ARB
NT_extern.cxx
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1 // =============================================================== //
2 // //
3 // File : NT_extern.cxx //
4 // Purpose : //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // =============================================================== //
10 
11 #include "map_viewer.h"
12 #include "NT_local.h"
13 #include "ad_trees.h"
14 #include "NT_group_search.h"
15 
16 #include <seq_quality.h>
17 #include <multi_probe.hxx>
18 #include <st_window.hxx>
19 #include <GEN.hxx>
20 #include <EXP.hxx>
21 
22 #include <TreeCallbacks.hxx>
23 #include <AW_rename.hxx>
24 #include <probe_gui.hxx>
25 #include <primer_design.hxx>
26 #include <gde.hxx>
27 #include <awtc_submission.hxx>
28 
29 #include <macros.hxx>
30 #include <xcmd.hxx>
31 #include <nds.h>
32 #include <db_query.h>
33 #include <dbui.h>
34 #include <refentries.h>
35 #include <insdel.h>
36 
37 #include <awti_export.hxx>
38 #include <awti_import.hxx>
39 
40 #include <awt.hxx>
41 #include <awt_input_mask.hxx>
42 #include <awt_sel_boxes.hxx>
43 #include <awt_www.hxx>
44 #include <awt_TreeAwars.hxx>
45 #include <awt_misc.hxx>
46 
47 #include <aw_color_groups.hxx>
48 #include <aw_advice.hxx>
49 #include <aw_preset.hxx>
50 #include <aw_awars.hxx>
51 #include <aw_global_awars.hxx>
52 #include <aw_file.hxx>
53 #include <aw_msg.hxx>
54 #include <arb_progress.h>
55 #include <aw_root.hxx>
56 #include <aw_question.hxx>
57 #include <aw_select.hxx>
58 #include <aw_system.hxx>
59 #include <rootAsWin.h>
60 
61 #include <ad_cb.h>
62 
63 #include <arb_strbuf.h>
64 #include <arb_file.h>
65 #include <arb_version.h>
66 #include <arb_sleep.h>
67 
68 #include <saicalc.h>
69 
70 #if defined(DEVEL_RALF)
71 # define TRACE_GROUP_SELECTION
72 #endif
73 
74 #define AWAR_EXPORT_NDS "tmp/export_nds"
75 #define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/delimiter"
76 #define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species"
77 #define AWAR_NTREE_TITLE_MODE "tmp/title_mode"
78 
79 void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
80 
81 void create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
82 AW_window *create_insertDeleteColumn_window(AW_root *root);
83 AW_window *create_insertDeleteBySAI_window(AW_root *root, GBDATA *gb_main);
84 
85 AW_window *create_tree_window(AW_root *aw_root, AWT_graphic *awd);
86 
87 enum Export_Type {
88  EXPORT_SPACE_PADDED_RIGHT_ALIGNED = 1, // format info (using spaces). slow - uses one extra pass for column width detection.
89  EXPORT_SPACE_PADDED_LEFT_ALIGNED = 4, // dito, but left aligned
90  EXPORT_TAB_SEPARATED = 2, // format info (using 1 tab per column - for easy import into star-calc, excel, etc. )
91  EXPORT_COMMA_SEPARATED = 3, // like EXPORT_TAB_SEPARATED, but using commas
92 };
93 
94 static void nt_changesecurity(AW_root *aw_root) {
95  int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
96  GB_push_transaction(GLOBAL.gb_main);
97  GB_change_my_security(GLOBAL.gb_main, level); // changes user security
98  GB_pop_transaction(GLOBAL.gb_main);
99 }
100 
101 static void export_nds_cb(AW_window *aww, bool do_print) {
102  AW_root *aw_root = aww->get_root();
103  char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
104  FILE *out = fopen(name, "w");
105 
106  if (!out) {
107  aw_message("Error: Cannot open and write to file");
108  }
109  else {
110  GB_transaction ta(GLOBAL.gb_main);
111 
112  char *tree_name = aw_root->awar(AWAR_TREE)->read_string();
113  const Export_Type export_type = (Export_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
114  const NDS_Type nds_type = export_type == EXPORT_COMMA_SEPARATED ? NDS_OUTPUT_COMMA_SEPARATED : NDS_OUTPUT_TAB_SEPARATED;
115  const bool spacePadded = export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED || export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED;
116  const int passesNeeded = spacePadded ? 2 : 1;
117  NDS_Labeler labeler(nds_type);
118 
119  arb_progress progress("Exporting data using NDS", passesNeeded*GBT_count_marked_species(GLOBAL.gb_main));
120 
121  const size_t max_col = std::max(labeler.max_columns(GLOBAL.gb_main), 1L);
122  size_t col_max_len[max_col];
123 
124  const char *col_format = NULp;
125 
126  if (spacePadded) {
127  for (size_t i = 0; i<max_col; ++i) {
128  col_max_len[i] = 0;
129  }
130  if (export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED) {
131  col_format = "%*s";
132  }
133  else {
134  col_format = "%-*s";
135  }
136  }
137 
138  for (int pass = 1; pass<=passesNeeded; ++pass) {
139  for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
140  gb_species;
141  gb_species = GBT_next_marked_species(gb_species))
142  {
143  const char *label = labeler.speciesLabel(GLOBAL.gb_main, gb_species, NULp, tree_name);
144 
145  if (spacePadded) {
146  ConstStrArray parts;
147  GBT_split_string(parts, label, "\t", SPLIT_KEEPEMPTY);
148 
149  size_t col_count = parts.size();
150  nt_assert(col_count<=max_col);
151 
152  if (pass == 1) { // track maximum used width for all columns
153  for (size_t i = 0; i<col_count; ++i) {
154  col_max_len[i] = std::max(col_max_len[i], strlen(parts[i]));
155  }
156  }
157  else { // format according to tracked widths
158  for (size_t i = 0; i<col_count; ++i) {
159  if (i) fputc(' ', out);
160 
161  arb_assert(col_max_len[i]>0); // otherwise empty, unused column (might be ok, but might need different handling)
162  arb_assert(col_max_len[i]<=INT_MAX); // (protect cast below)
163 
164  if (export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED && i == (col_count-1)) { // left aligned and last column
165  fputs(parts[i], out);
166  }
167  else {
168  fprintf(out, col_format, int(col_max_len[i]), parts[i]);
169  }
170  }
171  fputc('\n', out);
172  }
173  }
174  else {
175  fprintf(out, "%s\n", label);
176  }
177  ++progress;
178  }
179  }
180 
181  AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
182  fclose(out);
183  if (do_print) {
184  GB_ERROR error = GB_textprint(name);
185  if (error) aw_message(error);
186  }
187  free(tree_name);
188  }
189  free(name);
190 }
191 
192 static AW_window *create_nds_export_window(AW_root *root) {
193  AW_window_simple *aws = new AW_window_simple;
194  aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
195  aws->load_xfig("sel_box_nds.fig");
196 
197  aws->callback(AW_POPDOWN);
198  aws->at("close");
199  aws->create_button("CLOSE", "CLOSE", "C");
200 
201  aws->callback(makeHelpCallback("arb_export_nds.hlp"));
202  aws->at("help");
203  aws->create_button("HELP", "HELP", "H");
204 
205  aws->at("save");
206  aws->callback(makeWindowCallback(export_nds_cb, false));
207  aws->create_button("SAVE", "SAVE", "S");
208 
209  aws->at("print");
210  aws->callback(makeWindowCallback(export_nds_cb, true));
211  aws->create_button("PRINT", "PRINT", "P");
212 
213  aws->at("toggle1");
214  aws->label("Column output");
215  aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR);
216  aws->insert_option ("Space padded (left aligned)", "S", EXPORT_SPACE_PADDED_LEFT_ALIGNED);
217  aws->insert_option ("Space padded (right aligned)", "r", EXPORT_SPACE_PADDED_RIGHT_ALIGNED);
218  aws->insert_default_option("TAB separated", "T", EXPORT_TAB_SEPARATED);
219  aws->insert_option ("Comma separated", "C", EXPORT_COMMA_SEPARATED);
220  aws->update_option_menu();
221 
222  AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS);
223 
224  return aws;
225 }
226 
227 static void create_export_nds_awars(AW_root *awr, AW_default def) {
228  AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds");
229  awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, EXPORT_TAB_SEPARATED, def);
230 }
231 
232 static void selectedSpeciesChanged_cb(AW_root *awr) {
233  const char *value = awr->awar(AWAR_SPECIES_NAME)->read_char_pntr();
234  awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
235  if (value[0]) {
236  awr->awar(AWAR_GROUP)->write_pointer(NULp); // deselect group when species gets selected
237 #if defined(TRACE_GROUP_SELECTION)
238  fputs("clear AWAR_GROUP (because species selected)\n", stderr);
239 #endif
240  }
241 }
242 
243 static void expert_mode_changed_cb(AW_root *aw_root) {
244  aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
245 }
246 
247 static void NT_toggle_expert_mode(AW_window *aww) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
248 static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
249 
250 static void nt_create_all_awars(AW_root *awr) {
251  // creates awars for all modules reachable from ARB_NT main window
252 
