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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 <www.hxx>
45 #include <TreeAwars.hxx>
46 #include <arb_spec.hxx>
47 
48 #include <aw_color_groups.hxx>
49 #include <aw_advice.hxx>
50 #include <aw_preset.hxx>
51 #include <aw_awars.hxx>
52 #include <aw_global_awars.hxx>
53 #include <aw_file.hxx>
54 #include <arb_progress.h>
55 #include <aw_select.hxx>
56 #include <aw_system.hxx>
57 #include <rootAsWin.h>
58 
59 #include <ad_cb.h>
60 
61 #include <arb_strbuf.h>
62 #include <arb_file.h>
63 #include <arb_version.h>
64 
65 #include <saicalc.h>
66 
67 #include <string>
68 
69 #if defined(DEVEL_RALF)
70 # define TRACE_GROUP_SELECTION
71 #endif
72 
73 #define AWAR_EXPORT_NDS "tmp/export_nds"
74 #define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/delimiter"
75 #define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species"
76 #define AWAR_NTREE_TITLE_MODE "tmp/title_mode"
77 
78 void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
79 
80 void create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
81 AW_window *create_insertDeleteColumn_window(AW_root *root);
82 AW_window *create_insertDeleteBySAI_window(AW_root *root, GBDATA *gb_main);
83 
84 AW_window *create_tree_window(AW_root *aw_root, AWT_graphic *awd);
85 
86 enum Export_Type {
87  EXPORT_SPACE_PADDED_RIGHT_ALIGNED = 1, // format info (using spaces). slow - uses one extra pass for column width detection.
88  EXPORT_SPACE_PADDED_LEFT_ALIGNED = 4, // dito, but left aligned
89  EXPORT_TAB_SEPARATED = 2, // format info (using 1 tab per column - for easy import into star-calc, excel, etc. )
90  EXPORT_COMMA_SEPARATED = 3, // like EXPORT_TAB_SEPARATED, but using commas
91 };
92 
93 static void nt_changesecurity(AW_root *aw_root) {
94  int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
95  GB_push_transaction(GLOBAL.gb_main);
96  GB_change_my_security(GLOBAL.gb_main, level); // changes user security
97  GB_pop_transaction(GLOBAL.gb_main);
98 }
99 
100 static void export_nds_cb(AW_window *aww, bool do_print) {
101  AW_root *aw_root = aww->get_root();
102  char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
103  FILE *out = fopen(name, "w");
104 
105  if (!out) {
106  aw_message("Error: Cannot open and write to file");
107  }
108  else {
109  GB_transaction ta(GLOBAL.gb_main);
110 
111  char *tree_name = aw_root->awar(AWAR_TREE)->read_string();
112  const Export_Type export_type = (Export_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
113  const NDS_Type nds_type = export_type == EXPORT_COMMA_SEPARATED ? NDS_OUTPUT_COMMA_SEPARATED : NDS_OUTPUT_TAB_SEPARATED;
114  const bool spacePadded = export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED || export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED;
115  const int passesNeeded = spacePadded ? 2 : 1;
116  NDS_Labeler labeler(nds_type);
117 
118  arb_progress progress("Exporting data using NDS", passesNeeded*GBT_count_marked_species(GLOBAL.gb_main));
119 
120  const size_t max_col = std::max(labeler.max_columns(GLOBAL.gb_main), 1L);
121  size_t col_max_len[max_col];
122 
123  const char *col_format = NULp;
124 
125  if (spacePadded) {
126  for (size_t i = 0; i<max_col; ++i) {
127  col_max_len[i] = 0;
128  }
129  if (export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED) {
130  col_format = "%*s";
131  }
132  else {
133  col_format = "%-*s";
134  }
135  }
136 
137  for (int pass = 1; pass<=passesNeeded; ++pass) {
138  for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
139  gb_species;
140  gb_species = GBT_next_marked_species(gb_species))
141  {
142  const char *label = labeler.speciesLabel(GLOBAL.gb_main, gb_species, NULp, tree_name);
143 
144  if (spacePadded) {
145  ConstStrArray parts;
146  GBT_split_string(parts, label, "\t", SPLIT_KEEPEMPTY);
147 
148  size_t col_count = parts.size();
149  nt_assert(col_count<=max_col);
150 
151  if (pass == 1) { // track maximum used width for all columns
152  for (size_t i = 0; i<col_count; ++i) {
153  col_max_len[i] = std::max(col_max_len[i], strlen(parts[i]));
154  }
155  }
156  else { // format according to tracked widths
157  for (size_t i = 0; i<col_count; ++i) {
158  if (i) fputc(' ', out);
159 
160  arb_assert(col_max_len[i]>0); // otherwise empty, unused column (might be ok, but might need different handling)
161  arb_assert(col_max_len[i]<=INT_MAX); // (protect cast below)
162 
163  if (export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED && i == (col_count-1)) { // left aligned and last column
164  fputs(parts[i], out);
165  }
166  else {
167  fprintf(out, col_format, int(col_max_len[i]), parts[i]);
168  }
169  }
170  fputc('\n', out);
171  }
172  }
173  else {
174  fprintf(out, "%s\n", label);
175  }
176  ++progress;
177  }
178  }
179 
180  AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
181  fclose(out);
182  if (do_print) {
183  GB_ERROR error = GB_textprint(name);
184  if (error) aw_message(error);
185  }
186  free(tree_name);
187  }
188  free(name);
189 }
190 
191 static AW_window *create_nds_export_window(AW_root *root) {
192  AW_window_simple *aws = new AW_window_simple;
193  aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
194  aws->load_xfig("sel_box_nds.fig");
195 
196  aws->callback(AW_POPDOWN);
197  aws->at("close");
198  aws->create_button("CLOSE", "CLOSE", "C");
199 
200  aws->callback(makeHelpCallback("arb_export_nds.hlp"));
201  aws->at("help");
202  aws->create_button("HELP", "HELP", "H");
203 
204  aws->at("save");
205  aws->callback(makeWindowCallback(export_nds_cb, false));
206  aws->create_button("SAVE", "SAVE", "S");
207 
208  aws->at("print");
209  aws->callback(makeWindowCallback(export_nds_cb, true));
210  aws->create_button("PRINT", "PRINT", "P");
211 
212  aws->at("toggle1");
213  aws->label("Column output");
214  aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR);
215  aws->insert_option ("Space padded (left aligned)", "S", EXPORT_SPACE_PADDED_LEFT_ALIGNED);
216  aws->insert_option ("Space padded (right aligned)", "r", EXPORT_SPACE_PADDED_RIGHT_ALIGNED);
217  aws->insert_default_option("TAB separated", "T", EXPORT_TAB_SEPARATED);
218  aws->insert_option ("Comma separated", "C", EXPORT_COMMA_SEPARATED);
219  aws->update_option_menu();
220 
221  AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS);
222 
223  return aws;
224 }
225 
226 static void create_export_nds_awars(AW_root *awr, AW_default def) {
227  AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds");
228  awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, EXPORT_TAB_SEPARATED, def);
229 }
230 
231 static void selectedSpeciesChanged_cb(AW_root *awr) {
232  const char *value = awr->awar(AWAR_SPECIES_NAME)->read_char_pntr();
233  awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
234  if (value[0]) {
235  awr->awar(AWAR_GROUP)->write_pointer(NULp); // deselect group when species gets selected
236 #if defined(TRACE_GROUP_SELECTION)
237  fputs("clear AWAR_GROUP (because species selected)\n", stderr);
238 #endif
239  }
240 }
241 
242 static void expert_mode_changed_cb(AW_root *aw_root) {
243  aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
244 }
245 
246 static void NT_toggle_expert_mode(AW_window *aww) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
247 static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
248 
249 static void nt_create_all_awars(AW_root *awr) {
250  // creates awars for all modules reachable from ARB_NT main window
251 
252  awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT);
253  if (GB_read_clients(GLOBAL.gb_main)>=0) {
254  awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
255  }
256  else {
257  awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT);
258  }
259 
260  awr->awar_string(AWAR_TOPAREA_SAIS, "ECOLI;HELIX;HELIX_NR", AW_ROOT_DEFAULT);
261 
262  awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main);
263  awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main);
264  awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main);
265  awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown", 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().
