source: tags/ms_r17q3/NTREE/NT_extern.cxx

Last change on this file was 16391, checked in by westram, 7 years ago
  • full update from child 'aci' into 'trunk'
    • allow to view console from inside ARB
    • slightly tweaked ACI trace
  • adds: log:branches/aci@16386:16390
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 77.3 KB
Line 
1// =============================================================== //
2//                                                                 //
3//   File      : NT_extern.cxx                                     //
4//   Purpose   :                                                   //
5//                                                                 //
6//   Institute of Microbiology (Technical University Munich)       //
7//   http://www.arb-home.de/                                       //
8//                                                                 //
9// =============================================================== //
10
11#include "map_viewer.h"
12#include "NT_local.h"
13#include "ad_trees.h"
14#include "NT_group_search.h"
15
16#include <seq_quality.h>
17#include <multi_probe.hxx>
18#include <st_window.hxx>
19#include <GEN.hxx>
20#include <EXP.hxx>
21
22#include <TreeCallbacks.hxx>
23#include <AW_rename.hxx>
24#include <probe_gui.hxx>
25#include <primer_design.hxx>
26#include <gde.hxx>
27#include <awtc_submission.hxx>
28
29#include <macros.hxx>
30#include <nds.h>
31#include <db_query.h>
32#include <dbui.h>
33#include <refentries.h>
34#include <insdel.h>
35
36#include <awti_export.hxx>
37#include <awti_import.hxx>
38
39#include <awt.hxx>
40#include <awt_input_mask.hxx>
41#include <awt_sel_boxes.hxx>
42#include <awt_www.hxx>
43#include <awt_TreeAwars.hxx>
44#include <awt_misc.hxx>
45
46#include <aw_color_groups.hxx>
47#include <aw_advice.hxx>
48#include <aw_preset.hxx>
49#include <aw_awars.hxx>
50#include <aw_global_awars.hxx>
51#include <aw_file.hxx>
52#include <aw_msg.hxx>
53#include <arb_progress.h>
54#include <aw_root.hxx>
55#include <aw_question.hxx>
56#include <aw_select.hxx>
57#include <rootAsWin.h>
58
59#include <ad_cb.h>
60
61#include <arb_strbuf.h>
62#include <arb_strarray.h>
63#include <arb_file.h>
64#include <arb_version.h>
65
66#if defined(DEVEL_RALF)
67# define TRACE_GROUP_SELECTION
68#endif
69
70#define AWAR_EXPORT_NDS              "tmp/export_nds"
71#define AWAR_EXPORT_NDS_SEPARATOR    AWAR_EXPORT_NDS "/separator"
72#define AWAR_MARKED_SPECIES_COUNTER  "tmp/disp_marked_species"
73#define AWAR_NTREE_TITLE_MODE        "tmp/title_mode"
74
75void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
76
77void       create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
78AW_window *create_insertDeleteColumn_window(AW_root *root);
79AW_window *create_insertDeleteBySAI_window(AW_root *root, GBDATA *gb_main);
80
81AW_window *create_tree_window(AW_root *aw_root, AWT_graphic *awd);
82
83static void nt_changesecurity(AW_root *aw_root) {
84    int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
85    GB_push_transaction(GLOBAL.gb_main);
86    GB_change_my_security(GLOBAL.gb_main, level);
87    GB_pop_transaction(GLOBAL.gb_main);
88}
89
90static void export_nds_cb(AW_window *aww, bool do_print) {
91    AW_root *aw_root = aww->get_root();
92    char    *name    = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
93    FILE    *out     = fopen(name, "w");
94
95    if (!out) {
96        aw_message("Error: Cannot open and write to file");
97    }
98    else {
99        GB_transaction ta(GLOBAL.gb_main);
100
101        make_node_text_init(GLOBAL.gb_main);
102        NDS_Type  nds_type  = (NDS_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
103        char     *tree_name = aw_root->awar(AWAR_TREE)->read_string();
104
105        for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
106             gb_species;
107             gb_species = GBT_next_marked_species(gb_species))
108        {
109            const char *buf = make_node_text_nds(GLOBAL.gb_main, gb_species, nds_type, 0, tree_name);
110            fprintf(out, "%s\n", buf);
111        }
112        AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
113        fclose(out);
114        if (do_print) {
115            GB_ERROR error = GB_textprint(name);
116            if (error) aw_message(error);
117        }
118        free(tree_name);
119    }
120    free(name);
121}
122
123static AW_window *create_nds_export_window(AW_root *root) {
124    AW_window_simple *aws = new AW_window_simple;
125    aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
126    aws->load_xfig("sel_box_nds.fig");
127
128    aws->callback(AW_POPDOWN);
129    aws->at("close");
130    aws->create_button("CLOSE", "CLOSE", "C");
131
132    aws->callback(makeHelpCallback("arb_export_nds.hlp"));
133    aws->at("help");
134    aws->create_button("HELP", "HELP", "H");
135
136    aws->at("save");
137    aws->callback(makeWindowCallback(export_nds_cb, false));
138    aws->create_button("SAVE", "SAVE", "S");
139
140    aws->at("print");
141    aws->callback(makeWindowCallback(export_nds_cb, true));
142    aws->create_button("PRINT", "PRINT", "P");
143
144    aws->at("toggle1");
145    aws->label("Column output");
146    aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR, true);
147    aws->insert_default_option("Space padded",    "S", NDS_OUTPUT_SPACE_PADDED);
148    aws->insert_option        ("TAB separated",   "T", NDS_OUTPUT_TAB_SEPARATED);
149    aws->insert_option        ("Comma separated", "C", NDS_OUTPUT_COMMA_SEPARATED);
150    aws->update_option_menu();
151
152    AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS);
153
154    return aws;
155}
156
157static void create_export_nds_awars(AW_root *awr, AW_default def)
158{
159    AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds");
160    awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, NDS_OUTPUT_SPACE_PADDED, def);
161}
162
163static void selectedSpeciesChanged_cb(AW_root *awr) {
164    const char *value = awr->awar(AWAR_SPECIES_NAME)->read_char_pntr();
165    awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
166    if (value[0]) {
167        awr->awar(AWAR_GROUP)->write_pointer(NULL); // deselect group when species gets selected
168#if defined(TRACE_GROUP_SELECTION)
169        fputs("clear AWAR_GROUP (because species selected)\n", stderr);
170#endif
171    }
172}
173
174static void expert_mode_changed_cb(AW_root *aw_root) {
175    aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
176}
177
178static void NT_toggle_expert_mode(AW_window *aww) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
179#if defined(ARB_MOTIF)
180static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
181#endif
182
183static void nt_create_all_awars(AW_root *awr) {
184    // creates awars for all modules reachable from ARB_NT main window
185
186    awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT);
187    if (GB_read_clients(GLOBAL.gb_main)>=0) {
188        awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
189    }
190    else {
191        awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT);
192    }
193
194    awr->awar_string(AWAR_SPECIES_NAME, "",     GLOBAL.gb_main);
195    awr->awar_string(AWAR_SAI_NAME, "",     GLOBAL.gb_main);
196    awr->awar_string(AWAR_SAI_GLOBAL, "",     GLOBAL.gb_main);
197    awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown",    GLOBAL.gb_main);
198    awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info",    GLOBAL.gb_main);
199    awr->awar(AWAR_SPECIES_NAME)->add_callback(selectedSpeciesChanged_cb);
200    awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
201
202    awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
203
204    GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
205    EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
206#if defined(DEBUG)
207    AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT);
208#endif // DEBUG
209
210    AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
211
212    awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT);