253  awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT);
254  if (GB_read_clients(GLOBAL.gb_main)>=0) {
255  awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
256  }
257  else {
258  awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT);
259  }
260 
261  awr->awar_string(AWAR_TOPAREA_SAIS, "ECOLI;HELIX;HELIX_NR", AW_ROOT_DEFAULT);
262 
263  awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main);
264  awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main);
265  awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main);
266  awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown", GLOBAL.gb_main);
267  awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main);
268  awr->awar(AWAR_SPECIES_NAME)->add_callback(selectedSpeciesChanged_cb);
269  awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
270 
271  awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
272 
273  GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
274  EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
275 #if defined(DEBUG)
276  AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT);
277 #endif // DEBUG
278 
279  AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
280 
281  awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT);
282  awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
283 #if defined(DEBUG) && 0
284  awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
285 #endif // DEBUG
286 
287  create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT);
288  create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
289  create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
290  create_trees_var(awr, AW_ROOT_DEFAULT);
291  DBUI::create_dbui_awars(awr);
292  AP_create_consensus_var(awr, AW_ROOT_DEFAULT);
293  {
294  GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, NULp, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT);
295  if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
296  }
297  NT_create_transpro_variables(awr, AW_ROOT_DEFAULT);
298  NT_create_resort_awars(awr, AW_ROOT_DEFAULT);
299  NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT);
300  NT_create_trackAliChanges_Awars(awr, AW_ROOT_DEFAULT);
301 
302  NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
303  NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
304  NDS_create_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
305  create_export_nds_awars(awr, AW_ROOT_DEFAULT);
306  create_group_search_awars(awr, AW_ROOT_DEFAULT);
307  TREE_create_awars(awr, GLOBAL.gb_main);
308 
309  awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
310  awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
311 
312  AWTC_create_submission_variables(awr, GLOBAL.gb_main);
313  NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
314  NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar
315  SQ_create_awars(awr, AW_ROOT_DEFAULT);
316  RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT);
317 
318  NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT);
319 
320  GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
321  if (!error) {
322  AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
323  awar_expert->add_callback(expert_mode_changed_cb);
324  awar_expert->touch();
325 
326  awt_create_aww_vars(awr, AW_ROOT_DEFAULT);
327  }
328 
329  if (error) aw_message(error);
330 }
331 
332 // --------------------------------------------------------------------------------
333 
334 static bool nt_disconnect_from_db(AW_root *aw_root, GBDATA*& gb_main_ref, bool quitWithoutSaveQuestion) {
335  // ask user if DB was not saved in the last 15 seconds (dont ask if quitWithoutSaveQuestion is true).
336  // returns true if user allows to quit.
337 
338  // @@@ code here could as well be applied to both merge DBs
339  // - question about saving only with target DB!
340 
341 #if defined(DEBUG)
342  quitWithoutSaveQuestion = true; // do not ask about saving while developing
343 #endif
344 
345  if (gb_main_ref) {
346  if (GB_read_clients(gb_main_ref) >= 0 && // only in server
347  GB_read_clock(gb_main_ref) > GB_last_saved_clock(gb_main_ref) &&
348  quitWithoutSaveQuestion == false)
349  {
350  long secs = GB_last_saved_time(gb_main_ref);
351  const char *quit_buttons = "Quit ARB,Do NOT quit";
352  if (secs) {
353  secs = GB_time_of_day() - secs;
354  if (secs>15) {
355  char *question = GBS_global_string_copy("You last saved your data %li:%02li minutes ago\nSure to quit?", secs/60, secs%60);
356  int dontQuit = aw_question("quit_arb", question, quit_buttons);
357  free(question);
358  if (dontQuit) {
359  return false;
360  }
361  }
362  }
363  else {
364  if (aw_question("quit_arb", "You never saved any data.\nSure to quit?", quit_buttons)) {
365  return false;
366  }
367  }
368  }
369 
370  GBCMS_shutdown(gb_main_ref);
371 
372  GBDATA *gb_main = gb_main_ref;
373  gb_main_ref = NULp; // avoid further usage
374 
375  nt_assert(aw_root);
376 
377  // @@@ instead of directly calling the following functions, try to add them as GB_atclose_callback
378  aw_root->unlink_awars_from_DB(gb_main);
379  AWT_destroy_input_masks();
380 #if defined(DEBUG)
381  AWT_browser_forget_db(gb_main);
382 #endif // DEBUG
383 
384  GB_close(gb_main);
385  }
386  return true;
387 }
388 
389 static void nt_run(const char *command) {
390  GB_ERROR error = GBK_system(command);
391  if (error) {
392  fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
393 #if defined(DEBUG)
394  GBK_dump_backtrace(stderr, "nt_run-error");
395 #endif
396  }
397 }
398 
399 void NT_start(const char *arb_ntree_args, bool restart_with_new_ARB_PID) {
400  char *command = GBS_global_string_copy("arb_launcher --async %s %s", restart_with_new_ARB_PID ? "arb" : "arb_ntree", arb_ntree_args);
401  nt_run(command);
402  free(command);
403 }
404 
405 __ATTR__NORETURN static void really_exit(int exitcode, bool kill_my_clients) {
406  if (kill_my_clients) {
407  nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
408  }
409  exit(exitcode);
410 }
411 
412 static void exit_ignoring_running_macro(AW_root *aw_root, int exitcode, bool quitWithoutSaveQuestion) {
413  AWTI_cleanup_importer();
414  shutdown_macro_recording(aw_root);
415 
416  bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
417  if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main, quitWithoutSaveQuestion)) {
418  really_exit(exitcode, is_server_and_has_clients);
419  }
420 }
421 
422 #define TRY_TO_QUIT_ARB_FREQUENCY 250 // ms
423 
424 static unsigned NT_exit_when_macros_did_finish(AW_root *aw_root, int exitcode) {
425  if (is_server_and_executing_macro(aw_root)) {
426  static long milliSeconds = 0;
427  static int lastDecaSeconds = 0;
428 
429  milliSeconds += TRY_TO_QUIT_ARB_FREQUENCY;
430  int seconds = milliSeconds/1000;
431  int decaSeconds = seconds/10;
432 
433  if (decaSeconds != lastDecaSeconds) {
434  const char *msg = GBS_global_string("waited %i seconds for macro termination", seconds);
435  if (decaSeconds>3) {
436  int after = (10-decaSeconds)*10;
437  msg = GBS_global_string("%s. Will terminate unconditionally in %i seconds", msg, after);
438  }
439  aw_message(GBS_global_string("[%s]", msg));
440  lastDecaSeconds = decaSeconds;
441  }
442 
443  if (decaSeconds<10) {
444  return TRY_TO_QUIT_ARB_FREQUENCY;
445  }
446  // reached after 100s
447  aw_message("[forcing arb quit]");
448  }
449  else {
450  aw_message("[all macros have terminated. arb quits now]");
451  }
452  ARB_sleep(1, SEC);
453  exit_ignoring_running_macro(aw_root, exitcode, true); // never ask if sure to quit!
454  return 0;
455 }
456 
457 void NT_exit(AW_window *aws, int exitcode) {
458  AW_root *aw_root = aws->get_root();
459  if (is_server_and_executing_macro(aw_root)) {
460  static int suppressed = 0;
461  if (!suppressed) {
462  aw_message("[did not quit arb yet, because macro is still running. Would crash. Will retry ASAP]");
463  suppressed = 1;
464  }
465  else {
466  aw_message("[macro is still running. But time will pass faster because you are in a hurry]");
467  }
468 
469  // Note: this branch effectively suppresses the 'sure to quit?' question
470  aw_root->add_timed_callback(TRY_TO_QUIT_ARB_FREQUENCY,
471  makeTimedCallback(NT_exit_when_macros_did_finish, exitcode));
472  }
473  else {
474  exit_ignoring_running_macro(aw_root, exitcode, false);
475  }
476 }
477 
478 void NT_restart(AW_root *aw_root, const char *arb_ntree_args) {
479  // restarts arb_ntree (with new ARB_PID)
480  // @@@ do we need to call AWTI_cleanup_importer and/or shutdown_macro_recording here?