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 static void NT_update_marked_counter(GBDATA*, AW_window* aww) {
746  long count = GBT_count_marked_species(GLOBAL.gb_main);
747  const char *buffer = count ? GBS_global_string("%li marked", count) : "";
748  AW_awar *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
749  char *oldval = counter->read_string();
750  if (strcmp(oldval, buffer)) {
751  counter->write_string(buffer);
752  aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
753  }
754  free(oldval);
755 }
756 
757 // --------------------------------------------------------------------------------------------------
758 
759 static void NT_alltree_remove_leafs(AW_window *, GBT_TreeRemoveType mode, GBDATA *gb_main) {
760  GB_ERROR error = NULp;
761  GB_transaction ta(gb_main);
762 
763  ConstStrArray tree_names;
764  GBT_get_tree_names(tree_names, gb_main, false);
765 
766  if (!tree_names.empty()) {
767  long treeCount = tree_names.size();
768 
769  const char *whats_removed = NULp;
770  switch (mode) {
771  case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
772  case GBT_REMOVE_MARKED: whats_removed = "marked"; break;
773  default: nt_assert(0); break;
774  }
775 
776  const char *task = GBS_global_string("Deleting %s from %li trees", whats_removed, treeCount);
777 
778  arb_progress progress(task, treeCount);
779  GB_HASH *species_hash = GBT_create_species_hash(gb_main);
780 
781  int modified = 0;
782 
783  for (int t = 0; t<treeCount && !error; t++) {
784  progress.subtitle(tree_names[t]);
785  TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
786  if (!tree) {
787  aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
788  }
789  else {
790  int removed = 0;
791  int groups_removed = 0;
792 
793  tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
794 
795  nt_assert(removed >= groups_removed);
796 
797  if (!tree) {
798  aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
799  }
800  else {
801  if (removed>0) {
802  error = GBT_write_tree(gb_main, tree_names[t], tree);
803  if (error) {
804  aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
805  }
806  else {
807  if (groups_removed>0) {
808  aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
809  }
810  else {
811  aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
812  }
813  modified++;
814  }
815  }
816  UNCOVERED();
817  destroy(tree);
818  }
819  }
820  progress.inc_and_check_user_abort(error);
821  }
822 
823  if (modified) {
824  aw_message(GBS_global_string("Changed %i of %li trees.", modified, treeCount));
825  }
826  else {
827  aw_message("No tree modified");
828  }
829 
830  GBS_free_hash(species_hash);
831  }
832 
833  aw_message_if(ta.close(error));
834 }
835 
836 TreeNode *NT_get_tree_root_of_canvas(TREE_canvas *ntw) {
837  AWT_graphic_tree *tree = AWT_TREE(ntw);
838  if (tree) {
839  AP_tree *root = tree->get_root_node();
840  if (root) return root;
841  }
842  return NULp;
843 }
844 
845 // --------------------------------------------------------------------------------------------------
846 
847 static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
848  GB_transaction ta(gb_main);
849  GBT_mark_all(gb_main, 0);
850 
851  DBItemSetIter end = referred.end();
852  for (DBItemSetIter s = referred.begin(); s != end; ++s) {
853  GB_write_flag(*s, 1);
854  }
855  return ARB_ERROR();
856 }
857 
858 static AW_window *create_mark_by_refentries_window(AW_root *awr, GBDATA *gbmain) {
859  static AW_window *aws = NULp;
860  if (!aws) {
861  static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
862  aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULp, "Mark referenced", mark_referred_species);
863  }
864  return aws;
865 }
866 
867 // --------------------------------------------------------------------------------------------------
868 
869 static void merge_from_to(AW_root *awr, const char *db_awar_name, bool merge_to) {
870  const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
871  char *quotedDB = GBK_singlequote(db_name);
872 
873  AW_system(
874  GBS_global_string(
875  merge_to
876  ? "arb_ntree : %s &"
877  : "arb_ntree %s : &",
878  quotedDB)
879  );
880 
881  free(quotedDB);
882 }
883 
884 static void merge_from_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, false); }
885 static void merge_into_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, true); }
886 
887 static AW_window *NT_create_merge_from_window(AW_root *awr) {
888  static char *awar_name = NULp; // do not free, bound to callback
889  AW_window *aw_from =
890  awt_create_load_box(awr, "Merge data from", "other ARB database",
891  ".", ".arb", &awar_name,
892  makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
893  return aw_from;
894 }
895 static AW_window *NT_create_merge_to_window(AW_root *awr) {
896  static char *awar_name = NULp; // do not free, bound to callback
897  AW_window *aw_to =
898  awt_create_load_box(awr, "Merge data to", "other ARB database",
899  ".", ".arb", &awar_name,
900  makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
901  makeWindowCallback(AW_POPDOWN), NULp);
902  return aw_to;
903 }
904 
905 // --------------------------------------------------------------------------------------------------
906 
907 static void update_main_window_title(AW_root* awr, AW_window_menu_modes* aww, int clone) {
908  const char* filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
909  if (clone) {
910  aww->set_window_title(GBS_global_string("%s - ARB (%i)", filename, clone));
911  }
912  else {
913  aww->set_window_title(GBS_global_string("%s - ARB", filename));
914  }
915 }
916 
917 static void canvas_tree_awar_changed_cb(AW_awar *, bool, TREE_canvas *ntw) {
918  NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
919  AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
920  TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_TREE);
921 }
922 
923 class TREE_canvas_registry {
924  int count;
925  TREE_canvas *canvas[MAX_NT_WINDOWS];
926 
927  static TREE_canvas_registry *SINGLETON;
928 
929  TREE_canvas_registry() : count(0) {
930  AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
931  }
932 
933 public:
934  static TREE_canvas_registry& instance() {
935  if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
936  return *SINGLETON;
937  }
938 
939  void register_canvas(TREE_canvas *ntw) {
940  nt_assert(count<MAX_NT_WINDOWS);
941  nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
942  canvas[count++] = ntw;
943  ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
944  }
945 
946  int get_count() const { return count; }
947 
948  TREE_canvas *get_canvas(int idx) const {
949  if (idx<0 || idx>=count) return NULp;
950  return canvas[idx];
951  }
952 };
953 
954 TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULp;
955 
956 TREE_canvas *NT_get_canvas_by_index(int idx) {
958  nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
959  return TREE_canvas_registry::instance().get_canvas(idx);
960 }
961 
962 #if defined(TRACE_GROUP_SELECTION)
963 static TREE_canvas *find_canvas_showing(AWT_graphic_tree *agt) {
964  // look for (registered) canvas showing given AWT_graphic_tree
965  // returns NULp if none found
966  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
967 
968  int maxIdx = reg.get_count();
969  for (int32_t i = 0; i<maxIdx; ++i) {
970  TREE_canvas *ntw = reg.get_canvas(i);
971  if (ntw->gfx == agt) return ntw;
972  }
973  return NULp;
974 }
975 #endif
976 
977 void NT_fill_canvas_selection_list(class AW_selection_list *sellst, TREE_canvas *to_skip) {
980  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
981 
982  int maxIdx = reg.get_count();
983  for (int32_t i = 0; i<maxIdx; ++i) {
984  TREE_canvas *ntw = reg.get_canvas(i);
985  if (ntw && ntw != to_skip) {
986  nt_assert(ntw->get_awar_tree());
987  const char *treename = ntw->get_awar_tree()->read_char_pntr();
988  const char *description = i
989  ? GBS_global_string("ARB (%i): %s", i, treename)
990  : GBS_global_string("ARB main: %s", treename);
991  sellst->insert(description, i);
992  }
993  }
994 }
995 
996 // ----------------------------------
997 // group-selection handlers
998 
999 void NT_deselect_group(AW_root *awr) {
1000  awr->awar(AWAR_GROUP)->write_pointer(NULp);
1001 }
1002 
1003 static bool track_group_selection_by_canvas = true;
1004 
1005 static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) {
1006  const Group& group = gfx->get_selected_group();
1007 
1008 #if defined(TRACE_GROUP_SELECTION)
1009  fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track");
1010  TREE_canvas *ntw = find_canvas_showing(gfx);
1011  if (group.is_valid()) {
1012  fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name());
1013  }
1014  else {
1015  fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index());
1016  }
1017 #endif
1018 
1019  if (track_group_selection_by_canvas) {
1020  // set group-awar:
1021  gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULp if !group.is_valid()
1022  }
1023 }
1024 
1025 static void group_awar_changed_cb(AW_root *awr) {
1026  AW_awar *awar_group = awr->awar(AWAR_GROUP);
1027  GBDATA *gb_wanted_group = awar_group->read_pointer();
1028 
1029  GBDATA *gb_wanted_tree = NULp;
1030  {
1031  if (gb_wanted_group) {
1032  GB_transaction ta(gb_wanted_group);
1033  gb_wanted_tree = GB_get_father(gb_wanted_group);
1034  awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected
1035 #if defined(TRACE_GROUP_SELECTION)
1036  fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr);
1037 #endif
1038  }
1039 #if defined(TRACE_GROUP_SELECTION)
1040  const char *group_name = NULp;
1041  if (gb_wanted_group) {
1042  GB_transaction ta(gb_wanted_group);
1043  GBDATA *gb_name = GB_entry(gb_wanted_group, "group_name");
1044  if (gb_name) group_name = GB_read_char_pntr(gb_name);
1045  }
1046  fprintf(stderr, "group awar changed to %p", gb_wanted_group);
1047  if (group_name) fprintf(stderr, " (='%s')", group_name);
1048  fputc('\n', stderr);
1049 #endif
1050  }
1051 
1052  LocallyModify<bool> ignore_group_selection_by_canvas(track_group_selection_by_canvas, false);
1053 
1054  {
1055  const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1056 
1057  int maxIdx = reg.get_count();
1058  for (int32_t i = 0; i<maxIdx; ++i) {
1059  TREE_canvas *ntw = reg.get_canvas(i);
1060  AWT_graphic_tree *agt = AWT_TREE(ntw);
1061  const Group& curr_group = agt->get_selected_group();
1062 
