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 <nds.h>
31 #include <db_query.h>
32 #include <dbui.h>
33 #include <refentries.h>
34 #include <insdel.h>
35 
36 #include <awti_export.hxx>
37 #include <awti_import.hxx>
38 
39 #include <awt.hxx>
40 #include <awt_input_mask.hxx>
41 #include <awt_sel_boxes.hxx>
42 #include <awt_www.hxx>
43 #include <awt_TreeAwars.hxx>
44 #include <awt_misc.hxx>
45 
46 #include <aw_color_groups.hxx>
47 #include <aw_advice.hxx>
48 #include <aw_preset.hxx>
49 #include <aw_awars.hxx>
50 #include <aw_global_awars.hxx>
51 #include <aw_file.hxx>
52 #include <aw_msg.hxx>
53 #include <arb_progress.h>
54 #include <aw_root.hxx>
55 #include <aw_question.hxx>
56 #include <aw_select.hxx>
57 #include <rootAsWin.h>
58 
59 #include <ad_cb.h>
60 
61 #include <arb_strbuf.h>
62 #include <arb_file.h>
63 #include <arb_version.h>
64 #include <arb_sleep.h>
65 
66 #include <saicalc.h>
67 
68 #if defined(DEVEL_RALF)
69 # define TRACE_GROUP_SELECTION
70 #endif
71 
72 #define AWAR_EXPORT_NDS "tmp/export_nds"
73 #define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/delimiter"
74 #define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species"
75 #define AWAR_NTREE_TITLE_MODE "tmp/title_mode"
76 
77 void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
78 
79 void create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
80 AW_window *create_insertDeleteColumn_window(AW_root *root);
81 AW_window *create_insertDeleteBySAI_window(AW_root *root, GBDATA *gb_main);
82 
83 AW_window *create_tree_window(AW_root *aw_root, AWT_graphic *awd);
84 
85 enum Export_Type {
86  EXPORT_SPACE_PADDED_RIGHT_ALIGNED = 1, // format info (using spaces). slow - uses one extra pass for column width detection.
87  EXPORT_SPACE_PADDED_LEFT_ALIGNED = 4, // dito, but left aligned
88  EXPORT_TAB_SEPARATED = 2, // format info (using 1 tab per column - for easy import into star-calc, excel, etc. )
89  EXPORT_COMMA_SEPARATED = 3, // like EXPORT_TAB_SEPARATED, but using commas
90 };
91 
92 static void nt_changesecurity(AW_root *aw_root) {
93  int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
94  GB_push_transaction(GLOBAL.gb_main);
95  GB_change_my_security(GLOBAL.gb_main, level); // changes user security
96  GB_pop_transaction(GLOBAL.gb_main);
97 }
98 
99 static void export_nds_cb(AW_window *aww, bool do_print) {
100  AW_root *aw_root = aww->get_root();
101  char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
102  FILE *out = fopen(name, "w");
103 
104  if (!out) {
105  aw_message("Error: Cannot open and write to file");
106  }
107  else {
108  GB_transaction ta(GLOBAL.gb_main);
109 
110  char *tree_name = aw_root->awar(AWAR_TREE)->read_string();
111  const Export_Type export_type = (Export_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
112  const NDS_Type nds_type = export_type == EXPORT_COMMA_SEPARATED ? NDS_OUTPUT_COMMA_SEPARATED : NDS_OUTPUT_TAB_SEPARATED;
113  const bool spacePadded = export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED || export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED;
114  const int passesNeeded = spacePadded ? 2 : 1;
115  NDS_Labeler labeler(nds_type);
116 
117  arb_progress progress("Exporting data using NDS", passesNeeded*GBT_count_marked_species(GLOBAL.gb_main));
118 
119  const size_t max_col = std::max(labeler.max_columns(GLOBAL.gb_main), 1L);
120  size_t col_max_len[max_col];
121 
122  const char *col_format = NULp;
123 
124  if (spacePadded) {
125  for (size_t i = 0; i<max_col; ++i) {
126  col_max_len[i] = 0;
127  }
128  if (export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED) {
129  col_format = "%*s";
130  }
131  else {
132  col_format = "%-*s";
133  }
134  }
135 
136  for (int pass = 1; pass<=passesNeeded; ++pass) {
137  for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
138  gb_species;
139  gb_species = GBT_next_marked_species(gb_species))
140  {
141  const char *label = labeler.speciesLabel(GLOBAL.gb_main, gb_species, NULp, tree_name);
142 
143  if (spacePadded) {
144  ConstStrArray parts;
145  GBT_split_string(parts, label, "\t", SPLIT_KEEPEMPTY);
146 
147  size_t col_count = parts.size();
148  nt_assert(col_count<=max_col);
149 
150  if (pass == 1) { // track maximum used width for all columns
151  for (size_t i = 0; i<col_count; ++i) {
152  col_max_len[i] = std::max(col_max_len[i], strlen(parts[i]));
153  }
154  }
155  else { // format according to tracked widths
156  for (size_t i = 0; i<col_count; ++i) {
157  if (i) fputc(' ', out);
158 
159  arb_assert(col_max_len[i]>0); // otherwise empty, unused column (might be ok, but might need different handling)
160  arb_assert(col_max_len[i]<=INT_MAX); // (protect cast below)
161 
162  if (export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED && i == (col_count-1)) { // left aligned and last column
163  fputs(parts[i], out);
164  }
165  else {
166  fprintf(out, col_format, int(col_max_len[i]), parts[i]);
167  }
168  }
169  fputc('\n', out);
170  }
171  }
172  else {
173  fprintf(out, "%s\n", label);
174  }
175  ++progress;
176  }
177  }
178 
179  AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
180  fclose(out);
181  if (do_print) {
182  GB_ERROR error = GB_textprint(name);
183  if (error) aw_message(error);
184  }
185  free(tree_name);
186  }
187  free(name);
188 }
189 
190 static AW_window *create_nds_export_window(AW_root *root) {
191  AW_window_simple *aws = new AW_window_simple;
192  aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
193  aws->load_xfig("sel_box_nds.fig");
194 
195  aws->callback(AW_POPDOWN);
196  aws->at("close");
197  aws->create_button("CLOSE", "CLOSE", "C");
198 
199  aws->callback(makeHelpCallback("arb_export_nds.hlp"));
200  aws->at("help");
201  aws->create_button("HELP", "HELP", "H");
202 
203  aws->at("save");
204  aws->callback(makeWindowCallback(export_nds_cb, false));
205  aws->create_button("SAVE", "SAVE", "S");
206 
207  aws->at("print");
208  aws->callback(makeWindowCallback(export_nds_cb, true));
209  aws->create_button("PRINT", "PRINT", "P");
210 
211  aws->at("toggle1");
212  aws->label("Column output");
213  aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR);
214  aws->insert_option ("Space padded (left aligned)", "S", EXPORT_SPACE_PADDED_LEFT_ALIGNED);
215  aws->insert_option ("Space padded (right aligned)", "r", EXPORT_SPACE_PADDED_RIGHT_ALIGNED);
216  aws->insert_default_option("TAB separated", "T", EXPORT_TAB_SEPARATED);
217  aws->insert_option ("Comma separated", "C", EXPORT_COMMA_SEPARATED);
218  aws->update_option_menu();
219 
220  AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS);
221 
222  return aws;
223 }
224 
225 static void create_export_nds_awars(AW_root *awr, AW_default def) {
226  AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds");
227  awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, EXPORT_TAB_SEPARATED, def);
228 }
229 
230 static void selectedSpeciesChanged_cb(AW_root *awr) {
231  const char *value = awr->awar(AWAR_SPECIES_NAME)->read_char_pntr();
232  awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
233  if (value[0]) {
234  awr->awar(AWAR_GROUP)->write_pointer(NULp); // deselect group when species gets selected
235 #if defined(TRACE_GROUP_SELECTION)
236  fputs("clear AWAR_GROUP (because species selected)\n", stderr);
237 #endif
238  }
239 }
240 
241 static void expert_mode_changed_cb(AW_root *aw_root) {
242  aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
243 }
244 
245 static void NT_toggle_expert_mode(AW_window *aww) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
246 static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
247 
248 static void nt_create_all_awars(AW_root *awr) {
249  // creates awars for all modules reachable from ARB_NT main window
250 
251  awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT);
252  if (GB_read_clients(GLOBAL.gb_main)>=0) {
253  awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
254  }
255  else {
256  awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT);
257  }
258 
259  awr->awar_string(AWAR_TOPAREA_SAIS, "ECOLI;HELIX;HELIX_NR", AW_ROOT_DEFAULT);
260 
261  awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main);