481  // consider to delegate to normal exit-code (NT_exit, exit_ignoring_running_macro)
482  bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
483  if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main, false)) {
484  NT_start(arb_ntree_args, true);
485  really_exit(EXIT_SUCCESS, is_server_and_has_clients);
486  }
487 }
488 
489 static void nt_start_2nd_arb(AW_window *aww, bool quit) {
490  // start 2nd arb with intro window
491  AW_root *aw_root = aww->get_root();
492  char *dir4intro;
493  GB_split_full_path(aw_root->awar(AWAR_SAVED_DB_PATH)->read_char_pntr(), &dir4intro, NULp, NULp, NULp);
494  if (!dir4intro) {
495  dir4intro = ARB_strdup(".");
496  }
497 
498  if (quit) {
499  NT_restart(aw_root, dir4intro);
500  }
501  else {
502  NT_start(dir4intro, true);
503  }
504  free(dir4intro);
505 }
506 
507 // --------------------------------------------------------------------------------
508 
509 static void NT_save_quick_cb(AW_window *aww) {
510  AW_root *awr = aww->get_root();
511  char *filename = awr->awar(AWAR_DB_PATH)->read_string();
512 
513  awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
514 
515  GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
516  if (error) aw_message(error);
517  else {
518  awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
519  AW_refresh_fileselection(awr, AWAR_DBBASE);
520  }
521 
522  free(filename);
523 }
524 
525 
526 static void NT_save_quick_as_cb(AW_window *aww) {
527  AW_root *awr = aww->get_root();
528  char *filename = awr->awar(AWAR_DB_PATH)->read_string();
529 
530  // @@@ also use dont_save_awars_with_default_value here?
531 
532  GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename);
533  if (!error) {
534  awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
535  AW_refresh_fileselection(awr, AWAR_DBBASE);
536  }
537  aww->hide_or_notify(error);
538 
539  free(filename);
540 }
541 
542 #define AWAR_DB_TYPE AWAR_DBBASE "/type" // created by AWT_insert_DBsaveType_selector
543 #define AWAR_DB_COMPRESSION AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector
544 #define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name"
545 
546 static void NT_save_as_cb(AW_window *aww) {
547  AW_root *awr = aww->get_root();
548  char *filename = awr->awar(AWAR_DB_PATH)->read_string();
549  const char *atype = awr->awar(AWAR_DB_TYPE)->read_char_pntr();
550  const char *ctype = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr();
551  char *savetype = GBS_global_string_copy("%s%s", atype, ctype);
552 
553  awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
554 
555  GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype);
556  if (!error) {
557  awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
558  AW_refresh_fileselection(awr, AWAR_DBBASE);
559  }
560  aww->hide_or_notify(error);
561 
562  free(savetype);
563  free(filename);
564 }
565 
566 static AW_window *NT_create_save_quick_as_window(AW_root *aw_root, const char *base_name) {
567  static AW_window_simple *aws = NULp;
568  if (!aws) {
569  aws = new AW_window_simple;
570  aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as");
571  aws->load_xfig("save_as.fig");
572 
573  aws->at("close");
574  aws->callback(AW_POPDOWN);
575  aws->create_button("CLOSE", "CLOSE", "C");
576 
577  aws->callback(makeHelpCallback("save.hlp"));
578  aws->at("help");
579  aws->create_button("HELP", "HELP", "H");
580 
581  AW_create_standard_fileselection(aws, base_name);
582 
583  aws->at("comment");
584  aws->create_text_field(AWAR_DB_COMMENT);
585 
586  aws->at("save");
587  aws->callback(NT_save_quick_as_cb);
588  aws->create_button("SAVE", "SAVE", "S");
589  }
590  return aws;
591 }
592 
593 static void NT_database_optimization(AW_window *aww) {
594  arb_progress progress(WEIGHTED, "Optimizing database compression", 0.38);
595  // 38% for seq-compression is just a rough guess made with silvaNR99138
596  // (a real guess would have to depend on ali-count, ali-length + field-count)
597 
598  GB_topSecurityLevel unsecured(GLOBAL.gb_main);
599 
600  GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
601  if (!error) {
602  ConstStrArray ali_names;
603  GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
604 
605  arb_progress ali_progress("Optimizing sequence data", ali_names.size());
606  ali_progress.allow_title_reuse();
607 
608  error = GBT_check_data(GLOBAL.gb_main, NULp);
609  error = GB_end_transaction(GLOBAL.gb_main, error);
610 
611  if (!error) {
612  char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string();
613  for (int i = 0; ali_names[i]; ++i) {
614  error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
615  ali_progress.inc_and_check_user_abort(error);
616  }
617  free(tree_name);
618  }
619  }
620  progress.inc_and_check_user_abort(error);
621 
622  if (!error) {
623  error = GB_optimize(GLOBAL.gb_main);
624  progress.inc_and_check_user_abort(error);
625  }
626  aww->hide_or_notify(error);
627 }
628 
629 static AW_window *NT_create_database_optimization_window(AW_root *aw_root) {
630  static AW_window_simple *aws = NULp;
631  if (aws) return aws;
632  GB_transaction ta(GLOBAL.gb_main);
633 
634  const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
635  aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree);
636 
637  aws = new AW_window_simple;
638  aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression");
639  aws->load_xfig("optimize.fig");
640 
641  aws->at("trees");
642  awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME);
643 
644  aws->at("close");
645  aws->callback(AW_POPDOWN);
646  aws->create_button("CLOSE", "CLOSE", "C");
647 
648  aws->callback(makeHelpCallback("optimize.hlp"));
649  aws->at("help");
650  aws->create_button("HELP", "HELP", "H");
651 
652  aws->at("go");
653  aws->callback(NT_database_optimization);
654  aws->create_button("GO", "GO");
655  return aws;
656 }
657 
658 static AW_window *NT_create_save_as(AW_root *aw_root, const char *base_name) {
659  static AW_window_simple *aws = NULp;
660  if (aws) return aws;
661 
662  aws = new AW_window_simple;
663  aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
664  aws->load_xfig("save_as.fig");
665 
666  aws->at("close");
667  aws->callback(AW_POPDOWN);
668  aws->create_button("CLOSE", "CLOSE", "C");
669 
670  aws->at("help");
671  aws->callback(makeHelpCallback("save.hlp"));
672  aws->create_button("HELP", "HELP", "H");
673 
674  AW_create_standard_fileselection(aws, base_name);
675 
676  aws->at("type");
677  AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE);
678 
679  aws->at("compression");
680  AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION);
681 
682  aws->at("optimize");
683  aws->callback(NT_create_database_optimization_window);
684  aws->help_text("optimize.hlp");
685  aws->create_autosize_button("OPTIMIZE", "Optimize database compression");
686 
687  aws->at("save");
688  aws->callback(NT_save_as_cb);
689  aws->create_button("SAVE", "SAVE", "S");
690 
691  aws->at("comment");
692  aws->create_text_field(AWAR_DB_COMMENT);
693 
694  return aws;
695 }
696 
697 static void NT_undo_cb(AW_window*, GB_UNDO_TYPE undo_type, TREE_canvas *ntw) {
698  GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type);
699  if (error) aw_message(error);
700  else {
701  GB_transaction ta(GLOBAL.gb_main);
702  AWT_auto_refresh allowed_on(ntw);
703  ntw->request_refresh();
704  }
705 }
706 
707 static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) {
708  DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
709  nt_mode_event(NULp, canvas, mode);
710 }
711 
712 static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) {
713  AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
714  if (tree_root) {
715  AWT_auto_refresh allowed_on(ntw);
716  GB_transaction ta(ntw->gb_main);
717 
718  NT_mark_all_cb(NULp, ntw, 0); // unmark all
719  tree_root->mark_duplicates();
720  ntw->request_structure_update();
721  }
722 }
723 
724 static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) {
725  GB_transaction ta(ntw->gb_main);
726  AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
727 
728  if (tree_root) {
729  AWT_auto_refresh allowed_on(ntw);
730  tree_root->justify_branch_lenghs(ntw->gb_main);
731  ntw->request_save_and_zoom_reset();
732  }
733 }
734 
735 #if defined(DEBUG)
736 static void NT_fix_database(AW_window *) {
737  GB_ERROR err = NULp;
738  err = GB_fix_database(GLOBAL.gb_main);
739  if (err) aw_message(err);
740 }
741 #endif
742 
743 static void relink_pseudo_species_to_organisms(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash) {
744  if (ref_gb_node) {
745  if (GEN_is_pseudo_gene_species(ref_gb_node)) {
746  GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
747 
748  if (gb_organism) {
749  char *name = GBT_read_string(gb_organism, "name");
750 
751  if (name) {
752  freeset(ref_name, name);
753  ref_gb_node = gb_organism;
754  }
755  }
756  }
757  }
758 }
759 
760 static void NT_pseudo_species_to_organism(AW_window *, TREE_canvas *ntw) {
761  GB_transaction ta(ntw->gb_main);
762  AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
763 
764  if (tree_root) {
765  AWT_auto_refresh allowed_on(ntw);
766 
767  GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
768  tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
769  GBS_free_hash(organism_hash);
770  ntw->request_save();
771  }
772 }
773 
774 
775 // #########################################
776 // #########################################
777 // ### ###
778 // ## user mask section ##
779 // ### ###
780 // #########################################
781 // #########################################
782 
783 struct nt_item_type_species_selector FINAL_TYPE : public awt_item_type_selector {
784  nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
785  ~nt_item_type_species_selector() OVERRIDE {}
786 
787  const char *get_self_awar() const OVERRIDE {
788  return AWAR_SPECIES_NAME;
789  }
790  size_t get_self_awar_content_length() const OVERRIDE {
791  return 12; // should be enough for "nnaammee.999"
792  }
793  GBDATA *current(AW_root *root, GBDATA *gb_main) const OVERRIDE { // give the current item
794  char *species_name = root->awar(get_self_awar())->read_string();
795  GBDATA *gb_species = NULp;
796 
797  if (species_name[0]) {