1063  GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree();
1064  if (gb_curr_tree == gb_wanted_tree) {
1065  AWT_auto_refresh allowed_on(ntw);
1066  if (!curr_group.is_valid() || // no group selected
1067  curr_group.get_group_data() != gb_wanted_group) // wrong group selected
1068  {
1069  agt->select_group(gb_wanted_group);
1070  ntw->request_refresh();
1071  }
1072  // perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group)
1073  TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_GROUP);
1074  }
1075  else {
1076  if (curr_group.is_valid()) {
1077  AWT_auto_refresh allowed_on(ntw);
1078  agt->deselect_group();
1079  ntw->request_refresh();
1080  }
1081  }
1082  }
1083  }
1084 }
1085 
1086 // ----------------------------
1087 // create main window
1088 
1089 static AW_window *popup_new_main_window(AW_root *awr, int clone, TREE_canvas **result_ntw) {
1095  GB_push_transaction(GLOBAL.gb_main);
1096 
1097  char window_title[256];
1098  const char *awar_tree = NULp;
1099 
1100  if (clone) {
1101  awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
1102  sprintf(window_title, "ARB_NT_%i", clone);
1103  }
1104  else {
1105  awar_tree = AWAR_TREE;
1106  sprintf(window_title, "ARB_NT");
1107  }
1108  AW_window_menu_modes *awm = new AW_window_menu_modes;
1109  awm->init(awr, window_title, window_title, 0, 0);
1110 
1111  awr->awar(AWAR_DB_NAME)
1112  ->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1113  ->update();
1114 
1115  awm->button_length(5);
1116 
1117  if (!clone) AW_init_color_group_defaults("arb_ntree");
1118 
1119  AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1120 
1121  if (!clone) { // while creating initial window
1122  AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb));
1123  awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb);
1124  }
1125 
1126  TREE_canvas *ntw;
1127  {
1128  AW_awar *tree_awar = awr->awar_string(awar_tree);
1129  {
1130  AP_tree_display_style prev_style = tree->get_tree_style();
1131  tree->set_tree_style(AP_LIST_SIMPLE, NULp); // avoid NDS warnings during startup
1132 
1133  ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1134  tree->set_tree_style(prev_style, ntw);
1135  ntw->set_mode(AWT_MODE_SELECT);
1136  }
1137 
1138  if (result_ntw) *result_ntw = ntw;
1139 
1140  {
1141  const char *tree_name = tree_awar->read_char_pntr();
1142  const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1143 
1144  if (existing_tree_name) {
1145  tree_awar->write_string(existing_tree_name);
1146  NT_reload_tree_event(awr, ntw, true); // load first tree
1147  }
1148  else {
1149  AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, NULp, "no_tree.hlp");
1150  tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list
1151  }
1152 
1153  TREE_canvas_registry::instance().register_canvas(ntw);
1154  AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1155  }
1156  }
1157 
1158  TREE_install_update_callbacks(ntw);
1159 
1160  bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1161 
1162  WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1163 
1164  // --------------
1165  // File
1166 
1167 #if defined(DEBUG)
1168  AWT_create_debug_menu(awm);
1169 #endif // DEBUG
1170 
1171  bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1172 
1173  if (clone) {
1174  awm->create_menu("File", "F", AWM_ALL);
1175  if (allow_new_window) {
1176  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));
1177  }
1178  awm->insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN);
1179  }
1180  else {
1181 #if defined(DEBUG)
1182  // add more to debug-menu
1183  awm->sep______________();
1184  awm->insert_menu_topic("fix_db", "Fix database", "F", NULp, AWM_ALL, NT_fix_database);
1185  awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", NULp, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1186  awm->insert_menu_topic("test_compr", "Test compression", "T", NULp, AWM_ALL, makeWindowCallback(GBT_compression_test, GLOBAL.gb_main));
1187 #endif // DEBUG
1188 
1189  awm->create_menu("File", "F", AWM_ALL);
1190  {
1191  // keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1192  awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, NT_save_quick_cb);
1193  awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1194  if (allow_new_window) {
1195  awm->sep______________();
1196  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));
1197  }
1198  awm->sep______________();
1199  awm->insert_menu_topic("optimize_db", "Optimize database compression", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window);
1200  awm->sep______________();
1201 
1202  awm->insert_sub_menu("Import", "I");
1203  {
1204  awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1205  awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1206  GDE_load_menu(awm, AWM_EXP, "Import");
1207  }
1208  awm->close_sub_menu();
1209 
1210  awm->insert_sub_menu("Export", "E");
1211  {
1212  awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1213  awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1214  GDE_load_menu(awm, AWM_ALL, "Export");
1215  awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window);
1216  }
1217  awm->close_sub_menu();
1218  awm->sep______________();
1219 
1220  insert_macro_menu_entry(awm, false);
1221 
1222  awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1223  {
1224  awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp"));
1225  awm->insert_menu_topic("bug_report", "Report bug", "b", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1226  awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1227  }
1228  awm->close_sub_menu();
1229  awm->sep______________();
1230 
1231  awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1232  awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1233  awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_confirm_exit, EXIT_SUCCESS));
1234  }
1235 
1236  // -----------------
1237  // Species
1238 
1239  awm->create_menu("Species", "c", AWM_ALL);
1240  {
1241  awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1242  awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb);
1243 
1244  awm->sep______________();
1245 
1246  NT_insert_mark_submenus(awm, ntw, 1);
1247  awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1248  awm->insert_menu_topic("species_colors", "Colors ...", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window);
1249  awm->insert_menu_topic("selection_admin", "Selections ...", "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1250 
1251  awm->sep______________();
1252 
1253  awm->insert_sub_menu("Database fields admin", "f");
1254  DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1255  awm->close_sub_menu();
1256  NT_create_mask_submenu(awm);
1257 
1258  awm->sep______________();
1259 
1260  awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1261 
1262  awm->insert_sub_menu("Sort Species", "s");
1263  {
1264  awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window);
1265  awm->insert_menu_topic("$sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1266  }
1267  awm->close_sub_menu();
1268 
1269  awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1270  {
1271  awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1272  awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "species_join.hlp", AWM_EXP, NT_create_species_join_window);
1273  }
1274  awm->close_sub_menu();
1275 
1276  awm->sep______________();
1277 
1278  awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1279 
1280  awm->sep______________();
1281 
1282  awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1283 
1284  awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1285  {
1286  awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames);
1287  awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames);
1288  awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1289  awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window);
1290  }
1291  awm->close_sub_menu();
1292  }
1293 
1294  // ----------------------------
1295  // Genes + Experiment
1296 
1297  if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1298 
1299  // ------------------
1300  // Sequence
1301 
1302  awm->create_menu("Sequence", "S", AWM_ALL);
1303  {
1304  awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)NULp));
1305  awm->insert_sub_menu("Insert/delete", "I");
1306  {
1307  awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window);
1308  awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main));
1309  }
1310  awm->close_sub_menu();
1311  awm->sep______________();
1312 
1313  awm->insert_sub_menu("Edit Sequences", "E");
1314  {
1315  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));
1316  awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1317  awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1318  }
1319  awm->close_sub_menu();
1320 
1321  awm->sep______________();
1322 
1323  awm->insert_sub_menu("Align sequences", "l");
1324  {
1325  awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1326  GDE_load_menu(awm, AWM_ALL, "Align");
1327  }
1328  awm->close_sub_menu();
1329  awm->insert_menu_topic("seq_concat", "Concatenate sequences", "C", "concatenate.hlp", AWM_ALL, NT_createConcatenationWindow);
1330  awm->insert_menu_topic("seq_split", "Split sequences", "S", "split.hlp", AWM_ALL, NT_create_splitAlignment_window);
1331  awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1332  awm->sep______________();
1333 
1334  awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1335  awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist"));
1336  awm->sep______________();
1337 
1338  awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1339  awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1340 
1341  awm->sep______________();
1342 
1343  GDE_load_menu(awm, AWM_ALL, "Print");
1344  }
1345 
1346  // -------------
1347  // SAI
1348 
1349  awm->create_menu("SAI", "A", AWM_ALL);
1350  {
1351  awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1352  awm->insert_menu_topic("sai_calc", "Combine SAIs", "b", "saicalc.hlp", AWM_ALL, makeWindowCallback(SAI_popup_calculator_window, GLOBAL.gb_main));
1353  awm->insert_sub_menu("Create SAI using ...", "C");
1354  {
1355  awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window);
1356  awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window);
1357  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);
1358  awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_phylo"));