262  awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main);
263  awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main);
264  awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown", GLOBAL.gb_main);
265  awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main);
266  awr->awar(AWAR_SPECIES_NAME)->add_callback(selectedSpeciesChanged_cb);
267  awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
268 
269  awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
270 
271  GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
272  EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
273 #if defined(DEBUG)
274  AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT);
275 #endif // DEBUG
276 
277  AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
278 
279  awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT);
280  awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
281 #if defined(DEBUG) && 0
282  awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
283 #endif // DEBUG
284 
285  create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT);
286  create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
287  create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
288  create_trees_var(awr, AW_ROOT_DEFAULT);
289  DBUI::create_dbui_awars(awr);
290  AP_create_consensus_var(awr, AW_ROOT_DEFAULT);
291  {
292  GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, NULp, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT);
293  if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
294  }
295  NT_create_transpro_variables(awr, AW_ROOT_DEFAULT);
296  NT_create_resort_awars(awr, AW_ROOT_DEFAULT);
297  NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT);
298  NT_create_trackAliChanges_Awars(awr, AW_ROOT_DEFAULT);
299 
300  NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
301  NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
302  NDS_create_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
303  create_export_nds_awars(awr, AW_ROOT_DEFAULT);
304  create_group_search_awars(awr, AW_ROOT_DEFAULT);
305  TREE_create_awars(awr, GLOBAL.gb_main);
306 
307  awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
308  awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
309 
310  AWTC_create_submission_variables(awr, GLOBAL.gb_main);
311  NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
312  NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar
313  SQ_create_awars(awr, AW_ROOT_DEFAULT);
314  RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT);
315 
316  NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT);
317 
318  GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
319  if (!error) {
320  AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
321  awar_expert->add_callback(expert_mode_changed_cb);
322  awar_expert->touch();
323 
324  awt_create_aww_vars(awr, AW_ROOT_DEFAULT);
325  }
326 
327  if (error) aw_message(error);
328 }
329 
330 // --------------------------------------------------------------------------------
331 
332 static bool nt_disconnect_from_db(AW_root *aw_root, GBDATA*& gb_main_ref, bool quitWithoutSaveQuestion) {
333  // ask user if DB was not saved in the last 15 seconds (dont ask if quitWithoutSaveQuestion is true).
334  // returns true if user allows to quit.
335 
336  // @@@ code here could as well be applied to both merge DBs
337  // - question about saving only with target DB!
338 
339 #if defined(DEBUG)
340  quitWithoutSaveQuestion = true; // do not ask about saving while developing
341 #endif
342 
343  if (gb_main_ref) {
344  if (GB_read_clients(gb_main_ref) >= 0 && // only in server
345  GB_read_clock(gb_main_ref) > GB_last_saved_clock(gb_main_ref) &&
346  quitWithoutSaveQuestion == false)
347  {
348  long secs = GB_last_saved_time(gb_main_ref);
349  const char *quit_buttons = "Quit ARB,Do NOT quit";
350  if (secs) {
351  secs = GB_time_of_day() - secs;
352  if (secs>15) {
353  char *question = GBS_global_string_copy("You last saved your data %li:%02li minutes ago\nSure to quit?", secs/60, secs%60);
354  int dontQuit = aw_question("quit_arb", question, quit_buttons);
355  free(question);
356  if (dontQuit) {
357  return false;
358  }
359  }
360  }
361  else {
362  if (aw_question("quit_arb", "You never saved any data.\nSure to quit?", quit_buttons)) {
363  return false;
364  }
365  }
366  }
367 
368  GBCMS_shutdown(gb_main_ref);
369 
370  GBDATA *gb_main = gb_main_ref;
371  gb_main_ref = NULp; // avoid further usage
372 
373  nt_assert(aw_root);
374 
375  // @@@ instead of directly calling the following functions, try to add them as GB_atclose_callback
376  aw_root->unlink_awars_from_DB(gb_main);
377  AWT_destroy_input_masks();
378 #if defined(DEBUG)
379  AWT_browser_forget_db(gb_main);
380 #endif // DEBUG
381 
382  GB_close(gb_main);
383  }
384  return true;
385 }
386 
387 static void nt_run(const char *command) {
388  GB_ERROR error = GBK_system(command);
389  if (error) {
390  fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
391 #if defined(DEBUG)
392  GBK_dump_backtrace(stderr, "nt_run-error");
393 #endif
394  }
395 }
396 
397 void NT_start(const char *arb_ntree_args, bool restart_with_new_ARB_PID) {
398  char *command = GBS_global_string_copy("arb_launcher --async %s %s", restart_with_new_ARB_PID ? "arb" : "arb_ntree", arb_ntree_args);
399  nt_run(command);
400  free(command);
401 }
402 
403 __ATTR__NORETURN static void really_exit(int exitcode, bool kill_my_clients) {
404  if (kill_my_clients) {
405  nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
406  }
407  exit(exitcode);
408 }
409 
410 static void exit_ignoring_running_macro(AW_root *aw_root, int exitcode, bool quitWithoutSaveQuestion) {
411  AWTI_cleanup_importer();
412  shutdown_macro_recording(aw_root);
413 
414  bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
415  if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main, quitWithoutSaveQuestion)) {
416  really_exit(exitcode, is_server_and_has_clients);
417  }
418 }
419 
420 #define TRY_TO_QUIT_ARB_FREQUENCY 250 // ms
421 
422 static unsigned NT_exit_when_macros_did_finish(AW_root *aw_root, int exitcode) {
423  if (is_executing_macro_as_server(aw_root)) {
424  static long milliSeconds = 0;
425  static int lastDecaSeconds = 0;
426 
427  milliSeconds += TRY_TO_QUIT_ARB_FREQUENCY;
428  int seconds = milliSeconds/1000;
429  int decaSeconds = seconds/10;
430 
431  if (decaSeconds != lastDecaSeconds) {
432  const char *msg = GBS_global_string("waited %i seconds for macro termination", seconds);
433  if (decaSeconds>3) {
434  int after = (10-decaSeconds)*10;
435  msg = GBS_global_string("%s. Will terminate unconditionally in %i seconds", msg, after);
436  }
437  aw_message(GBS_global_string("[%s]", msg));
438  lastDecaSeconds = decaSeconds;
439  }
440 
441  if (decaSeconds<10) {
442  return TRY_TO_QUIT_ARB_FREQUENCY;
443  }
444  // reached after 100s
445  aw_message("[forcing arb quit]");
446  }
447  else {
448  aw_message("[all macros have terminated. arb quits now]");
449  }
450  ARB_sleep(1, SEC);
451  exit_ignoring_running_macro(aw_root, exitcode, true); // never ask if sure to quit!
452  return 0;
453 }
454 
455 void NT_exit(AW_window *aws, int exitcode) {
456  AW_root *aw_root = aws->get_root();
457  if (is_executing_macro_as_server(aw_root)) {
458  static int suppressed = 0;
459  if (!suppressed) {
460  aw_message("[did not quit arb yet, because macro is still running. Would crash. Will retry ASAP]");
461  suppressed = 1;
462  }
463  else {
464  aw_message("[macro is still running. But time will pass faster because you are in a hurry]");
465  }
466 
467  // Note: this branch effectively suppresses the 'sure to quit?' question
468  aw_root->add_timed_callback(TRY_TO_QUIT_ARB_FREQUENCY,
469  makeTimedCallback(NT_exit_when_macros_did_finish, exitcode));
470  }
471  else {
472  exit_ignoring_running_macro(aw_root, exitcode, false);
473  }
474 }
475 
476 void NT_restart(AW_root *aw_root, const char *arb_ntree_args) {
477  // restarts arb_ntree (with new ARB_PID)
478  // @@@ do we need to call AWTI_cleanup_importer and/or shutdown_macro_recording here?