798  GB_transaction ta(gb_main);
799  gb_species = GBT_find_species(gb_main, species_name);
800  }
801 
802  free(species_name);
803  return gb_species;
804  }
805  const char *getKeyPath() const OVERRIDE { // give the keypath for items
806  return CHANGE_KEY_PATH;
807  }
808 };
809 
810 static nt_item_type_species_selector item_type_species;
811 
812 static void NT_open_mask_window(AW_window *aww, int id, GBDATA *gb_main) {
813  const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
814  nt_assert(descriptor);
815  if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
816 }
817 
818 static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
819  AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
820 }
821 static AW_window *create_colorize_species_window(AW_root *aw_root) {
822  return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
823 }
824 
825 static void NT_update_marked_counter(GBDATA*, AW_window* aww) {
829  long count = GBT_count_marked_species(GLOBAL.gb_main);
830  const char *buffer = count ? GBS_global_string("%li marked", count) : "";
831  AW_awar *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
832  char *oldval = counter->read_string();
833  if (strcmp(oldval, buffer)) {
834  counter->write_string(buffer);
835  aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
836  }
837  free(oldval);
838 }
839 
840 // --------------------------------------------------------------------------------------------------
841 
842 static void NT_alltree_remove_leafs(AW_window *, GBT_TreeRemoveType mode, GBDATA *gb_main) {
843  GB_ERROR error = NULp;
844  GB_transaction ta(gb_main);
845 
846  ConstStrArray tree_names;
847  GBT_get_tree_names(tree_names, gb_main, false);
848 
849  if (!tree_names.empty()) {
850  long treeCount = tree_names.size();
851 
852  const char *whats_removed = NULp;
853  switch (mode) {
854  case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
855  case GBT_REMOVE_MARKED: whats_removed = "marked"; break;
856  default: nt_assert(0); break;
857  }
858 
859  const char *task = GBS_global_string("Deleting %s from %li trees", whats_removed, treeCount);
860 
861  arb_progress progress(task, treeCount);
862  GB_HASH *species_hash = GBT_create_species_hash(gb_main);
863 
864  int modified = 0;
865 
866  for (int t = 0; t<treeCount && !error; t++) {
867  progress.subtitle(tree_names[t]);
868  TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
869  if (!tree) {
870  aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
871  }
872  else {
873  int removed = 0;
874  int groups_removed = 0;
875 
876  tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
877 
878  nt_assert(removed >= groups_removed);
879 
880  if (!tree) {
881  aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
882  }
883  else {
884  if (removed>0) {
885  error = GBT_write_tree(gb_main, tree_names[t], tree);
886  if (error) {
887  aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
888  }
889  else {
890  if (groups_removed>0) {
891  aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
892  }
893  else {
894  aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
895  }
896  modified++;
897  }
898  }
899  UNCOVERED();
900  destroy(tree);
901  }
902  }
903  progress.inc_and_check_user_abort(error);
904  }
905 
906  if (modified) {
907  aw_message(GBS_global_string("Changed %i of %li trees.", modified, treeCount));
908  }
909  else {
910  aw_message("No tree modified");
911  }
912 
913  GBS_free_hash(species_hash);
914  }
915 
916  aw_message_if(ta.close(error));
917 }
918 
919 TreeNode *NT_get_tree_root_of_canvas(TREE_canvas *ntw) {
920  AWT_graphic_tree *tree = AWT_TREE(ntw);
921  if (tree) {
922  AP_tree *root = tree->get_root_node();
923  if (root) return root;
924  }
925  return NULp;
926 }
927 
928 // --------------------------------------------------------------------------------------------------
929 
930 static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
931  GB_transaction ta(gb_main);
932  GBT_mark_all(gb_main, 0);
933 
934  DBItemSetIter end = referred.end();
935  for (DBItemSetIter s = referred.begin(); s != end; ++s) {
936  GB_write_flag(*s, 1);
937  }
938  return ARB_ERROR();
939 }
940 
941 static AW_window *create_mark_by_refentries_window(AW_root *awr, GBDATA *gbmain) {
942  static AW_window *aws = NULp;
943  if (!aws) {
944  static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
945  aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULp, "Mark referenced", mark_referred_species);
946  }
947  return aws;
948 }
949 
950 // --------------------------------------------------------------------------------------------------
951 
952 static void merge_from_to(AW_root *awr, const char *db_awar_name, bool merge_to) {
953  const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
954  char *quotedDB = GBK_singlequote(db_name);
955 
956  AW_system(
957  GBS_global_string(
958  merge_to
959  ? "arb_ntree : %s &"
960  : "arb_ntree %s : &",
961  quotedDB)
962  );
963 
964  free(quotedDB);
965 }
966 
967 static void merge_from_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, false); }
968 static void merge_into_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, true); }
969 
970 static AW_window *NT_create_merge_from_window(AW_root *awr) {
971  static char *awar_name = NULp; // do not free, bound to callback
972  AW_window *aw_from =
973  awt_create_load_box(awr, "Merge data from", "other ARB database",
974  ".", ".arb", &awar_name,
975  makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
976  return aw_from;
977 }
978 static AW_window *NT_create_merge_to_window(AW_root *awr) {
979  static char *awar_name = NULp; // do not free, bound to callback
980  AW_window *aw_to =
981  awt_create_load_box(awr, "Merge data to", "other ARB database",
982  ".", ".arb", &awar_name,
983  makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
984  makeWindowCallback(AW_POPDOWN), NULp);
985  return aw_to;
986 }
987 
988 // --------------------------------------------------------------------------------------------------
989 
990 static void update_main_window_title(AW_root* awr, AW_window_menu_modes* aww, int clone) {
991  const char* filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
992  if (clone) {
993  aww->set_window_title(GBS_global_string("%s - ARB (%i)", filename, clone));
994  }
995  else {
996  aww->set_window_title(GBS_global_string("%s - ARB", filename));
997  }
998 }
999 
1000 static void canvas_tree_awar_changed_cb(AW_awar *, bool, TREE_canvas *ntw) {
1001  NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
1002  AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
1003  TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_TREE);
1004 }
1005 
1006 class TREE_canvas_registry {
1007  int count;
1008  TREE_canvas *canvas[MAX_NT_WINDOWS];
1009 
1010  static TREE_canvas_registry *SINGLETON;
1011 
1012  TREE_canvas_registry() : count(0) {
1013  AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
1014  }
1015 
1016 public:
1017  static TREE_canvas_registry& instance() {
1018  if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
1019  return *SINGLETON;
1020  }
1021 
1022  void register_canvas(TREE_canvas *ntw) {
1023  nt_assert(count<MAX_NT_WINDOWS);
1024  nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
1025  canvas[count++] = ntw;
1026  ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
1027  }
1028 
1029  int get_count() const { return count; }
1030 
1031  TREE_canvas *get_canvas(int idx) const {
1032  if (idx<0 || idx>=count) return NULp;
1033  return canvas[idx];
1034  }
1035 };
1036 
1037 TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULp;
1038 
1039 TREE_canvas *NT_get_canvas_by_index(int idx) {
1041  nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
1042  return TREE_canvas_registry::instance().get_canvas(idx);
1043 }
1044 
1045 #if defined(TRACE_GROUP_SELECTION)
1046 static TREE_canvas *find_canvas_showing(AWT_graphic_tree *agt) {
1047  // look for (registered) canvas showing given AWT_graphic_tree
1048  // returns NULp if none found
1049  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1050 
1051  int maxIdx = reg.get_count();
1052  for (int32_t i = 0; i<maxIdx; ++i) {
1053  TREE_canvas *ntw = reg.get_canvas(i);
1054  if (ntw->gfx == agt) return ntw;
1055  }
1056  return NULp;
1057 }
1058 #endif
1059 
1060 void NT_fill_canvas_selection_list(class AW_selection_list *sellst, TREE_canvas *to_skip) {
1063  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1064 
1065  int maxIdx = reg.get_count();
1066  for (int32_t i = 0; i<maxIdx; ++i) {
1067  TREE_canvas *ntw = reg.get_canvas(i);
1068  if (ntw && ntw != to_skip) {
1069  nt_assert(ntw->get_awar_tree());
1070  const char *treename = ntw->get_awar_tree()->read_char_pntr();
1071  const char *description = i
1072  ? GBS_global_string("ARB (%i): %s", i, treename)
1073  : GBS_global_string("ARB main: %s", treename);
1074  sellst->insert(description, i);
1075  }
1076  }
1077 }
1078 
1079 // ----------------------------------
1080 // group-selection handlers
1081 
1082 void NT_deselect_group(AW_root *awr) {
1083  awr->awar(AWAR_GROUP)->write_pointer(NULp);
1084 }
1085 
1086 static bool track_group_selection_by_canvas = true;
1087 
1088 static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) {
1089  const Group& group = gfx->get_selected_group();
1090 
1091 #if defined(TRACE_GROUP_SELECTION)
1092  fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track");
1093  TREE_canvas *ntw = find_canvas_showing(gfx);
1094  if (group.is_valid()) {
1095  fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name());
1096  }
1097  else {
1098  fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index());
1099  }
1100 #endif
1101 
1102  if (track_group_selection_by_canvas) {
1103  // set group-awar:
1104  gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULp if !group.is_valid()
1105  }
1106 }
1107 
1108 static void group_awar_changed_cb(AW_root *awr) {
1109  AW_awar *awar_group = awr->awar(AWAR_GROUP);
1110  GBDATA *gb_wanted_group = awar_group->read_pointer();
1111 
1112  GBDATA *gb_wanted_tree = NULp;
1113  {
1114  if (gb_wanted_group) {
1115  GB_transaction ta(gb_wanted_group);
1116  gb_wanted_tree = GB_get_father(gb_wanted_group);
1117  awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected
