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 <MacroExitor.hxx>
31 #include <xcmd.hxx>
32 #include <nds.h>
33 #include <db_query.h>
34 #include <dbui.h>
35 #include <refentries.h>
36 #include <insdel.h>
37 
38 #include <awti_export.hxx>
39 #include <awti_import.hxx>
40 
41 #include <app.hxx>
42 #include <input_mask.hxx>
43 #include <sel_boxes.hxx>
44 #include <selection_admin.h>
45 #include <www.hxx>
46 #include <TreeAwars.hxx>
47 #include <arb_spec.hxx>
48 
49 #include <aw_color_groups.hxx>
50 #include <aw_advice.hxx>
51 #include <aw_preset.hxx>
52 #include <aw_awars.hxx>
53 #include <aw_global_awars.hxx>
54 #include <aw_file.hxx>
55 #include <arb_progress.h>
56 #include <aw_select.hxx>
57 #include <aw_system.hxx>
58 #include <rootAsWin.h>
59 
60 #include <ad_cb.h>
61 
62 #include <arb_strbuf.h>
63 #include <arb_file.h>
64 #include <arb_version.h>
65 
66 #include <saicalc.h>
67 
68 #include <string>
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_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main);
267  awr->awar(AWAR_SPECIES_NAME)->add_callback(selectedSpeciesChanged_cb);
268  awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
269 
270  awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
271 
272  GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
273  EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
274 #if defined(DEBUG)
275  AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT);
276 #endif // DEBUG
277 
278  AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
279 
280  awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT);
281  awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
282 #if defined(DEBUG) && 0
283  awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
284 #endif // DEBUG
285 
286  create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT);
287  create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
288  create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
289  create_trees_var(awr, AW_ROOT_DEFAULT);
290  DBUI::create_dbui_awars(awr);
291  AP_create_consensus_var(awr, AW_ROOT_DEFAULT);
292  {
293  GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, NULp, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT);
294  if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
295  }
296  NT_create_transpro_variables(awr, AW_ROOT_DEFAULT);
297  NT_create_resort_awars(awr, AW_ROOT_DEFAULT);
298  NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT);
299  NT_create_trackAliChanges_Awars(awr, AW_ROOT_DEFAULT);
300 
301  NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
302  NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
303  NDS_create_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
304  create_export_nds_awars(awr, AW_ROOT_DEFAULT);
305  create_group_search_awars(awr, AW_ROOT_DEFAULT);
306  TREE_create_awars(awr, GLOBAL.gb_main);
307 
308  awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
309  awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
310 
311  AWTC_create_submission_variables(awr, GLOBAL.gb_main);
312  NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
313  NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar
314  SQ_create_awars(awr, AW_ROOT_DEFAULT);
315  RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT);
316 
317  NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT);
318 
319  GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
320  if (!error) {
321  AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
322  awar_expert->add_callback(expert_mode_changed_cb);
323  awar_expert->touch();
324 
325  awt_create_aww_vars(awr, AW_ROOT_DEFAULT);
326  }
327 
328  if (error) aw_message(error);
329 }
330 
331 // --------------------------------------------------------------------------------
332 
333 static void nt_run(const char *command) {
334  GB_ERROR error = GBK_system(command);
335  if (error) {
336  fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
337 #if defined(DEBUG)
338  GBK_dump_backtrace(stderr, "nt_run-error");
339 #endif
340  }
341 }
342 
343 void NT_start_if(const char *arb_ntree_args) {
344  if (arb_ntree_args && arb_ntree_args[0]) {
345  char *command = GBS_global_string_copy("arb_launcher --async arb %s", arb_ntree_args);
346  nt_run(command);
347  free(command);
348  }
349 }
350 
351 void NT_exit_now_restart_if(AW_root *aw_root, int exitcode, const char *restart_ntree_args) { // goes to header: __ATTR__NORETURN
352  // Exit arb_ntree + optionally restart arb.
353  //
354  // 'exitcode': exit with this code.
355  // 'restart_ntree_args': if null or empty -> just exit;
356  // otherwise -> restarts arb_ntree (with new ARB_PID).
357 
358  AWTI_cleanup_importer(aw_root);
359 
360  bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
361  ARB_disconnect_from_db(aw_root, GLOBAL.gb_main);
362  NT_start_if(restart_ntree_args);
363  if (is_server_and_has_clients) {
364  nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
365  }
366  exit(exitcode);
367 }
368 
369 class NT_MacroExitor: public MacroExitor {
370  int exitcode;
371  std::string restart_ntree_args; // [if non-empty] restart arb with these arguments
372 
373  __ATTR__NORETURN void perform_exit() OVERRIDE {
374  NT_exit_now_restart_if(get_root(), exitcode, restart_ntree_args.c_str());
375  }
376 
377  GBDATA* get_gbmain_checked_for_save() OVERRIDE {
378  return GLOBAL.gb_main;
379  }
380 
381 public:
382  NT_MacroExitor(AW_root *aw_root_, int exitcode_, const char *restart_ntree_args_)
383  : MacroExitor(aw_root_, "ARB"),
384  exitcode(exitcode_),
385  restart_ntree_args(null2empty(restart_ntree_args_)) // restart arb if not empty/null
386  {}
387 };
388 
389 void NT_confirm_exit_restart_if(AW_root *aw_root, int exitcode, const char *restart_ntree_args) {
390  // finally (may) exit ARB using NT_exit_now_restart_if(). see there for arguments.
391  //
392  // Beforehand this will happen:
393  // - if no macro running -> asks user to confirm quit (and maybe aborts exit/restart).
394  // - otherwise waits for macro to finish, then quits w/o question.
395 
396  static SmartPtr<NT_MacroExitor> exitor;
397  if (exitor.isNull()) exitor = new NT_MacroExitor(aw_root, exitcode, restart_ntree_args);
398  exitor->maybe_exit_delayed();
399  if (!exitor->is_performing_delayed_exit()) exitor.setNull();
400 }
401 
402 void NT_confirm_exit(AW_window *aws, int exitcode) {
403  NT_confirm_exit_restart_if(aws->get_root(), exitcode, NULp);
404 }
405 
406 static void nt_start_2nd_arb(AW_window *aww, bool quit) {
407  // start 2nd arb with intro window
408  AW_root *aw_root = aww->get_root();
409  char *dir4intro;
410  GB_split_full_path(aw_root->awar(AWAR_SAVED_DB_PATH)->read_char_pntr(), &dir4intro, NULp, NULp, NULp);
411  if (!dir4intro) {
412  dir4intro = ARB_strdup(".");
413  }
414 
415  if (quit) {
416  NT_confirm_exit_restart_if(aww->get_root(), EXIT_SUCCESS, dir4intro);
417  }
418  else {
419  NT_start_if(dir4intro);
420  }
421  free(dir4intro);
422 }
423 
424 // --------------------------------------------------------------------------------
425 
426 static void NT_save_quick_cb(AW_window *aww) {
427  AW_root *awr = aww->get_root();
428  char *filename = awr->awar(AWAR_DB_PATH)->read_string();
429 
430  awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
431 
432  GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
433  if (error) aw_message(error);
434  else {
435  awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
436  AW_refresh_fileselection(awr, AWAR_DBBASE);
437  }
438 
439  free(filename);
440 }
441 
442 
443 static void NT_save_quick_as_cb(AW_window *aww) {
444  AW_root *awr = aww->get_root();
445  char *filename = awr->awar(AWAR_DB_PATH)->read_string();
446 
447  // @@@ also use dont_save_awars_with_default_value here?
448 
449  GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename);
450  if (!error) {
451  awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
452  AW_refresh_fileselection(awr, AWAR_DBBASE);
453  }
454  aww->hide_or_notify(error);
455 
456  free(filename);
457 }
458 
459 #define AWAR_DB_TYPE AWAR_DBBASE "/type" // created by AWT_insert_DBsaveType_selector
460 #define AWAR_DB_COMPRESSION AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector
461 #define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name"
462 
463 static void NT_save_as_cb(AW_window *aww) {
464  AW_root *awr = aww->get_root();
465  char *filename = awr->awar(AWAR_DB_PATH)->read_string();
466  const char *atype = awr->awar(AWAR_DB_TYPE)->read_char_pntr();
467  const char *ctype = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr();
468  char *savetype = GBS_global_string_copy("%s%s", atype, ctype);
469 
470  awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
471 
472  GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype);
473  if (!error) {
474  awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
475  AW_refresh_fileselection(awr, AWAR_DBBASE);
476  }
477  aww->hide_or_notify(error);
478 
479  free(savetype);
480  free(filename);
481 }
482 
483 static AW_window *NT_create_save_quick_as_window(AW_root *aw_root, const char *base_name) {
484  static AW_window_simple *aws = NULp;
485  if (!aws) {
486  aws = new AW_window_simple;
487  aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as");
488  aws->load_xfig("save_as.fig");
489 
490  aws->at("close");
491  aws->callback(AW_POPDOWN);
492  aws->create_button("CLOSE", "CLOSE", "C");
493 
494  aws->callback(makeHelpCallback("save.hlp"));
495  aws->at("help");
496  aws->create_button("HELP", "HELP", "H");
497 
498  AW_create_standard_fileselection(aws, base_name);
499 
500  aws->at("comment");
501  aws->create_text_field(AWAR_DB_COMMENT);
502 
503  aws->at("save");
504  aws->callback(NT_save_quick_as_cb);
505  aws->create_button("SAVE", "SAVE", "S");
506  }
507  return aws;
508 }
509 
510 static void NT_database_optimization(AW_window *aww) {
511  arb_progress progress(WEIGHTED, "Optimizing database compression", 0.38);
512  // 38% for seq-compression is just a rough guess made with silvaNR99138
513  // (a real guess would have to depend on ali-count, ali-length + field-count)
514 
515  GB_topSecurityLevel unsecured(GLOBAL.gb_main);
516 
517  GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
518  if (!error) {
519  ConstStrArray ali_names;
520  GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
521 
522  arb_progress ali_progress("Optimizing sequence data", ali_names.size());
523  ali_progress.allow_title_reuse();
524 
525  error = GBT_check_data(GLOBAL.gb_main, NULp);
526  error = GB_end_transaction(GLOBAL.gb_main, error);
527 
528  if (!error) {
529  char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string();
530  for (int i = 0; ali_names[i]; ++i) {
531  error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
532  ali_progress.inc_and_check_user_abort(error);
533  }
534  free(tree_name);
535  }
536  }
537  progress.inc_and_check_user_abort(error);
538 
539  if (!error) {
540  error = GB_optimize(GLOBAL.gb_main);
541  progress.inc_and_check_user_abort(error);
542  }
543  aww->hide_or_notify(error);
544 }
545 
546 static AW_window *NT_create_database_optimization_window(AW_root *aw_root) {
547  static AW_window_simple *aws = NULp;
548  if (aws) return aws;
549  GB_transaction ta(GLOBAL.gb_main);
550 
551  const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
552  aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree);
553 
554  aws = new AW_window_simple;
555  aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression");
556  aws->load_xfig("optimize.fig");
557 
558  aws->at("trees");
559  awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME);
560 
561  aws->at("close");
562  aws->callback(AW_POPDOWN);
563  aws->create_button("CLOSE", "CLOSE", "C");
564 
565  aws->callback(makeHelpCallback("optimize.hlp"));
566  aws->at("help");
567  aws->create_button("HELP", "HELP", "H");
568 
569  aws->at("go");
570  aws->callback(NT_database_optimization);
571  aws->create_button("GO", "GO");
572  return aws;
573 }
574 
575 static AW_window *NT_create_save_as(AW_root *aw_root, const char *base_name) {
576  static AW_window_simple *aws = NULp;
577  if (aws) return aws;
578 
579  aws = new AW_window_simple;
580  aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
581  aws->load_xfig("save_as.fig");
582 
583  aws->at("close");
584  aws->callback(AW_POPDOWN);
585  aws->create_button("CLOSE", "CLOSE", "C");
586 
587  aws->at("help");
588  aws->callback(makeHelpCallback("save.hlp"));
589  aws->create_button("HELP", "HELP", "H");
590 
591  AW_create_standard_fileselection(aws, base_name);
592 