479  // consider to delegate to normal exit-code (NT_exit, exit_ignoring_running_macro)
480  bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
481  if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main, false)) {
482  NT_start(arb_ntree_args, true);
483  really_exit(EXIT_SUCCESS, is_server_and_has_clients);
484  }
485 }
486 
487 static void nt_start_2nd_arb(AW_window *aww, bool quit) {
488  // start 2nd arb with intro window
489  AW_root *aw_root = aww->get_root();
490  char *dir4intro;
491  GB_split_full_path(aw_root->awar(AWAR_SAVED_DB_PATH)->read_char_pntr(), &dir4intro, NULp, NULp, NULp);
492  if (!dir4intro) {
493  dir4intro = ARB_strdup(".");
494  }
495 
496  if (quit) {
497  NT_restart(aw_root, dir4intro);
498  }
499  else {
500  NT_start(dir4intro, true);
501  }
502  free(dir4intro);
503 }
504 
505 // --------------------------------------------------------------------------------
506 
507 static void NT_save_quick_cb(AW_window *aww) {
508  AW_root *awr = aww->get_root();
509  char *filename = awr->awar(AWAR_DB_PATH)->read_string();
510 
511  awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
512 
513  GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
514  if (error) aw_message(error);
515  else {
516  awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
517  AW_refresh_fileselection(awr, AWAR_DBBASE);
518  }
519 
520  free(filename);
521 }
522 
523 
524 static void NT_save_quick_as_cb(AW_window *aww) {
525  AW_root *awr = aww->get_root();
526  char *filename = awr->awar(AWAR_DB_PATH)->read_string();
527 
528  // @@@ also use dont_save_awars_with_default_value here?
529 
530  GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename);
531  if (!error) {
532  awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
533  AW_refresh_fileselection(awr, AWAR_DBBASE);
534  }
535  aww->hide_or_notify(error);
536 
537  free(filename);
538 }
539 
540 #define AWAR_DB_TYPE AWAR_DBBASE "/type" // created by AWT_insert_DBsaveType_selector
541 #define AWAR_DB_COMPRESSION AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector
542 #define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name"
543 
544 static void NT_save_as_cb(AW_window *aww) {
545  AW_root *awr = aww->get_root();
546  char *filename = awr->awar(AWAR_DB_PATH)->read_string();
547  const char *atype = awr->awar(AWAR_DB_TYPE)->read_char_pntr();
548  const char *ctype = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr();
549  char *savetype = GBS_global_string_copy("%s%s", atype, ctype);
550 
551  awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
552 
553  GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype);
554  if (!error) {
555  awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
556  AW_refresh_fileselection(awr, AWAR_DBBASE);
557  }
558  aww->hide_or_notify(error);
559 
560  free(savetype);
561  free(filename);
562 }
563 
564 static AW_window *NT_create_save_quick_as_window(AW_root *aw_root, const char *base_name) {
565  static AW_window_simple *aws = NULp;
566  if (!aws) {
567  aws = new AW_window_simple;
568  aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as");
569  aws->load_xfig("save_as.fig");
570 
571  aws->at("close");
572  aws->callback(AW_POPDOWN);
573  aws->create_button("CLOSE", "CLOSE", "C");
574 
575  aws->callback(makeHelpCallback("save.hlp"));
576  aws->at("help");
577  aws->create_button("HELP", "HELP", "H");
578 
579  AW_create_standard_fileselection(aws, base_name);
580 
581  aws->at("comment");
582  aws->create_text_field(AWAR_DB_COMMENT);
583 
584  aws->at("save");
585  aws->callback(NT_save_quick_as_cb);
586  aws->create_button("SAVE", "SAVE", "S");
587  }
588  return aws;
589 }
590 
591 static void NT_database_optimization(AW_window *aww) {
592  arb_progress progress(WEIGHTED, "Optimizing database compression", 0.38);
593  // 38% for seq-compression is just a rough guess made with silvaNR99138
594  // (a real guess would have to depend on ali-count, ali-length + field-count)
595 
596  GB_topSecurityLevel unsecured(GLOBAL.gb_main);
597 
598  GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
599  if (!error) {
600  ConstStrArray ali_names;
601  GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
602 
603  arb_progress ali_progress("Optimizing sequence data", ali_names.size());
604  ali_progress.allow_title_reuse();
605 
606  error = GBT_check_data(GLOBAL.gb_main, NULp);
607  error = GB_end_transaction(GLOBAL.gb_main, error);
608 
609  if (!error) {
610  char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string();
611  for (int i = 0; ali_names[i]; ++i) {
612  error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
613  ali_progress.inc_and_check_user_abort(error);
614  }
615  free(tree_name);
616  }
617  }
618  progress.inc_and_check_user_abort(error);
619 
620  if (!error) {
621  error = GB_optimize(GLOBAL.gb_main);
622  progress.inc_and_check_user_abort(error);
623  }
624  aww->hide_or_notify(error);
625 }
626 
627 static AW_window *NT_create_database_optimization_window(AW_root *aw_root) {
628  static AW_window_simple *aws = NULp;
629  if (aws) return aws;
630  GB_transaction ta(GLOBAL.gb_main);
631 
632  const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
633  aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree);
634 
635  aws = new AW_window_simple;
636  aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression");
637  aws->load_xfig("optimize.fig");
638 
639  aws->at("trees");
640  awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME);
641 
642  aws->at("close");
643  aws->callback(AW_POPDOWN);
644  aws->create_button("CLOSE", "CLOSE", "C");
645 
646  aws->callback(makeHelpCallback("optimize.hlp"));
647  aws->at("help");
648  aws->create_button("HELP", "HELP", "H");
649 
650  aws->at("go");
651  aws->callback(NT_database_optimization);
652  aws->create_button("GO", "GO");
653  return aws;
654 }
655 
656 static AW_window *NT_create_save_as(AW_root *aw_root, const char *base_name) {
657  static AW_window_simple *aws = NULp;
658  if (aws) return aws;
659 
660  aws = new AW_window_simple;
661  aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
662  aws->load_xfig("save_as.fig");
663 
664  aws->at("close");
665  aws->callback(AW_POPDOWN);
666  aws->create_button("CLOSE", "CLOSE", "C");
667 
668  aws->at("help");
669  aws->callback(makeHelpCallback("save.hlp"));
670  aws->create_button("HELP", "HELP", "H");
671 
672  AW_create_standard_fileselection(aws, base_name);
673 
674  aws->at("type");
675  AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE);
676 
677  aws->at("compression");
678  AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION);
679 
680  aws->at("optimize");
681  aws->callback(NT_create_database_optimization_window);
682  aws->help_text("optimize.hlp");
683  aws->create_autosize_button("OPTIMIZE", "Optimize database compression");
684 
685  aws->at("save");
686  aws->callback(NT_save_as_cb);
687  aws->create_button("SAVE", "SAVE", "S");
688 
689  aws->at("comment");
690  aws->create_text_field(AWAR_DB_COMMENT);
691 
692  return aws;
693 }
694 
695 static void NT_undo_cb(AW_window*, GB_UNDO_TYPE undo_type, TREE_canvas *ntw) {
696  GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type);
697  if (error) aw_message(error);
698  else {
699  GB_transaction ta(GLOBAL.gb_main);
700  AWT_auto_refresh allowed_on(ntw);
701  ntw->request_refresh();
702  }
703 }
704 
705 static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) {
706  DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
707  nt_mode_event(NULp, canvas, mode);
708 }
709 
710 static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) {
711  AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
712  if (tree_root) {
713  AWT_auto_refresh allowed_on(ntw);
714  GB_transaction ta(ntw->gb_main);
715 
716  NT_mark_all_cb(NULp, ntw, 0); // unmark all
717  tree_root->mark_duplicates();
718  ntw->request_structure_update();
719  }
720 }
721 
722 static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) {
723  GB_transaction ta(ntw->gb_main);
724  AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
725 
726  if (tree_root) {
727  AWT_auto_refresh allowed_on(ntw);
728  tree_root->justify_branch_lenghs(ntw->gb_main);
729  ntw->request_save_and_zoom_reset();
730  }
731 }
732 
733 #if defined(DEBUG)
734 static void NT_fix_database(AW_window *) {
735  GB_ERROR err = NULp;
736  err = GB_fix_database(GLOBAL.gb_main);
737  if (err) aw_message(err);
738 }
739 #endif
740 
741 static void relink_pseudo_species_to_organisms(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash) {
742  if (ref_gb_node) {
743  if (GEN_is_pseudo_gene_species(ref_gb_node)) {
744  GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
745 
746  if (gb_organism) {
747  char *name = GBT_read_string(gb_organism, "name");
748 
749  if (name) {
750  freeset(ref_name, name);
751  ref_gb_node = gb_organism;
752  }
753  }
754  }
755  }
756 }
757 
758 static void NT_pseudo_species_to_organism(AW_window *, TREE_canvas *ntw) {
759  GB_transaction ta(ntw->gb_main);
760  AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
761 
762  if (tree_root) {
763  AWT_auto_refresh allowed_on(ntw);
764 
765  GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
766  tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
767  GBS_free_hash(organism_hash);
768  ntw->request_save();
769  }
770 }
771 
772 
773 // #########################################
774 // #########################################