213    awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
214#if defined(DEBUG) && 0
215    awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
216#endif // DEBUG
217
218    create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT);
219    create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
220    create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
221    create_trees_var(awr, AW_ROOT_DEFAULT);
222    DBUI::create_dbui_awars(awr);
223    AP_create_consensus_var(awr, AW_ROOT_DEFAULT);
224    {
225        GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, 0, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT);
226        if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
227    }
228    NT_create_transpro_variables(awr, AW_ROOT_DEFAULT);
229    NT_create_resort_awars(awr, AW_ROOT_DEFAULT);
230    NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT);
231    NT_create_trackAliChanges_Awars(awr, GLOBAL.gb_main);
232
233    NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
234    NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
235    create_nds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, false);
236    create_export_nds_awars(awr, AW_ROOT_DEFAULT);
237    create_group_search_awars(awr, AW_ROOT_DEFAULT);
238    TREE_create_awars(awr, GLOBAL.gb_main);
239
240    awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
241    awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
242
243    AWTC_create_submission_variables(awr, GLOBAL.gb_main);
244    NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
245    NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar
246    SQ_create_awars(awr, AW_ROOT_DEFAULT);
247    RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT);
248
249    NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT);
250
251    GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
252    if (!error) {
253        AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
254        awar_expert->add_callback(expert_mode_changed_cb);
255        awar_expert->touch();
256
257        awt_create_aww_vars(awr, AW_ROOT_DEFAULT);
258    }
259
260    if (error) aw_message(error);
261}
262
263// --------------------------------------------------------------------------------
264
265bool nt_disconnect_from_db(AW_root *aw_root, GBDATA*& gb_main_ref) {
266    // ask user if DB was not saved
267    // returns true if user allows to quit
268
269    // @@@ code here could as well be applied to both merge DBs
270    // - question about saving only with target DB!
271
272    if (gb_main_ref) {
273        if (GB_read_clients(gb_main_ref)>=0) {
274            if (GB_read_clock(gb_main_ref) > GB_last_saved_clock(gb_main_ref)) {
275                long secs;
276                secs = GB_last_saved_time(gb_main_ref);
277
278#if defined(DEBUG)
279                secs =  GB_time_of_day(); // simulate "just saved"
280#endif // DEBUG
281
282                const char *quit_buttons = "Quit ARB,Do NOT quit";
283                if (secs) {
284                    secs = GB_time_of_day() - secs;
285                    if (secs>10) {
286                        char *question = GBS_global_string_copy("You last saved your data %li:%li minutes ago\nSure to quit ?", secs/60, secs%60);
287                        int   dontQuit = aw_question("quit_arb", question, quit_buttons);
288                        free(question);
289                        if (dontQuit) {
290                            return false;
291                        }
292                    }
293                }
294                else {
295                    if (aw_question("quit_arb", "You never saved any data\nSure to quit ???", quit_buttons)) {
296                        return false;
297                    }
298                }
299            }
300        }
301
302        GBCMS_shutdown(gb_main_ref);
303
304        GBDATA *gb_main = gb_main_ref;
305        gb_main_ref     = NULL;                  // avoid further usage
306
307        nt_assert(aw_root);
308#if defined(WARN_TODO)
309#warning instead of directly calling the following functions, try to add them as GB_atclose-callbacks
310#endif
311        aw_root->unlink_awars_from_DB(gb_main);
312        AWT_destroy_input_masks();
313#if defined(DEBUG)
314        AWT_browser_forget_db(gb_main);
315#endif // DEBUG
316
317        GB_close(gb_main);
318    }
319    return true;
320}
321
322static void nt_run(const char *command) {
323    GB_ERROR error = GBK_system(command);
324    if (error) {
325        fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
326#if defined(DEBUG)
327        GBK_dump_backtrace(stderr, "nt_run-error");
328#endif
329    }
330}
331
332void NT_start(const char *arb_ntree_args, bool restart_with_new_ARB_PID) {
333    char *command = GBS_global_string_copy("arb_launcher --async %s %s", restart_with_new_ARB_PID ? "arb" : "arb_ntree", arb_ntree_args);
334    nt_run(command);
335    free(command);
336}
337
338__ATTR__NORETURN static void really_exit(int exitcode, bool kill_my_clients) {
339    if (kill_my_clients) {
340        nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
341    }
342    exit(exitcode);
343}
344
345void NT_exit(AW_window *aws, int exitcode) {
346    AW_root *aw_root = aws->get_root();
347    AWTI_cleanup_importer();
348    shutdown_macro_recording(aw_root);
349    bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
350    if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
351        really_exit(exitcode, is_server_and_has_clients);
352    }
353}
354void NT_restart(AW_root *aw_root, const char *arb_ntree_args) {
355    // restarts arb_ntree (with new ARB_PID)
356    bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
357    if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main))  {
358        NT_start(arb_ntree_args, true);
359        really_exit(EXIT_SUCCESS, is_server_and_has_clients);
360    }
361}
362
363static void nt_start_2nd_arb(AW_window *aww, bool quit) {
364    // start 2nd arb with intro window
365    AW_root *aw_root = aww->get_root();
366    char    *dir4intro;
367    GB_split_full_path(aw_root->awar(AWAR_DB_PATH)->read_char_pntr(), &dir4intro, NULL, NULL, NULL);
368    if (!dir4intro) {
369        dir4intro = ARB_strdup(".");
370    }
371
372    if (quit) {
373        NT_restart(aw_root, dir4intro);
374    }
375    else {
376        NT_start(dir4intro, true);
377    }
378    free(dir4intro);
379}
380
381// --------------------------------------------------------------------------------
382
383static void NT_save_quick_cb(AW_window *aww) {
384    AW_root *awr      = aww->get_root();
385    char    *filename = awr->awar(AWAR_DB_PATH)->read_string();
386
387    awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
388
389    GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
390    free( filename);
391    if (error) aw_message(error);
392    else       AW_refresh_fileselection(awr, AWAR_DBBASE);
393}
394
395
396static void NT_save_quick_as_cb(AW_window *aww) {
397    AW_root  *awr      = aww->get_root();
398    char     *filename = awr->awar(AWAR_DB_PATH)->read_string();
399    GB_ERROR  error    = GB_save_quick_as(GLOBAL.gb_main, filename);
400    if (!error) AW_refresh_fileselection(awr, AWAR_DBBASE);
401    aww->hide_or_notify(error);
402
403    free(filename);
404}
405
406#define AWAR_DB_TYPE          AWAR_DBBASE "/type"      // created by AWT_insert_DBsaveType_selector
407#define AWAR_DB_COMPRESSION   AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector
408#define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name"
409
410static void NT_save_as_cb(AW_window *aww) {
411    AW_root    *awr      = aww->get_root();
412    char       *filename = awr->awar(AWAR_DB_PATH)->read_string();
413    const char *atype    = awr->awar(AWAR_DB_TYPE)->read_char_pntr();
414    const char *ctype    = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr();
415    char       *savetype = GBS_global_string_copy("%s%s", atype, ctype);
416
417    awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
