITION, info2bio(0), gb_main); |
---|
290 | root->awar_int(AWAR_CURSOR_POSITION_LOCAL, 0, gb_main); |
---|
291 | root->awar_int(AWAR_SET_CURSOR_POSITION, 1, gb_main); |
---|
292 | |
---|
293 | root->awar_string(AWAR_FIELD_CHOSEN, NO_FIELD_SELECTED, gb_main); |
---|
294 | |
---|
295 | root->awar_string(AWAR_RANGE, "", gb_main); |
---|
296 | root->awar_string(AWAR_SPECIES_NAME, "", gb_main); |
---|
297 | root->awar_string(AWAR_SAI_NAME, "", gb_main); |
---|
298 | root->awar_string(AWAR_SAI_GLOBAL, "", gb_main); |
---|
299 | } |
---|
300 | |
---|
301 | static void ed4_create_all_awars(AW_root *root, const char *config_name) { |
---|
302 | // Note: cursor awars are created in window constructor |
---|
303 | |
---|
304 | root->awar_string(AWAR_EDIT_CONFIGURATION, config_name, AW_ROOT_DEFAULT); |
---|
305 | |
---|
306 | ed4_create_mainDB_awars(root); |
---|
307 | ED4_create_search_awars(root); |
---|
308 | |
---|
309 | #if defined(DEBUG) |
---|
310 | AWT_create_db_browser_awars(root, AW_ROOT_DEFAULT); |
---|
311 | #endif // DEBUG |
---|
312 | |
---|
313 | create_naligner_variables(root, AW_ROOT_DEFAULT); |
---|
314 | create_sina_variables(root, AW_ROOT_DEFAULT); |
---|
315 | |
---|
316 | awar_edit_mode = AD_ALIGN; |
---|
317 | |
---|
318 | int def_sec_level = 0; |
---|
319 | #ifdef DEBUG |
---|
320 | def_sec_level = 6; // don't nag developers |
---|
321 | #endif |
---|
322 | root->awar_int(AWAR_EDIT_SECURITY_LEVEL, def_sec_level, AW_ROOT_DEFAULT); |
---|
323 | |
---|
324 | root->awar_int(AWAR_EDIT_SECURITY_LEVEL_ALIGN, def_sec_level, AW_ROOT_DEFAULT)->add_callback(ed4_changesecurity); |
---|
325 | root->awar_int(AWAR_EDIT_SECURITY_LEVEL_CHANGE, def_sec_level, AW_ROOT_DEFAULT)->add_callback(ed4_changesecurity); |
---|
326 | |
---|
327 | root->awar_int(AWAR_EDIT_MODE, 0)->add_callback(ed4_change_edit_mode); |
---|
328 | root->awar_int(AWAR_INSERT_MODE, 1)->add_callback(ed4_change_edit_mode); |
---|
329 | |
---|
330 | root->awar_int(AWAR_EDIT_RIGHTWARD, 1)->add_target_var(&awar_edit_rightward)->add_callback(ED4_edit_direction_changed); |
---|
331 | root->awar_int(AWAR_EDIT_TITLE_MODE, 0); |
---|
332 | |
---|
333 | root->awar_int(AWAR_EDIT_HELIX_SPACING, 0) ->set_minmax(-30, 30) ->add_target_var(&ED4_ROOT->helix_add_spacing) ->add_callback(makeRootCallback(ED4_request_relayout)); |
---|
334 | root->awar_int(AWAR_EDIT_TERMINAL_SPACING, 0) ->set_minmax(-30, 30) ->add_target_var(&ED4_ROOT->terminal_add_spacing) ->add_callback(makeRootCallback(ED4_request_relayout)); |
---|
335 | |
---|
336 | ed4_changesecurity(root); |
---|
337 | |
---|
338 | root->awar_int(ED4_AWAR_COMPRESS_SEQUENCE_GAPS, 0)->add_callback(makeRootCallback(ED4_compression_toggle_changed_cb, false)); |
---|
339 | root->awar_int(ED4_AWAR_COMPRESS_SEQUENCE_HIDE, 0)->add_callback(makeRootCallback(ED4_compression_toggle_changed_cb, true)); |
---|
340 | root->awar_int(ED4_AWAR_COMPRESS_SEQUENCE_TYPE, 0)->add_callback(ED4_compression_changed_cb); |
---|