1118 #if defined(TRACE_GROUP_SELECTION)
1119  fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr);
1120 #endif
1121  }
1122 #if defined(TRACE_GROUP_SELECTION)
1123  const char *group_name = NULp;
1124  if (gb_wanted_group) {
1125  GB_transaction ta(gb_wanted_group);
1126  GBDATA *gb_name = GB_entry(gb_wanted_group, "group_name");
1127  if (gb_name) group_name = GB_read_char_pntr(gb_name);
1128  }
1129  fprintf(stderr, "group awar changed to %p", gb_wanted_group);
1130  if (group_name) fprintf(stderr, " (='%s')", group_name);
1131  fputc('\n', stderr);
1132 #endif
1133  }
1134 
1135  LocallyModify<bool> ignore_group_selection_by_canvas(track_group_selection_by_canvas, false);
1136 
1137  {
1138  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1139 
1140  int maxIdx = reg.get_count();
1141  for (int32_t i = 0; i<maxIdx; ++i) {
1142  TREE_canvas *ntw = reg.get_canvas(i);
1143  AWT_graphic_tree *agt = AWT_TREE(ntw);
1144  const Group& curr_group = agt->get_selected_group();
1145 
1146  GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree();
1147  if (gb_curr_tree == gb_wanted_tree) {
1148  AWT_auto_refresh allowed_on(ntw);
1149  if (!curr_group.is_valid() || // no group selected
1150  curr_group.get_group_data() != gb_wanted_group) // wrong group selected
1151  {
1152  agt->select_group(gb_wanted_group);
1153  ntw->request_refresh();
1154  }
1155  // perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group)
1156  TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_GROUP);
1157  }
1158  else {
1159  if (curr_group.is_valid()) {
1160  AWT_auto_refresh allowed_on(ntw);
1161  agt->deselect_group();
1162  ntw->request_refresh();
1163  }
1164  }
1165  }
1166  }
1167 }
1168 
1169 // ----------------------------
1170 // create main window
1171 
1172 static AW_window *popup_new_main_window(AW_root *awr, int clone, TREE_canvas **result_ntw) {
1178  GB_push_transaction(GLOBAL.gb_main);
1179 
1180  char window_title[256];
1181  const char *awar_tree = NULp;
1182 
1183  if (clone) {
1184  awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
1185  sprintf(window_title, "ARB_NT_%i", clone);
1186  }
1187  else {
1188  awar_tree = AWAR_TREE;
1189  sprintf(window_title, "ARB_NT");
1190  }
1191  AW_window_menu_modes *awm = new AW_window_menu_modes;
1192  awm->init(awr, window_title, window_title, 0, 0);
1193 
1194  awr->awar(AWAR_DB_NAME)
1195  ->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1196  ->update();
1197 
1198  awm->button_length(5);
1199 
1200  if (!clone) AW_init_color_group_defaults("arb_ntree");
1201 
1202  AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1203 
1204  if (!clone) { // while creating initial window
1205  AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb));
1206  awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb);
1207  }
1208 
1209  TREE_canvas *ntw;
1210  {
1211  AW_awar *tree_awar = awr->awar_string(awar_tree);
1212  {
1213  AP_tree_display_style prev_style = tree->get_tree_style();
1214  tree->set_tree_style(AP_LIST_SIMPLE, NULp); // avoid NDS warnings during startup
1215 
1216  ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1217  tree->set_tree_style(prev_style, ntw);
1218  ntw->set_mode(AWT_MODE_SELECT);
1219  }
1220 
1221  if (result_ntw) *result_ntw = ntw;
1222 
1223  {
1224  const char *tree_name = tree_awar->read_char_pntr();
1225  const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1226 
1227  if (existing_tree_name) {
1228  tree_awar->write_string(existing_tree_name);
1229  NT_reload_tree_event(awr, ntw, true); // load first tree
1230  }
1231  else {
1232  AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, NULp, "no_tree.hlp");
1233  tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list
1234  }
1235 
1236  TREE_canvas_registry::instance().register_canvas(ntw);
1237  AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1238  }
1239  }
1240 
1241  TREE_install_update_callbacks(ntw);
1242 
1243  bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1244 
1245  WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1246 
1247  // --------------
1248  // File
1249 
1250 #if defined(DEBUG)
1251  AWT_create_debug_menu(awm);
1252 #endif // DEBUG
1253 
1254  bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1255 
1256  if (clone) {
1257  awm->create_menu("File", "F", AWM_ALL);
1258  if (allow_new_window) {
1259  awm->insert_menu_topic(awm->local_id("new_window"), "New window (same database)", "N", "newwindow.hlp", AWM_ALL, makeCreateWindowCallback(popup_new_main_window, clone+1, (TREE_canvas**)NULp));
1260  }
1261  awm->insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN);
1262  }
1263  else {
1264 #if defined(DEBUG)
1265  // add more to debug-menu
1266  awm->sep______________();
1267  awm->insert_menu_topic("fix_db", "Fix database", "F", NULp, AWM_ALL, NT_fix_database);
1268  awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", NULp, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1269  awm->insert_menu_topic("test_compr", "Test compression", "T", NULp, AWM_ALL, makeWindowCallback(GBT_compression_test, GLOBAL.gb_main));
1270 #endif // DEBUG
1271 
1272  awm->create_menu("File", "F", AWM_ALL);
1273  {
1274  // keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1275  awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, NT_save_quick_cb);
1276  awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1277  if (allow_new_window) {
1278  awm->sep______________();
1279  awm->insert_menu_topic("new_window", "New window (same database)", "N", "newwindow.hlp", AWM_ALL, makeCreateWindowCallback(popup_new_main_window, clone+1, (TREE_canvas**)NULp));
1280  }
1281  awm->sep______________();
1282  awm->insert_menu_topic("optimize_db", "Optimize database compression", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window);
1283  awm->sep______________();
1284 
1285  awm->insert_sub_menu("Import", "I");
1286  {
1287  awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1288  awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1289  GDE_load_menu(awm, AWM_EXP, "Import");
1290  }
1291  awm->close_sub_menu();
1292 
1293  awm->insert_sub_menu("Export", "E");
1294  {
1295  awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1296  awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1297  GDE_load_menu(awm, AWM_ALL, "Export");
1298  awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window);
1299  }
1300  awm->close_sub_menu();
1301  awm->sep______________();
1302 
1303  insert_macro_menu_entry(awm, false);
1304 
1305  awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1306  {
1307  awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp"));
1308  awm->insert_menu_topic("bug_report", "Report bug", "b", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1309  awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1310  }
1311  awm->close_sub_menu();
1312  awm->sep______________();
1313 
1314  awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1315  awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1316  awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_exit, EXIT_SUCCESS));
1317  }
1318 
1319  // -----------------
1320  // Species
1321 
1322  awm->create_menu("Species", "c", AWM_ALL);
1323  {
1324  awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1325  awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb);
1326 
1327  awm->sep______________();
1328 
1329  NT_insert_mark_submenus(awm, ntw, 1);
1330  awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1331  awm->insert_menu_topic("species_colors", "Colors ...", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window);
1332  awm->insert_menu_topic("selection_admin", "Selections ...", "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1333 
1334  awm->sep______________();
1335 
1336  awm->insert_sub_menu("Database fields admin", "f");
1337  DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1338  awm->close_sub_menu();
1339  NT_create_mask_submenu(awm);
1340 
1341  awm->sep______________();
1342 
1343  awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1344 
1345  awm->insert_sub_menu("Sort Species", "s");
1346  {
1347  awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window);
1348  awm->insert_menu_topic("$sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1349  }
1350  awm->close_sub_menu();
1351 
1352  awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1353  {
1354  awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1355  awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "species_join.hlp", AWM_EXP, NT_create_species_join_window);
1356  }
1357  awm->close_sub_menu();
1358 
1359  awm->sep______________();
1360 
1361  awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1362 
1363  awm->sep______________();
1364 
1365  awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1366 
1367  awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1368  {
1369  awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames);
1370  awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames);
1371  awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1372  awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window);
1373  }
1374  awm->close_sub_menu();
1375  }
1376 
1377  // ----------------------------
1378  // Genes + Experiment
1379 
1380  if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1381 
1382  // ------------------
1383  // Sequence
1384 
1385  awm->create_menu("Sequence", "S", AWM_ALL);
1386  {
1387  awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)NULp));
1388  awm->insert_sub_menu("Insert/delete", "I");
1389  {
1390  awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window);
1391  awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main));
1392  }
1393  awm->close_sub_menu();
1394  awm->sep______________();
1395 
1396  awm->insert_sub_menu("Edit Sequences", "E");
1397  {
1398  awm->insert_menu_topic("new_arb_edit4", "Using marked species and tree", "m", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1399  awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1400  awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1401  }
1402  awm->close_sub_menu();
1403 
1404  awm->sep______________();
1405 
1406  awm->insert_sub_menu("Align sequences", "l");
1407  {