593  aws->at("type");
594  AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE);
595 
596  aws->at("compression");
597  AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION);
598 
599  aws->at("optimize");
600  aws->callback(NT_create_database_optimization_window);
601  aws->help_text("optimize.hlp");
602  aws->create_autosize_button("OPTIMIZE", "Optimize database compression");
603 
604  aws->at("save");
605  aws->callback(NT_save_as_cb);
606  aws->create_button("SAVE", "SAVE", "S");
607 
608  aws->at("comment");
609  aws->create_text_field(AWAR_DB_COMMENT);
610 
611  return aws;
612 }
613 
614 static void NT_undo_cb(AW_window*, GB_UNDO_TYPE undo_type, TREE_canvas *ntw) {
615  GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type);
616  if (error) aw_message(error);
617  else {
618  GB_transaction ta(GLOBAL.gb_main);
619  AWT_auto_refresh allowed_on(ntw);
620  ntw->request_refresh();
621  }
622 }
623 
624 static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) {
625  DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
626  nt_mode_event(NULp, canvas, mode);
627 }
628 
629 static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) {
630  AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
631  if (tree_root) {
632  AWT_auto_refresh allowed_on(ntw);
633  GB_transaction ta(ntw->gb_main);
634 
635  NT_mark_all_cb(NULp, ntw, 0); // unmark all
636  tree_root->mark_duplicates();
637  ntw->request_structure_update();
638  }
639 }
640 
641 static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) {
642  GB_transaction ta(ntw->gb_main);
643  AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
644 
645  if (tree_root) {
646  AWT_auto_refresh allowed_on(ntw);
647  tree_root->justify_branch_lenghs(ntw->gb_main);
648  ntw->request_save_and_zoom_reset();
649  }
650 }
651 
652 #if defined(DEBUG)
653 static void NT_fix_database(AW_window *) {
654  GB_ERROR err = NULp;
655  err = GB_fix_database(GLOBAL.gb_main);
656  if (err) aw_message(err);
657 }
658 #endif
659 
660 static void relink_pseudo_species_to_organisms(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash) {
661  if (ref_gb_node) {
662  if (GEN_is_pseudo_gene_species(ref_gb_node)) {
663  GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
664 
665  if (gb_organism) {
666  char *name = GBT_read_string(gb_organism, "name");
667 
668  if (name) {
669  freeset(ref_name, name);
670  ref_gb_node = gb_organism;
671  }
672  }
673  }
674  }
675 }
676 
677 static void NT_pseudo_species_to_organism(AW_window *, TREE_canvas *ntw) {
678  GB_transaction ta(ntw->gb_main);
679  AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
680 
681  if (tree_root) {
682  AWT_auto_refresh allowed_on(ntw);
683 
684  GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
685  tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
686  GBS_free_hash(organism_hash);
687  ntw->request_save();
688  }
689 }
690 
691 
692 // #########################################
693 // #########################################
694 // ### ###
695 // ## user mask section ##
696 // ### ###
697 // #########################################
698 // #########################################
699 
700 struct nt_item_type_species_selector FINAL_TYPE : public awt_item_type_selector {
701  nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
702  ~nt_item_type_species_selector() OVERRIDE {}
703 
704  const char *get_self_awar() const OVERRIDE {
705  return AWAR_SPECIES_NAME;
706  }
707  size_t get_self_awar_content_length() const OVERRIDE {
708  return 12; // should be enough for "nnaammee.999"
709  }
710  GBDATA *current(AW_root *root, GBDATA *gb_main) const OVERRIDE { // give the current item
711  char *species_name = root->awar(get_self_awar())->read_string();
712  GBDATA *gb_species = NULp;
713 
714  if (species_name[0]) {
715  GB_transaction ta(gb_main);
716  gb_species = GBT_find_species(gb_main, species_name);
717  }
718 
719  free(species_name);
720  return gb_species;
721  }
722  const char *getKeyPath() const OVERRIDE { // give the keypath for items
723  return CHANGE_KEY_PATH;
724  }
725 };
726 
727 static nt_item_type_species_selector item_type_species;
728 
729 static void NT_open_mask_window(AW_window *aww, int id, GBDATA *gb_main) {
730  const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
731  nt_assert(descriptor);
732  if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
733 }
734 
735 static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
736  AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
737 }
738 static AW_window *create_colorize_species_window(AW_root *aw_root) {
739  return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
740 }
741 
742 // --------------------------------------------------------------------------------------------------
743 
744 static void NT_alltree_remove_leafs(AW_window *, GBT_TreeRemoveType mode, GBDATA *gb_main) {
745  GB_ERROR error = NULp;
746  GB_transaction ta(gb_main);
747 
748  ConstStrArray tree_names;
749  GBT_get_tree_names(tree_names, gb_main, false);
750 
751  if (!tree_names.empty()) {
752  long treeCount = tree_names.size();
753 
754  const char *whats_removed = NULp;
755  switch (mode) {
756  case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
757  case GBT_REMOVE_MARKED: whats_removed = "marked"; break;
758  default: nt_assert(0); break;
759  }
760 
761  const char *task = GBS_global_string("Deleting %s from %li trees", whats_removed, treeCount);
762 
763  arb_progress progress(task, treeCount);
764  GB_HASH *species_hash = GBT_create_species_hash(gb_main);
765 
766  int modified = 0;
767 
768  for (int t = 0; t<treeCount && !error; t++) {
769  progress.subtitle(tree_names[t]);
770  TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
771  if (!tree) {
772  aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
773  }
774  else {
775  int removed = 0;
776  int groups_removed = 0;
777 
778  tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
779 
780  nt_assert(removed >= groups_removed);
781 
782  if (!tree) {
783  aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
784  }
785  else {
786  if (removed>0) {
787  error = GBT_write_tree(gb_main, tree_names[t], tree);
788  if (error) {
789  aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
790  }
791  else {
792  if (groups_removed>0) {
793  aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
794  }
795  else {
796  aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
797  }
798  modified++;
799  }
800  }
801  UNCOVERED();
802  destroy(tree);
803  }
804  }
805  progress.inc_and_check_user_abort(error);
806  }
807 
808  if (modified) {
809  aw_message(GBS_global_string("Changed %i of %li trees.", modified, treeCount));
810  }
811  else {
812  aw_message("No tree modified");
813  }
814 
815  GBS_free_hash(species_hash);
816  }
817 
818  aw_message_if(ta.close(error));
819 }
820 
821 // --------------------------------------------------------------------------------------------------
822 
823 static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
824  GB_transaction ta(gb_main);
825  GBT_mark_all(gb_main, 0);
826 
827  DBItemSetIter end = referred.end();
828  for (DBItemSetIter s = referred.begin(); s != end; ++s) {
829  GB_write_flag(*s, 1);
830  }
831  return ARB_ERROR();
832 }
833 
834 static AW_window *create_mark_by_refentries_window(AW_root *awr, GBDATA *gbmain) {
835  static AW_window *aws = NULp;
836  if (!aws) {
837  static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
838  aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULp, "Mark referenced", mark_referred_species);
839  }
840  return aws;
841 }
842 
843 // --------------------------------------------------------------------------------------------------
844 
845 static void merge_from_to(AW_root *awr, const char *db_awar_name, bool merge_to) {
846  const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
847  char *quotedDB = GBK_singlequote(db_name);
848 
849  AW_system(
850  GBS_global_string(
851  merge_to
852  ? "arb_ntree : %s &"
853  : "arb_ntree %s : &",
854  quotedDB)
855  );
856 
857  free(quotedDB);
858 }
859 
860 static void merge_from_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, false); }
861 static void merge_into_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, true); }
862 
863 static AW_window *NT_create_merge_from_window(AW_root *awr) {
864  static char *awar_name = NULp; // do not free, bound to callback
865  AW_window *aw_from =
866  awt_create_load_box(awr, "Merge data from", "other ARB database",
867  ".", ".arb", &awar_name,
868  makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
869  return aw_from;
870 }
871 static AW_window *NT_create_merge_to_window(AW_root *awr) {
872  static char *awar_name = NULp; // do not free, bound to callback
873  AW_window *aw_to =
874  awt_create_load_box(awr, "Merge data to", "other or new ARB database",
875  ".", ".arb", &awar_name,
876  makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
877  makeWindowCallback(AW_POPDOWN), NULp);
878  return aw_to;
879 }
880 
881 // --------------------------------------------------------------------------------------------------
882 
883 static void update_main_window_title(AW_root *awr, AW_window_menu_modes *aww, int clone) {
884  const char *filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
885  const char *base_title = GBS_global_string("%s - ARB", filename);
886  aww->set_window_title(TREE_canvas::suffixed_title_for_index(base_title, clone));
887 }
888 
889 static void canvas_tree_awar_changed_cb(AW_awar *, bool, TREE_canvas *ntw) {
890  NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
891  AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
892  TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_TREE);
893 }
894 
895 class TREE_canvas_registry {
896  int count;
897  TREE_canvas *canvas[MAX_NT_WINDOWS];
898 
899  static TREE_canvas_registry *SINGLETON;
900 
901  TREE_canvas_registry() : count(0) {
902  AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
903  }
904 
905 public:
906  static TREE_canvas_registry& instance() {
907  if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
908  return *SINGLETON;
909  }
910 
911  void register_canvas(TREE_canvas *ntw) {
912  nt_assert(count<MAX_NT_WINDOWS);
913  nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
914  canvas[count++] = ntw;
915  ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
916  }
917 
918  int get_count() const { return count; }
919 
920  TREE_canvas *get_canvas(int idx) const {
921  if (idx<0 || idx>=count) return NULp;
922  return canvas[idx];
923  }
924 };
925 
926 TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULp;
927 
928 TREE_canvas *NT_get_canvas_by_index(int idx) {
930  nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
931  return TREE_canvas_registry::instance().get_canvas(idx);
932 }
933 
934 #if defined(TRACE_GROUP_SELECTION)
935 static TREE_canvas *find_canvas_showing(AWT_graphic_tree *agt) {
936  // look for (registered) canvas showing given AWT_graphic_tree
937  // returns NULp if none found
938  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
939 
940  int maxIdx = reg.get_count();
941  for (int32_t i = 0; i<maxIdx; ++i) {
942  TREE_canvas *ntw = reg.get_canvas(i);
943  if (ntw->gfx == agt) return ntw;
944  }
945  return NULp;
946 }
947 #endif
948 
949 void NT_fill_canvas_selection_list(class AW_selection_list *sellst, TREE_canvas *to_skip) {
952  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
953 
954  int maxIdx = reg.get_count();
955  for (int32_t i = 0; i<maxIdx; ++i) {
956  TREE_canvas *ntw = reg.get_canvas(i);
957  if (ntw && ntw != to_skip) {
958  nt_assert(ntw->get_awar_tree());
959  const char *treename = ntw->get_awar_tree()->read_char_pntr();
960  const char *description = i
961  ? GBS_global_string("%s: %s", TREE_canvas::suffixed_title_for_index("ARB", i), treename)
962  : GBS_global_string("ARB main: %s", treename);
963  sellst->insert(description, i);
964  }
965  }
966 }
967 
968 // ----------------------------------
969 // group-selection handlers
970 
971 void NT_deselect_group(AW_root *awr) {
972  awr->awar(AWAR_GROUP)->write_pointer(NULp);
973 }
974 
975 static bool track_group_selection_by_canvas = true;
976 
977 static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) {
978  const Group& group = gfx->get_selected_group();
979 
980 #if defined(TRACE_GROUP_SELECTION)
981  fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track");
982  TREE_canvas *ntw = find_canvas_showing(gfx);
983  if (group.is_valid()) {
984  fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name());