341 | root->awar_int(ED4_AWAR_COMPRESS_SEQUENCE_PERCENT, 1)->add_callback(ED4_compression_changed_cb)->set_minmax(1, 99); |
---|
342 | |
---|
343 | root->awar_int(ED4_AWAR_DIGITS_AS_REPEAT, 0); |
---|
344 | root->awar_int(ED4_AWAR_FAST_CURSOR_JUMP, 0); |
---|
345 | root->awar_int(ED4_AWAR_CURSOR_TYPE, (int)ED4_RIGHT_ORIENTED_CURSOR); |
---|
346 | |
---|
347 | ED4_create_consensus_awars(root); |
---|
348 | ED4_create_NDS_awars(root); |
---|
349 | |
---|
350 | root->awar_string(ED4_AWAR_REP_SEARCH_PATTERN, "."); |
---|
351 | root->awar_string(ED4_AWAR_REP_REPLACE_PATTERN, "-"); |
---|
352 | |
---|
353 | root->awar_int(ED4_AWAR_SCROLL_SPEED_X, 40); |
---|
354 | root->awar_int(ED4_AWAR_SCROLL_SPEED_Y, 20); |
---|
355 | root->awar_int(ED4_AWAR_SCROLL_MARGIN, 5); |
---|
356 | |
---|
357 | root->awar_string(ED4_AWAR_SPECIES_TO_CREATE, ""); |
---|
358 | |
---|
359 | root->awar_string(ED4_AWAR_GAP_CHARS, GAP::anyGapChars())->add_callback(ED4_gap_chars_changed); |
---|
360 | ED4_gap_chars_changed(root); |
---|
361 | root->awar_int(ED4_AWAR_ANNOUNCE_CHECKSUM_CHANGES, 0); |
---|
362 | |
---|
363 | GBDATA *gb_main = ED4_ROOT->get_gb_main(); |
---|
364 | { |
---|
365 | GB_ERROR gde_err = GDE_init(ED4_ROOT->aw_root, ED4_ROOT->props_db, gb_main, ED4_create_sequences_for_gde, NULp, GDE_WINDOWTYPE_EDIT4); |
---|
366 | if (gde_err) GBK_terminatef("Fatal error: %s", gde_err); |
---|
367 | } |
---|
368 | |
---|
369 | root->awar_string(ED4_AWAR_CREATE_FROM_CONS_REPL_EQUAL, "-"); |
---|
370 | root->awar_string(ED4_AWAR_CREATE_FROM_CONS_REPL_POINT, "?"); |
---|
371 | root->awar_int(ED4_AWAR_CREATE_FROM_CONS_CREATE_POINTS, 1); |
---|
372 | root->awar_int(ED4_AWAR_CREATE_FROM_CONS_ALL_UPPER, 1); |
---|
373 | root->awar_int(ED4_AWAR_CREATE_FROM_CONS_DATA_SOURCE, 0); |
---|
374 | |
---|
375 | ED4_createVisualizeSAI_Awars(root, AW_ROOT_DEFAULT); |
---|
376 | ED4_create_dot_missing_bases_awars(root, AW_ROOT_DEFAULT); |
---|
377 | ED4_create_detect_bad_alignment_awars(root, AW_ROOT_DEFAULT); |
---|
378 | |
---|
379 | // Create Awars To Be Used In Protein Viewer |
---|
380 | if (ED4_ROOT->alignment_type == GB_AT_DNA) { |
---|
381 | PV_CreateAwars(root, AW_ROOT_DEFAULT); |
---|
382 | } |
---|
383 | |
---|
384 | // create awars to be used for protein secondary structure match |
---|
385 | if (ED4_ROOT->alignment_type == GB_AT_AA) { |
---|
386 | root->awar_int(PFOLD_AWAR_ENABLE, 1); |
---|
387 | root->awar_string(PFOLD_AWAR_SELECTED_SAI, "PFOLD"); |
---|
388 | root->awar_int(PFOLD_AWAR_MATCH_METHOD, SECSTRUCT_SEQUENCE); |
---|
389 | int pt; |
---|
390 | char awar[256]; |
---|
391 | for (int i = 0; pfold_match_type_awars[i].name; i++) { |
---|
392 | e4_assert(i<PFOLD_PAIRS); |
---|
393 | pt = pfold_match_type_awars[i].value; |
---|
394 | sprintf(awar, PFOLD_AWAR_PAIR_TEMPLATE, pfold_match_type_awars[i].name); |
---|
395 | root->awar_string(awar, pfold_pairs[pt])->add_target_var(&pfold_pairs[pt]); |
---|
396 | sprintf(awar, PFOLD_AWAR_SYMBOL_TEMPLATE, pfold_match_type_awars[i].name); |
---|