1408  awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1409  GDE_load_menu(awm, AWM_ALL, "Align");
1410  }
1411  awm->close_sub_menu();
1412  awm->insert_menu_topic("seq_concat", "Concatenate sequences", "C", "concatenate.hlp", AWM_ALL, NT_createConcatenationWindow);
1413  awm->insert_menu_topic("seq_split", "Split sequences", "S", "split.hlp", AWM_ALL, NT_create_splitAlignment_window);
1414  awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1415  awm->sep______________();
1416 
1417  awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1418  awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist"));
1419  awm->sep______________();
1420 
1421  awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1422  awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1423 
1424  awm->sep______________();
1425 
1426  GDE_load_menu(awm, AWM_ALL, "Print");
1427  }
1428 
1429  // -------------
1430  // SAI
1431 
1432  awm->create_menu("SAI", "A", AWM_ALL);
1433  {
1434  awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1435  awm->insert_menu_topic("sai_calc", "Combine SAIs", "b", "saicalc.hlp", AWM_ALL, makeWindowCallback(SAI_popup_calculator_window, GLOBAL.gb_main));
1436  awm->insert_sub_menu("Create SAI using ...", "C");
1437  {
1438  awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window);
1439  awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window);
1440  awm->insert_menu_topic("pos_var_pars", "Positional variability + Column statistic (parsimony method)", "a", "pos_var_pars.hlp", AWM_ALL, AP_create_pos_var_pars_window);
1441  awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_phylo"));
1442  awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold);
1443 
1444  GDE_load_menu(awm, AWM_EXP, "SAI");
1445  }
1446  awm->close_sub_menu();
1447 
1448  awm->insert_sub_menu("Other functions", "O");
1449  {
1450  awm->insert_menu_topic("count_different_chars", "Count different chars/column", "C", "count_chars.hlp", AWM_EXP, makeWindowCallback(NT_count_different_chars, GLOBAL.gb_main));
1451  awm->insert_menu_topic("corr_mutat_analysis", "Compute clusters of correlated positions", "m", "", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_rnacma", new XCmdType(XCMD_SERVSYNC_WAIT_ON_ERROR, GLOBAL.gb_main)));
1452  awm->insert_menu_topic("export_pos_var", "Export Column Statistic (GNUPLOT format)", "E", "csp_2_gnuplot.hlp", AWM_ALL, NT_create_colstat_2_gnuplot_window);
1453  }
1454  awm->close_sub_menu();
1455  }
1456 
1457  // ----------------
1458  // Probes
1459 
1460  awm->create_menu("Probes", "P", AWM_ALL);
1461  {
1462  awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1463  awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1464  awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1465  awm->sep______________();
1466  awm->insert_menu_topic("probe_match_sp", "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window, ntw));
1467  awm->sep______________();
1468  awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1469  awm->insert_menu_topic("primer_design", "Design Sequencing Primers", "S", "primer.hlp", AWM_EXP, makeWindowCallback(ARB_system_in_console_cb, "arb_primer", new XCmdType(XCMD_SERVSYNC_WAIT_ON_ERROR, GLOBAL.gb_main)));
1470  awm->sep______________();
1471  awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1472  }
1473 
1474  }
1475 
1476  // --------------
1477  // Tree
1478 
1479  awm->create_menu("Tree", "T", AWM_ALL);
1480  {
1481  if (!clone) {
1482  awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1483  awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(NDS_create_window, GLOBAL.gb_main));
1484  awm->sep______________();
1485  awm->insert_sub_menu("Add Species to Existing Tree", "A");
1486  {
1487  awm->insert_menu_topic("arb_pars_quick", "ARB Parsimony (Quick add marked)", "Q", "pars.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_pars -add_marked -quit"));
1488  awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_pars"));
1489  GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1490  }
1491  awm->close_sub_menu();
1492  }
1493 
1494  awm->insert_sub_menu("Remove Species from Tree", "R");
1495  {
1496  awm->insert_menu_topic(awm->local_id("tree_remove_deleted"), "Remove zombies", "z", "trm_del.hlp", AWM_ALL, makeWindowCallback(NT_remove_leafs, ntw, AWT_REMOVE_ZOMBIES));
1497  awm->insert_menu_topic(awm->local_id("tree_remove_marked"), "Remove marked", "m", "trm_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_remove_leafs, ntw, AWT_REMOVE_MARKED));
1498  awm->insert_menu_topic(awm->local_id("tree_keep_marked"), "Keep marked", "K", "tkeep_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_remove_leafs, ntw, AWT_KEEP_MARKED));
1499  awm->sep______________();
1500  awm->insert_menu_topic("all_tree_remove_deleted", "Remove zombies from ALL trees", "A", "trm_del.hlp", AWM_ALL, makeWindowCallback(NT_alltree_remove_leafs, GBT_REMOVE_ZOMBIES, GLOBAL.gb_main));
1501  awm->insert_menu_topic("all_tree_remove_marked", "Remove marked from ALL trees", "L", "trm_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_alltree_remove_leafs, GBT_REMOVE_MARKED, GLOBAL.gb_main));
1502  }
1503  awm->close_sub_menu();
1504 
1505  if (!clone) {
1506  awm->insert_sub_menu("Build tree from sequence data", "B");
1507  {
1508  awm->insert_sub_menu("Distance matrix methods", "D");
1509  awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist"));
1510  GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1511  awm->close_sub_menu();
1512 
1513  awm->insert_sub_menu("Maximum Parsimony methods", "P");
1514  GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1515  awm->close_sub_menu();
1516 
1517  awm->insert_sub_menu("Maximum Likelihood methods", "L");
1518  GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1519  GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1520  awm->close_sub_menu();
1521 
1522  awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1523  GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1524  awm->close_sub_menu();
1525  }
1526  awm->close_sub_menu();
1527  }
1528 
1529  awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1530 
1531  awm->sep______________();
1532 
1533  awm->insert_sub_menu("Reset zoom", "z");
1534  {
1535  awm->insert_menu_topic(awm->local_id("reset_logical_zoom"), "Logical zoom", "L", "rst_log_zoom.hlp", AWM_ALL, makeWindowCallback(NT_reset_lzoom_cb, ntw));
1536  awm->insert_menu_topic(awm->local_id("reset_physical_zoom"), "Physical zoom", "P", "rst_phys_zoom.hlp", AWM_ALL, makeWindowCallback(NT_reset_pzoom_cb, ntw));
1537  }
1538  awm->close_sub_menu();
1539 
1540  awm->sep______________();
1541 
1542  // taxonomic groups
1543  NT_insert_collapse_submenu(awm, ntw);
1544  if (!clone) {
1545  awm->insert_menu_topic("group_search", "Search groups...", "g", "group_search.hlp", AWM_ALL, makeWindowCallback (popup_group_search_window, GLOBAL.gb_main));
1546  awm->insert_menu_topic("compare_taxonomy", "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1547  awm->insert_menu_topic("move_groups", "Move groups...", "v", "move_groups.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_moveGroupInfo_window));
1548  }
1549 
1550  awm->sep______________();
1551 
1552  if (!clone) {
1553  awm->insert_menu_topic("compare_topology", "Compare topology...", "o", "compare_topo.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compareTopologies_window));
1554  }
1555 
1556  awm->insert_sub_menu("Modify branches", "M");
1557  {
1558  awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw));
1559  awm->insert_menu_topic(awm->local_id("tree_edit_remark"), "Edit bootstraps", "E", "ted_boot.hlp", AWM_ALL, makeWindowCallback(NT_edit_bootstrap, ntw));
1560  awm->sep______________();
1561  awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw));
1562  awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1563  awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw));
1564  awm->sep______________();
1565  awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1566  awm->sep______________();
1567  awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1568  awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1569 
1570  }
1571  awm->close_sub_menu();
1572  awm->insert_sub_menu("Beautify tree", "u");
1573  {
1574  awm->insert_menu_topic(awm->local_id("beautifyt_tree"), "#beautifyt.xpm", "", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_TOP));
1575  awm->insert_menu_topic(awm->local_id("beautifyc_tree"), "#beautifyc.xpm", "", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_EDGE));
1576  awm->insert_menu_topic(awm->local_id("beautifyb_tree"), "#beautifyb.xpm", "", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_BOTTOM));
1577  awm->insert_menu_topic(awm->local_id("beautifyr_tree"), "Radial tree (1)", "1", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_CENTER));
1578  awm->insert_menu_topic(awm->local_id("beautifyr2_tree"), "Radial tree (2)", "2", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_ALTERNATING));
1579  awm->sep______________();
1580  awm->insert_menu_topic(awm->local_id("sort_by_other"), "By other tree", "o", "resortbyother.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_sort_tree_by_other_tree_window, ntw));
1581  }
1582  awm->close_sub_menu();
1583 
1584  awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "h", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1585  awm->insert_menu_topic(awm->local_id("syncroots"), "Adjust roots...", "j", "syncroots.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncroot_window, GLOBAL.gb_main));
1586  awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "k", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback (NT_mark_duplicates, ntw));
1587 
1588  awm->sep______________();
1589  awm->insert_menu_topic(awm->local_id("shade"), "Tree shading...", "s", "tree_shading.hlp", AWM_ALL, makeWindowCallback (NT_configure_treeShader));
1590  awm->insert_menu_topic(awm->local_id("syncscroll"), "Sync tree scrolling..", "e", "syncscroll.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1591 
1592  awm->sep______________();
1593  awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", NULp, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1594 
1595  awm->sep______________();
1596  awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1597 