1359  awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold);
1360 
1361  GDE_load_menu(awm, AWM_EXP, "SAI");
1362  }
1363  awm->close_sub_menu();
1364 
1365  awm->insert_sub_menu("Other functions", "O");
1366  {
1367  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));
1368  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)));
1369  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);
1370  }
1371  awm->close_sub_menu();
1372  }
1373 
1374  // ----------------
1375  // Probes
1376 
1377  awm->create_menu("Probes", "P", AWM_ALL);
1378  {
1379  awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1380  awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1381  awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1382  awm->sep______________();
1383  awm->insert_menu_topic("probe_match_sp", "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window, ntw));
1384  awm->sep______________();
1385  awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1386  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)));
1387  awm->sep______________();
1388  awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1389  }
1390 
1391  }
1392 
1393  // --------------
1394  // Tree
1395 
1396  awm->create_menu("Tree", "T", AWM_ALL);
1397  {
1398  if (!clone) {
1399  awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1400  awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(NDS_create_window, GLOBAL.gb_main));
1401  awm->sep______________();
1402  awm->insert_sub_menu("Add Species to Existing Tree", "A");
1403  {
1404  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"));
1405  awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_pars"));
1406  GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1407  }
1408  awm->close_sub_menu();
1409  }
1410 
1411  awm->insert_sub_menu("Remove Species from Tree", "R");
1412  {
1413  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));
1414  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));
1415  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));
1416  awm->sep______________();
1417  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));
1418  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));
1419  }
1420  awm->close_sub_menu();
1421 
1422  if (!clone) {
1423  awm->insert_sub_menu("Build tree from sequence data", "B");
1424  {
1425  awm->insert_sub_menu("Distance matrix methods", "D");
1426  awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist"));
1427  GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1428  awm->close_sub_menu();
1429 
1430  awm->insert_sub_menu("Maximum Parsimony methods", "P");
1431  GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1432  awm->close_sub_menu();
1433 
1434  awm->insert_sub_menu("Maximum Likelihood methods", "L");
1435  GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1436  GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1437  awm->close_sub_menu();
1438 
1439  awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1440  GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1441  awm->close_sub_menu();
1442  }
1443  awm->close_sub_menu();
1444  }
1445 
1446  awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1447 
1448  awm->sep______________();
1449 
1450  awm->insert_sub_menu("Reset zoom", "z");
1451  {
1452  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));
1453  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));
1454  }
1455  awm->close_sub_menu();
1456 
1457  awm->sep______________();
1458 
1459  // taxonomic groups
1460  NT_insert_collapse_submenu(awm, ntw);
1461  if (!clone) {
1462  awm->insert_menu_topic("group_search", "Search groups...", "g", "group_search.hlp", AWM_ALL, makeWindowCallback (popup_group_search_window, GLOBAL.gb_main));
1463  awm->insert_menu_topic("compare_taxonomy", "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1464  awm->insert_menu_topic("move_groups", "Move groups...", "v", "move_groups.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_moveGroupInfo_window));
1465  }
1466 
1467  awm->sep______________();
1468 
1469  if (!clone) {
1470  awm->insert_menu_topic("compare_topology", "Compare topology...", "o", "compare_topo.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compareTopologies_window));
1471  }
1472 
1473  awm->insert_sub_menu("Modify branches", "M");
1474  {
1475  awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw));
1476  awm->insert_menu_topic(awm->local_id("tree_edit_remark"), "Edit bootstraps", "E", "ted_boot.hlp", AWM_ALL, makeWindowCallback(NT_edit_bootstrap, ntw));
1477  awm->sep______________();
1478  awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw));
1479  awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1480  awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw));
1481  awm->sep______________();
1482  awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1483  awm->sep______________();
1484  awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1485  awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1486 
1487  }
1488  awm->close_sub_menu();
1489  awm->insert_sub_menu("Beautify tree", "u");
1490  {
1491  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));
1492  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));
1493  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));
1494  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));
1495  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));
1496  awm->sep______________();
1497  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));
1498  }
1499  awm->close_sub_menu();
1500 
1501  awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "h", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1502  awm->insert_menu_topic(awm->local_id("syncroots"), "Adjust roots...", "j", "syncroots.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncroot_window, GLOBAL.gb_main));
1503  awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "k", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback (NT_mark_duplicates, ntw));
1504 
1505  awm->sep______________();
1506  awm->insert_menu_topic(awm->local_id("shade"), "Tree shading...", "s", "tree_shading.hlp", AWM_ALL, makeWindowCallback (NT_configure_treeShader));
1507  awm->insert_menu_topic(awm->local_id("syncscroll"), "Sync tree scrolling..", "e", "syncscroll.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1508 
1509  awm->sep______________();
1510  awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", NULp, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1511 
1512  awm->sep______________();
1513  awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1514 
1515  if (is_genome_db) {
1516  awm->sep______________();
1517  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));
1518  }
1519 
1520  if (!clone) {
1521  awm->sep______________();
1522  awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1523  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)));
1524  }
1525 
1526  }
1527 
1528  if (!clone) {
1529  // ---------------
1530  // Tools
1531 
1532  awm->create_menu("Tools", "o", AWM_ALL);
1533  {
1534  awm->insert_menu_topic("names_admin", "Nameserver admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeWindowCallback(AW_popup_namesadmin_window, GLOBAL.gb_main));
1535  awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1536  {
1537  awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1538  }
1539  awm->close_sub_menu();
1540  awm->sep______________();
1541 
1542  awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1543  {
1544  GDE_load_menu(awm, AWM_EXP, NULp);
1545  }
1546  awm->close_sub_menu();
1547 
1548  awm->sep______________();
1549  awm->insert_menu_topic("xterm", "Start XTERM", "X", "xterm.hlp", AWM_ALL, AW_console_cb);
1550  XCmdType *showlog_cmdtype = new XCmdType(XCMD_ASYNC_WAIT_ON_ERROR, GLOBAL.gb_main); // do not free (used in callback)
1551  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
1552  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));
1553  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));
1554  awm->sep______________();
1555  GDE_load_menu(awm, AWM_EXP, "User");
1556  }
1557  // --------------------
1558  // Properties
1559 
1560  awm->create_menu("Properties", "r", AWM_ALL);
1561  {
1562  awm->insert_menu_topic("props_menu", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1563  awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1564  awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1565  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));
1566  awm->sep______________();
1567  awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", NULp, AWM_ALL, NT_toggle_expert_mode);
1568  awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", NULp, AWM_ALL, NT_toggle_focus_policy);
1569  awm->sep______________();
1570  AW_insert_common_property_menu_entries(awm);
1571  awm->sep______________();
1572  awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1573  }
1574  }
1575 
1576  awm->insert_help_topic("ARB_NT help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1577 
1578  // ----------------------
1579  // mode buttons
1580  //
1581  // keep them synchronized as far as possible with those in ARB_PARSIMONY
1582  // see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1583 
1584  awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1585  awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1586  awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1587  awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1588  awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1589 
1590  awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1591  awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW));
1592 
1593  // topology-modification-modes
1594  awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1595  awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1596  awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1597  awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1598  awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1599 
1600  // layout-modes
1601  awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1602  awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1603  awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1604 
1605  awm->set_info_area_height(250);
1606  awm->at(5, 2);
1607  awm->auto_space(-2, -2);
1608  awm->shadow_width(1);