397 | root->awar_string(awar, pfold_pair_chars[pt])->add_target_var(&pfold_pair_chars[pt]); |
---|
398 | } |
---|
399 | root->awar_string(PFOLD_AWAR_SYMBOL_TEMPLATE_2, PFOLD_PAIR_CHARS_2); |
---|
400 | root->awar_string(PFOLD_AWAR_SAI_FILTER, "pfold"); |
---|
401 | } |
---|
402 | |
---|
403 | GB_ERROR error = ARB_init_global_awars(root, AW_ROOT_DEFAULT, gb_main); |
---|
404 | if (error) aw_message(error); |
---|
405 | } |
---|
406 | |
---|
407 | static void ED4_postcbcb(AW_window *aww) { |
---|
408 | ED4_ROOT->announce_useraction_in(aww); |
---|
409 | ED4_trigger_instant_refresh(); |
---|
410 | } |
---|
411 | static void seq_colors_changed_cb() { |
---|
412 | ED4_ROOT->request_refresh_for_sequence_terminals(); |
---|
413 | } |
---|
414 | |
---|
415 | int ARB_main(int argc, char *argv[]) { |
---|
416 | const char *data_path = ":"; |
---|
417 | char *config_name = NULp; |
---|
418 | |
---|
419 | if (argc > 1 && ((strcmp(argv[1], "-h") == 0) || (strcmp(argv[1], "--help") == 0))) { |
---|
420 | fprintf(stderr, |
---|
421 | "Usage: arb_edit4 [options] database\n" |
---|
422 | " database name of database or ':' to connect to arb-database-server\n" |
---|
423 | "\n" |
---|
424 | " options:\n" |
---|
425 | " -c config loads configuration 'config' (default: '" DEFAULT_CONFIGURATION "')\n" |
---|
426 | ); |
---|
427 | return EXIT_SUCCESS; |
---|
428 | } |
---|
429 | |
---|
430 | if (argc > 1 && strcmp(argv[1], "-c") == 0) { |
---|
431 | config_name = new char[strlen(argv[2])+1]; |
---|
432 | strcpy(config_name, argv[2]); |
---|
433 | argc -= 2; argv += 2; |
---|
434 | } |
---|
435 | else { // load default configuration if no command line is given |
---|
436 | config_name = ARB_strdup(DEFAULT_CONFIGURATION); |
---|
437 | printf("Using '%s'\n", DEFAULT_CONFIGURATION); |
---|
438 | } |
---|
439 | |
---|
440 | if (argc>1) { |
---|
441 | data_path = argv[1]; |
---|
442 | argc--; argv++; |
---|
443 | } |
---|
444 | |
---|
445 | aw_initstatus(); |
---|
446 | |
---|
447 | GB_shell shell; |
---|
448 | ARB_ERROR error; |
---|
449 | GBDATA *gb_main = GB_open(data_path, "rwt"); |
---|
450 | |
---|
451 | if (!gb_main) { |
---|
452 | error = GB_await_error(); |
---|
453 | } |
---|
454 | else { |
---|
455 | #if defined(DEBUG) |
---|
456 | AWT_announce_db_to_browser(gb_main, GBS_global_string("ARB database (%s)", data_path)); |
---|
457 | #endif // DEBUG |
---|
458 | |
---|
459 | ED4_ROOT = new ED4_root(gb_main); |
---|
460 | |
---|
461 | error = configure_macro_recording(ED4_ROOT->aw_root, "ARB_EDIT4", gb_main); |
---|
462 | if (!error) error = ED4_ROOT->init_alignment(); |
---|
463 | if (!error) { |
---|
464 | ed4_create_all_awars(ED4_ROOT->aw_root, config_name); |
---|
465 | |
---|
466 | ED4_ROOT->st_ml = STAT_create_ST_ML(gb_main); |
---|
467 | ED4_ROOT->sequence_colors = new ED4_seq_colors(ED4_G_SEQUENCES, seq_colors_changed_cb); |
---|
468 | |
---|
469 | ED4_ROOT->edk = new ed_key; |
---|
470 | ED4_ROOT->edk->create_awars(ED4_ROOT->aw_root); |
---|
471 | |