985  }
986  else {
987  fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index());
988  }
989 #endif
990 
991  if (track_group_selection_by_canvas) {
992  // set group-awar:
993  gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULp if !group.is_valid()
994  }
995 }
996 
997 static void group_awar_changed_cb(AW_root *awr) {
998  AW_awar *awar_group = awr->awar(AWAR_GROUP);
999  GBDATA *gb_wanted_group = awar_group->read_pointer();
1000 
1001  GBDATA *gb_wanted_tree = NULp;
1002  {
1003  if (gb_wanted_group) {
1004  GB_transaction ta(gb_wanted_group);
1005  gb_wanted_tree = GB_get_father(gb_wanted_group);
1006  awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected
1007 #if defined(TRACE_GROUP_SELECTION)
1008  fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr);
1009 #endif
1010  }
1011 #if defined(TRACE_GROUP_SELECTION)
1012  const char *group_name = NULp;
1013  if (gb_wanted_group) {
1014  GB_transaction ta(gb_wanted_group);
1015  GBDATA *gb_name = GB_entry(gb_wanted_group, "group_name");
1016  if (gb_name) group_name = GB_read_char_pntr(gb_name);
1017  }
1018  fprintf(stderr, "group awar changed to %p", gb_wanted_group);
1019  if (group_name) fprintf(stderr, " (='%s')", group_name);
1020  fputc('\n', stderr);
1021 #endif
1022  }
1023 
1024  LocallyModify<bool> ignore_group_selection_by_canvas(track_group_selection_by_canvas, false);
1025 
1026  {
1027  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1028 
1029  int maxIdx = reg.get_count();
1030  for (int32_t i = 0; i<maxIdx; ++i) {
1031  TREE_canvas *ntw = reg.get_canvas(i);
1032  AWT_graphic_tree *agt = AWT_TREE(ntw);
1033  const Group& curr_group = agt->get_selected_group();
1034 
1035  GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree();
1036  if (gb_curr_tree == gb_wanted_tree) {
1037  AWT_auto_refresh allowed_on(ntw);
1038  if (!curr_group.is_valid() || // no group selected
1039  curr_group.get_group_data() != gb_wanted_group) // wrong group selected
1040  {
1041  agt->select_group(gb_wanted_group);
1042  ntw->request_refresh();
1043  }
1044  // perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group)
1045  TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_GROUP);
1046  }
1047  else {
1048  if (curr_group.is_valid()) {
1049  AWT_auto_refresh allowed_on(ntw);
1050  agt->deselect_group();
1051  ntw->request_refresh();
1052  }
1053  }
1054  }
1055  }
1056 }
1057 
1058 // ----------------------------
1059 // create main window
1060 
1061 static AW_window *popup_new_main_window(AW_root *awr, int clone, TREE_canvas **result_ntw) {
1067  GB_push_transaction(GLOBAL.gb_main);
1068 
1069  const char *awar_tree = NULp;
1070  AW_window_menu_modes *awm = new AW_window_menu_modes;
1071 
1072  {
1073  char window_id[256];
1074  if (clone) {
1075  awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
1076  sprintf(window_id, "ARB_NT_%i", clone);
1077  }
1078  else {
1079  awar_tree = AWAR_TREE;
1080  sprintf(window_id, "ARB_NT");
1081  }
1082  awm->init(awr, window_id, "[starting arb]", 0, 0); // effective title is generated by update_main_window_title
1083  }
1084 
1085  awr->awar(AWAR_DB_NAME)
1086  ->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1087  ->update();
1088 
1089  awm->button_length(5);
1090 
1091  if (!clone) AW_init_color_group_defaults("arb_ntree");
1092 
1093  AWT_graphic_tree *tree = TREE_generate_display(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1094 
1095  if (!clone) { // while creating initial window
1096  AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb));
1097  awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb);
1098  }
1099 
1100  TREE_canvas *ntw;
1101  {
1102  AW_awar *tree_awar = awr->awar_string(awar_tree);
1103  {
1104  AP_tree_display_style prev_style = tree->get_tree_style();
1105  tree->set_tree_style(AP_LIST_SIMPLE, NULp); // avoid NDS warnings during startup
1106 
1107  ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1108  nt_assert(ntw->get_index() == clone); // required for proper title enumeration.
1109 
1110  tree->set_tree_style(prev_style, ntw);
1111  ntw->set_mode(AWT_MODE_SELECT);
1112  }
1113 
1114  if (result_ntw) *result_ntw = ntw;
1115 
1116  {
1117  const char *tree_name = tree_awar->read_char_pntr();
1118  const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1119 
1120  if (existing_tree_name) {
1121  tree_awar->write_string(existing_tree_name);
1122  NT_reload_tree_event(awr, ntw, true); // load first tree
1123  }
1124  else {
1125  AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, NULp, "no_tree.hlp");
1126  tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list
1127  }
1128 
1129  TREE_canvas_registry::instance().register_canvas(ntw);
1130  AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1131  }
1132  }
1133 
1134  TREE_install_update_callbacks(ntw);
1135 
1136  bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1137 
1138  WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1139 
1140  // --------------
1141  // File
1142 
1143 #if defined(DEBUG)
1144  AWT_create_debug_menu(awm);
1145 #endif // DEBUG
1146 
1147  bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1148 
1149  if (clone) {
1150  awm->create_menu("File", "F", AWM_ALL);
1151  if (allow_new_window) {
1152  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));
1153  }
1154  awm->insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN);
1155  }
1156  else {
1157 #if defined(DEBUG)
1158  // add more to debug-menu
1159  awm->sep______________();
1160  awm->insert_menu_topic("fix_db", "Fix database", "F", NULp, AWM_ALL, NT_fix_database);
1161  awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", NULp, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1162  awm->insert_menu_topic("test_compr", "Test compression", "T", NULp, AWM_ALL, makeWindowCallback(GBT_compression_test, GLOBAL.gb_main));
1163 #endif // DEBUG
1164 
1165  awm->create_menu("File", "F", AWM_ALL);
1166  {
1167  // keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1168  awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, NT_save_quick_cb);
1169  awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1170  if (allow_new_window) {
1171  awm->sep______________();
1172  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));
1173  }
1174  awm->sep______________();
1175  awm->insert_menu_topic("optimize_db", "Optimize database compression", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window);
1176  awm->sep______________();
1177 
1178  awm->insert_sub_menu("Import", "I");
1179  {
1180  awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1181  awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1182  GDE_load_menu(awm, AWM_EXP, "Import");
1183  }
1184  awm->close_sub_menu();
1185 
1186  awm->insert_sub_menu("Export", "E");
1187  {
1188  awm->insert_menu_topic("export_to_ARB", "Merge to other or new ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1189  awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1190  GDE_load_menu(awm, AWM_ALL, "Export");
1191  awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window);
1192  }
1193  awm->close_sub_menu();
1194  awm->sep______________();
1195 
1196  insert_macro_menu_entry(awm, false);
1197 
1198  awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1199  {
1200  awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp"));
1201  awm->insert_menu_topic("bug_report", "Report bug", "b", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1202  awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1203  }
1204  awm->close_sub_menu();
1205  awm->sep______________();
1206 
1207  awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1208  awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1209  awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_confirm_exit, EXIT_SUCCESS));
1210  }
1211 
1212  // -----------------
1213  // Species
1214 
1215  awm->create_menu("Species", "c", AWM_ALL);
1216  {
1217  awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1218  awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb);
1219 
1220  awm->sep______________();
1221 
1222  NT_insert_mark_submenus(awm, ntw, 1);
1223  awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1224  awm->insert_menu_topic("species_colors", "Colors ...", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window);
1225  awm->insert_menu_topic("selection_admin", "Selections ...", "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1226 
1227  awm->sep______________();
1228 
1229  awm->insert_sub_menu("Database fields admin", "f");
1230  DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1231  awm->close_sub_menu();
1232  NT_create_mask_submenu(awm);
1233 
1234  awm->sep______________();
1235 
1236  awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1237 
1238  awm->insert_sub_menu("Sort Species", "s");
1239  {
1240  awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window);
1241  awm->insert_menu_topic("$sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1242  }
1243  awm->close_sub_menu();
1244 
1245  awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1246  {
1247  awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1248  awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "species_join.hlp", AWM_EXP, NT_create_species_join_window);
1249  }
1250  awm->close_sub_menu();
1251 
1252  awm->sep______________();
1253 
1254  awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1255 
1256  awm->sep______________();
1257 
1258  awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1259 
1260  awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1261  {
1262  awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames);
1263  awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames);
1264  awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1265  awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window);
1266  }
1267  awm->close_sub_menu();
1268  }
1269 
1270  // ----------------------------
1271  // Genes + Experiment
1272 
1273  if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1274 
1275  // ------------------
1276  // Sequence
1277 
1278  awm->create_menu("Sequence", "S", AWM_ALL);
1279  {
1280  awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)NULp));
1281  awm->insert_sub_menu("Insert/delete", "I");
1282  {
1283  awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window);
1284  awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main));
1285  }
1286  awm->close_sub_menu();
1287  awm->sep______________();
1288 
1289  awm->insert_sub_menu("Edit Sequences", "E");
1290  {
1291  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));
1292  awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1293  awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1294  }
1295  awm->close_sub_menu();
1296 
1297  awm->sep______________();
1298 
1299  awm->insert_sub_menu("Align sequences", "l");
1300  {
1301  awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1302  GDE_load_menu(awm, AWM_ALL, "Align");
1303  }
1304  awm->close_sub_menu();
1305  awm->insert_menu_topic("seq_concat", "Concatenate sequences", "C", "concatenate.hlp", AWM_ALL, NT_createConcatenationWindow);
1306  awm->insert_menu_topic("seq_split", "Split sequences", "S", "split.hlp", AWM_ALL, NT_create_splitAlignment_window);
1307  awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1308  awm->sep______________();
1309 
1310  awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1311  awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist"));
1312  awm->sep______________();
1313 
1314  awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1315  awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1316 
1317  awm->sep______________();
1318 
1319  GDE_load_menu(awm, AWM_ALL, "Print");
1320  }
1321 
1322  // -------------
1323  // SAI
1324 
1325  awm->create_menu("SAI", "A", AWM_ALL);
1326  {
1327  awm->insert_menu_topic("sai_admin", "SAI Admin", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1328  awm->insert_menu_topic("sai_calc", "Combine SAIs", "b", "saicalc.hlp", AWM_ALL, makeWindowCallback(SAI_popup_calculator_window, GLOBAL.gb_main));
1329  awm->insert_sub_menu("Create SAI using ...", "C");
1330  {
1331  awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window);
1332  awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window);
1333  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);
1334  awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_phylo"));
1335  awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold);
1336 
1337  GDE_load_menu(awm, AWM_EXP, "SAI");
1338  }