1609 
1610  // -------------------------
1611  // create top area
1612 
1613  int first_liney;
1614  int leftx;
1615  awm->get_at_position(&leftx, &first_liney);
1616 
1617  // ---------------------
1618  // quit + help
1619 
1620  awm->button_length(0);
1621 
1622  if (clone) {
1623  awm->callback(AW_POPDOWN);
1624  awm->create_button("CLOSE", "#close.xpm");
1625  }
1626  else {
1627  awm->callback(makeWindowCallback(NT_confirm_exit, EXIT_SUCCESS));
1628  awm->help_text("quit.hlp");
1629  awm->create_button("QUIT", "#quit.xpm");
1630  }
1631 
1632  int db_pathx = awm->get_at_xposition();
1633 
1634  // now fetch the yposition for the 2nd button line
1635  awm->at_newline();
1636  int second_liney = awm->get_at_yposition();
1637 
1638  awm->callback(AW_help_entry_pressed);
1639  awm->help_text("arb_ntree.hlp");
1640  awm->create_button("?", "#help.xpm");
1641 
1642  // --------------------------
1643  // save + undo/redo
1644 
1645  awm->callback(NT_save_quick_cb);
1646  awm->help_text("save.hlp");
1647  awm->create_button("SAVE", "#save.xpm");
1648 
1649  awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1650  awm->help_text("save.hlp");
1651  awm->create_button("SAVE_AS", "#saveAs.xpm");
1652 
1653  // undo/redo:
1654  awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1655  awm->help_text("undo.hlp");
1656  awm->create_button("UNDO", "#undo.xpm");
1657 
1658  awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1659  awm->help_text("undo.hlp");
1660  awm->create_button("REDO", "#redo.xpm");
1661 
1662  int db_pathx2 = awm->get_at_xposition();
1663 
1664  // fetch position for mode help-line:
1665  awm->at_newline();
1666  int third_liney = awm->get_at_yposition();
1667 
1668  awm->at(db_pathx, first_liney);
1669  // size of DB-name button is determined by buttons below:
1670  awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1671  awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1672  awm->help_text("save.hlp");
1673  awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1674 
1675  // -----------------------------
1676  // tree + tree display
1677 
1678 #define TREE_BUTTON_OVERSIZE 6
1679 
1680  int db_treex = awm->get_at_xposition();
1681  int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1682 
1683  awm->at(db_treex, second_uppery);
1684  awm->button_length(0);
1685 
1686  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1687  awm->help_text("tr_type_radial.hlp");
1688  awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1689 
1690  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1691  awm->help_text("tr_type_dendro.hlp");
1692  awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1693 
1694  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1695  awm->help_text("tr_type_irs.hlp");
1696  awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1697 
1698  awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1699  awm->help_text("tr_type_nds.hlp");
1700  awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1701 
1702  int db_treex2 = awm->get_at_xposition();
1703 
1704  awm->at(db_treex, first_liney);
1705  // size of tree-name button is determined by buttons below:
1706  awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1707  awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1708  awm->help_text("nt_tree_select.hlp");
1709  awm->create_button("SELECT_A_TREE", awar_tree);
1710 
1711  // ---------------------------------------------------------------
1712  // protection, alignment + editor (and maybe Genome Map)
1713 
1714  int db_alignx = awm->get_at_xposition();
1715 
1716  // editor and genemap buttons have to be 44x24 sized
1717 #define EDIT_XSIZE 50
1718 #define EDIT_YSIZE 30 // same as 'save as' buttons
1719 
1720  // first draw protection:
1721  int protectx = db_alignx + 2*EDIT_XSIZE;
1722 
1723  awm->at(protectx+2, first_liney+1);
1724  awm->button_length(0);
1725  awm->create_button(NULp, "#protect.xpm");
1726 
1727  awm->at(protectx, second_liney+2);
1728  awm->create_option_menu(AWAR_SECURITY_LEVEL);
1729  awm->insert_option ("0", NULp, 0);
1730  awm->insert_option ("1", NULp, 1);
1731  awm->insert_option ("2", NULp, 2);
1732  awm->insert_option ("3", NULp, 3);
1733  awm->insert_option ("4", NULp, 4);
1734  awm->insert_option ("5", NULp, 5);
1735  awm->insert_default_option("6", NULp, 6);
1736  awm->update_option_menu();
1737 
1738  int db_searchx = awm->get_at_xposition() - 7;
1739 
1740  // draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1741  awm->at(db_alignx, second_liney);
1742 
1743  awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1744  awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1745  awm->help_text("arb_edit4.hlp");
1746  if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1747  else awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1748 
1749  if (is_genome_db) {
1750  awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1751  awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1752  awm->help_text("gene_map.hlp");
1753  awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1754  }
1755 
1756  int db_alignx2 = awm->get_at_xposition();
1757 
1758  awm->at(db_alignx, first_liney);
1759  awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1760  awm->callback(NT_create_select_alignment_window);
1761  awm->help_text("nt_align_select.hlp");
1762  awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1763 
1764  // -------------------------------
1765  // create mode-help line
1766 
1767  awm->at(leftx, third_liney);
1768  awm->button_length(AWAR_FOOTER_MAX_LEN);
1769  awm->create_button(NULp, AWAR_FOOTER);
1770 
1771  awm->at_newline();
1772  int bottomy = awm->get_at_yposition();
1773 
1774  // ---------------------------------------
1775  // Info / marked / Search / Jump
1776 
1777  awm->button_length(7);
1778 
1779  awm->at(db_searchx, first_liney);
1780  awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1781  awm->help_text("sp_search.hlp");
1782  awm->create_button("SEARCH", "Search");
1783 
1784  awm->at(db_searchx, second_uppery);
1785  awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1786  awm->help_text("tr_jump.hlp");
1787  awm->create_button("JUMP", "Jump");
1788 
1789  int db_infox = awm->get_at_xposition();
1790 
1791  awm->at(db_infox, first_liney);
1792  awm->button_length(13);
1793  awm->callback(popupinfo_wcb);
1794  awm->help_text("sp_info.hlp");
1795  awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1796 
1797  awm->at(db_infox, second_uppery);
1798  awm->button_length(13);
1799  awm->help_text("species_configs.hlp");
1800  awm->callback(makeWindowCallback(NT_popup_configuration_admin, ntw));
1801  awm->create_button("selection_admin2", AWAR_MARKED_SPECIES_COUNTER);
1802  {
1803  GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1804  GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(NT_update_marked_counter, static_cast<AW_window*>(awm)));
1805  NT_update_marked_counter(NULp, awm);
1806  }
1807 
1808  // set height of top area:
1809  awm->set_info_area_height(bottomy+2);
1810  awm->set_bottom_area_height(0);
1811 
1812  NT_activate_configMarkers_display(ntw);
1813 
1814  // ------------------------------------
1815  // Autostarts for development
1816 
1817 #if defined(DEVEL_RALF)
1818  // if (is_genome_db) GEN_map_first(awr)->show();
1819 #endif // DEVEL_RALF
1820 
1821  GB_pop_transaction(GLOBAL.gb_main);
1822 
1823 #if defined(DEBUG)
1824  AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1825 #endif
1826 
1827  return awm;
1828 }
1829 
1830 TREE_canvas *NT_create_main_window(AW_root *aw_root) {
1831  GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1832  if (error) aw_message(error);
1833 
1834  nt_create_all_awars(aw_root);
1835 
1836  TREE_canvas *ntw = NULp;
1837  AW_window *aww = popup_new_main_window(aw_root, 0, &ntw);
1838  NT_install_treeShader(ntw, GLOBAL.gb_main);
1839  aww->show();
1840 
1841  error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1842  if (error) aw_message(error);
1843 
1844  return ntw;
1845 }
WEIGHTED
Definition: arb_progress.h:225
GB_begin_transaction
GB_ERROR GB_begin_transaction(GBDATA *gbd)
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Definition: NT_edconf.cxx:1253
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Definition: NT_extern.cxx:89
group_selected_by_canvas_cb
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Definition: NT_extern.cxx:1005
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Definition: AP_Tree.hxx:36
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Definition: arb_msg.cxx:571
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Definition: arb_assert.h:245
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Definition: NT_extern.cxx:546
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awt_item_type_selector::get_self_awar
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NT_database_optimization
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Definition: NT_extern.cxx:510
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Definition: TreeDisplay.hxx:507
GBT_TreeRemoveType
GBT_TreeRemoveType
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update_main_window_title
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Definition: NT_extern.cxx:907
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Definition: aw_global_awars.hxx:20
GBT_compression_test
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Definition: AW_rename.cxx:573
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Definition: arb_strarray.h:85
NT_create_startEditorOnOldConfiguration_window
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NT_edit_bootstrap
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AW_awar::read_pointer
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Definition: aw_window.hxx:652
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Definition: ad_save_load.cxx:804
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Definition: NT_concatenate.cxx:52
FINAL_TYPE::current
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Definition: NT_extern.cxx:710
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Definition: NT_extern.cxx:242
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Definition: AW_window.cxx:595
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Definition: AWTC_submission.cxx:31
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Definition: AW_window.cxx:720