1598  if (is_genome_db) {
1599  awm->sep______________();
1600  awm->insert_menu_topic(awm->local_id("tree_pseudo_species_to_organism"), "Relink tree to organisms", "i", "tree_pseudo.hlp", AWM_EXP, makeWindowCallback(NT_pseudo_species_to_organism, ntw));
1601  }
1602 
1603  if (!clone) {
1604  awm->sep______________();
1605  awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1606  awm->insert_menu_topic("tree_2_xfig", "Export tree to XFIG", "F", "tree2file.hlp", AWM_ALL, makeWindowCallback(AWT_popup_tree_export_window, static_cast<AWT_canvas*>(ntw)));
1607  }
1608 
1609  }
1610 
1611  if (!clone) {
1612  // ---------------
1613  // Tools
1614 
1615  awm->create_menu("Tools", "o", AWM_ALL);
1616  {
1617  awm->insert_menu_topic("names_admin", "Nameserver admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeWindowCallback(AW_popup_namesadmin_window, GLOBAL.gb_main));
1618  awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1619  {
1620  awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1621  }
1622  awm->close_sub_menu();
1623  awm->sep______________();
1624 
1625  awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1626  {
1627  GDE_load_menu(awm, AWM_EXP, NULp);
1628  }
1629  awm->close_sub_menu();
1630 
1631  awm->sep______________();
1632  awm->insert_menu_topic("xterm", "Start XTERM", "X", "xterm.hlp", AWM_ALL, AW_console_cb);
1633  XCmdType *showlog_cmdtype = new XCmdType(XCMD_ASYNC_WAIT_ON_ERROR, GLOBAL.gb_main); // do not free (used in callback)
1634  awm->insert_menu_topic("viewlog", "View ARB log", "l", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl run", showlog_cmdtype)); // ../SH/arb_show_log.pl
1635  awm->insert_menu_topic("viewserv", "View server log", "V", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl server", showlog_cmdtype));
1636  awm->insert_menu_topic("viewsys", "View sysinfo", "i", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl sysinf", showlog_cmdtype));
1637  awm->sep______________();
1638  GDE_load_menu(awm, AWM_EXP, "User");
1639  }
1640  // --------------------
1641  // Properties
1642 
1643  awm->create_menu("Properties", "r", AWM_ALL);
1644  {
1645  awm->insert_menu_topic("props_menu", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1646  awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1647  awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1648  awm->insert_menu_topic("props_www", "Search world wide web (WWW)", "b", "props_www.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_www_window, GLOBAL.gb_main));
1649  awm->sep______________();
1650  awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", NULp, AWM_ALL, NT_toggle_expert_mode);
1651  awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", NULp, AWM_ALL, NT_toggle_focus_policy);
1652  awm->sep______________();
1653  AW_insert_common_property_menu_entries(awm);
1654  awm->sep______________();
1655  awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1656  }
1657  }
1658 
1659  awm->insert_help_topic("ARB_NT help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1660 
1661  // ----------------------
1662  // mode buttons
1663  //
1664  // keep them synchronized as far as possible with those in ARB_PARSIMONY
1665  // see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1666 
1667  awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1668  awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1669  awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1670  awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1671  awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1672 
1673  awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1674  awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW));
1675 
1676  // topology-modification-modes
1677  awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1678  awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1679  awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1680  awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1681  awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1682 
1683  // layout-modes
1684  awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1685  awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1686  awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1687 
1688  awm->set_info_area_height(250);
1689  awm->at(5, 2);
1690  awm->auto_space(-2, -2);
1691  awm->shadow_width(1);
1692 
1693  // -------------------------
1694  // create top area
1695 
1696  int first_liney;
1697  int leftx;
1698  awm->get_at_position(&leftx, &first_liney);
1699 
1700  // ---------------------
1701  // quit + help
1702 
1703  awm->button_length(0);
1704 
1705  if (clone) {
1706  awm->callback(AW_POPDOWN);
1707  awm->create_button("CLOSE", "#close.xpm");
1708  }
1709  else {
1710  awm->callback(makeWindowCallback(NT_exit, EXIT_SUCCESS));
1711  awm->help_text("quit.hlp");
1712  awm->create_button("QUIT", "#quit.xpm");
1713  }
1714 
1715  int db_pathx = awm->get_at_xposition();
1716 
1717  // now fetch the yposition for the 2nd button line
1718  awm->at_newline();
1719  int second_liney = awm->get_at_yposition();
1720 
1721  awm->callback(AW_help_entry_pressed);
1722  awm->help_text("arb_ntree.hlp");
1723  awm->create_button("?", "#help.xpm");
1724 
1725  // --------------------------
1726  // save + undo/redo
1727 
1728  awm->callback(NT_save_quick_cb);
1729  awm->help_text("save.hlp");
1730  awm->create_button("SAVE", "#save.xpm");
1731 
1732  awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1733  awm->help_text("save.hlp");
1734  awm->create_button("SAVE_AS", "#saveAs.xpm");
1735 
1736  // undo/redo:
1737  awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1738  awm->help_text("undo.hlp");
1739  awm->create_button("UNDO", "#undo.xpm");
1740 
1741  awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1742  awm->help_text("undo.hlp");
1743  awm->create_button("REDO", "#redo.xpm");
1744 
1745  int db_pathx2 = awm->get_at_xposition();
1746 
1747  // fetch position for mode help-line:
1748  awm->at_newline();
1749  int third_liney = awm->get_at_yposition();
1750 
1751  awm->at(db_pathx, first_liney);
1752  // size of DB-name button is determined by buttons below:
1753  awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1754  awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1755  awm->help_text("save.hlp");
1756  awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1757 
1758  // -----------------------------
1759  // tree + tree display
1760 
1761 #define TREE_BUTTON_OVERSIZE 6
1762 
1763  int db_treex = awm->get_at_xposition();
1764  int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1765 
1766  awm->at(db_treex, second_uppery);
1767  awm->button_length(0);
1768 
1769  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1770  awm->help_text("tr_type_radial.hlp");
1771  awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1772 
1773  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1774  awm->help_text("tr_type_dendro.hlp");
1775  awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1776 
1777  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1778  awm->help_text("tr_type_irs.hlp");
1779  awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1780 
1781  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1782  awm->help_text("tr_type_nds.hlp");
1783  awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1784 
1785  int db_treex2 = awm->get_at_xposition();
1786 
1787  awm->at(db_treex, first_liney);
1788  // size of tree-name button is determined by buttons below:
1789  awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1790  awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1791  awm->help_text("nt_tree_select.hlp");
1792  awm->create_button("SELECT_A_TREE", awar_tree);
1793 
1794  // ---------------------------------------------------------------
1795  // protection, alignment + editor (and maybe Genome Map)
1796 
1797  int db_alignx = awm->get_at_xposition();
1798 
1799  // editor and genemap buttons have to be 44x24 sized
1800 #define EDIT_XSIZE 50
1801 #define EDIT_YSIZE 30 // same as 'save as' buttons
1802 
1803  // first draw protection:
1804  int protectx = db_alignx + 2*EDIT_XSIZE;
1805 
1806  awm->at(protectx+2, first_liney+1);
1807  awm->button_length(0);
1808  awm->create_button(NULp, "#protect.xpm");
1809 
1810  awm->at(protectx, second_liney+2);
1811  awm->create_option_menu(AWAR_SECURITY_LEVEL);
1812  awm->insert_option ("0", NULp, 0);
1813  awm->insert_option ("1", NULp, 1);
1814  awm->insert_option ("2", NULp, 2);
1815  awm->insert_option ("3", NULp, 3);
1816  awm->insert_option ("4", NULp, 4);
1817  awm->insert_option ("5", NULp, 5);
1818  awm->insert_default_option("6", NULp, 6);
1819  awm->update_option_menu();
1820 
1821  int db_searchx = awm->get_at_xposition() - 7;
1822 
1823  // draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1824  awm->at(db_alignx, second_liney);
1825 
1826  awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1827  awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1828  awm->help_text("arb_edit4.hlp");
1829  if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1830  else awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1831 
1832  if (is_genome_db) {
1833  awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1834  awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1835  awm->help_text("gene_map.hlp");
1836  awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1837  }
1838 
1839  int db_alignx2 = awm->get_at_xposition();
1840 
1841  awm->at(db_alignx, first_liney);
1842  awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1843  awm->callback(NT_create_select_alignment_window);
1844  awm->help_text("nt_align_select.hlp");
1845  awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1846 
1847  // -------------------------------
1848  // create mode-help line
1849 
1850  awm->at(leftx, third_liney);
1851  awm->button_length(AWAR_FOOTER_MAX_LEN);
1852  awm->create_button(NULp, AWAR_FOOTER);
1853 
1854  awm->at_newline();
1855  int bottomy = awm->get_at_yposition();
1856 
1857  // ---------------------------------------
1858  // Info / marked / Search / Jump
1859 
1860  awm->button_length(7);
1861 
1862  awm->at(db_searchx, first_liney);