1339  awm->close_sub_menu();
1340 
1341  awm->insert_sub_menu("Other functions", "O");
1342  {
1343  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));
1344  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)));
1345  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);
1346  }
1347  awm->close_sub_menu();
1348  }
1349 
1350  // ----------------
1351  // Probes
1352 
1353  awm->create_menu("Probes", "P", AWM_ALL);
1354  {
1355  awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1356  awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1357  awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1358  awm->sep______________();
1359  awm->insert_menu_topic("probe_match_sp", "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window, ntw));
1360  awm->sep______________();
1361  awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1362  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)));
1363  awm->sep______________();
1364  awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1365  }
1366 
1367  }
1368 
1369  // --------------
1370  // Tree
1371 
1372  awm->create_menu("Tree", "T", AWM_ALL);
1373  {
1374  if (!clone) {
1375  awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1376  awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(NDS_create_window, GLOBAL.gb_main));
1377  awm->sep______________();
1378  awm->insert_sub_menu("Add Species to Existing Tree", "A");
1379  {
1380  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"));
1381  awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_pars"));
1382  GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1383  }
1384  awm->close_sub_menu();
1385  }
1386 
1387  awm->insert_sub_menu("Remove Species from Tree", "R");
1388  {
1389  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));
1390  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));
1391  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));
1392  awm->sep______________();
1393  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));
1394  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));
1395  }
1396  awm->close_sub_menu();
1397 
1398  if (!clone) {
1399  awm->insert_sub_menu("Build tree from sequence data", "B");
1400  {
1401  awm->insert_sub_menu("Distance matrix methods", "D");
1402  awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist"));
1403  GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1404  awm->close_sub_menu();
1405 
1406  awm->insert_sub_menu("Maximum Parsimony methods", "P");
1407  GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1408  awm->close_sub_menu();
1409 
1410  awm->insert_sub_menu("Maximum Likelihood methods", "L");
1411  GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1412  GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1413  awm->close_sub_menu();
1414 
1415  awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1416  GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1417  awm->close_sub_menu();
1418  }
1419  awm->close_sub_menu();
1420  }
1421 
1422  awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1423 
1424  awm->sep______________();
1425 
1426  awm->insert_sub_menu("Reset zoom", "z");
1427  {
1428  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));
1429  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));
1430  }
1431  awm->close_sub_menu();
1432 
1433  awm->sep______________();
1434 
1435  // taxonomic groups
1436  NT_insert_collapse_submenu(awm, ntw);
1437  if (!clone) {
1438  awm->insert_menu_topic("group_search", "Search groups...", "g", "group_search.hlp", AWM_ALL, makeWindowCallback (popup_group_search_window, GLOBAL.gb_main));
1439  awm->insert_menu_topic("compare_taxonomy", "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1440  awm->insert_menu_topic("move_groups", "Move groups...", "v", "move_groups.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_moveGroupInfo_window));
1441  }
1442 
1443  awm->sep______________();
1444 
1445  if (!clone) {
1446  awm->insert_menu_topic("compare_topology", "Compare topology...", "o", "compare_topo.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compareTopologies_window));
1447  }
1448 
1449  awm->insert_sub_menu("Modify branches", "M");
1450  {
1451  awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw));
1452  awm->insert_menu_topic(awm->local_id("tree_edit_remark"), "Edit bootstraps", "E", "ted_boot.hlp", AWM_ALL, makeWindowCallback(NT_edit_bootstrap, ntw));
1453  awm->sep______________();
1454  awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw));
1455  awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1456  awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw));
1457  awm->sep______________();
1458  awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1459  awm->sep______________();
1460  awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1461  awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1462 
1463  }
1464  awm->close_sub_menu();
1465  awm->insert_sub_menu("Beautify tree", "u");
1466  {
1467  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));
1468  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));
1469  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));
1470  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));
1471  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));
1472  awm->sep______________();
1473  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));
1474  }
1475  awm->close_sub_menu();
1476 
1477  awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "h", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1478  awm->insert_menu_topic(awm->local_id("syncroots"), "Adjust roots...", "j", "syncroots.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncroot_window, GLOBAL.gb_main));
1479  awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "k", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback (NT_mark_duplicates, ntw));
1480 
1481  awm->sep______________();
1482  awm->insert_menu_topic(awm->local_id("shade"), "Tree shading...", "s", "tree_shading.hlp", AWM_ALL, makeWindowCallback (NT_configure_treeShader));
1483  awm->insert_menu_topic(awm->local_id("syncscroll"), "Sync tree scrolling..", "e", "syncscroll.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1484 
1485  awm->sep______________();
1486  awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", NULp, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1487 
1488  awm->sep______________();
1489  awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1490 
1491  if (is_genome_db) {
1492  awm->sep______________();
1493  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));
1494  }
1495 
1496  if (!clone) {
1497  awm->sep______________();
1498  awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1499  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)));
1500  }
1501 
1502  }
1503 
1504  if (!clone) {
1505  // ---------------
1506  // Tools
1507 
1508  awm->create_menu("Tools", "o", AWM_ALL);
1509  {
1510  awm->insert_menu_topic("names_admin", "Nameserver admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeWindowCallback(AW_popup_namesadmin_window, GLOBAL.gb_main));
1511  awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1512  {
1513  awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1514  }
1515  awm->close_sub_menu();
1516  awm->sep______________();
1517 
1518  awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1519  {
1520  GDE_load_menu(awm, AWM_EXP, NULp);
1521  }
1522  awm->close_sub_menu();
1523 
1524  awm->sep______________();
1525  awm->insert_menu_topic("xterm", "Start XTERM", "X", "xterm.hlp", AWM_ALL, AW_console_cb);
1526  XCmdType *showlog_cmdtype = new XCmdType(XCMD_ASYNC_WAIT_ON_ERROR, GLOBAL.gb_main); // do not free (used in callback)
1527  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
1528  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));
1529  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));
1530  awm->sep______________();
1531  GDE_load_menu(awm, AWM_EXP, "User");
1532  }
1533  // --------------------
1534  // Properties
1535 
1536  awm->create_menu("Properties", "r", AWM_ALL);
1537  {
1538  awm->insert_menu_topic("props_menu", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1539  awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1540  awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1541  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));
1542  awm->sep______________();
1543  awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", NULp, AWM_ALL, NT_toggle_expert_mode);
1544  awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", NULp, AWM_ALL, NT_toggle_focus_policy);
1545  awm->sep______________();
1546  AW_insert_common_property_menu_entries(awm);
1547  awm->sep______________();
1548  awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1549  }
1550  }
1551 
1552  awm->insert_help_topic("ARB NTREE help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1553 
1554  // ----------------------
1555  // mode buttons
1556  //
1557  // keep them synchronized as far as possible with those in ARB_PARSIMONY
1558  // see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1559 
1560  awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1561  awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1562  awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1563  awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1564  awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1565 
1566  awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1567  awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW));
1568 
1569  // topology-modification-modes
1570  awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1571  awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1572  awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1573  awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1574  awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1575 
1576  // layout-modes
1577  awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1578  awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1579  awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1580 
1581  awm->set_info_area_height(250);
1582  awm->at(5, 2);
1583  awm->auto_space(-2, -2);
1584  awm->shadow_width(1);
1585 
1586  // -------------------------
1587  // create top area
1588 
1589  int first_liney;
1590  int leftx;
1591  awm->get_at_position(&leftx, &first_liney);
1592 
1593  // ---------------------
1594  // quit + help
1595 
1596  awm->button_length(0);
1597 
1598  if (clone) {
1599  awm->callback(AW_POPDOWN);
1600  awm->create_button("CLOSE", "#close.xpm");
1601  }
1602  else {
1603  awm->callback(makeWindowCallback(NT_confirm_exit, EXIT_SUCCESS));
1604  awm->help_text("quit.hlp");
1605  awm->create_button("QUIT", "#quit.xpm");
1606  }
1607 
1608  int db_pathx = awm->get_at_xposition();
1609 
1610  // now fetch the yposition for the 2nd button line
1611  awm->at_newline();
1612  int second_liney = awm->get_at_yposition();
1613 
1614  awm->callback(AW_help_entry_pressed);
1615  awm->help_text("arb_ntree.hlp");
1616  awm->create_button("?", "#help.xpm");
1617 
1618  // --------------------------
1619  // save + undo/redo
1620 
1621  awm->callback(NT_save_quick_cb);
1622  awm->help_text("save.hlp");
1623  awm->create_button("SAVE", "#save.xpm");
1624 
1625  awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1626  awm->help_text("save.hlp");
1627  awm->create_button("SAVE_AS", "#saveAs.xpm");
1628 
1629  // undo/redo:
1630  awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1631  awm->help_text("undo.hlp");
1632  awm->create_button("UNDO", "#undo.xpm");
1633 
1634  awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1635  awm->help_text("undo.hlp");
1636  awm->create_button("REDO", "#redo.xpm");
1637 
1638  int db_pathx2 = awm->get_at_xposition();
1639 
1640  // fetch position for mode help-line:
1641  awm->at_newline();
1642  int third_liney = awm->get_at_yposition();
1643 
1644  awm->at(db_pathx, first_liney);
1645  // size of DB-name button is determined by buttons below:
1646  awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1647  awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1648  awm->help_text("save.hlp");
1649  awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1650 
1651  // -----------------------------
1652  // tree + tree display
1653 
1654 #define TREE_BUTTON_OVERSIZE 6
1655 
1656  int db_treex = awm->get_at_xposition();
1657  int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1658 
1659  awm->at(db_treex, second_uppery);
1660  awm->button_length(0);