SQ_create_awars
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Definition: SQ_main.cxx:48
DBUI::create_dbui_awars
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Definition: ui_species.cxx:85
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Definition: arb_progress.h:227
AWAR_DB_OPTI_TREENAME
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Definition: NT_extern.cxx:461
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AW_window * create_AWTC_export_window(AW_root *awr, GBDATA *gb_main)
Definition: AWTI_export.cxx:303
GB_add_callback
GB_ERROR GB_add_callback(GBDATA *gbd, GB_CB_TYPE type, const DatabaseCallback &dbcb)
Definition: ad_cb.cxx:356
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Definition: NT_extern.cxx:86
GEN_create_awars
void GEN_create_awars(AW_root *aw_root, AW_default aw_def, GBDATA *gb_main)
Definition: GEN_interface.cxx:350
NT_create_transpro_variables
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Definition: ad_transpro.cxx:215
GBT_mark_all
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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:1488
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GB_ERROR write_pointer(GBDATA *aw_pointer)
ARB_keep_string
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Definition: arb_string.cxx:72
AWT_graphic
Definition: canvas.hxx:248
GB_CB_CHANGED
Definition: arbdb_base.h:49
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Definition: TreeCallbacks.cxx:144
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Definition: canvas.hxx:372
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Definition: AWTC_submission.cxx:225
AWT_IT_SPECIES
Definition: input_mask.hxx:31
NT_remove_bootstrap
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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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GB_ERROR GB_end_transaction(GBDATA *gbd, GB_ERROR error)
Definition: arbdb.cxx:2561
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Definition: AW_at.cxx:93
NT_move_boot_branch
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Definition: TreeCallbacks.cxx:650
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Definition: arb_progress.h:319
AWT_REMOVE_ZOMBIES
Definition: AP_Tree.hxx:38
AWT_auto_refresh
Definition: canvas.hxx:410
NT_reset_pzoom_cb
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Definition: TreeCallbacks.cxx:548
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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:88
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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
create_primer_design_variables
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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: ST_window.cxx:270
NT_create_mask_submenu
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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:29
NT_create_multifurcate_tree_window
AW_window * NT_create_multifurcate_tree_window(AW_root *aw_root, TREE_canvas *ntw)
Definition: ad_trees.cxx:1126
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AW_window * create_insertDeleteBySAI_window(AW_root *root, GBDATA *gb_main)
Definition: NT_ins_col.cxx:268
NT_start_editor_on_tree
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Definition: NT_edconf.cxx:1294
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Definition: arb_msg.cxx:203
NT_create_syncScroll_window
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Definition: NT_sync_scroll.cxx:89
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AW_root * awr
Definition: canvas.hxx:348
AW_advice
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Show a message box with an advice for the user.
Definition: AW_advice.cxx:160
export_nds_cb
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Definition: NT_extern.cxx:100
NT_toggle_focus_policy
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Definition: NT_extern.cxx:247
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Definition: arb_msg.cxx:523
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Definition: AW_window.cxx:52
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Definition: TreeCallbacks.cxx:864
AWT_COMMAND_MODE
AWT_COMMAND_MODE
Definition: canvas.hxx:35
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Definition: AW_preset.cxx:1445
canvas_tree_awar_changed_cb
static void canvas_tree_awar_changed_cb(AW_awar *, bool, TREE_canvas *ntw)
Definition: NT_extern.cxx:917
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const char * GBT_existing_tree(GBDATA *gb_main, const char *tree_name)
Definition: adtree.cxx:1056
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void NT_create_alignment_vars(AW_root *aw_root, AW_default aw_def, GBDATA *gb_main)
Definition: NT_cb.cxx:97
NT_confirm_exit
void NT_confirm_exit(AW_window *aws, int exitcode)
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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bool isNull() const
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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static void NT_save_as_cb(AW_window *aww)
Definition: NT_extern.cxx:463
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Definition: arb_a2ps.c:154
NT_get_canvas_by_index
TREE_canvas * NT_get_canvas_by_index(int idx)
Definition: NT_extern.cxx:956
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static bool track_group_selection_by_canvas
Definition: NT_extern.cxx:1003
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#define AWAR_FOOTER_MAX_LEN
Definition: aw_awar_defs.hxx:57
AW_window::set_window_title
void set_window_title(const char *title)
Definition: AW_window.cxx:1069
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bool is_valid() const
Definition: Group.hxx:48
create_multiprobe_window
AW_window * create_multiprobe_window(AW_root *root, TREE_canvas *canvas)
Definition: MP_main.cxx:100
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AW_window * create_primer_design_window(AW_root *root, GBDATA *gb_main)
Definition: primer_design.cxx:462
AWM_EXP
Definition: aw_window.hxx:180
NT_create_save_as
static AW_window * NT_create_save_as(AW_root *aw_root, const char *base_name)
Definition: NT_extern.cxx:575
FINAL_TYPE::getKeyPath
const char * getKeyPath() const OVERRIDE
Definition: NT_extern.cxx:722
GB_fix_database
GB_ERROR GB_fix_database(GBDATA *gb_main)
Definition: adTest.cxx:237
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void insert_field_admin_menuitems(AW_window *aws, GBDATA *gb_main)
Definition: ui_species.cxx:888
AWAR_GROUP
#define AWAR_GROUP
Definition: ad_trees.h:19
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set SmartPtr to NULp
Definition: smartptr.h:251
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char buffer[MESSAGE_BUFFERSIZE]
Definition: seq_search.cxx:34
GB_get_father
GBDATA * GB_get_father(GBDATA *gbd)
Definition: arbdb.cxx:1722
AW_window::update_option_menu
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Definition: AW_option_toggle.cxx:268
NT_update_marked_counter
static void NT_update_marked_counter(GBDATA *, AW_window *aww)
Definition: NT_extern.cxx:742
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
NT_delete_mark_all_cb
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Definition: NT_cb.cxx:30
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Definition: AW_preset.cxx:1113
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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bool empty() const
Definition: arb_strarray.h:86
TREE_canvas_registry
Definition: NT_extern.cxx:923
GB_HASH
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
AW_awar
Definition: aw_awar.hxx:53
AWT_create_mask_submenu
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Definition: input_mask.cxx:2446
AWT_registerTreeAwarCallback
void AWT_registerTreeAwarCallback(AW_awar *awar, const TreeAwarCallback &tacb, bool triggerIfTreeDataChanges)
Definition: TreeAwars.cxx:208
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void SAI_popup_calculator_window(AW_window *awp, GBDATA *gb_main)
Definition: saicalc.cxx:1138
AWAR_MARKED_SPECIES_COUNTER
#define AWAR_MARKED_SPECIES_COUNTER
Definition: NT_extern.cxx:75
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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:87
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Definition: AW_select.cxx:380
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void AW_create_namesadmin_awars(AW_root *awr, GBDATA *gb_main)
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:858
NT_mark_duplicates
static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw)
Definition: NT_extern.cxx:629
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void set_tree_style(AP_tree_display_style style, AWT_canvas *ntw)
Definition: TreeDisplay.cxx:2265
GB_UNDO_TYPE
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
NT_create_syncroot_window
AW_window * NT_create_syncroot_window(AW_root *awr, GBDATA *gb_main)
Definition: NT_syncroot.cxx:220
AW_awar::read_char_pntr
const char * read_char_pntr() const
Definition: AW_awar.cxx:168
AW_system
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Definition: AW_help.cxx:32
MacroExitor::is_performing_delayed_exit
bool is_performing_delayed_exit() const
Definition: MacroExitor.hxx:176
merge_from_cb
static void merge_from_cb(AW_window *aww, AW_CL cl_awarNamePtr)
Definition: NT_extern.cxx:884
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static void install_group_changed_callback(const GraphicTreeCallback &gccb)
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:2986
GB_optimize
GB_ERROR GB_optimize(GBDATA *gb_main)
Definition: adoptimize.cxx:2556
NT_generate_tree
AWT_graphic_tree * NT_generate_tree(AW_root *root, GBDATA *gb_main, AD_map_viewer_cb map_viewer_cb)
Definition: TreeDisplay.cxx:3931
NT_create_resort_window
AW_window * NT_create_resort_window(AW_root *awr)
Definition: NT_sort.cxx:209
NT_create_select_alignment_window
AW_window * NT_create_select_alignment_window(AW_root *awr)
Definition: NT_cb.cxx:118
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AW_root::SINGLETON
static AW_root * SINGLETON
Definition: aw_root.hxx:102
AW_window::show
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Definition: AW_window.cxx:1683
NT_get_tree_root_of_canvas
TreeNode * NT_get_tree_root_of_canvas(TREE_canvas *ntw)
Definition: NT_extern.cxx:836
GDE_load_menu