418    GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype);
419    if (!error) AW_refresh_fileselection(awr, AWAR_DBBASE);
420    aww->hide_or_notify(error);
421
422    free(savetype);
423    free(filename);
424}
425
426static AW_window *NT_create_save_quick_as_window(AW_root *aw_root, const char *base_name) {
427    static AW_window_simple *aws = 0;
428    if (!aws) {
429        aws = new AW_window_simple;
430        aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as");
431        aws->load_xfig("save_as.fig");
432
433        aws->at("close");
434        aws->callback(AW_POPDOWN);
435        aws->create_button("CLOSE", "CLOSE", "C");
436
437        aws->callback(makeHelpCallback("save.hlp"));
438        aws->at("help");
439        aws->create_button("HELP", "HELP", "H");
440
441        AW_create_standard_fileselection(aws, base_name);
442
443        aws->at("comment");
444        aws->create_text_field(AWAR_DB_COMMENT);
445
446        aws->at("save");
447        aws->callback(NT_save_quick_as_cb);
448        aws->create_button("SAVE", "SAVE", "S");
449    }
450    return aws;
451}
452
453static void NT_database_optimization(AW_window *aww) {
454    arb_progress progress("Optimizing database compression", 2);
455
456    GB_push_my_security(GLOBAL.gb_main);
457    GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
458    if (!error) {
459        ConstStrArray ali_names;
460        GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
461
462        arb_progress ali_progress("Optimizing sequence data", ali_names.size());
463        ali_progress.allow_title_reuse();
464
465        error = GBT_check_data(GLOBAL.gb_main, 0);
466        error = GB_end_transaction(GLOBAL.gb_main, error);
467
468        if (!error) {
469            char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string();
470            for (int i = 0; ali_names[i]; ++i) {
471                error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
472                ali_progress.inc_and_check_user_abort(error);
473            }
474            free(tree_name);
475        }
476    }
477    progress.inc_and_check_user_abort(error);
478
479    if (!error) {
480        error = GB_optimize(GLOBAL.gb_main);
481        progress.inc_and_check_user_abort(error);
482    }
483
484    GB_pop_my_security(GLOBAL.gb_main);
485    aww->hide_or_notify(error);
486}
487
488static AW_window *NT_create_database_optimization_window(AW_root *aw_root) {
489    static AW_window_simple *aws = 0;
490    if (aws) return (AW_window *)aws;
491    GB_transaction ta(GLOBAL.gb_main);
492
493    const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
494    aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree);
495
496    aws = new AW_window_simple;
497    aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression");
498    aws->load_xfig("optimize.fig");
499
500    aws->at("trees");
501    awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME, true);
502
503    aws->at("close");
504    aws->callback(AW_POPDOWN);
505    aws->create_button("CLOSE", "CLOSE", "C");
506
507    aws->callback(makeHelpCallback("optimize.hlp"));
508    aws->at("help");
509    aws->create_button("HELP", "HELP", "H");
510
511    aws->at("go");
512    aws->callback(NT_database_optimization);
513    aws->create_button("GO", "GO");
514    return aws;
515}
516
517static AW_window *NT_create_save_as(AW_root *aw_root, const char *base_name)
518{
519    static AW_window_simple *aws = 0;
520    if (aws) return (AW_window *)aws;
521
522    aws = new AW_window_simple;
523    aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
524    aws->load_xfig("save_as.fig");
525
526    aws->at("close");
527    aws->callback(AW_POPDOWN);
528    aws->create_button("CLOSE", "CLOSE", "C");
529
530    aws->at("help");
531    aws->callback(makeHelpCallback("save.hlp"));
532    aws->create_button("HELP", "HELP", "H");
533
534    AW_create_standard_fileselection(aws, base_name);
535
536    aws->at("type");
537    AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE);
538
539    aws->at("compression");
540    AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION);
541
542    aws->at("optimize");
543    aws->callback(NT_create_database_optimization_window);
544    aws->help_text("optimize.hlp");
545    aws->create_autosize_button("OPTIMIZE", "Optimize database compression");
546
547    aws->at("save");
548    aws->callback(NT_save_as_cb);
549    aws->create_button("SAVE", "SAVE", "S");
550
551    aws->at("comment");
552    aws->create_text_field(AWAR_DB_COMMENT);
553
554    return aws;
555}
556
557static void NT_undo_cb(AW_window*, GB_UNDO_TYPE undo_type, TREE_canvas *ntw) {
558    GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type);
559    if (error) aw_message(error);
560    else {
561        GB_transaction ta(GLOBAL.gb_main);
562        AWT_auto_refresh allowed_on(ntw);
563        ntw->request_refresh();
564    }
565}
566
567enum streamSource { FROM_PIPE, FROM_FILE };
568static char *stream2str(streamSource source, const char *commandOrFile) {
569    char *output = 0;
570    FILE *in     = 0;
571
572    switch (source) {
573        case FROM_PIPE: in = popen(commandOrFile, "r"); break;
574        case FROM_FILE: in = fopen(commandOrFile, "rt"); break;
575    }
576
577    if (in) {
578        GBS_strstruct *out = GBS_stropen(2000);
579        int c;
580
581        while (EOF != (c = fgetc(in))) GBS_chrcat(out, c);
582
583        switch (source) {
584            case FROM_PIPE: pclose(in); break;
585            case FROM_FILE: fclose(in); break;
586        }
587
588        // skip trailing linefeeds
589        long offset = GBS_memoffset(out);
590        while (offset>0 && GBS_mempntr(out)[offset-1] == '\n') {
591            GBS_str_cut_tail(out, 1);
592            offset--;
593        }
594
595        output = GBS_strclose(out);
596    }
597    return output;
598}
599
600inline void removeTrailingNewlines(char *str) {
601    char *eos = strchr(str, 0)-1;
602    while (eos >= str && eos[0] == '\n') *eos-- = 0;
603}
604
605inline void append_named_value(GBS_strstruct *out, const char *prefix, const char *value) {
606    GBS_strcat(out, GBS_global_string("%-*s: %s\n", 12, prefix, value));
607}
608inline void append_command_output(GBS_strstruct *out, const char *prefix, const char *command) {
609    char *output = stream2str(FROM_PIPE, command);
610    if (output) {
611        removeTrailingNewlines(output);
612        if (strcmp(output, "unknown") != 0) append_named_value(out, prefix, output);
613        free(output);
614    }
615}
616
617static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) {
618    DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
619    nt_mode_event(NULL, canvas, mode);
620}
621
622static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) {
623    AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
624    if (tree_root) {
625        AWT_auto_refresh allowed_on(ntw);
626        GB_transaction   ta(ntw->gb_main);
627
628        NT_mark_all_cb(NULL, ntw, 0); // unmark all
629        tree_root->mark_duplicates();
630        ntw->request_structure_update();
631    }
632}
633
634static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) {
635    GB_transaction  ta(ntw->gb_main);
636    AP_tree        *tree_root = AWT_TREE(ntw)->get_root_node();
637
638    if (tree_root) {
639        AWT_auto_refresh allowed_on(ntw);
640        tree_root->justify_branch_lenghs(ntw->gb_main);
641        ntw->request_save_and_zoom_reset();
642    }
643}
644
645#if defined(DEBUG)
646static void NT_fix_database(AW_window *) {
647    GB_ERROR err = 0;
648    err = GB_fix_database(GLOBAL.gb_main);
649    if (err) aw_message(err);
650}
651#endif
652
653static void relink_pseudo_species_to_organisms(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash) {
654    if (ref_gb_node) {
655        if (GEN_is_pseudo_gene_species(ref_gb_node)) {
656            GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
657
658            if (gb_organism) {
659                char *name = GBT_read_string(gb_organism, "name");
660
661                if (name) {