1661 
1662  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1663  awm->help_text("tr_type_radial.hlp");
1664  awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1665 
1666  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1667  awm->help_text("tr_type_dendro.hlp");
1668  awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1669 
1670  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1671  awm->help_text("tr_type_irs.hlp");
1672  awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1673 
1674  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1675  awm->help_text("tr_type_nds.hlp");
1676  awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1677 
1678  int db_treex2 = awm->get_at_xposition();
1679 
1680  awm->at(db_treex, first_liney);
1681  // size of tree-name button is determined by buttons below:
1682  awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1683  awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree, ntw));
1684  awm->help_text("nt_tree_select.hlp");
1685  awm->create_button("SELECT_A_TREE", awar_tree);
1686 
1687  // ---------------------------------------------------------------
1688  // protection, alignment + editor (and maybe Genome Map)
1689 
1690  int db_alignx = awm->get_at_xposition();
1691 
1692  // editor and genemap buttons have to be 44x24 sized
1693 #define EDIT_XSIZE 50
1694 #define EDIT_YSIZE 30 // same as 'save as' buttons
1695 
1696  // first draw protection:
1697  int protectx = db_alignx + 2*EDIT_XSIZE;
1698 
1699  awm->at(protectx+2, first_liney+1);
1700  awm->button_length(0);
1701  awm->create_button(NULp, "#protect.xpm");
1702 
1703  awm->at(protectx, second_liney+2);
1704  awm->create_option_menu(AWAR_SECURITY_LEVEL);
1705  awm->insert_option ("0", NULp, 0);
1706  awm->insert_option ("1", NULp, 1);
1707  awm->insert_option ("2", NULp, 2);
1708  awm->insert_option ("3", NULp, 3);
1709  awm->insert_option ("4", NULp, 4);
1710  awm->insert_option ("5", NULp, 5);
1711  awm->insert_default_option("6", NULp, 6);
1712  awm->update_option_menu();
1713 
1714  int db_searchx = awm->get_at_xposition() - 7;
1715 
1716  // draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1717  awm->at(db_alignx, second_liney);
1718 
1719  awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1720  awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1721  awm->help_text("arb_edit4.hlp");
1722  if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1723  else awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1724 
1725  if (is_genome_db) {
1726  awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1727  awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1728  awm->help_text("gene_map.hlp");
1729  awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1730  }
1731 
1732  int db_alignx2 = awm->get_at_xposition();
1733 
1734  awm->at(db_alignx, first_liney);
1735  awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1736  awm->callback(NT_create_select_alignment_window);
1737  awm->help_text("nt_align_select.hlp");
1738  awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1739 
1740  // -------------------------------
1741  // create mode-help line
1742 
1743  awm->at(leftx, third_liney);
1744  awm->button_length(AWAR_FOOTER_MAX_LEN);
1745  awm->create_button(NULp, AWAR_FOOTER);
1746 
1747  awm->at_newline();
1748  int bottomy = awm->get_at_yposition();
1749 
1750  // ---------------------------------------
1751  // Info / marked / Search / Jump
1752 
1753  awm->button_length(7);
1754 
1755  awm->at(db_searchx, first_liney);
1756  awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1757  awm->help_text("sp_search.hlp");
1758  awm->create_button("SEARCH", "Search");
1759 
1760  awm->at(db_searchx, second_uppery);
1761  awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1762  awm->help_text("tr_jump.hlp");
1763  awm->create_button("JUMP", "Jump");
1764 
1765  int db_infox = awm->get_at_xposition();
1766 
1767  awm->at(db_infox, first_liney);
1768  awm->button_length(13);
1769  awm->callback(popupinfo_wcb);
1770  awm->help_text("sp_info.hlp");
1771  awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1772 
1773  awm->at(db_infox, second_uppery);
1774  create_species_selection_button(awm, makeWindowCallback(NT_popup_configuration_admin, ntw), "selection_admin2", AWAR_MARKED_SPECIES_COUNTER, GLOBAL.gb_main);
1775 
1776  // set height of top area:
1777  awm->set_info_area_height(bottomy+2);
1778  awm->set_bottom_area_height(0);
1779 
1780  NT_activate_configMarkers_display(ntw);
1781 
1782  // ------------------------------------
1783  // Autostarts for development
1784 
1785 #if defined(DEVEL_RALF)
1786  // if (is_genome_db) GEN_map_first(awr)->show();
1787 #endif // DEVEL_RALF
1788 
1789  GB_pop_transaction(GLOBAL.gb_main);
1790 
1791 #if defined(DEBUG)
1792  AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1793 #endif
1794 
1795  return awm;
1796 }
1797 
1798 TREE_canvas *NT_create_main_window(AW_root *aw_root) {
1799  GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1800  if (error) aw_message(error);
1801 
1802  nt_create_all_awars(aw_root);
1803 
1804  TREE_canvas *ntw = NULp;
1805  AW_window *aww = popup_new_main_window(aw_root, 0, &ntw);
1806  NT_install_treeShader(ntw, GLOBAL.gb_main);
1807  aww->show();
1808 
1809  error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1810  if (error) aw_message(error);
1811 
1812  return ntw;
1813 }
WEIGHTED
Definition: arb_progress.h:225
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GB_ERROR GB_begin_transaction(GBDATA *gbd)
Definition: arbdb.cxx:2528
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Definition: NT_edconf.cxx:406
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Definition: AW_option_toggle.cxx:260
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Definition: arb_msg.cxx:571
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Definition: arb_assert.h:245
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Definition: ui_species.cxx:1481
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Definition: NT_extern.cxx:546
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Definition: AW_at.cxx:296
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Definition: Group.hxx:55
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Definition: aw_awar_defs.hxx:6
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Definition: NT_shadeTree.cxx:143
NT_database_optimization
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Definition: NT_extern.cxx:510
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Definition: TreeDisplay.hxx:507
GBT_TreeRemoveType
GBT_TreeRemoveType
Definition: arbdbt.h:32
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Definition: NT_extern.cxx:883
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Definition: aw_global_awars.hxx:20
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Definition: ad_spec.cxx:253
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Definition: AW_at.cxx:288
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Definition: AW_rename.cxx:573
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Definition: aditem.cxx:113
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Definition: arb_strarray.h:85
NT_create_startEditorOnOldConfiguration_window
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Definition: NT_edconf.cxx:445
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Definition: TreeCallbacks.cxx:567
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Definition: AW_at.cxx:301
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Definition: NT_extern.cxx:443
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Definition: AW_awar.cxx:191
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Definition: ad_save_load.cxx:804
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NT_createConcatenationAwars
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Definition: NT_concatenate.cxx:52
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Definition: NT_extern.cxx:710
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Definition: NT_extern.cxx:243
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Definition: AW_window.cxx:707
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Definition: SQ_main.cxx:48
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Definition: ui_species.cxx:85
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Definition: arb_progress.h:227
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Definition: NT_extern.cxx:461
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Definition: AWTI_export.cxx:303
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Definition: NT_extern.cxx:87
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Definition: GEN_interface.cxx:350
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Definition: ad_transpro.cxx:215
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Definition: aditem.cxx:295
NT_create_compare_taxonomy_awars
void NT_create_compare_taxonomy_awars(AW_root *aw_root, AW_default props)
Definition: NT_taxonomy.cxx:335
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Definition: ui_species.cxx:1468
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Definition: arb_string.cxx:72
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Definition: canvas.hxx:248
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Definition: TreeCallbacks.cxx:144
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Definition: canvas.hxx:372
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Definition: ad_ext.cxx:318
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Definition: AWTC_submission.cxx:225
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Definition: input_mask.hxx:31
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Definition: TreeCallbacks.cxx:581
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Definition: adtree.cxx:34
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Definition: ad_ext.cxx:286
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Definition: arbdb.cxx:2561
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Definition: AW_at.cxx:93
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Definition: TreeCallbacks.cxx:650
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Definition: arb_progress.h:319
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Definition: AP_Tree.hxx:38
AWT_auto_refresh
Definition: canvas.hxx:410
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Definition: TreeCallbacks.cxx:548
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Definition: AW_root.cxx:657
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Definition: aw_file.hxx:30
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Definition: adtree.cxx:1103
EXPORT_SPACE_PADDED_LEFT_ALIGNED
Definition: NT_extern.cxx:89
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Definition: canvas.hxx:376
ARB_bind_global_awars
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Definition: AW_global_awars.cxx:146
ARB_VERSION_DETAILED
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Definition: arb_build.h:2
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Definition: adali.cxx:317
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Definition: MacroExitor.hxx:128
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Definition: primer_design.cxx:94
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Definition: arb_string.h:27
AWAR_DEFAULT_ALIGNMENT
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Definition: aw_awar_defs.hxx:8
create_probe_match_with_specificity_window
AW_window * create_probe_match_with_specificity_window(AW_root *root, TREE_canvas *ntw)
Definition: probe_design.cxx:2554
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Definition: NT_extern.cxx:735
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Definition: adtree.cxx:837
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Definition: AW_awar.cxx:184
AWAR_SAI_COLOR_STR
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Definition: aw_awar_defs.hxx:28
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Definition: ad_trees.cxx:1126
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Definition: NT_ins_col.cxx:268
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Definition: arb_msg.cxx:203
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Definition: NT_sync_scroll.cxx:89
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AW_root * awr
Definition: canvas.hxx:348
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Show a message box with an advice for the user.