---|
472 | ED4_ROOT->helix = new AW_helix(ED4_ROOT->aw_root); |
---|
473 | |
---|
474 | { |
---|
475 | GB_ERROR warning = NULp; |
---|
476 | switch (ED4_ROOT->alignment_type) { |
---|
477 | case GB_AT_RNA: |
---|
478 | case GB_AT_DNA: |
---|
479 | warning = ED4_ROOT->helix->init(gb_main); |
---|
480 | break; |
---|
481 | |
---|
482 | case GB_AT_AA: |
---|
483 | warning = ED4_pfold_set_SAI(&ED4_ROOT->protstruct, gb_main, ED4_ROOT->get_alignment_name(), &ED4_ROOT->protstruct_len); |
---|
484 | break; |
---|
485 | |
---|
486 | default: |
---|
487 | e4_assert(0); |
---|
488 | break; |
---|
489 | } |
---|
490 | |
---|
491 | if (warning) aw_message(warning); // write to console |
---|
492 | ED4_ROOT->create_first_window(); |
---|
493 | if (warning) { aw_message(warning); warning = NULp; } // write again to status window |
---|
494 | } |
---|
495 | |
---|
496 | ED4_objspec::init_object_specs(); |
---|
497 | { |
---|
498 | bool found_config = false; |
---|
499 | ED4_LocalWinContext uses(ED4_ROOT->first_window); |
---|
500 | |
---|
501 | if (config_name) { |
---|
502 | GB_transaction ta(gb_main); |
---|
503 | GB_ERROR cfg_error; |
---|
504 | GBT_config cfg(gb_main, config_name, cfg_error); |
---|
505 | |
---|
506 | if (cfg.exists()) { |
---|
507 | ED4_ROOT->create_hierarchy(cfg.get_definition(GBT_config::MIDDLE_AREA), cfg.get_definition(GBT_config::TOP_AREA)); // create internal hierarchy |
---|
508 | found_config = true; |
---|
509 | } |
---|
510 | else { |
---|
511 | aw_message(GBS_global_string("Could not find configuration '%s'", config_name)); |
---|
512 | } |
---|
513 | } |
---|
514 | |
---|
515 | if (!found_config) { |
---|
516 | aw_popup_ok("The editor needs a configuration stored in database.\n" |
---|
517 | "Cannot continue and will terminate now."); |
---|
518 | ED4_exit(); |
---|
519 | } |
---|
520 | } |
---|
521 | |
---|
522 | // now bind DB depending callbacks |
---|
523 | ed4_bind_mainDB_awar_callbacks(ED4_ROOT->aw_root); |
---|
524 | |
---|
525 | // Create Additional sequence (aminoacid) terminals to be used in Protein Viewer |
---|
526 | if (ED4_ROOT->alignment_type == GB_AT_DNA) { |
---|
527 | PV_CallBackFunction(ED4_ROOT->aw_root); |
---|
528 | } |
---|
529 | |
---|
530 | AWT_install_postcb_cb(ED4_postcbcb); |
---|
531 | AWT_install_cb_guards(); |
---|
532 | e4_assert(!ED4_WinContext::have_context()); // no global context shall be active |
---|
533 | ED4_ROOT->aw_root->main_loop(); // enter main-loop |
---|
534 | } |
---|
535 | |
---|
536 | shutdown_macro_recording(ED4_ROOT->aw_root); |
---|
537 | GB_close(gb_main); |
---|
538 | } |
---|
539 | |
---|
540 | bool have_aw_root = ED4_ROOT && ED4_ROOT->aw_root; |
---|
541 | if (error) { |
---|
542 | if (have_aw_root) aw_popup_ok(error.deliver()); |
---|
543 | else fprintf(stderr, "arb_edit4: Error: %s\n", error.deliver()); |
---|
544 | } |
---|
545 | if (have_aw_root) delete ED4_ROOT->aw_root; |
---|
546 | |
---|
547 | return EXIT_SUCCESS; |
---|
548 | } |
---|
549 | |
---|