662                    freeset(ref_name, name);
663                    ref_gb_node = gb_organism;
664                }
665            }
666        }
667    }
668}
669
670static void NT_pseudo_species_to_organism(AW_window *, TREE_canvas *ntw) {
671    GB_transaction  ta(ntw->gb_main);
672    AP_tree        *tree_root = AWT_TREE(ntw)->get_root_node();
673
674    if (tree_root) {
675        AWT_auto_refresh allowed_on(ntw);
676
677        GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
678        tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
679        GBS_free_hash(organism_hash);
680        ntw->request_save();
681    }
682}
683
684
685// #########################################
686// #########################################
687// ###                                   ###
688// ##          user mask section          ##
689// ###                                   ###
690// #########################################
691// #########################################
692
693struct nt_item_type_species_selector FINAL_TYPE : public awt_item_type_selector {
694    nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
695    ~nt_item_type_species_selector() OVERRIDE {}
696
697    const char *get_self_awar() const OVERRIDE {
698        return AWAR_SPECIES_NAME;
699    }
700    size_t get_self_awar_content_length() const OVERRIDE {
701        return 12; // should be enough for "nnaammee.999"
702    }
703    GBDATA *current(AW_root *root, GBDATA *gb_main) const OVERRIDE { // give the current item
704        char           *species_name = root->awar(get_self_awar())->read_string();
705        GBDATA         *gb_species   = 0;
706
707        if (species_name[0]) {
708            GB_transaction ta(gb_main);
709            gb_species = GBT_find_species(gb_main, species_name);
710        }
711
712        free(species_name);
713        return gb_species;
714    }
715    const char *getKeyPath() const OVERRIDE { // give the keypath for items
716        return CHANGE_KEY_PATH;
717    }
718};
719
720static nt_item_type_species_selector item_type_species;
721
722static void NT_open_mask_window(AW_window *aww, int id, GBDATA *gb_main) {
723    const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
724    nt_assert(descriptor);
725    if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
726}
727
728static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
729    AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
730}
731static AW_window *create_colorize_species_window(AW_root *aw_root) {
732    return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
733}
734
735static void NT_update_marked_counter(GBDATA*, AW_window* aww) {
736    /*! Updates marked counter and issues redraw on tree if number of marked species changes.
737     * Called on any change of species_information container.
738     */
739    long        count   = GBT_count_marked_species(GLOBAL.gb_main);
740    const char *buffer  = count ? GBS_global_string("%li marked", count) : "";
741    AW_awar    *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
742    char       *oldval  = counter->read_string();
743    if (strcmp(oldval, buffer)) {
744        counter->write_string(buffer);
745        aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
746    }
747    free(oldval);
748}
749
750// --------------------------------------------------------------------------------------------------
751
752static void NT_alltree_remove_leafs(AW_window *, GBT_TreeRemoveType mode, GBDATA *gb_main) {
753    GB_ERROR       error = 0;
754    GB_transaction ta(gb_main);
755
756    ConstStrArray tree_names;
757    GBT_get_tree_names(tree_names, gb_main, false);
758
759    if (!tree_names.empty()) {
760        int treeCount = tree_names.size();
761
762        const char *whats_removed = NULL;
763        switch (mode) {
764            case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
765            case GBT_REMOVE_MARKED:  whats_removed = "marked";  break;
766            default: nt_assert(0); break;
767        }
768
769        const char *task = GBS_global_string("Deleting %s from %i trees", whats_removed, treeCount);
770
771        arb_progress  progress(task, treeCount);
772        GB_HASH      *species_hash = GBT_create_species_hash(gb_main);
773
774        int modified = 0;
775
776        for (int t = 0; t<treeCount && !error; t++) {
777            progress.subtitle(tree_names[t]);
778            TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
779            if (!tree) {
780                aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
781            }
782            else {
783                int removed        = 0;
784                int groups_removed = 0;
785
786                tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
787
788                nt_assert(removed >= groups_removed);
789
790                if (!tree) {
791                    aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
792                }
793                else {
794                    if (removed>0) {
795                        error = GBT_write_tree(gb_main, tree_names[t], tree);
796                        if (error) {
797                            aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
798                        }
799                        else {
800                            if (groups_removed>0) {
801                                aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
802                            }
803                            else {
804                                aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
805                            }
806                            modified++;
807                        }
808                    }
809                    UNCOVERED();
810                    destroy(tree);
811                }
812            }
813            progress.inc_and_check_user_abort(error);
814        }
815
816        if (modified) {
817            aw_message(GBS_global_string("Changed %i of %i trees.", modified, treeCount));
818        }
819        else {
820            aw_message("No tree modified");
821        }
822
823        GBS_free_hash(species_hash);
824    }
825
826    aw_message_if(ta.close(error));
827}
828
829TreeNode *NT_get_tree_root_of_canvas(TREE_canvas *ntw) {
830    AWT_graphic_tree *tree = AWT_TREE(ntw);
831    if (tree) {
832        AP_tree *root = tree->get_root_node();
833        if (root) return root;
834    }
835    return NULL;
836}
837
838// --------------------------------------------------------------------------------------------------
839
840static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
841    GB_transaction ta(gb_main);
842    GBT_mark_all(gb_main, 0);
843
844    DBItemSetIter end = referred.end();
845    for (DBItemSetIter s = referred.begin(); s != end; ++s) {
846        GB_write_flag(*s, 1);
847    }
848    return ARB_ERROR();
849}
850
851static AW_window *create_mark_by_refentries_window(AW_root *awr, GBDATA *gbmain) {
852    static AW_window *aws = NULL;
853    if (!aws) {
854        static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
855        aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULL, "Mark referenced", mark_referred_species);
856    }
857    return aws;
858}
859
860// --------------------------------------------------------------------------------------------------
861
862static void merge_from_to(AW_root *awr, const char *db_awar_name, bool merge_to) {
863    const char *db_name  = awr->awar(db_awar_name)->read_char_pntr();
864    char       *quotedDB = GBK_singlequote(db_name);
865
866    AWT_system_cb(
867        GBS_global_string(
868            merge_to
869            ? "arb_ntree : %s &"
870            : "arb_ntree %s : &",
871            quotedDB)
872        );
873
874    free(quotedDB);
875}
876
877static void merge_from_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, false); }
878static void merge_into_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, true); }
879
880static AW_window *NT_create_merge_from_window(AW_root *awr) {