Definition: AW_advice.cxx:160
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Definition: NT_extern.cxx:101
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Definition: NT_extern.cxx:248
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Definition: arb_msg.cxx:523
AW_POPDOWN
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Definition: AW_window.cxx:52
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Definition: TreeCallbacks.cxx:864
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Definition: canvas.hxx:35
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Definition: AW_preset.cxx:1450
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Definition: NT_extern.cxx:889
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Definition: adtree.cxx:1056
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Definition: NT_cb.cxx:101
NT_confirm_exit
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Definition: NT_extern.cxx:402
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void GBS_free_hash(GB_HASH *hs)
Definition: adhash.cxx:538
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GB_HASH * GBT_create_species_hash(GBDATA *gb_main)
Definition: adhashtools.cxx:36
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test if SmartPtr is NULp
Definition: smartptr.h:248
AWT_look_input_mask
const awt_input_mask_descriptor * AWT_look_input_mask(int id)
Definition: input_mask.cxx:2171
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Definition: NT_extern.cxx:463
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Definition: arb_a2ps.c:154
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Definition: NT_extern.cxx:928
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Definition: NT_extern.cxx:975
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Definition: aw_awar_defs.hxx:56
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Definition: AW_window.cxx:1062
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static const char * suffixed_title_for_index(const char *primary_title, int index)
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Definition: Group.hxx:48
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Definition: MP_main.cxx:100
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Definition: primer_design.cxx:462
AWM_EXP
Definition: aw_window.hxx:180
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static AW_window * NT_create_save_as(AW_root *aw_root, const char *base_name)
Definition: NT_extern.cxx:575
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const char * getKeyPath() const OVERRIDE
Definition: NT_extern.cxx:722
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Definition: adTest.cxx:237
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Definition: ui_species.cxx:868
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Definition: ad_trees.h:19
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set SmartPtr to NULp
Definition: smartptr.h:251
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Definition: arbdb.cxx:1722
AW_window::update_option_menu
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Definition: AW_option_toggle.cxx:268
GB_push_transaction
GB_ERROR GB_push_transaction(GBDATA *gbd)
Definition: arbdb.cxx:2494
AW_awar::toggle_toggle
GB_ERROR toggle_toggle()
Definition: AW_awar.cxx:573
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Definition: NT_cb.cxx:30
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Definition: AW_preset.cxx:1115
NT_exit_now_restart_if
void NT_exit_now_restart_if(AW_root *aw_root, int exitcode, const char *restart_ntree_args)
Definition: NT_extern.cxx:351
EDIT_YSIZE
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Definition: arb_strarray.h:86
TREE_canvas_registry
Definition: NT_extern.cxx:895
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Definition: adhash.cxx:28
NT_create_sort_tree_by_other_tree_window
AW_window * NT_create_sort_tree_by_other_tree_window(AW_root *aw_root, TREE_canvas *ntw)
Definition: ad_trees.cxx:1088
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NT_createMergeSimilarSpeciesWindow
AW_window * NT_createMergeSimilarSpeciesWindow(AW_root *aw_root)
Definition: NT_concatenate.cxx:753
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Definition: aw_awar.hxx:53
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Definition: input_mask.cxx:2446
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Definition: TreeAwars.cxx:208
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Definition: saicalc.cxx:1138
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#define AWAR_MARKED_SPECIES_COUNTER
Definition: NT_extern.cxx:76
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AW_awar * add_callback(const RootCallback &cb)
Definition: AW_awar.cxx:231
UNFIXED
struct Unfixed_cb_parameter * UNFIXED
Definition: cb_base.h:15
EXPORT_SPACE_PADDED_RIGHT_ALIGNED
Definition: NT_extern.cxx:88
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Definition: AW_select.cxx:380
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void NT_start_editor_on_tree(AW_window *, int use_species_aside, TREE_canvas *ntw)
Definition: NT_edconf.cxx:468
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Definition: AW_names_admin.cxx:90
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static AW_window * create_mark_by_refentries_window(AW_root *awr, GBDATA *gbmain)
Definition: NT_extern.cxx:834
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Definition: NT_extern.cxx:629
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Definition: TreeDisplay.cxx:2265
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GB_UNDO_TYPE
Definition: arbdb.h:107
GDE_init
GB_ERROR GDE_init(AW_root *aw_root, AW_default aw_def, GBDATA *gb_main, GDE_get_sequences_cb get_sequences, GDE_format_alignment_cb format_ali, gde_window_type window_type)
Definition: GDE.cxx:489
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void GB_change_my_security(GBDATA *gbd, int level)
Definition: arbdb.cxx:1627
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AW_window * NT_create_syncroot_window(AW_root *awr, GBDATA *gb_main)
Definition: NT_syncroot.cxx:220
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const char * read_char_pntr() const
Definition: AW_awar.cxx:168
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Definition: AW_help.cxx:32
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bool is_performing_delayed_exit() const
Definition: MacroExitor.hxx:176
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static void merge_from_cb(AW_window *aww, AW_CL cl_awarNamePtr)
Definition: NT_extern.cxx:860
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Definition: TreeDisplay.hxx:572
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int create_mode(const char *pixmap, const char *help_text_, AW_active mask, const WindowCallback &cb)
Definition: AW_window.cxx:2980
GB_optimize
GB_ERROR GB_optimize(GBDATA *gb_main)
Definition: adoptimize.cxx:2556
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AW_window * NT_create_resort_window(AW_root *awr)
Definition: NT_sort.cxx:210
NT_create_select_alignment_window
AW_window * NT_create_select_alignment_window(AW_root *awr)
Definition: NT_cb.cxx:122
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AW_root::SINGLETON
static AW_root * SINGLETON
Definition: aw_root.hxx:102
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Definition: AW_window.cxx:1676
GDE_load_menu
void GDE_load_menu(AW_window *awm, AW_active, const char *menulabel)
Definition: GDE.cxx:436
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Definition: aw_window.hxx:106
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Definition: insdel.cxx:1439
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Definition: NT_extern.cxx:94
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Definition: NT_group_search.cxx:870
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Definition: canio.cxx:863
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Definition: ad_trees.cxx:796
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Definition: aw_awar_defs.hxx:55
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Definition: TreeCallbacks.cxx:498
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Definition: GEN_map.cxx:1482
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Definition: NT_ins_col.cxx:135
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GBDATA * get_gb_tree() const
Definition: ARB_Tree.hxx:82
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size_t get_self_awar_content_length() const OVERRIDE
Definition: NT_extern.cxx:707
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Definition: NT_extern.cxx:727
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#define AWAR_SAI_GLOBAL
Definition: aw_awar_defs.hxx:49
SPLIT_KEEPEMPTY
Definition: arb_strarray.h:218
DBItemSet
std::set< GBDATA * > DBItemSet
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NT_create_sai_from_pfold
void NT_create_sai_from_pfold(AW_window *aww)
Definition: ad_spec.cxx:126
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AW_window * create_refentries_window(AW_root *aw_root, ReferringEntriesHandler *reh, const char *window_id, const char *title, const char *help, client_area_builder build_client_area, const char *action, referred_item_handler action_cb)
Definition: refentries.cxx:253
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AW_root * get_root() const
Definition: TreeDisplay.hxx:504
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AW_window * NT_create_compareTopologies_window(AW_root *root)
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#define AWAR_DB_PATH
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void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global)
Definition: probe_design.cxx:1236
awt_item_type_selector
Definition: input_mask.hxx:50
create_nds_export_window
static AW_window * create_nds_export_window(AW_root *root)
Definition: NT_extern.cxx:192
SmartPtr
Generic smart pointer.
Definition: smartptr.h:149
AWT_create_www_window
AW_window * AWT_create_www_window(AW_root *aw_root, GBDATA *gb_main)
Definition: www.cxx:193
group
static int group[MAXN+1]
Definition: ClustalV.cxx:65
AW_save_properties
void AW_save_properties(AW_window *aw)
Definition: AW_preset.cxx:1457
AW_awar::update
void update()
Definition: AW_awar.cxx:390
aw_file.hxx
AW_selection_list
Definition: aw_select.hxx:58
MAX_NT_WINDOWS
#define MAX_NT_WINDOWS
Definition: NT_local.h:32
NT_MacroExitor::NT_MacroExitor
NT_MacroExitor(AW_root *aw_root_, int exitcode_, const char *restart_ntree_args_)
Definition: NT_extern.cxx:382
NT_create_dna_2_pro_window
AW_window * NT_create_dna_2_pro_window(AW_root *root)
Definition: ad_transpro.cxx:72
create_export_nds_awars
static void create_export_nds_awars(AW_root *awr, AW_default def)