1863  awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1864  awm->help_text("sp_search.hlp");
1865  awm->create_button("SEARCH", "Search");
1866 
1867  awm->at(db_searchx, second_uppery);
1868  awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1869  awm->help_text("tr_jump.hlp");
1870  awm->create_button("JUMP", "Jump");
1871 
1872  int db_infox = awm->get_at_xposition();
1873 
1874  awm->at(db_infox, first_liney);
1875  awm->button_length(13);
1876  awm->callback(popupinfo_wcb);
1877  awm->help_text("sp_info.hlp");
1878  awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1879 
1880  awm->at(db_infox, second_uppery);
1881  awm->button_length(13);
1882  awm->help_text("species_configs.hlp");
1883  awm->callback(makeWindowCallback(NT_popup_configuration_admin, ntw));
1884  awm->create_button("selection_admin2", AWAR_MARKED_SPECIES_COUNTER);
1885  {
1886  GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1887  GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(NT_update_marked_counter, static_cast<AW_window*>(awm)));
1888  NT_update_marked_counter(NULp, awm);
1889  }
1890 
1891  // set height of top area:
1892  awm->set_info_area_height(bottomy+2);
1893  awm->set_bottom_area_height(0);
1894 
1895  NT_activate_configMarkers_display(ntw);
1896 
1897  // ------------------------------------
1898  // Autostarts for development
1899 
1900 #if defined(DEVEL_RALF)
1901  // if (is_genome_db) GEN_map_first(awr)->show();
1902 #endif // DEVEL_RALF
1903 
1904  GB_pop_transaction(GLOBAL.gb_main);
1905 
1906 #if defined(DEBUG)
1907  AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1908 #endif
1909 
1910  return awm;
1911 }
1912 
1913 TREE_canvas *NT_create_main_window(AW_root *aw_root) {
1914  GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1915  if (error) aw_message(error);
1916 
1917  nt_create_all_awars(aw_root);
1918 
1919  TREE_canvas *ntw = NULp;
1920  AW_window *aww = popup_new_main_window(aw_root, 0, &ntw);
1921  NT_install_treeShader(ntw, GLOBAL.gb_main);
1922  aww->show();
1923 
1924  error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1925  if (error) aw_message(error);
1926 
1927  return ntw;
1928 }
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Definition: refentries.cxx:253
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Definition: NT_cb.cxx:60
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Definition: TreeDisplay.hxx:504
NT_create_compareTopologies_window
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Definition: adname.cxx:33
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Definition: aw_awar_defs.hxx:5
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Definition: probe_design.cxx:1236
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Definition: NT_extern.cxx:192
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Definition: awt_canvas.hxx:34
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Definition: AW_preset.cxx:1452
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Definition: AW_awar.cxx:390
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Definition: NT_extern.cxx:478
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Definition: NT_extern.cxx:227
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Definition: adtree.cxx:523
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Definition: aw_window.hxx:181
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Definition: NT_ins_col.cxx:201
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Definition: AW_window.cxx:472
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Definition: NT_extern.cxx:930
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Definition: NT_local.h:29
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Definition: AW_preset.cxx:1373
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Definition: AW_window.cxx:116
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Definition: AW_awar.cxx:207
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Definition: arb_error.h:99
NT_rerepair_DB
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Definition: NT_dbrepair.cxx:1040
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Definition: AP_Tree.cxx:1530
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Definition: TreeCallbacks.cxx:694
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AW_window * NT_create_alignment_admin_window(AW_root *root, AW_window *aw_popmedown)
Definition: NT_cb.cxx:109
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Definition: AW_window.cxx:2402
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Definition: AP_consensus.cxx:248
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Definition: Group.hxx:56
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Definition: aw_awar_defs.hxx:11
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void AW_create_fileselection_awars(AW_root *awr, const char *awar_base, const char *directories, const char *filter, const char *file_name)
Definition: AW_file.cxx:72
AWM_BASIC
Definition: aw_window.hxx:179
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Definition: nds.h:35
NT_create_searchManuallyNames_window
AW_window * NT_create_searchManuallyNames_window(AW_root *aw_root)
Definition: NT_validManual.cxx:154
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Definition: AW_preset.cxx:1920
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Definition: aw_awar_defs.hxx:10
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AW_ADVICE_TOGGLE_AND_HELP
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Definition: aw_system.hxx:25
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Definition: AW_window.cxx:569
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Definition: TreeDisplay.hxx:594
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Definition: adcomm.cxx:1682
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Definition: NT_import.cxx:48
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Definition: dbitem_set.h:23
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Definition: aw_awar_defs.hxx:59
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Definition: aw_awar_defs.hxx:49
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Definition: NT_extern.cxx:1172
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Definition: NT_extern.cxx:543
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Definition: AWT_input_mask.cxx:2491
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Definition: aw_awar_defs.hxx:43
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Definition: NT_extern.cxx:250
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Definition: TreeDisplay.hxx:553
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Definition: AW_awar.cxx:198
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Definition: rootAsWin.h:47
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Definition: arb_sleep.h:32
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Definition: AW_root.cxx:554
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Definition: awt_canvas.hxx:43
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Definition: AW_window.cxx:645
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Definition: NT_extern.cxx:707
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Definition: AWT_misc.cxx:39
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Definition: arbdb.cxx:2814
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Definition: NT_extern.cxx:232
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Definition: NT_extern.cxx:75
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Definition: NT_extern.cxx:784
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Definition: TreeDisplay.hxx:745
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Definition: AW_root.cxx:635
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Definition: NT_local.h:27
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Definition: NT_extern.cxx:422
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Definition: NT_extern.cxx:970
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Definition: NT_extern.cxx:968
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Definition: NT_join.cxx:143
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Definition: NT_extern.cxx:1108
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Definition: AW_window.cxx:796
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Definition: awt_canvas.hxx:339
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AW_window * NT_create_colstat_2_gnuplot_window(AW_root *root)
Definition: ColumnStat_2_gnuplot.cxx:589
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Definition: NT_local.h:30
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Definition: NT_extern.cxx:1913
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Definition: db_query.cxx:1965
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const Group & get_selected_group() const
Definition: TreeDisplay.hxx:597
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Definition: awt_canvas.hxx:382
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Definition: AW_window.cxx:801
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Definition: NT_extern.cxx:697
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Definition: AW_at.cxx:259
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Definition: NT_extern.cxx:724
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GBDATA * GEN_find_origin_organism(GBDATA *gb_pseudo, const GB_HASH *organism_hash)
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const char * get_self_awar() const OVERRIDE
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Definition: awt_canvas.hxx:51
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Definition: NT_extern.cxx:812
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Definition: awt_canvas.hxx:365
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AW_gc_manager * gc_manager
Definition: awt_canvas.hxx:341
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Definition: GEN_map.cxx:1585
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Definition: AW_button.cxx:448
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Definition: f2c.h:154
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