881    static char *awar_name = NULL; // do not free, bound to callback
882    AW_window *aw_from     =
883        awt_create_load_box(awr, "Merge data from", "other ARB database",
884                            ".", ".arb", &awar_name,
885                            makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
886    return aw_from;
887}
888static AW_window *NT_create_merge_to_window(AW_root *awr) {
889    static char *awar_name = NULL; // do not free, bound to callback
890    AW_window *aw_to       =
891        awt_create_load_box(awr, "Merge data to", "other ARB database",
892                            ".", ".arb", &awar_name,
893                            makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
894                            makeWindowCallback(AW_POPDOWN), NULL);
895    return aw_to;
896}
897
898// --------------------------------------------------------------------------------------------------
899
900static void update_main_window_title(AW_root* awr, AW_window_menu_modes* aww, int clone) {
901    const char* filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
902    if (clone) {
903        aww->set_window_title(GBS_global_string("%s - ARB (%i)",  filename, clone));
904    }
905    else {
906        aww->set_window_title(GBS_global_string("%s - ARB", filename));
907    }
908}
909
910static void canvas_tree_awar_changed_cb(AW_awar *, bool, TREE_canvas *ntw) {
911    NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
912    AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
913    TREE_auto_jump_cb(NULL, ntw, AP_JUMP_REASON_TREE);
914}
915
916class TREE_canvas_registry {
917    int          count;
918    TREE_canvas *canvas[MAX_NT_WINDOWS];
919
920    static TREE_canvas_registry *SINGLETON;
921
922    TREE_canvas_registry() : count(0) {
923        AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
924    }
925
926public:
927    static TREE_canvas_registry& instance() {
928        if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
929        return *SINGLETON;
930    }
931
932    void register_canvas(TREE_canvas *ntw) {
933        nt_assert(count<MAX_NT_WINDOWS);
934        nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
935        canvas[count++] = ntw;
936        ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
937    }
938
939    int get_count() const  { return count; }
940
941    TREE_canvas *get_canvas(int idx) const {
942        if (idx<0 || idx>=count) return NULL;
943        return canvas[idx];
944    }
945};
946
947TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULL;
948
949TREE_canvas *NT_get_canvas_by_index(int idx) {
950    /*! return canvas with index 'idx' [0...MAX_NT_WINDOWS-1] */
951    nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
952    return TREE_canvas_registry::instance().get_canvas(idx);
953}
954
955#if defined(TRACE_GROUP_SELECTION)
956static TREE_canvas *find_canvas_showing(AWT_graphic_tree *agt) {
957    // look for (registered) canvas showing given AWT_graphic_tree
958    // returns NULL if none found
959    const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
960
961    int maxIdx = reg.get_count();
962    for (int32_t i = 0; i<maxIdx; ++i) {
963        TREE_canvas *ntw = reg.get_canvas(i);
964        if (ntw->gfx == agt) return ntw;
965    }
966    return NULL;
967}
968#endif
969
970void NT_fill_canvas_selection_list(class AW_selection_list *sellst, TREE_canvas *to_skip) {
971    /*! insert canvases into selection list (using canvas-indices as values)
972     */
973    const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
974
975    int maxIdx = reg.get_count();
976    for (int32_t i = 0; i<maxIdx; ++i) {
977        TREE_canvas *ntw = reg.get_canvas(i);
978        if (ntw && ntw != to_skip) {
979            nt_assert(ntw->get_awar_tree());
980            const char *treename    = ntw->get_awar_tree()->read_char_pntr();
981            const char *description = i
982                ? GBS_global_string("ARB (%i):  %s", i, treename)
983                : GBS_global_string("ARB main: %s", treename);
984            sellst->insert(description, i);
985        }
986    }
987}
988
989// ----------------------------------
990//      group-selection handlers
991
992static bool track_group_selection_by_canvas = true;
993
994static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) {
995    const Group& group = gfx->get_selected_group();
996
997#if defined(TRACE_GROUP_SELECTION)
998    fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track");
999    TREE_canvas *ntw = find_canvas_showing(gfx);
1000    if (group.is_valid()) {
1001        fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name());
1002    }
1003    else {
1004        fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index());
1005    }
1006#endif
1007
1008    if (track_group_selection_by_canvas) {
1009        // set group-awar:
1010        gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULL if !group.is_valid()
1011    }
1012}
1013
1014static void group_awar_changed_cb(AW_root *awr) {
1015    AW_awar *awar_group      = awr->awar(AWAR_GROUP);
1016    GBDATA  *gb_wanted_group = awar_group->read_pointer();
1017
1018    GBDATA *gb_wanted_tree = NULL;
1019    {
1020        if (gb_wanted_group) {
1021            GB_transaction ta(gb_wanted_group);
1022            gb_wanted_tree = GB_get_father(gb_wanted_group);
1023            awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected
1024#if defined(TRACE_GROUP_SELECTION)
1025            fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr);
1026#endif
1027        }
1028#if defined(TRACE_GROUP_SELECTION)
1029        const char *group_name = NULL;
1030        if (gb_wanted_group) {
1031            GB_transaction  ta(gb_wanted_group);
1032            GBDATA         *gb_name = GB_entry(gb_wanted_group, "group_name");
1033            if (gb_name) group_name = GB_read_char_pntr(gb_name);
1034        }
1035        fprintf(stderr, "group awar changed to %p", gb_wanted_group);
1036        if (group_name) fprintf(stderr, " (='%s')", group_name);
1037        fputc('\n', stderr);
1038#endif
1039    }
1040
1041    LocallyModify<bool> ignore_group_selection_by_canvas(track_group_selection_by_canvas, false);
1042
1043    {
1044        const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1045
1046        int maxIdx = reg.get_count();
1047        for (int32_t i = 0; i<maxIdx; ++i) {
1048            TREE_canvas      *ntw        = reg.get_canvas(i);
1049            AWT_graphic_tree *agt        = AWT_TREE(ntw);
1050            const Group&      curr_group = agt->get_selected_group();
1051
1052            GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree();
1053            if (gb_curr_tree == gb_wanted_tree) {
1054                AWT_auto_refresh allowed_on(ntw);
1055                if (!curr_group.is_valid() ||                       // no group selected
1056                    curr_group.get_group_data() != gb_wanted_group) // wrong group selected
1057                {
1058                    agt->select_group(gb_wanted_group);
1059                    ntw->request_refresh();
1060                }
1061                // perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group)
1062                TREE_auto_jump_cb(NULL, ntw, AP_JUMP_REASON_GROUP);
1063            }
1064            else {
1065                if (curr_group.is_valid()) {
1066                    AWT_auto_refresh allowed_on(ntw);
1067                    agt->deselect_group();
1068                    ntw->request_refresh();
1069                }
1070            }
1071        }
1072    }
1073}
1074
1075// ----------------------------
1076//      create main window
1077
1078static AW_window *popup_new_main_window(AW_root *awr, int clone, TREE_canvas **result_ntw) {
1079    /*! create ARB_NTREE main window
1080     * @param awr application root
1081     * @param clone == 0 -> first window (full functionality); >0 -> additional tree views (restricted functionality)
1082     * @param result_ntw is set to the created TREE_canvas (passed pointer may be NULL if result is not needed)