void GDE_load_menu(AW_window *awm, AW_active, const char *menulabel)
Definition: GDE.cxx:436
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WindowCallback makeHelpCallback(const char *helpfile)
Definition: aw_window.hxx:106
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GB_ERROR ARB_format_alignment(GBDATA *Main, const char *alignment_name)
Definition: insdel.cxx:1439
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static void nt_changesecurity(AW_root *aw_root)
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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:56
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Definition: TreeCallbacks.cxx:498
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void GEN_create_genes_submenu(AW_window_menu_modes *awm, GBDATA *gb_main, bool for_ARB_NTREE)
Definition: GEN_map.cxx:1482
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void create_insertDeleteColumn_variables(AW_root *root, AW_default db1)
Definition: NT_ins_col.cxx:135
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GBDATA * get_gb_tree() const
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FINAL_TYPE::get_self_awar_content_length
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AWAR_SAI_GLOBAL
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Definition: aw_awar_defs.hxx:50
SPLIT_KEEPEMPTY
Definition: arb_strarray.h:218
DBItemSet
std::set< GBDATA * > DBItemSet
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NT_create_sai_from_pfold
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Definition: ad_spec.cxx:126
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Definition: refentries.cxx:253
NT_create_select_tree_window
AW_window * NT_create_select_tree_window(AW_root *awr, const char *awar_tree)
Definition: NT_cb.cxx:59
AWT_graphic_tree::get_root
AW_root * get_root() const
Definition: TreeDisplay.hxx:504
NT_create_compareTopologies_window
AW_window * NT_create_compareTopologies_window(AW_root *root)
Definition: ad_trees.cxx:637
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Definition: adname.cxx:33
AWAR_DB_PATH
#define AWAR_DB_PATH
Definition: aw_awar_defs.hxx:5
create_probe_design_variables
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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:191
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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
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Definition: AW_preset.cxx:1452
AW_awar::update
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Definition: AW_awar.cxx:390
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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_)
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NT_create_dna_2_pro_window
AW_window * NT_create_dna_2_pro_window(AW_root *root)
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static void create_export_nds_awars(AW_root *awr, AW_default def)
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AWM_ALL
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create_insertDeleteColumn_window
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AW_window::create_menu
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AWAR_NTREE_MAIN_WINDOW_COUNT
#define AWAR_NTREE_MAIN_WINDOW_COUNT
Definition: NT_local.h:29
AW_create_gc_window
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Definition: AW_preset.cxx:1373
AW_window::help_text
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Definition: AW_window.cxx:116
AW_awar::touch
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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
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NT_start_if
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Definition: TreeCallbacks.cxx:694
NT_create_alignment_admin_window
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Definition: NT_cb.cxx:108
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Definition: mkptypes.cxx:96
TREE_canvas_registry::get_canvas
TREE_canvas * get_canvas(int idx) const
Definition: NT_extern.cxx:948
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Definition: AW_window.cxx:2402
AP_create_consensus_var
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Definition: AP_consensus.cxx:248
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const char * get_name() const
Definition: Group.hxx:56
AWAR_TREE_REFRESH
#define AWAR_TREE_REFRESH
Definition: aw_awar_defs.hxx:11
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:1920
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)
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Definition: aw_awar_defs.hxx:10
AWAR_DBBASE
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AW_ADVICE_TOGGLE_AND_HELP
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AW_console_cb
void AW_console_cb(AW_window *)
Definition: aw_system.hxx:25
AW_window::insert_help_topic
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Definition: AW_window.cxx:569
AWT_graphic_tree::deselect_group
void deselect_group()
Definition: TreeDisplay.hxx:594
AWTI_cleanup_importer
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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
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AWAR_SPECIES_NAME
#define AWAR_SPECIES_NAME
Definition: aw_awar_defs.hxx:42
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:59
AWAR_SAI_NAME
#define AWAR_SAI_NAME
Definition: aw_awar_defs.hxx:49
popup_new_main_window
static AW_window * popup_new_main_window(AW_root *awr, int clone, TREE_canvas **result_ntw)
Definition: NT_extern.cxx:1089
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:43
nt_create_all_awars
static void nt_create_all_awars(AW_root *awr)
Definition: NT_extern.cxx:249
AWT_popup_tree_export_window
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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:15
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:554
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:645
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:167
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
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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:231
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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:74
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
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#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
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void create_trees_var(AW_root *aw_root, AW_default aw_def)
Definition: ad_trees.cxx:203
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static AW_window * NT_create_merge_from_window(AW_root *awr)
Definition: NT_extern.cxx:887
merge_into_cb
static void merge_into_cb(AW_window *aww, AW_CL cl_awarNamePtr)
Definition: NT_extern.cxx:885
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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:1025
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:796
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
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fputs(TRACE_PREFIX, stderr)
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#define AWAR_AW_FOCUS_FOLLOWS_MOUSE
Definition: aw_global_awars.hxx:19
AWAR_TOPAREA_SAIS
#define AWAR_TOPAREA_SAIS
Definition: NT_local.h:30
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NT_create_main_window
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Definition: NT_extern.cxx:1830
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AW_window * create_colorize_items_window(AW_root *aw_root, GBDATA *gb_main, ItemSelector &sel)
Definition: db_query.cxx:1965
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#define EDIT_XSIZE
AWT_graphic_tree::get_selected_group
const Group & get_selected_group() const
Definition: TreeDisplay.hxx:597
AWT_canvas::set_mode
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Definition: canvas.hxx:392
AW_window::set_bottom_area_height
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Definition: AW_window.cxx:801
NT_undo_cb
static void NT_undo_cb(AW_window *, GB_UNDO_TYPE undo_type, TREE_canvas *ntw)
Definition: NT_extern.cxx:614
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AW_awar * awar_int(const char *var_name, long default_value=0, AW_default default_file=AW_ROOT_DEFAULT)
Definition: AW_root.cxx:580
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
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Definition: AW_at.cxx:259
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FINAL_TYPE
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Definition: aisc_commands.c:804
NT_activate_configMarkers_display
void NT_activate_configMarkers_display(TREE_canvas *ntw)
Definition: NT_edconf.cxx:254
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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:37
GBK_singlequote
char * GBK_singlequote(const char *arg)
Definition: arb_msg.cxx:599
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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
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#define AWAR_ERROR_MESSAGES
Definition: aw_awar_defs.hxx:54
AW_CL
long AW_CL
Definition: cb.h:21
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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
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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
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Definition: NT_validNames.cxx:28
AP_create_con_expert_window
AW_window * AP_create_con_expert_window(AW_root *aw_root)
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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
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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
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#define AWAR_DB_COMMENT
Definition: aw_awar_defs.hxx:20
AWT_graphic_tree::get_root_node
AP_tree * get_root_node()
Definition: TreeDisplay.hxx:509
NT_importValidNames
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Definition: NT_validNames.cxx:49
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CHANGE_KEY_PATH
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Definition: arbdb.h:200
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GB_ERROR GB_textprint(const char *path) __ATTR__USERESULT