775 // ### ###
776 // ## user mask section ##
777 // ### ###
778 // #########################################
779 // #########################################
780 
781 struct nt_item_type_species_selector FINAL_TYPE : public awt_item_type_selector {
782  nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
783  ~nt_item_type_species_selector() OVERRIDE {}
784 
785  const char *get_self_awar() const OVERRIDE {
786  return AWAR_SPECIES_NAME;
787  }
788  size_t get_self_awar_content_length() const OVERRIDE {
789  return 12; // should be enough for "nnaammee.999"
790  }
791  GBDATA *current(AW_root *root, GBDATA *gb_main) const OVERRIDE { // give the current item
792  char *species_name = root->awar(get_self_awar())->read_string();
793  GBDATA *gb_species = NULp;
794 
795  if (species_name[0]) {
796  GB_transaction ta(gb_main);
797  gb_species = GBT_find_species(gb_main, species_name);
798  }
799 
800  free(species_name);
801  return gb_species;
802  }
803  const char *getKeyPath() const OVERRIDE { // give the keypath for items
804  return CHANGE_KEY_PATH;
805  }
806 };
807 
808 static nt_item_type_species_selector item_type_species;
809 
810 static void NT_open_mask_window(AW_window *aww, int id, GBDATA *gb_main) {
811  const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
812  nt_assert(descriptor);
813  if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
814 }
815 
816 static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
817  AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
818 }
819 static AW_window *create_colorize_species_window(AW_root *aw_root) {
820  return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
821 }
822 
823 static void NT_update_marked_counter(GBDATA*, AW_window* aww) {
827  long count = GBT_count_marked_species(GLOBAL.gb_main);
828  const char *buffer = count ? GBS_global_string("%li marked", count) : "";
829  AW_awar *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
830  char *oldval = counter->read_string();
831  if (strcmp(oldval, buffer)) {
832  counter->write_string(buffer);
833  aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
834  }
835  free(oldval);
836 }
837 
838 // --------------------------------------------------------------------------------------------------
839 
840 static void NT_alltree_remove_leafs(AW_window *, GBT_TreeRemoveType mode, GBDATA *gb_main) {
841  GB_ERROR error = NULp;
842  GB_transaction ta(gb_main);
843 
844  ConstStrArray tree_names;
845  GBT_get_tree_names(tree_names, gb_main, false);
846 
847  if (!tree_names.empty()) {
848  long treeCount = tree_names.size();
849 
850  const char *whats_removed = NULp;
851  switch (mode) {
852  case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
853  case GBT_REMOVE_MARKED: whats_removed = "marked"; break;
854  default: nt_assert(0); break;
855  }
856 
857  const char *task = GBS_global_string("Deleting %s from %li trees", whats_removed, treeCount);
858 
859  arb_progress progress(task, treeCount);
860  GB_HASH *species_hash = GBT_create_species_hash(gb_main);
861 
862  int modified = 0;
863 
864  for (int t = 0; t<treeCount && !error; t++) {
865  progress.subtitle(tree_names[t]);
866  TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
867  if (!tree) {
868  aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
869  }
870  else {
871  int removed = 0;
872  int groups_removed = 0;
873 
874  tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
875 
876  nt_assert(removed >= groups_removed);
877 
878  if (!tree) {
879  aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
880  }
881  else {
882  if (removed>0) {
883  error = GBT_write_tree(gb_main, tree_names[t], tree);
884  if (error) {
885  aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
886  }
887  else {
888  if (groups_removed>0) {
889  aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
890  }
891  else {
892  aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
893  }
894  modified++;
895  }
896  }
897  UNCOVERED();
898  destroy(tree);
899  }
900  }
901  progress.inc_and_check_user_abort(error);
902  }
903 
904  if (modified) {
905  aw_message(GBS_global_string("Changed %i of %li trees.", modified, treeCount));
906  }
907  else {
908  aw_message("No tree modified");
909  }
910 
911  GBS_free_hash(species_hash);
912  }
913 
914  aw_message_if(ta.close(error));
915 }
916 
917 TreeNode *NT_get_tree_root_of_canvas(TREE_canvas *ntw) {
918  AWT_graphic_tree *tree = AWT_TREE(ntw);
919  if (tree) {
920  AP_tree *root = tree->get_root_node();
921  if (root) return root;
922  }
923  return NULp;
924 }
925 
926 // --------------------------------------------------------------------------------------------------
927 
928 static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
929  GB_transaction ta(gb_main);
930  GBT_mark_all(gb_main, 0);
931 
932  DBItemSetIter end = referred.end();
933  for (DBItemSetIter s = referred.begin(); s != end; ++s) {
934  GB_write_flag(*s, 1);
935  }
936  return ARB_ERROR();
937 }
938 
939 static AW_window *create_mark_by_refentries_window(AW_root *awr, GBDATA *gbmain) {
940  static AW_window *aws = NULp;
941  if (!aws) {
942  static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
943  aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULp, "Mark referenced", mark_referred_species);
944  }
945  return aws;
946 }
947 
948 // --------------------------------------------------------------------------------------------------
949 
950 static void merge_from_to(AW_root *awr, const char *db_awar_name, bool merge_to) {
951  const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
952  char *quotedDB = GBK_singlequote(db_name);
953 
954  AWT_system_cb(
955  GBS_global_string(
956  merge_to
957  ? "arb_ntree : %s &"
958  : "arb_ntree %s : &",
959  quotedDB)
960  );
961 
962  free(quotedDB);
963 }
964 
965 static void merge_from_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, false); }
966 static void merge_into_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, true); }
967 
968 static AW_window *NT_create_merge_from_window(AW_root *awr) {
969  static char *awar_name = NULp; // do not free, bound to callback
970  AW_window *aw_from =
971  awt_create_load_box(awr, "Merge data from", "other ARB database",
972  ".", ".arb", &awar_name,
973  makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
974  return aw_from;
975 }
976 static AW_window *NT_create_merge_to_window(AW_root *awr) {
977  static char *awar_name = NULp; // do not free, bound to callback
978  AW_window *aw_to =
979  awt_create_load_box(awr, "Merge data to", "other ARB database",
980  ".", ".arb", &awar_name,
981  makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
982  makeWindowCallback(AW_POPDOWN), NULp);
983  return aw_to;
984 }
985 
986 // --------------------------------------------------------------------------------------------------
987 
988 static void update_main_window_title(AW_root* awr, AW_window_menu_modes* aww, int clone) {
989  const char* filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
990  if (clone) {
991  aww->set_window_title(GBS_global_string("%s - ARB (%i)", filename, clone));
992  }
993  else {
994  aww->set_window_title(GBS_global_string("%s - ARB", filename));
995  }
996 }
997 
998 static void canvas_tree_awar_changed_cb(AW_awar *, bool, TREE_canvas *ntw) {
999  NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
1000  AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
1001  TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_TREE);
1002 }
1003 
1004 class TREE_canvas_registry {
1005  int count;
1006  TREE_canvas *canvas[MAX_NT_WINDOWS];
1007 
1008  static TREE_canvas_registry *SINGLETON;
1009 
1010  TREE_canvas_registry() : count(0) {
1011  AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
1012  }
1013 
1014 public:
1015  static TREE_canvas_registry& instance() {
1016  if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
1017  return *SINGLETON;
1018  }
1019 
1020  void register_canvas(TREE_canvas *ntw) {
1021  nt_assert(count<MAX_NT_WINDOWS);
1022  nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
1023  canvas[count++] = ntw;
1024  ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
1025  }
1026 
1027  int get_count() const { return count; }
1028 
1029  TREE_canvas *get_canvas(int idx) const {
1030  if (idx<0 || idx>=count) return NULp;
1031  return canvas[idx];
1032  }
1033 };
1034 
1035 TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULp;
1036 
1037 TREE_canvas *NT_get_canvas_by_index(int idx) {
1039  nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
1040  return TREE_canvas_registry::instance().get_canvas(idx);
1041 }
1042 
1043 #if defined(TRACE_GROUP_SELECTION)
1044 static TREE_canvas *find_canvas_showing(AWT_graphic_tree *agt) {
1045  // look for (registered) canvas showing given AWT_graphic_tree
1046  // returns NULp if none found
1047  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1048 
1049  int maxIdx = reg.get_count();
1050  for (int32_t i = 0; i<maxIdx; ++i) {
1051  TREE_canvas *ntw = reg.get_canvas(i);
1052  if (ntw->gfx == agt) return ntw;
1053  }
1054  return NULp;
1055 }
1056 #endif
1057 
1058 void NT_fill_canvas_selection_list(class AW_selection_list *sellst, TREE_canvas *to_skip) {
1061  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1062 
1063  int maxIdx = reg.get_count();
1064  for (int32_t i = 0; i<maxIdx; ++i) {
1065  TREE_canvas *ntw = reg.get_canvas(i);