1083     */
1084    GB_push_transaction(GLOBAL.gb_main);
1085
1086    char        window_title[256];
1087    const char *awar_tree = NULL;
1088
1089    if (clone) {
1090        awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
1091        sprintf(window_title, "ARB_NT_%i", clone);
1092    }
1093    else {
1094        awar_tree = AWAR_TREE;
1095        sprintf(window_title, "ARB_NT");
1096    }
1097    AW_window_menu_modes *awm = new AW_window_menu_modes;
1098    awm->init(awr, window_title, window_title, 0, 0);
1099
1100    awr->awar(AWAR_DB_NAME)
1101       ->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1102       ->update();
1103
1104    awm->button_length(5);
1105
1106    if (!clone) AW_init_color_group_defaults("arb_ntree");
1107
1108    AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1109
1110    if (!clone) { // while creating initial window
1111        AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb));
1112        awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb);
1113    }
1114
1115    TREE_canvas *ntw;
1116    {
1117        AW_awar *tree_awar = awr->awar_string(awar_tree);
1118        {
1119            AP_tree_display_style prev_style = tree->get_tree_style();
1120            tree->set_tree_style(AP_LIST_SIMPLE, NULL); // avoid NDS warnings during startup
1121
1122            ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1123            tree->set_tree_style(prev_style, ntw);
1124            ntw->set_mode(AWT_MODE_SELECT);
1125        }
1126
1127        if (result_ntw) *result_ntw = ntw;
1128
1129        {
1130            const char *tree_name          = tree_awar->read_char_pntr();
1131            const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1132
1133            if (existing_tree_name) {
1134                tree_awar->write_string(existing_tree_name);
1135                NT_reload_tree_event(awr, ntw, true); // load first tree
1136            }
1137            else {
1138                AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, 0, "no_tree.hlp");
1139                tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list
1140            }
1141
1142            TREE_canvas_registry::instance().register_canvas(ntw);
1143            AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1144        }
1145    }
1146
1147    TREE_install_update_callbacks(ntw);
1148
1149    bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); //  is this a genome database ? (default = 0 = not a genom db)
1150
1151    WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1152
1153    // --------------
1154    //      File
1155
1156#if defined(DEBUG)
1157    AWT_create_debug_menu(awm);
1158#endif // DEBUG
1159
1160    bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1161
1162    if (clone) {
1163        awm->create_menu("File", "F", AWM_ALL);
1164        if (allow_new_window) {
1165            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**)NULL));
1166        }
1167        awm->insert_menu_topic("close", "Close", "C", 0, AWM_ALL, AW_POPDOWN);
1168    }
1169    else {
1170#if defined(DEBUG)
1171        // add more to debug-menu
1172        awm->sep______________();
1173        awm->insert_menu_topic("fix_db",      "Fix database",            "F", 0, AWM_ALL, NT_fix_database);
1174        awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", 0, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1175        awm->insert_menu_topic("test_compr",  "Test compression",        "T", 0, AWM_ALL, makeWindowCallback(GBT_compression_test,       GLOBAL.gb_main));
1176#endif // DEBUG
1177
1178        awm->create_menu("File", "F", AWM_ALL);
1179        {
1180            // keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1181            awm->insert_menu_topic("save_changes", "Quicksave changes",          "s", "save.hlp",      AWM_ALL, NT_save_quick_cb);
1182            awm->insert_menu_topic("save_all_as",  "Save whole database as ...", "w", "save.hlp",      AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1183            if (allow_new_window) {
1184                awm->sep______________();
1185                awm->insert_menu_topic("new_window", "New window (same database)", "N", "newwindow.hlp", AWM_ALL, makeCreateWindowCallback(popup_new_main_window, clone+1, (TREE_canvas**)NULL));
1186            }
1187            awm->sep______________();
1188            awm->insert_menu_topic("optimize_db",  "Optimize database compression", "O", "optimize.hlp",  AWM_ALL, NT_create_database_optimization_window);
1189            awm->sep______________();
1190
1191            awm->insert_sub_menu("Import",      "I");
1192            {
1193                awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1194                awm->insert_menu_topic("import_seq", "Import from external format",   "I", "arb_import.hlp",     AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1195                GDE_load_menu(awm, AWM_EXP, "Import");
1196            }
1197            awm->close_sub_menu();
1198
1199            awm->insert_sub_menu("Export",      "E");
1200            {
1201                awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1202                awm->insert_menu_topic("export_seqs",   "Export to external format",   "f", "arb_export.hlp",      AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1203                GDE_load_menu(awm, AWM_ALL, "Export");
1204                awm->insert_menu_topic("export_nds",    "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp",  AWM_ALL, create_nds_export_window);
1205            }
1206            awm->close_sub_menu();
1207            awm->sep______________();
1208
1209            insert_macro_menu_entry(awm, false);
1210
1211            awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1212            {
1213                awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback  ("version.hlp"));
1214                awm->insert_menu_topic("bug_report",   "Report bug",                              "b", NULL,          AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1215                awm->insert_menu_topic("mailing_list", "Mailing list",                            "M", NULL,          AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1216            }
1217            awm->close_sub_menu();
1218            awm->sep______________();
1219
1220            awm->insert_menu_topic("new_arb",     "Start second database",      "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1221            awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1222            awm->insert_menu_topic("quit",        "Quit",                       "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_exit, EXIT_SUCCESS));
1223        }
1224
1225        // -----------------
1226        //      Species
1227
1228        awm->create_menu("Species", "c", AWM_ALL);
1229        {
1230            awm->insert_menu_topic("species_search", "Search and query",    "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1231            awm->insert_menu_topic("species_info",   "Species information", "i", "sp_info.hlp",   AWM_ALL, popupinfo_wcb);
1232
1233            awm->sep______________();
1234
1235            NT_insert_mark_submenus(awm, ntw, 1);
1236            awm->insert_menu_topic("mark_by_ref",     "Mark by reference..", "r", "markbyref.hlp",       AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1237            awm->insert_menu_topic("species_colors",  "Colors ...",          "l", "colorize.hlp",        AWM_ALL, create_colorize_species_window);
1238            awm->insert_menu_topic("selection_admin", "Selections ...",      "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1239
1240            awm->sep______________();
1241
1242            awm->insert_sub_menu("Database fields admin", "f");
1243            DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1244            awm->close_sub_menu();
1245            NT_create_mask_submenu(awm);
1246
1247            awm->sep______________();