Definition: NT_extern.cxx:227
st_window.hxx
GBT_write_tree
GB_ERROR GBT_write_tree(GBDATA *gb_main, const char *tree_name, TreeNode *tree)
Definition: adtree.cxx:523
AWM_ALL
Definition: aw_window.hxx:181
create_insertDeleteColumn_window
AW_window * create_insertDeleteColumn_window(AW_root *root)
Definition: NT_ins_col.cxx:201
AW_window::create_menu
void create_menu(const char *name, const char *mnemonic, AW_active mask=AWM_ALL)
Definition: AW_window.cxx:459
mark_referred_species
static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet &referred)
Definition: NT_extern.cxx:823
AWAR_NTREE_MAIN_WINDOW_COUNT
#define AWAR_NTREE_MAIN_WINDOW_COUNT
Definition: NT_local.h:29
AW_create_gc_window
AW_window * AW_create_gc_window(AW_root *aw_root, AW_gc_manager *gcman)
Definition: AW_preset.cxx:1378
AW_window::help_text
void help_text(const char *id)
Definition: AW_window.cxx:125
AW_awar::touch
void touch()
Definition: AW_awar.cxx:207
ARB_ERROR
Definition: arb_error.h:99
NT_rerepair_DB
void NT_rerepair_DB(AW_window *, GBDATA *gb_main)
Definition: NT_dbrepair.cxx:1040
AP_tree::mark_duplicates
void mark_duplicates()
Definition: AP_Tree.cxx:1530
NT_start_if
void NT_start_if(const char *arb_ntree_args)
Definition: NT_extern.cxx:343
NT_jump_cb
void NT_jump_cb(UNFIXED, TREE_canvas *ntw, AP_tree_jump_type jumpType)
Definition: TreeCallbacks.cxx:694
NT_create_alignment_admin_window
AW_window * NT_create_alignment_admin_window(AW_root *root, AW_window *aw_popmedown)
Definition: NT_cb.cxx:112
error
static void error(const char *msg)
Definition: mkptypes.cxx:96
TREE_canvas_registry::get_canvas
TREE_canvas * get_canvas(int idx) const
Definition: NT_extern.cxx:920
AW_window_menu_modes::init
void init(AW_root *root, const char *wid, const char *windowname, int width, int height)
Definition: AW_window.cxx:2400
AP_create_consensus_var
void AP_create_consensus_var(AW_root *aw_root, AW_default aw_def)
Definition: AP_consensus.cxx:248
Group::get_name
const char * get_name() const
Definition: Group.hxx:56
AW_create_fileselection_awars
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
NDS_Type
NDS_Type
Definition: nds.h:35
NT_create_searchManuallyNames_window
AW_window * NT_create_searchManuallyNames_window(AW_root *aw_root)
Definition: NT_validManual.cxx:154
fputc
fputc('\n', stderr)
AW_preset_window
AW_window * AW_preset_window(AW_root *root)
Definition: AW_preset.cxx:1925
GBT_next_marked_species
GBDATA * GBT_next_marked_species(GBDATA *gb_species)
Definition: aditem.cxx:116
AP_tree::relink_tree
void relink_tree(GBDATA *gb_main, void(*relinker)(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash), GB_HASH *organism_hash)
Definition: AP_Tree.cxx:1575
AWAR_TREE
#define AWAR_TREE
Definition: aw_awar_defs.hxx:10
AWAR_DBBASE
#define AWAR_DBBASE
Definition: aw_awar_defs.hxx:4
AW_ADVICE_TOGGLE_AND_HELP
Definition: aw_advice.hxx:31
AW_console_cb
void AW_console_cb(AW_window *)
Definition: aw_system.hxx:25
AW_window::insert_help_topic
void insert_help_topic(const char *labeli, const char *mnemonic, const char *helpText, AW_active mask, const WindowCallback &cb)
Definition: AW_window.cxx:556
AWT_graphic_tree::deselect_group
void deselect_group()
Definition: TreeDisplay.hxx:594
AWTI_cleanup_importer
void AWTI_cleanup_importer(AW_root *awr)
Definition: AWTI_import.cxx:1415
awt_create_aww_vars
void awt_create_aww_vars(AW_root *aw_root, AW_default aw_def)
Definition: www.cxx:53
NT_create_realign_dna_window
AW_window * NT_create_realign_dna_window(AW_root *root)
Definition: ad_transpro.cxx:180
NT_count_different_chars
void NT_count_different_chars(AW_window *, GBDATA *gb_main)
Definition: ad_spec.cxx:29
GB_read_clients
long GB_read_clients(GBDATA *gbd)
Definition: adcomm.cxx:1682
NT_import_sequences
void NT_import_sequences(AW_window *aww, TREE_canvas *ntw)
Definition: NT_import.cxx:47
seq_quality.h
AWAR_SPECIES_NAME
#define AWAR_SPECIES_NAME
Definition: aw_awar_defs.hxx:41
DBItemSetIter
DBItemSet::const_iterator DBItemSetIter
Definition: dbitem_set.h:23
TREE_canvas
Definition: TreeDisplay.hxx:723
AWAR_AWM_MASK
#define AWAR_AWM_MASK
Definition: aw_awar_defs.hxx:58
AWAR_SAI_NAME
#define AWAR_SAI_NAME
Definition: aw_awar_defs.hxx:48
popup_new_main_window
static AW_window * popup_new_main_window(AW_root *awr, int clone, TREE_canvas **result_ntw)
Definition: NT_extern.cxx:1061
AWAR_DB_COMPRESSION
#define AWAR_DB_COMPRESSION
Definition: NT_extern.cxx:460
AWAR_INFO_BUTTON_TEXT
#define AWAR_INFO_BUTTON_TEXT
Definition: aw_awar_defs.hxx:42
nt_create_all_awars
static void nt_create_all_awars(AW_root *awr)
Definition: NT_extern.cxx:250
AWT_popup_tree_export_window
void AWT_popup_tree_export_window(AW_window *parent_win, AWT_canvas *scr)
Definition: canio.cxx:765
AWT_graphic_tree::get_tree_style
AP_tree_display_style get_tree_style() const
Definition: TreeDisplay.hxx:553
AWAR_SECURITY_LEVEL
#define AWAR_SECURITY_LEVEL
Definition: aw_awar_defs.hxx:14
AW_awar::read_string
char * read_string() const
Definition: AW_awar.cxx:198
RootAsWindowCallback::simple
static WindowCallback simple(void(*root_cb)(AW_root *, T), T t)
Definition: rootAsWin.h:47
AW_root::awar
AW_awar * awar(const char *awar)
Definition: AW_root.cxx:606
GB_pop_transaction
GB_ERROR GB_pop_transaction(GBDATA *gbd)
Definition: arbdb.cxx:2524
AW_window::insert_sub_menu
void insert_sub_menu(const char *name, const char *mnemonic, AW_active mask=AWM_ALL)
Definition: AW_window.cxx:632
NT_create_trackAliChanges_Awars
void NT_create_trackAliChanges_Awars(AW_root *root, AW_default properties)
Definition: NT_trackAliChanges.cxx:191
GB_save_quick_as
GB_ERROR GB_save_quick_as(GBDATA *gbd, const char *path)
Definition: ad_save_load.cxx:1511
NT_resort_data_by_phylogeny
void NT_resort_data_by_phylogeny(AW_window *, TREE_canvas *ntw)
Definition: NT_sort.cxx:168
NT_infomode_cb
static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode)
Definition: NT_extern.cxx:624
NT_set_tree_style
void NT_set_tree_style(UNFIXED, TREE_canvas *ntw, AP_tree_display_style style)
Definition: TreeCallbacks.cxx:554
awt_create_TREE_selection_list
AW_DB_selection * awt_create_TREE_selection_list(GBDATA *gb_main, AW_window *aws, const char *varname)
Definition: sel_boxes.cxx:225
AW_refresh_fileselection
void AW_refresh_fileselection(AW_root *awr, const char *awar_prefix)
Definition: AW_file.cxx:944
awm
static AW_window_menu_modes_opengl * awm
Definition: RNA3D_Interface.cxx:26
GB_print_debug_information
void GB_print_debug_information(struct Unfixed_cb_parameter *, GBDATA *gb_main)
Definition: arbdb.cxx:2814
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selectedSpeciesChanged_cb
static void selectedSpeciesChanged_cb(AW_root *awr)
Definition: NT_extern.cxx:232
db_query.h
ad_trees.h
ARB_system_in_console_cb
void ARB_system_in_console_cb(AW_window *, const char *command, const XCmdType *exectype)
Definition: xcmd.cxx:183
AWAR_EXPORT_NDS_SEPARATOR
#define AWAR_EXPORT_NDS_SEPARATOR
Definition: NT_extern.cxx:75
GBT_count_marked_species
long GBT_count_marked_species(GBDATA *gb_main)
Definition: aditem.cxx:372
FINAL_TYPE::nt_item_type_species_selector
nt_item_type_species_selector()
Definition: NT_extern.cxx:701
TREE_canvas::get_index
int get_index() const
Definition: TreeDisplay.hxx:745
NT_insert_mark_submenus
void NT_insert_mark_submenus(AW_window_menu_modes *awm, TREE_canvas *ntw, int insert_as_submenu)
Definition: TreeCallbacks.cxx:403
AW_window::insert_default_option
void insert_default_option(AW_label choice_label, const char *mnemonic, const char *var_value, const char *name_of_color=NULp)
Definition: AW_option_toggle.cxx:261
AWT_initialize_input_mask
GB_ERROR AWT_initialize_input_mask(AW_root *root, GBDATA *gb_main, const awt_item_type_selector *sel, const char *internal_mask_name, bool local)
Definition: input_mask.cxx:2014
nt_assert
#define nt_assert(cond)
Definition: NT_local.h:27
AWT_graphic_tree
Definition: TreeDisplay.hxx:361
NT_create_splitAlignment_window
AW_window * NT_create_splitAlignment_window(AW_root *awr)
Definition: NT_split_ali.cxx:549
NT_create_multifurcate_tree_awars
void NT_create_multifurcate_tree_awars(AW_root *aw_root, AW_default props)
Definition: ad_trees.cxx:1107
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SQ_create_seq_quality_window
AW_window * SQ_create_seq_quality_window(AW_root *aw_root, GBDATA *gb_main)
Definition: SQ_main.cxx:249
create_trees_var
void create_trees_var(AW_root *aw_root, AW_default aw_def)
Definition: ad_trees.cxx:203
NT_create_merge_from_window
static AW_window * NT_create_merge_from_window(AW_root *awr)
Definition: NT_extern.cxx:863
merge_into_cb
static void merge_into_cb(AW_window *aww, AW_CL cl_awarNamePtr)
Definition: NT_extern.cxx:861
GB_undo
GB_ERROR GB_undo(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT
Definition: adindex.cxx:755
NT_create_species_join_window
AW_window * NT_create_species_join_window(AW_root *root)
Definition: NT_join.cxx:143
group_awar_changed_cb
static void group_awar_changed_cb(AW_root *awr)
Definition: NT_extern.cxx:997
NT_suggestValidNames
void NT_suggestValidNames(AW_window *)
Definition: NT_validNames.cxx:162
AW_window::set_info_area_height
void set_info_area_height(int height)
Definition: AW_window.cxx:806
AWT_canvas::gfx
AWT_graphic * gfx
Definition: canvas.hxx:349
NT_create_colstat_2_gnuplot_window
AW_window * NT_create_colstat_2_gnuplot_window(AW_root *root)
Definition: ColumnStat_2_gnuplot.cxx:589
fputs
fputs(TRACE_PREFIX, stderr)
AWAR_AW_FOCUS_FOLLOWS_MOUSE
#define AWAR_AW_FOCUS_FOLLOWS_MOUSE
Definition: aw_global_awars.hxx:19
AWAR_TOPAREA_SAIS
#define AWAR_TOPAREA_SAIS
Definition: NT_local.h:30
aw_global_awars.hxx
NT_create_main_window
TREE_canvas * NT_create_main_window(AW_root *aw_root)
Definition: NT_extern.cxx:1798
QUERY::create_colorize_items_window
AW_window * create_colorize_items_window(AW_root *aw_root, GBDATA *gb_main, ItemSelector &sel)
Definition: db_query.cxx:1953
EDIT_XSIZE
#define EDIT_XSIZE
AWT_graphic_tree::get_selected_group
const Group & get_selected_group() const
Definition: TreeDisplay.hxx:597
AWT_canvas::set_mode
void set_mode(AWT_COMMAND_MODE mo)
Definition: canvas.hxx:392
AW_window::set_bottom_area_height
void set_bottom_area_height(int height)
Definition: AW_window.cxx:811
NT_undo_cb
static void NT_undo_cb(AW_window *, GB_UNDO_TYPE undo_type, TREE_canvas *ntw)
Definition: NT_extern.cxx:614
AW_root::awar_int
AW_awar * awar_int(const char *var_name, long default_value=0, AW_default default_file=AW_ROOT_DEFAULT)
Definition: AW_root.cxx:632
NT_resort_tree_cb
void NT_resort_tree_cb(UNFIXED, TREE_canvas *ntw, TreeOrder order)
Definition: TreeCallbacks.cxx:531
AWT_canvas::request_save_and_zoom_reset
void request_save_and_zoom_reset()
Definition: canvas.hxx:378
AW_window::auto_space
void auto_space(int xspace, int yspace)
Definition: AW_at.cxx:259
NT_group_search.h
FINAL_TYPE
xml element
Definition: aisc_commands.c:804