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static AW_window * NT_create_merge_to_window(AW_root *awr)
Definition: NT_extern.cxx:895
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Definition: species.cxx:139
NT_alltree_remove_leafs
static void NT_alltree_remove_leafs(AW_window *, GBT_TreeRemoveType mode, GBDATA *gb_main)
Definition: NT_extern.cxx:759
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int get_count() const
Definition: NT_extern.cxx:946
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void close_sub_menu()
Definition: AW_window.cxx:486
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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
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#define AWAR_EXPORT_NDS
Definition: NT_extern.cxx:73
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GB_ERROR GBT_compress_sequence_tree2(GBDATA *gbd, const char *tree_name, const char *ali_name) __ATTR__USERESULT
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AW_window * TREE_create_settings_window(AW_root *aw_root)
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void NT_createValidNamesAwars(AW_root *aw_root, AW_default aw_def)
Definition: NT_validManual.cxx:36
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AW_window::create_option_menu
AW_option_menu_struct * create_option_menu(const char *awar_name)
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Definition: aw_root.hxx:86
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void insert_macro_menu_entry(AW_window *awm, bool prepend_separator)
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AW_root * get_root()
Definition: aw_window.hxx:359
EXPORT_COMMA_SEPARATED
Definition: NT_extern.cxx:90
AP_create_pos_var_pars_window
AW_window * AP_create_pos_var_pars_window(AW_root *root)
Definition: AP_pos_var_pars.cxx:48
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static void nt_start_2nd_arb(AW_window *aww, bool quit)
Definition: NT_extern.cxx:406
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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
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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
NT_select_bottom_tree
void NT_select_bottom_tree(AW_window *aww, const char *awar_tree)
Definition: NT_cb.cxx:91
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Definition: arbdb.h:131
AWAR_NTREE_TITLE_MODE
#define AWAR_NTREE_TITLE_MODE
Definition: NT_extern.cxx:76
__ATTR__NORETURN
#define __ATTR__NORETURN
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AWT_KEEP_MARKED
Definition: AP_Tree.hxx:45
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void create_refentries_awars(AW_root *aw_root, AW_default aw_def)
Definition: refentries.cxx:223
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GB_ERROR write_string(const char *aw_string)
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static char * command
Definition: arb_a2ps.c:319
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static AW_window * NT_create_save_quick_as_window(AW_root *aw_root, const char *base_name)
Definition: NT_extern.cxx:483
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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:753
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static TREE_canvas_registry & instance()
Definition: NT_extern.cxx:934
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:747
input_mask.hxx
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GB_ERROR GB_request_undo_type(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT_TODO
Definition: adindex.cxx:721
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void NT_fill_canvas_selection_list(class AW_selection_list *sellst, TREE_canvas *to_skip)
Definition: NT_extern.cxx:977
ta
GB_transaction ta(gb_var)
AW_window::callback
void callback(const WindowCallback &cb)
Definition: AW_window.cxx:133
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Definition: TreeNode.h:600
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GB_CSTR GB_read_char_pntr(GBDATA *gbd)
Definition: arbdb.cxx:904
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#define AWAR_DB_TYPE
Definition: NT_extern.cxx:459
AWAR_EXPERT
#define AWAR_EXPERT
Definition: aw_awar_defs.hxx:27
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)
Definition: AW_root.cxx:570
GBT_check_data
GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name)
Definition: adali.cxx:218
AW_window::hide_or_notify
void hide_or_notify(const char *error)
Definition: AW_window.cxx:1845
NT_create_branch_analysis_window
AW_window * NT_create_branch_analysis_window(AW_root *aw_root, TREE_canvas *ntw)
Definition: NT_branchAnalysis.cxx:306
NT_deselect_group
void NT_deselect_group(AW_root *awr)
Definition: NT_extern.cxx:999
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bool GEN_is_genome_db(GBDATA *gb_main, int default_value)
Definition: adGene.cxx:20
AW_window::shadow_width
void shadow_width(int shadow_thickness)
Definition: AW_window.cxx:1078
MacroExitor::get_root
AW_root * get_root() const
Definition: MacroExitor.hxx:175
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AW_window * awt_create_load_box(AW_root *aw_root, const char *action, const char *what, const char *default_directory, const char *file_extension, char **set_file_name_awar, const WindowCallback &ok_cb, const WindowCallback &close_cb, const char *close_button_text)
Definition: sel_boxes.cxx:896
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AW_window * create_probe_match_window(AW_root *root, GBDATA *gb_main)
Definition: probe_design.cxx:1775
NT_create_trackAliChanges_window
AW_window * NT_create_trackAliChanges_window(AW_root *root)
Definition: NT_trackAliChanges.cxx:196
ARB_disconnect_from_db
void ARB_disconnect_from_db(AW_root *aw_root, GBDATA *&gb_main_ref)
Definition: app.cxx:40
NT_confirm_exit_restart_if
void NT_confirm_exit_restart_if(AW_root *aw_root, int exitcode, const char *restart_ntree_args)
Definition: NT_extern.cxx:389
GEN_is_pseudo_gene_species
bool GEN_is_pseudo_gene_species(GBDATA *gb_species)
Definition: adGene.cxx:558
sel_boxes.hxx
NT_MacroExitor
Definition: NT_extern.cxx:369
relink_pseudo_species_to_organisms
static void relink_pseudo_species_to_organisms(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash)
Definition: NT_extern.cxx:660
AP_tree
Definition: AP_Tree.hxx:210
NT_configure_treeShader
void NT_configure_treeShader(void)
Definition: NT_shadeTree.cxx:147
AW_window::at_newline
void at_newline()
Definition: AW_at.cxx:119
ad_cb.h
merge_from_to
static void merge_from_to(AW_root *awr, const char *db_awar_name, bool merge_to)
Definition: NT_extern.cxx:869
TREE_canvas::get_awar_tree
AW_awar * get_awar_tree() const
Definition: TreeDisplay.hxx:744
TREE_create_awars
void TREE_create_awars(AW_root *aw_root, AW_default db)
Definition: TreeDisplay.cxx:3960
FINAL_TYPE::~nt_item_type_species_selector
~nt_item_type_species_selector() OVERRIDE
Definition: NT_extern.cxx:702
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void NDS_create_vars(AW_root *aw_root, AW_default awdef, GBDATA *gb_main)
Definition: nds.cxx:366
AW_window::at_attach_to
void at_attach_to(bool attach_x, bool attach_y, int xoff, int yoff)
Definition: AW_at.cxx:187
AW_ROOT_DEFAULT
#define AW_ROOT_DEFAULT
Definition: aw_base.hxx:106
NT_reset_branchlengths
void NT_reset_branchlengths(UNFIXED, TREE_canvas *ntw)
Definition: TreeCallbacks.cxx:622
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void AWT_insert_DBsaveType_selector(AW_window *aww, const char *awar_name)
Definition: arb_spec.cxx:39
AW_awar::write_int
GB_ERROR write_int(long aw_int)
NT_toggle_expert_mode
static void NT_toggle_expert_mode(AW_window *aww)
Definition: NT_extern.cxx:246
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void NT_reset_lzoom_cb(UNFIXED, TREE_canvas *ntw)
Definition: TreeCallbacks.cxx:539
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AW_window * create_probe_admin_window(AW_root *root, GBDATA *gb_main)
Definition: probe_design.cxx:2080
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void create_group_search_awars(AW_root *aw_root, AW_default props)
Definition: NT_group_search.cxx:615
GB_entry
GBDATA * GB_entry(GBDATA *father, const char *key)
Definition: adquery.cxx:334
arb_progress::inc_and_check_user_abort
void inc_and_check_user_abort(GB_ERROR &error)
Definition: arb_progress.h:332
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void TREE_install_update_callbacks(TREE_canvas *ntw)
Definition: TreeDisplay.cxx:4049
primer_design.hxx
GB_save_quick
GB_ERROR GB_save_quick(GBDATA *gbd, const char *refpath)
Definition: ad_save_load.cxx:1593
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Definition: Group.hxx:20
AW_system_async_cb
void AW_system_async_cb(AW_window *, const char *command)
Definition: aw_system.hxx:24
awti_import.hxx
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void aw_message_if(GB_ERROR error)
Definition: aw_msg.hxx:21
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AW_window * create_tree_window(AW_root *aw_root, AWT_graphic *awd)
GBS_global_string_copy
char * GBS_global_string_copy(const char *templat,...)
Definition: arb_msg.cxx:194
AWT_insert_DBcompression_selector
void AWT_insert_DBcompression_selector(AW_window *aww, const char *awar_name)
Definition: arb_spec.cxx:62
GLOBAL
NT_global GLOBAL
Definition: NT_main.cxx:46
AWT_canvas::gb_main
GBDATA * gb_main
Definition: canvas.hxx:346
NT_pseudo_species_to_organism
static void NT_pseudo_species_to_organism(AW_window *, TREE_canvas *ntw)
Definition: NT_extern.cxx:677
label
const char * label
Definition: item_sel_list.cxx:118
AW_window::create_button
void create_button(const char *macro_name, AW_label label, const char *mnemonic=NULp, const char *color=NULp)
Definition: AW_button.cxx:448
AWT_openURL
void AWT_openURL(AW_window *aww, const char *url)
Definition: www.cxx:267
UNCOVERED
#define UNCOVERED()
Definition: arb_assert.h:380
NT_create_resort_awars
void NT_create_resort_awars(AW_root *awr, AW_default aw_def)
Definition: NT_sort.cxx:199
NT_reload_tree_event
void NT_reload_tree_event(AW_root *, TREE_canvas *ntw, bool unzoom_and_expose)
Definition: TreeCallbacks.cxx:887
GBT_get_species_data
GBDATA * GBT_get_species_data(GBDATA *gb_main)
Definition: aditem.cxx:105
s
GB_write_int const char s
Definition: AW_awar.cxx:154
max
#define max(a, b)
Definition: f2c.h:154
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