1066  if (ntw && ntw != to_skip) {
1067  nt_assert(ntw->get_awar_tree());
1068  const char *treename = ntw->get_awar_tree()->read_char_pntr();
1069  const char *description = i
1070  ? GBS_global_string("ARB (%i): %s", i, treename)
1071  : GBS_global_string("ARB main: %s", treename);
1072  sellst->insert(description, i);
1073  }
1074  }
1075 }
1076 
1077 // ----------------------------------
1078 // group-selection handlers
1079 
1080 void NT_deselect_group(AW_root *awr) {
1081  awr->awar(AWAR_GROUP)->write_pointer(NULp);
1082 }
1083 
1084 static bool track_group_selection_by_canvas = true;
1085 
1086 static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) {
1087  const Group& group = gfx->get_selected_group();
1088 
1089 #if defined(TRACE_GROUP_SELECTION)
1090  fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track");
1091  TREE_canvas *ntw = find_canvas_showing(gfx);
1092  if (group.is_valid()) {
1093  fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name());
1094  }
1095  else {
1096  fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index());
1097  }
1098 #endif
1099 
1100  if (track_group_selection_by_canvas) {
1101  // set group-awar:
1102  gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULp if !group.is_valid()
1103  }
1104 }
1105 
1106 static void group_awar_changed_cb(AW_root *awr) {
1107  AW_awar *awar_group = awr->awar(AWAR_GROUP);
1108  GBDATA *gb_wanted_group = awar_group->read_pointer();
1109 
1110  GBDATA *gb_wanted_tree = NULp;
1111  {
1112  if (gb_wanted_group) {
1113  GB_transaction ta(gb_wanted_group);
1114  gb_wanted_tree = GB_get_father(gb_wanted_group);
1115  awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected
1116 #if defined(TRACE_GROUP_SELECTION)
1117  fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr);
1118 #endif
1119  }
1120 #if defined(TRACE_GROUP_SELECTION)
1121  const char *group_name = NULp;
1122  if (gb_wanted_group) {
1123  GB_transaction ta(gb_wanted_group);
1124  GBDATA *gb_name = GB_entry(gb_wanted_group, "group_name");
1125  if (gb_name) group_name = GB_read_char_pntr(gb_name);
1126  }
1127  fprintf(stderr, "group awar changed to %p", gb_wanted_group);
1128  if (group_name) fprintf(stderr, " (='%s')", group_name);
1129  fputc('\n', stderr);
1130 #endif
1131  }
1132 
1133  LocallyModify<bool> ignore_group_selection_by_canvas(track_group_selection_by_canvas, false);
1134 
1135  {
1136  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1137 
1138  int maxIdx = reg.get_count();
1139  for (int32_t i = 0; i<maxIdx; ++i) {
1140  TREE_canvas *ntw = reg.get_canvas(i);
1141  AWT_graphic_tree *agt = AWT_TREE(ntw);
1142  const Group& curr_group = agt->get_selected_group();
1143 
1144  GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree();
1145  if (gb_curr_tree == gb_wanted_tree) {
1146  AWT_auto_refresh allowed_on(ntw);
1147  if (!curr_group.is_valid() || // no group selected
1148  curr_group.get_group_data() != gb_wanted_group) // wrong group selected
1149  {
1150  agt->select_group(gb_wanted_group);
1151  ntw->request_refresh();
1152  }
1153  // perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group)
1154  TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_GROUP);
1155  }
1156  else {
1157  if (curr_group.is_valid()) {
1158  AWT_auto_refresh allowed_on(ntw);
1159  agt->deselect_group();
1160  ntw->request_refresh();
1161  }
1162  }
1163  }
1164  }
1165 }
1166 
1167 // ----------------------------
1168 // create main window
1169 
1170 static AW_window *popup_new_main_window(AW_root *awr, int clone, TREE_canvas **result_ntw) {
1176  GB_push_transaction(GLOBAL.gb_main);
1177 
1178  char window_title[256];
1179  const char *awar_tree = NULp;
1180 
1181  if (clone) {
1182  awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
1183  sprintf(window_title, "ARB_NT_%i", clone);
1184  }
1185  else {
1186  awar_tree = AWAR_TREE;
1187  sprintf(window_title, "ARB_NT");
1188  }
1189  AW_window_menu_modes *awm = new AW_window_menu_modes;
1190  awm->init(awr, window_title, window_title, 0, 0);
1191 
1192  awr->awar(AWAR_DB_NAME)
1193  ->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1194  ->update();
1195 
1196  awm->button_length(5);
1197 
1198  if (!clone) AW_init_color_group_defaults("arb_ntree");
1199 
1200  AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1201 
1202  if (!clone) { // while creating initial window
1203  AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb));
1204  awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb);
1205  }
1206 
1207  TREE_canvas *ntw;
1208  {
1209  AW_awar *tree_awar = awr->awar_string(awar_tree);
1210  {
1211  AP_tree_display_style prev_style = tree->get_tree_style();
1212  tree->set_tree_style(AP_LIST_SIMPLE, NULp); // avoid NDS warnings during startup
1213 
1214  ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1215  tree->set_tree_style(prev_style, ntw);
1216  ntw->set_mode(AWT_MODE_SELECT);
1217  }
1218 
1219  if (result_ntw) *result_ntw = ntw;
1220 
1221  {
1222  const char *tree_name = tree_awar->read_char_pntr();
1223  const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1224 
1225  if (existing_tree_name) {
1226  tree_awar->write_string(existing_tree_name);
1227  NT_reload_tree_event(awr, ntw, true); // load first tree
1228  }
1229  else {
1230  AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, NULp, "no_tree.hlp");
1231  tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list
1232  }
1233 
1234  TREE_canvas_registry::instance().register_canvas(ntw);
1235  AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1236  }
1237  }
1238 
1239  TREE_install_update_callbacks(ntw);
1240 
1241  bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1242 
1243  WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1244 
1245  // --------------
1246  // File
1247 
1248 #if defined(DEBUG)
1249  AWT_create_debug_menu(awm);
1250 #endif // DEBUG
1251 
1252  bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1253 
1254  if (clone) {
1255  awm->create_menu("File", "F", AWM_ALL);
1256  if (allow_new_window) {
1257  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));
1258  }
1259  awm->insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN);
1260  }
1261  else {
1262 #if defined(DEBUG)
1263  // add more to debug-menu
1264  awm->sep______________();
1265  awm->insert_menu_topic("fix_db", "Fix database", "F", NULp, AWM_ALL, NT_fix_database);
1266  awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", NULp, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1267  awm->insert_menu_topic("test_compr", "Test compression", "T", NULp, AWM_ALL, makeWindowCallback(GBT_compression_test, GLOBAL.gb_main));
1268 #endif // DEBUG
1269 
1270  awm->create_menu("File", "F", AWM_ALL);
1271  {
1272  // keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1273  awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, NT_save_quick_cb);
1274  awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1275  if (allow_new_window) {
1276  awm->sep______________();
1277  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));
1278  }
1279  awm->sep______________();
1280  awm->insert_menu_topic("optimize_db", "Optimize database compression", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window);
1281  awm->sep______________();
1282 
1283  awm->insert_sub_menu("Import", "I");
1284  {
1285  awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1286  awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1287  GDE_load_menu(awm, AWM_EXP, "Import");
1288  }
1289  awm->close_sub_menu();
1290 
1291  awm->insert_sub_menu("Export", "E");
1292  {
1293  awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1294  awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1295  GDE_load_menu(awm, AWM_ALL, "Export");
1296  awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window);
1297  }
1298  awm->close_sub_menu();
1299  awm->sep______________();
1300 
1301  insert_macro_menu_entry(awm, false);
1302 
1303  awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1304  {
1305  awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp"));
1306  awm->insert_menu_topic("bug_report", "Report bug", "b", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1307  awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1308  }
1309  awm->close_sub_menu();
1310  awm->sep______________();
1311 
1312  awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1313  awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1314  awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_exit, EXIT_SUCCESS));
1315  }
1316 
1317  // -----------------
1318  // Species
1319 
1320  awm->create_menu("Species", "c", AWM_ALL);
1321  {
1322  awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1323  awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb);
1324 
1325  awm->sep______________();
1326 
1327  NT_insert_mark_submenus(awm, ntw, 1);
1328  awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1329  awm->insert_menu_topic("species_colors", "Colors ...", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window);
1330  awm->insert_menu_topic("selection_admin", "Selections ...", "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1331 
1332  awm->sep______________();
1333 
1334  awm->insert_sub_menu("Database fields admin", "f");
1335  DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1336  awm->close_sub_menu();
1337  NT_create_mask_submenu(awm);
1338 
1339  awm->sep______________();
1340 