NT_activate_configMarkers_display
void NT_activate_configMarkers_display(TREE_canvas *ntw)
Definition: NT_edconf.cxx:240
GB_transaction::close
GB_ERROR close(GB_ERROR error)
Definition: arbdbpp.cxx:35
AW_help_entry_pressed
void AW_help_entry_pressed(AW_window *aww)
Definition: AW_root.cxx:38
GBK_singlequote
char * GBK_singlequote(const char *arg)
Definition: arb_msg.cxx:599
GB_write_flag
void GB_write_flag(GBDATA *gbd, long flag)
Definition: arbdb.cxx:2773
NDS_create_window
AW_window * NDS_create_window(AW_root *aw_root, GBDATA *gb_main)
Definition: nds.cxx:586
NT_justify_branch_lenghs
static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw)
Definition: NT_extern.cxx:641
AWAR_ERROR_MESSAGES
#define AWAR_ERROR_MESSAGES
Definition: aw_awar_defs.hxx:53
AW_CL
long AW_CL
Definition: cb.h:21
aw_awars.hxx
GEN_find_origin_organism
GBDATA * GEN_find_origin_organism(GBDATA *gb_pseudo, const GB_HASH *organism_hash)
Definition: adGene.cxx:643
FINAL_TYPE::get_self_awar
const char * get_self_awar() const OVERRIDE
Definition: NT_extern.cxx:704
NT_open_mask_window
static void NT_open_mask_window(AW_window *aww, int id, GBDATA *gb_main)
Definition: NT_extern.cxx:729
AWT_canvas::request_structure_update
void request_structure_update()
Definition: canvas.hxx:375
OVERRIDE
#define OVERRIDE
Definition: cxxforward.h:112
AWT_canvas::gc_manager
AW_gc_manager * gc_manager
Definition: canvas.hxx:351
NT_deleteValidNames
void NT_deleteValidNames(AW_window *)
Definition: NT_validNames.cxx:28
AP_create_con_expert_window
AW_window * AP_create_con_expert_window(AW_root *aw_root)
Definition: AP_consensus.cxx:289
GEN_create_first_map
AW_window * GEN_create_first_map(AW_root *aw_root, GBDATA *gb_main)
Definition: GEN_map.cxx:1584
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AW_popup_namesadmin_window
void AW_popup_namesadmin_window(AW_window *parent_win, GBDATA *gb_main)
Definition: AW_names_admin.cxx:95
AP_tree_display_style
AP_tree_display_style
Definition: TreeDisplay.hxx:87
AP_tree::justify_branch_lenghs
void justify_branch_lenghs(GBDATA *gb_main)
Definition: AP_Tree.cxx:1559
AWAR_DB_COMMENT
#define AWAR_DB_COMMENT
Definition: aw_awar_defs.hxx:19
NT_importValidNames
void NT_importValidNames(AW_window *)
Definition: NT_validNames.cxx:49
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void subtitle(const char *stitle)
Definition: arb_progress.h:321
CHANGE_KEY_PATH
#define CHANGE_KEY_PATH
Definition: arbdbt.h:87
GB_topSecurityLevel
Definition: arbdb.h:200
GB_textprint
GB_ERROR GB_textprint(const char *path) __ATTR__USERESULT
Definition: adsocket.cxx:364
GBK_dump_backtrace
void GBK_dump_backtrace(FILE *out, const char *message)
Definition: arb_msg.cxx:416
NT_create_merge_to_window
static AW_window * NT_create_merge_to_window(AW_root *awr)
Definition: NT_extern.cxx:871
SPECIES_get_selector
ItemSelector & SPECIES_get_selector()
Definition: species.cxx:140
NT_alltree_remove_leafs
static void NT_alltree_remove_leafs(AW_window *, GBT_TreeRemoveType mode, GBDATA *gb_main)
Definition: NT_extern.cxx:744
TREE_canvas_registry::get_count
int get_count() const
Definition: NT_extern.cxx:918
AW_rename.hxx
AW_window::close_sub_menu
void close_sub_menu()
Definition: AW_window.cxx:473
GBT_get_tree_names
void GBT_get_tree_names(ConstStrArray &names, GBDATA *gb_main, bool sorted)
Definition: adtree.cxx:1187
NT_save_quick_cb
static void NT_save_quick_cb(AW_window *aww)
Definition: NT_extern.cxx:426
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static AW_window * create_colorize_species_window(AW_root *aw_root)
Definition: NT_extern.cxx:738
AWAR_EXPORT_NDS
#define AWAR_EXPORT_NDS
Definition: NT_extern.cxx:74
GBT_compress_sequence_tree2
GB_ERROR GBT_compress_sequence_tree2(GBDATA *gbd, const char *tree_name, const char *ali_name) __ATTR__USERESULT
Definition: adseqcompr.cxx:889
TREE_create_settings_window
AW_window * TREE_create_settings_window(AW_root *aw_root)
Definition: TreeDisplay.cxx:4305
NT_createValidNamesAwars
void NT_createValidNamesAwars(AW_root *aw_root, AW_default aw_def)
Definition: NT_validManual.cxx:36
aw_message
void aw_message(const char *msg)
Definition: AW_status.cxx:1142
AW_window::create_option_menu
AW_option_menu_struct * create_option_menu(const char *awar_name)
Definition: AW_option_toggle.cxx:32
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Definition: aw_root.hxx:86
insert_macro_menu_entry
void insert_macro_menu_entry(AW_window *awm, bool prepend_separator)
Definition: macro_gui.cxx:233
AW_window::get_root
AW_root * get_root()
Definition: aw_window.hxx:362
EXPORT_COMMA_SEPARATED
Definition: NT_extern.cxx:91
AP_create_pos_var_pars_window
AW_window * AP_create_pos_var_pars_window(AW_root *root)
Definition: AP_pos_var_pars.cxx:48
nt_start_2nd_arb
static void nt_start_2nd_arb(AW_window *aww, bool quit)
Definition: NT_extern.cxx:406
GB_split_full_path
void GB_split_full_path(const char *fullpath, char **res_dir, char **res_fullname, char **res_name_only, char **res_suffix)
Definition: adsocket.cxx:1259
NT_createConcatenationWindow
AW_window * NT_createConcatenationWindow(AW_root *aw_root)
Definition: NT_concatenate.cxx:789
NULp
#define NULp
Definition: cxxforward.h:116
NT_global::gb_main
GBDATA * gb_main
Definition: NT_local.h:37
GBT_find_species
GBDATA * GBT_find_species(GBDATA *gb_main, const char *name)
Definition: aditem.cxx:139
GBT_create_organism_hash
GB_HASH * GBT_create_organism_hash(GBDATA *gb_main)
Definition: adhashtools.cxx:48
create_species_selection_button
void create_species_selection_button(AW_window *awm, WindowCallback wcb, const char *macro_id, const char *awarname_buttontext, GBDATA *gb_main)
Definition: selection_admin.cxx:863
NT_select_bottom_tree
void NT_select_bottom_tree(AW_window *aww, const char *awar_tree)
Definition: NT_cb.cxx:95
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Definition: arbdb.h:131
AWAR_NTREE_TITLE_MODE
#define AWAR_NTREE_TITLE_MODE
Definition: NT_extern.cxx:77
__ATTR__NORETURN
#define __ATTR__NORETURN
Definition: attributes.h:56
AWT_KEEP_MARKED
Definition: AP_Tree.hxx:45
RefEntries::create_refentries_awars
void create_refentries_awars(AW_root *aw_root, AW_default aw_def)
Definition: refentries.cxx:223
AW_awar::write_string
GB_ERROR write_string(const char *aw_string)
command
static char * command
Definition: arb_a2ps.c:319
NT_create_save_quick_as_window
static AW_window * NT_create_save_quick_as_window(AW_root *aw_root, const char *base_name)
Definition: NT_extern.cxx:483
GBT_split_string
void GBT_split_string(ConstStrArray &dest, const char *namelist, const char *separator, SplitMode mode)
Definition: arb_strarray.h:223
arb_strbuf.h
arb_spec.hxx
AW_window
Definition: aw_window.hxx:245
AW_window::sep______________
void sep______________()
Definition: AW_window.cxx:763
TREE_canvas_registry::instance
static TREE_canvas_registry & instance()
Definition: NT_extern.cxx:906
NT_scale_tree
void NT_scale_tree(UNFIXED, TREE_canvas *ntw)
Definition: TreeCallbacks.cxx:671
AW_window::local_id
const char * local_id(const char *id) const
Definition: AW_window.cxx:738
input_mask.hxx
GB_request_undo_type
GB_ERROR GB_request_undo_type(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT_TODO
Definition: adindex.cxx:721
NT_fill_canvas_selection_list
void NT_fill_canvas_selection_list(class AW_selection_list *sellst, TREE_canvas *to_skip)
Definition: NT_extern.cxx:949
ta
GB_transaction ta(gb_var)
AW_window::callback
void callback(const WindowCallback &cb)
Definition: AW_window.cxx:142
destroy
void destroy(TreeNode *that)
Definition: TreeNode.h:600
GB_read_char_pntr
GB_CSTR GB_read_char_pntr(GBDATA *gbd)
Definition: arbdb.cxx:904
AWAR_DB_TYPE
#define AWAR_DB_TYPE
Definition: NT_extern.cxx:459
AWAR_EXPERT
#define AWAR_EXPERT
Definition: aw_awar_defs.hxx:26
AW_window::get_at_yposition
int get_at_yposition() const
Definition: AW_at.cxx:305
NT_create_compare_taxonomy_window
AW_window * NT_create_compare_taxonomy_window(AW_root *aw_root, TREE_canvas *ntw)
Definition: NT_taxonomy.cxx:345
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GBDATA * gb_main
Definition: adname.cxx:32
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static void nt_run(const char *command)
Definition: NT_extern.cxx:333
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AW_awar * awar_string(const char *var_name, const char *default_value="", AW_default default_file=AW_ROOT_DEFAULT)
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Definition: MacroExitor.hxx:175
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Definition: probe_design.cxx:1775
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Definition: NT_trackAliChanges.cxx:196
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Definition: adGene.cxx:558
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Definition: NT_extern.cxx:660
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Definition: AP_Tree.hxx:210
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Definition: NT_shadeTree.cxx:147
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Definition: AW_at.cxx:119
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Definition: TreeDisplay.hxx:744
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Definition: TreeDisplay.cxx:3976
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~nt_item_type_species_selector() OVERRIDE
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Definition: aw_base.hxx:106
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Definition: arb_progress.h:332
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Definition: Group.hxx:20
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Definition: aw_system.hxx:24
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Definition: aw_msg.hxx:21
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Definition: arb_msg.cxx:194
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Definition: arb_spec.cxx:62
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NT_global GLOBAL
Definition: NT_main.cxx:47
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Definition: canvas.hxx:346
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Definition: NT_extern.cxx:677
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Definition: item_sel_list.cxx:118
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Definition: AW_button.cxx:448
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Definition: www.cxx:267
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#define UNCOVERED()
Definition: arb_assert.h:380
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Definition: NT_sort.cxx:200
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Definition: TreeCallbacks.cxx:887
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Definition: AW_awar.cxx:154
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Definition: f2c.h:154
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