1248
1249            awm->insert_menu_topic("del_marked",    "Delete Marked Species",    "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1250
1251            awm->insert_sub_menu("Sort Species",         "s");
1252            {
1253                awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp",  AWM_ALL, NT_create_resort_window);
1254                awm->insert_menu_topic("$sort_by_tree",  "According to Phylogeny",        "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1255            }
1256            awm->close_sub_menu();
1257
1258            awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1259            {
1260                awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1261                awm->insert_menu_topic("join_marked",   "Join Marked Species",                        "J", "species_join.hlp",  AWM_EXP, NT_create_species_join_window);
1262            }
1263            awm->close_sub_menu();
1264
1265            awm->sep______________();
1266
1267            awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1268
1269            awm->sep______________();
1270
1271            awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1272
1273            awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1274            {
1275                awm->insert_menu_topic("imp_names",    "Import names from file", "I", "vn_import.hlp",  AWM_EXP, NT_importValidNames);
1276                awm->insert_menu_topic("del_names",    "Delete names from DB",   "D", "vn_delete.hlp",  AWM_EXP, NT_deleteValidNames);
1277                awm->insert_menu_topic("sug_names",    "Suggest valid names",    "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1278                awm->insert_menu_topic("search_names", "Search manually",        "m", "vn_search.hlp",  AWM_EXP, NT_create_searchManuallyNames_window);
1279            }
1280            awm->close_sub_menu();
1281        }
1282
1283        // ----------------------------
1284        //      Genes + Experiment
1285
1286        if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1287
1288        // ------------------
1289        //      Sequence
1290
1291        awm->create_menu("Sequence", "S", AWM_ALL);
1292        {
1293            awm->insert_menu_topic("seq_admin",   "Sequence/Alignment Admin", "A", "ad_align.hlp",   AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)0));
1294            awm->insert_sub_menu("Insert/delete", "I");
1295            {
1296                awm->insert_menu_topic("ins_del_col", ".. column",     "c", "insdel.hlp",     AWM_ALL, create_insertDeleteColumn_window);
1297                awm->insert_menu_topic("ins_del_sai", ".. using SAI",  "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window,  GLOBAL.gb_main));
1298            }
1299            awm->close_sub_menu();
1300            awm->sep______________();
1301
1302            awm->insert_sub_menu("Edit Sequences", "E");
1303            {
1304                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));
1305                awm->insert_menu_topic("new2_arb_edit4", "... plus relatives",            "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1306                awm->insert_menu_topic("old_arb_edit4",  "Using earlier configuration",   "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1307            }
1308            awm->close_sub_menu();
1309
1310            awm->sep______________();
1311
1312            awm->insert_sub_menu("Align Sequences",  "S");
1313            {
1314                awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1315                GDE_load_menu(awm, AWM_ALL, "Align");
1316            }
1317            awm->close_sub_menu();
1318            awm->insert_menu_topic("seq_concat",    "Concatenate Sequences/Alignments", "C", "concatenate.hlp",       AWM_ALL, NT_createConcatenationWindow);
1319            awm->insert_menu_topic("track_changes", "Track alignment changes",          "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1320            awm->sep______________();
1321
1322            awm->insert_menu_topic("dna_2_pro", "Perform translation",      "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1323            awm->insert_menu_topic("arb_dist",  "Distance Matrix + ARB NJ", "D", "dist.hlp",                AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1324            awm->sep______________();
1325
1326            awm->insert_menu_topic("seq_quality",   "Check Sequence Quality", "Q", "seq_quality.hlp",   AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1327            awm->insert_menu_topic("chimera_check", "Chimera Check",          "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1328
1329            awm->sep______________();
1330
1331            GDE_load_menu(awm, AWM_ALL, "Print");
1332        }
1333
1334        // -------------
1335        //      SAI
1336
1337        awm->create_menu("SAI", "A", AWM_ALL);
1338        {
1339            awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1340            awm->insert_sub_menu("Create SAI using ...", "C");
1341            {
1342                awm->insert_menu_topic("sai_max_freq",  "Max. Frequency",                                               "M", "max_freq.hlp",     AWM_EXP, AP_create_max_freq_window);
1343                awm->insert_menu_topic("sai_consensus", "Consensus",                                                    "C", "consensus.hlp",    AWM_ALL, AP_create_con_expert_window);
1344                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);
1345                awm->insert_menu_topic("arb_phyl",      "Filter by base frequency",                                     "F", "phylo.hlp",        AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_phylo &"));
1346                awm->insert_menu_topic("sai_pfold",     "Protein secondary structure (field \"sec_struct\")",           "P", "pfold.hlp",        AWM_EXP, NT_create_sai_from_pfold);
1347
1348                GDE_load_menu(awm, AWM_EXP, "SAI");
1349            }
1350            awm->close_sub_menu();
1351
1352            awm->insert_sub_menu("Other functions", "O");
1353            {
1354                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));
1355                awm->insert_menu_topic("corr_mutat_analysis",   "Compute clusters of correlated positions", "m", "",                   AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_rnacma", XCMD_ASYNC_WAIT_ON_ERROR));
1356                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);
1357            }
1358            awm->close_sub_menu();
1359        }
1360
1361        // ----------------
1362        //      Probes
1363
1364        awm->create_menu("Probes", "P", AWM_ALL);
1365        {
1366            awm->insert_menu_topic("probe_design", "Design Probes",          "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1367            awm->insert_menu_topic("probe_multi",  "Calculate Multi-Probes", "u", "multiprobe.hlp",  AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1368            awm->insert_menu_topic("probe_match",  "Match Probes",           "M", "probematch.hlp",  AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1369            awm->sep______________();
1370            awm->insert_menu_topic("probe_match_sp",   "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window,    ntw));
1371            awm->sep______________();
1372            awm->insert_menu_topic("primer_design_new", "Design Primers",            "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1373            awm->insert_menu_topic("primer_design",     "Design Sequencing Primers", "S", "primer.hlp",     AWM_EXP, makeWindowCallback(AWT_system_in_console_cb, "arb_primer", XCMD_ASYNC_WAITKEY));
1374            awm->sep______________();
1375            awm->insert_menu_topic("pt_server_admin",   "PT_SERVER Admin",           "A", "probeadmin.hlp",  AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1376        }
1377
1378    }
1379
1380    // --------------
1381    //      Tree
1382