1341  awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1342 
1343  awm->insert_sub_menu("Sort Species", "s");
1344  {
1345  awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window);
1346  awm->insert_menu_topic("$sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1347  }
1348  awm->close_sub_menu();
1349 
1350  awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1351  {
1352  awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1353  awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "species_join.hlp", AWM_EXP, NT_create_species_join_window);
1354  }
1355  awm->close_sub_menu();
1356 
1357  awm->sep______________();
1358 
1359  awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1360 
1361  awm->sep______________();
1362 
1363  awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1364 
1365  awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1366  {
1367  awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames);
1368  awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames);
1369  awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1370  awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window);
1371  }
1372  awm->close_sub_menu();
1373  }
1374 
1375  // ----------------------------
1376  // Genes + Experiment
1377 
1378  if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1379 
1380  // ------------------
1381  // Sequence
1382 
1383  awm->create_menu("Sequence", "S", AWM_ALL);
1384  {
1385  awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)NULp));
1386  awm->insert_sub_menu("Insert/delete", "I");
1387  {
1388  awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window);
1389  awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main));
1390  }
1391  awm->close_sub_menu();
1392  awm->sep______________();
1393 
1394  awm->insert_sub_menu("Edit Sequences", "E");
1395  {
1396  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));
1397  awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1398  awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1399  }
1400  awm->close_sub_menu();
1401 
1402  awm->sep______________();
1403 
1404  awm->insert_sub_menu("Align sequences", "l");
1405  {
1406  awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1407  GDE_load_menu(awm, AWM_ALL, "Align");
1408  }
1409  awm->close_sub_menu();
1410  awm->insert_menu_topic("seq_concat", "Concatenate sequences", "C", "concatenate.hlp", AWM_ALL, NT_createConcatenationWindow);
1411  awm->insert_menu_topic("seq_split", "Split sequences", "S", "split.hlp", AWM_ALL, NT_create_splitAlignment_window);
1412  awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1413  awm->sep______________();
1414 
1415  awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1416  awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1417  awm->sep______________();
1418 
1419  awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1420  awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1421 
1422  awm->sep______________();
1423 
1424  GDE_load_menu(awm, AWM_ALL, "Print");
1425  }
1426 
1427  // -------------
1428  // SAI
1429 
1430  awm->create_menu("SAI", "A", AWM_ALL);
1431  {
1432  awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1433  awm->insert_menu_topic("sai_calc", "Combine SAIs", "b", "saicalc.hlp", AWM_ALL, makeWindowCallback(SAI_popup_calculator_window, GLOBAL.gb_main));
1434  awm->insert_sub_menu("Create SAI using ...", "C");
1435  {
1436  awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window);
1437  awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window);
1438  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);
1439  awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_phylo &"));
1440  awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold);
1441 
1442  GDE_load_menu(awm, AWM_EXP, "SAI");
1443  }
1444  awm->close_sub_menu();
1445 
1446  awm->insert_sub_menu("Other functions", "O");
1447  {
1448  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));
1449  awm->insert_menu_topic("corr_mutat_analysis", "Compute clusters of correlated positions", "m", "", AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_rnacma", XCMD_ASYNC_WAIT_ON_ERROR));
1450  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);
1451  }
1452  awm->close_sub_menu();
1453  }
1454 
1455  // ----------------
1456  // Probes
1457 
1458  awm->create_menu("Probes", "P", AWM_ALL);
1459  {
1460  awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1461  awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1462  awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1463  awm->sep______________();
1464  awm->insert_menu_topic("probe_match_sp", "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window, ntw));
1465  awm->sep______________();
1466  awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1467  awm->insert_menu_topic("primer_design", "Design Sequencing Primers", "S", "primer.hlp", AWM_EXP, makeWindowCallback(AWT_system_in_console_cb, "arb_primer", XCMD_ASYNC_WAITKEY));
1468  awm->sep______________();
1469  awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1470  }
1471 
1472  }
1473 
1474  // --------------
1475  // Tree
1476 
1477  awm->create_menu("Tree", "T", AWM_ALL);
1478  {
1479  if (!clone) {
1480  awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1481  awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(NDS_create_window, GLOBAL.gb_main));
1482  awm->sep______________();
1483  awm->insert_sub_menu("Add Species to Existing Tree", "A");
1484  {
1485  awm->insert_menu_topic("arb_pars_quick", "ARB Parsimony (Quick add marked)", "Q", "pars.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_pars -add_marked -quit &"));
1486  awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_pars &"));
1487  GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1488  }
1489  awm->close_sub_menu();
1490  }
1491 
1492  awm->insert_sub_menu("Remove Species from Tree", "R");
1493  {
1494  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));
1495  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));
1496  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));
1497  awm->sep______________();
1498  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));
1499  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));
1500  }
1501  awm->close_sub_menu();
1502 
1503  if (!clone) {
1504  awm->insert_sub_menu("Build tree from sequence data", "B");
1505  {
1506  awm->insert_sub_menu("Distance matrix methods", "D");
1507  awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1508  GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1509  awm->close_sub_menu();
1510 
1511  awm->insert_sub_menu("Maximum Parsimony methods", "P");
1512  GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1513  awm->close_sub_menu();
1514 
1515  awm->insert_sub_menu("Maximum Likelihood methods", "L");
1516  GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1517  GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1518  awm->close_sub_menu();
1519 
1520  awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1521  GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1522  awm->close_sub_menu();
1523  }
1524  awm->close_sub_menu();
1525  }
1526 
1527  awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1528 
1529  awm->sep______________();
1530 
1531  awm->insert_sub_menu("Reset zoom", "z");
1532  {
1533  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));
1534  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));
1535  }
1536  awm->close_sub_menu();
1537 
1538  awm->sep______________();
1539 
1540  // taxonomic groups
1541  NT_insert_collapse_submenu(awm, ntw);
1542  if (!clone) {
1543  awm->insert_menu_topic("group_search", "Search groups...", "g", "group_search.hlp", AWM_ALL, makeWindowCallback (popup_group_search_window, GLOBAL.gb_main));
1544  awm->insert_menu_topic("compare_taxonomy", "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1545  awm->insert_menu_topic("move_groups", "Move groups...", "v", "move_groups.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_moveGroupInfo_window));
1546  }
1547 
1548  awm->sep______________();
1549 
1550  if (!clone) {
1551  awm->insert_menu_topic("compare_topology", "Compare topology...", "o", "compare_topo.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compareTopologies_window));
1552  }
1553 
1554  awm->insert_sub_menu("Modify branches", "M");
1555  {
1556  awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw));
1557  awm->insert_menu_topic(awm->local_id("tree_edit_remark"), "Edit bootstraps", "E", "ted_boot.hlp", AWM_ALL, makeWindowCallback(NT_edit_bootstrap, ntw));
1558  awm->sep______________();
1559  awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw));
1560  awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1561  awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw));
1562  awm->sep______________();
1563  awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1564  awm->sep______________();
1565  awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1566  awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1567 
1568  }
1569  awm->close_sub_menu();
1570  awm->insert_sub_menu("Beautify tree", "u");
1571  {
1572  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));
1573  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));
1574  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));
1575  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));
1576  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));
1577  awm->sep______________();
1578  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));
1579  }
1580  awm->close_sub_menu();
1581 
1582  awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "h", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1583  awm->insert_menu_topic(awm->local_id("syncroots"), "Adjust roots...", "j", "syncroots.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncroot_window, GLOBAL.gb_main));
1584  awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "k", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback (NT_mark_duplicates, ntw));
1585 
1586  awm->sep______________();
1587  awm->insert_menu_topic(awm->local_id("shade"), "Tree shading...", "s", "tree_shading.hlp", AWM_ALL, makeWindowCallback (NT_configure_treeShader));
1588  awm->insert_menu_topic(awm->local_id("syncscroll"), "Sync tree scrolling..", "e", "syncscroll.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1589 
1590  awm->sep______________();
1591  awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", NULp, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1592 
1593  awm->sep______________();
1594  awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1595 
1596  if (is_genome_db) {
1597  awm->sep______________();
1598  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));
1599  }
1600 
1601  if (!clone) {
1602  awm->sep______________();
1603  awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1604  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)));
1605  }
1606 
1607  }
1608 
1609  if (!clone) {
1610  // ---------------
1611  // Tools
1612 
1613  awm->create_menu("Tools", "o", AWM_ALL);
1614  {
1615  awm->insert_menu_topic("names_admin", "Nameserver admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeWindowCallback(AW_popup_namesadmin_window, GLOBAL.gb_main));
1616  awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1617  {
1618  awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1619  }
1620  awm->close_sub_menu();
1621  awm->sep______________();
1622 
1623  awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1624  {
1625  GDE_load_menu(awm, AWM_EXP, NULp);
1626  }
1627  awm->close_sub_menu();
1628 
1629  awm->sep______________();
1630  awm->insert_menu_topic("xterm", "Start XTERM", "X", "xterm.hlp", AWM_ALL, AWT_console);
1631  awm->insert_menu_topic("viewlog", "View ARB log", "l", "console.hlp", AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_show_log.pl run", XCMD_ASYNC_WAIT_ON_ERROR)); // ../SH/arb_show_log.pl
1632  awm->insert_menu_topic("viewserv", "View server log", "V", "console.hlp", AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_show_log.pl server", XCMD_ASYNC_WAIT_ON_ERROR));
1633  awm->insert_menu_topic("viewsys", "View sysinfo", "i", "console.hlp", AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_show_log.pl sysinf", XCMD_ASYNC_WAIT_ON_ERROR));
1634  awm->sep______________();
1635  GDE_load_menu(awm, AWM_EXP, "User");
1636  }
1637  // --------------------
1638  // Properties
1639 
1640  awm->create_menu("Properties", "r", AWM_ALL);
1641  {
1642  awm->insert_menu_topic("props_menu", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1643  awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1644  awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1645  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));
1646  awm->sep______________();
1647  awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", NULp, AWM_ALL, NT_toggle_expert_mode);
1648  awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", NULp, AWM_ALL, NT_toggle_focus_policy);
1649  awm->sep______________();
1650  AW_insert_common_property_menu_entries(awm);
1651  awm->sep______________();
1652  awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1653  }
1654  }
1655 
1656  awm->insert_help_topic("ARB_NT help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1657 
1658  // ----------------------
1659  // mode buttons
1660  //
1661  // keep them synchronized as far as possible with those in ARB_PARSIMONY
1662  // see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1663 
1664  awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1665  awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1666  awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1667  awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1668  awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1669 
1670  awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1671  awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW));
1672 
1673  // topology-modification-modes
1674  awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1675  awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1676  awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1677  awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1678  awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1679 
1680  // layout-modes
1681  awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1682  awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1683  awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1684 
1685  awm->set_info_area_height(250);
1686  awm->at(5, 2);
1687  awm->auto_space(-2, -2);
1688  awm->shadow_width(1);
1689 
1690  // -------------------------
1691  // create top area
1692 
1693  int first_liney;
1694  int leftx;
1695  awm->get_at_position(&leftx, &first_liney);
1696 
1697  // ---------------------
1698  // quit + help
1699 
1700  awm->button_length(0);
1701 
1702  if (clone) {
1703  awm->callback(AW_POPDOWN);
1704  awm->create_button("CLOSE", "#close.xpm");
1705  }
1706  else {
1707  awm->callback(makeWindowCallback(NT_exit, EXIT_SUCCESS));
1708  awm->help_text("quit.hlp");
1709  awm->create_button("QUIT", "#quit.xpm");
1710  }
1711 
1712  int db_pathx = awm->get_at_xposition();
1713 
1714  // now fetch the yposition for the 2nd button line
1715  awm->at_newline();
1716  int second_liney = awm->get_at_yposition();
1717 
1718  awm->callback(AW_help_entry_pressed);
1719  awm->help_text("arb_ntree.hlp");
1720  awm->create_button("?", "#help.xpm");
1721 
1722  // --------------------------
1723  // save + undo/redo
1724 
1725  awm->callback(NT_save_quick_cb);
1726  awm->help_text("save.hlp");
1727  awm->create_button("SAVE", "#save.xpm");
1728 
1729  awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1730  awm->help_text("save.hlp");
1731  awm->create_button("SAVE_AS", "#saveAs.xpm");
1732 
1733  // undo/redo:
1734  awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1735  awm->help_text("undo.hlp");
1736  awm->create_button("UNDO", "#undo.xpm");
1737 
1738  awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1739  awm->help_text("undo.hlp");
1740  awm->create_button("REDO", "#redo.xpm");
1741 
1742  int db_pathx2 = awm->get_at_xposition();
1743 
1744  // fetch position for mode help-line:
1745  awm->at_newline();
1746  int third_liney = awm->get_at_yposition();
1747 
1748  awm->at(db_pathx, first_liney);
1749  // size of DB-name button is determined by buttons below:
1750  awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1751  awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1752  awm->help_text("save.hlp");
1753  awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1754 
1755  // -----------------------------
1756  // tree + tree display
1757 
1758 #define TREE_BUTTON_OVERSIZE 6
1759 
1760  int db_treex = awm->get_at_xposition();
1761  int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1762 
1763  awm->at(db_treex, second_uppery);
1764  awm->button_length(0);
1765 
1766  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1767  awm->help_text("tr_type_radial.hlp");
1768  awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1769 
1770  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1771  awm->help_text("tr_type_dendro.hlp");
1772  awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1773 
1774  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1775  awm->help_text("tr_type_irs.hlp");
1776  awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1777 
1778  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1779  awm->help_text("tr_type_nds.hlp");
1780  awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1781 
1782  int db_treex2 = awm->get_at_xposition();
1783 
1784  awm->at(db_treex, first_liney);
1785  // size of tree-name button is determined by buttons below:
1786  awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1787  awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1788  awm->help_text("nt_tree_select.hlp");
1789  awm->create_button("SELECT_A_TREE", awar_tree);
1790 
1791  // ---------------------------------------------------------------
1792  // protection, alignment + editor (and maybe Genome Map)
1793 
1794  int db_alignx = awm->get_at_xposition();
1795 
1796  // editor and genemap buttons have to be 44x24 sized
1797 #define EDIT_XSIZE 50
1798 #define EDIT_YSIZE 30 // same as 'save as' buttons
1799 
1800  // first draw protection:
1801  int protectx = db_alignx + 2*EDIT_XSIZE;
1802 
1803  awm->at(protectx+2, first_liney+1);
1804  awm->button_length(0);
1805  awm->create_button(NULp, "#protect.xpm");
1806 
1807  awm->at(protectx, second_liney+2);
1808  awm->create_option_menu(AWAR_SECURITY_LEVEL);
1809  awm->insert_option ("0", NULp, 0);
1810  awm->insert_option ("1", NULp, 1);
1811  awm->insert_option ("2", NULp, 2);
1812  awm->insert_option ("3", NULp, 3);
1813  awm->insert_option ("4", NULp, 4);
1814  awm->insert_option ("5", NULp, 5);
1815  awm->insert_default_option("6", NULp, 6);
1816  awm->update_option_menu();
1817 
1818  int db_searchx = awm->get_at_xposition() - 7;
1819 
1820  // draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1821  awm->at(db_alignx, second_liney);
1822 
1823  awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1824  awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1825  awm->help_text("arb_edit4.hlp");
1826  if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1827  else awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1828 
1829  if (is_genome_db) {
1830  awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1831  awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1832  awm->help_text("gene_map.hlp");
1833  awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1834  }
1835 
1836  int db_alignx2 = awm->get_at_xposition();
1837 
1838  awm->at(db_alignx, first_liney);
1839  awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1840  awm->callback(NT_create_select_alignment_window);
1841  awm->help_text("nt_align_select.hlp");
1842  awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1843 
1844  // -------------------------------
1845  // create mode-help line
1846 
1847  awm->at(leftx, third_liney);
1848  awm->button_length(AWAR_FOOTER_MAX_LEN);
1849  awm->create_button(NULp, AWAR_FOOTER);
1850 
1851  awm->at_newline();
1852  int bottomy = awm->get_at_yposition();
1853 
1854  // ---------------------------------------
1855  // Info / marked / Search / Jump
1856 
1857  awm->button_length(7);
1858 
1859  awm->at(db_searchx, first_liney);
1860  awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1861  awm->help_text("sp_search.hlp");
1862  awm->create_button("SEARCH", "Search");
1863 
1864  awm->at(db_searchx, second_uppery);
1865  awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1866  awm->help_text("tr_jump.hlp");
1867  awm->create_button("JUMP", "Jump");
1868 
1869  int db_infox = awm->get_at_xposition();
1870 
1871  awm->at(db_infox, first_liney);
1872  awm->button_length(13);
1873  awm->callback(popupinfo_wcb);
1874  awm->help_text("sp_info.hlp");
1875  awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1876 
1877  awm->at(db_infox, second_uppery);
1878  awm->button_length(13);
1879  awm->help_text("species_configs.hlp");
1880  awm->callback(makeWindowCallback(NT_popup_configuration_admin, ntw));
1881  awm->create_button("selection_admin2", AWAR_MARKED_SPECIES_COUNTER);
1882  {
1883  GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1884  GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(NT_update_marked_counter, static_cast<AW_window*>(awm)));
1885  NT_update_marked_counter(NULp, awm);
1886  }
1887 
1888  // set height of top area:
1889  awm->set_info_area_height(bottomy+2);
1890  awm->set_bottom_area_height(0);
1891 
1892  NT_activate_configMarkers_display(ntw);
1893 
1894  // ------------------------------------
1895  // Autostarts for development
1896 
1897 #if defined(DEVEL_RALF)
1898  // if (is_genome_db) GEN_map_first(awr)->show();
1899 #endif // DEVEL_RALF
1900 
1901  GB_pop_transaction(GLOBAL.gb_main);
1902 
1903 #if defined(DEBUG)
1904  AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1905 #endif
1906 
1907  return awm;
1908 }
1909 
1910 TREE_canvas *NT_create_main_window(AW_root *aw_root) {
1911  GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1912  if (error) aw_message(error);
1913 
1914  nt_create_all_awars(aw_root);
1915 
1916  TREE_canvas *ntw = NULp;
1917  AW_window *aww = popup_new_main_window(aw_root, 0, &ntw);
1918  NT_install_treeShader(ntw, GLOBAL.gb_main);
1919  aww->show();
1920 
1921  error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1922  if (error) aw_message(error);
1923 
1924  return ntw;
1925 }
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Definition: NT_extern.cxx:710
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Definition: adoptimize.cxx:2556
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Definition: aw_awar_defs.hxx:50
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Definition: ad_spec.cxx:127
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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: ad_trees.cxx:636
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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:1235
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Definition: NT_extern.cxx:190
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Definition: awt_canvas.hxx:34
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Definition: ClustalV.cxx:65
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Definition: AW_awar.cxx:390
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Definition: NT_local.h:32
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Definition: NT_extern.cxx:476
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Definition: NT_extern.cxx:225
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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:928
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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: mkptypes.cxx:96
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Definition: NT_extern.cxx:1029
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Definition: AW_window.cxx:2402
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Definition: AP_consensus.cxx:248
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const char * get_name() const
Definition: Group.hxx:56
AWAR_TREE_REFRESH
#define AWAR_TREE_REFRESH
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
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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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Definition: aw_awar_defs.hxx:4
AW_ADVICE_TOGGLE_AND_HELP
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Definition: adsocket.cxx:357
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Definition: AW_window.cxx:569
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Definition: TreeDisplay.hxx:594
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Definition: ad_spec.cxx:30
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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: TreeDisplay.hxx:723
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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:1170
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Definition: NT_extern.cxx:541
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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:248
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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: arbdb.cxx:2524
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Definition: AW_window.cxx:645
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Definition: NT_trackAliChanges.cxx:152
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Definition: NT_extern.cxx:705
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Definition: TreeCallbacks.cxx:554
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Definition: AW_file.cxx:944
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static void selectedSpeciesChanged_cb(AW_root *awr)
Definition: NT_extern.cxx:230
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Definition: NT_extern.cxx:782
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Definition: awt_canvas.hxx:44
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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:420
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Definition: TreeDisplay.hxx:361
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Definition: ad_trees.cxx:1106
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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:1106
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Definition: NT_validNames.cxx:162
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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:588
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Definition: NT_local.h:30
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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:695
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Definition: AW_root.cxx:580
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Definition: AW_at.cxx:259
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Definition: adGene.cxx:643
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const char * get_self_awar() const OVERRIDE
Definition: NT_extern.cxx:785
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Definition: awt_canvas.hxx:51
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Definition: NT_extern.cxx:810
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Definition: awt_canvas.hxx:365
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Definition: cxxforward.h:112
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Definition: GEN_map.cxx:1585
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~nt_item_type_species_selector() OVERRIDE
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Definition: arbdb.cxx:655
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Definition: AW_button.cxx:448
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Definition: f2c.h:154
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