1383    awm->create_menu("Tree", "T", AWM_ALL);
1384    {
1385        if (!clone) {
1386            awm->insert_sub_menu("Add Species to Existing Tree", "A");
1387            {
1388                awm->insert_menu_topic("arb_pars_quick", "ARB Parsimony (Quick add marked)", "Q", "pars.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_pars -add_marked -quit &"));
1389                awm->insert_menu_topic("arb_pars",       "ARB Parsimony interactive",        "i", "pars.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_pars &"));
1390                GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1391            }
1392            awm->close_sub_menu();
1393        }
1394
1395        awm->insert_sub_menu("Remove Species from Tree",     "R");
1396        {
1397            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));
1398            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));
1399            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));
1400            awm->sep______________();
1401            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));
1402            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));
1403        }
1404        awm->close_sub_menu();
1405
1406        if (!clone) {
1407            awm->insert_sub_menu("Build tree from sequence data",    "B");
1408            {
1409                awm->insert_sub_menu("Distance matrix methods", "D");
1410                awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1411                GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1412                awm->close_sub_menu();
1413
1414                awm->insert_sub_menu("Maximum Parsimony methods", "P");
1415                GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1416                awm->close_sub_menu();
1417
1418                awm->insert_sub_menu("Maximum Likelihood methods", "L");
1419                GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1420                GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1421                awm->close_sub_menu();
1422
1423                awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1424                GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1425                awm->close_sub_menu();
1426            }
1427            awm->close_sub_menu();
1428        }
1429
1430        awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1431
1432        awm->sep______________();
1433
1434        awm->insert_sub_menu("Reset zoom",         "z");
1435        {
1436            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));
1437            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));
1438        }
1439        awm->close_sub_menu();
1440
1441        awm->sep______________();
1442
1443        // taxonomic groups
1444        NT_insert_collapse_submenu(awm, ntw);
1445        awm->insert_menu_topic("group_search",                    "Search groups...",    "g", "group_search.hlp",     AWM_ALL, makeWindowCallback      (popup_group_search_window,         GLOBAL.gb_main));
1446        awm->insert_menu_topic(awm->local_id("compare_taxonomy"), "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1447
1448        awm->sep______________();
1449
1450        awm->insert_sub_menu("Beautify tree", "e");
1451        {
1452            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));
1453            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));
1454            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));
1455            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));
1456            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));
1457            awm->sep______________();
1458            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));
1459        }
1460        awm->close_sub_menu();
1461        awm->insert_sub_menu("Modify branches", "M");
1462        {
1463            awm->insert_menu_topic(awm->local_id("tree_remove_remark"),     "Remove bootstraps",      "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap,    ntw));
1464            awm->insert_menu_topic(awm->local_id("tree_toggle_bootstraps"), "Toggle 100% bootstraps", "1", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_toggle_bootstrap100, ntw));
1465            awm->sep______________();
1466            awm->insert_menu_topic(awm->local_id("tree_reset_lengths"),     "Reset branchlengths",   "R", "tbl_reset.hlp",   AWM_ALL, makeWindowCallback(NT_reset_branchlengths,   ntw));
1467            awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1468            awm->insert_menu_topic(awm->local_id("tree_scale_lengths"),     "Scale Branchlengths",   "S", "tbl_scale.hlp",   AWM_ALL, makeWindowCallback(NT_scale_tree,            ntw));
1469            awm->sep______________();
1470            awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1471            awm->sep______________();
1472            awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1473            awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1474
1475        }
1476        awm->close_sub_menu();
1477
1478        awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "s", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1479        awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "u", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback(NT_mark_duplicates, ntw));
1480
1481        awm->sep______________();
1482
1483        awm->insert_menu_topic(awm->local_id("shade"),            "Tree shading...",       "s", "tree_shading.hlp",     AWM_ALL, makeWindowCallback      (NT_configure_treeShader));
1484        awm->insert_menu_topic(awm->local_id("syncscroll"),       "Sync tree scrolling..", "y", "syncscroll.hlp",       AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1485
1486        awm->sep______________();
1487
1488        awm->insert_menu_topic(awm->local_id("tree_select"),        "Select Tree",      "T", 0, AWM_ALL, makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1489        awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", 0, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1490
1491        if (!clone) {
1492            awm->sep______________();
1493            awm->insert_menu_topic("tree_admin", "Tree admin",               "i", "treeadm.hlp",   AWM_ALL, popup_tree_admin_window);
1494            awm->insert_menu_topic("nds",        "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_nds_window, GLOBAL.gb_main));
1495        }
1496
1497        awm->sep______________();
1498        awm->insert_menu_topic("transversion",       "Transversion analysis",   "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1499
1500        if (!clone) {
1501            awm->sep______________();
1502            awm->insert_menu_topic("print_tree",  "Print tree",          "P", "tree2prt.hlp",  AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1503            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)));
1504        }
1505
1506        if (is_genome_db) {
1507            awm->sep______________();
1508            awm->insert_sub_menu("Other..",  "O", AWM_EXP);
1509            {
1510                awm->insert_menu_topic(awm->local_id("tree_pseudo_species_to_organism"), "Relink tree to organisms", "o", "tree_pseudo.hlp", AWM_EXP, makeWindowCallback(NT_pseudo_species_to_organism, ntw));
1511            }
1512            awm->close_sub_menu();
1513        }
1514    }
1515
1516    if (!clone) {
1517        // ---------------
1518        //      Tools
1519
1520        awm->create_menu("Tools", "o", AWM_ALL);
1521        {
1522            awm->insert_menu_topic("names_admin",      "Name server admin (IDs)",    "s", "namesadmin.hlp",  AWM_ALL, makeCreateWindowCallback(AW_create_namesadmin_window, GLOBAL.gb_main));
1523            awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1524            {
1525                awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1526            }
1527            awm->close_sub_menu();
1528            awm->insert_sub_menu("Network", "N", AWM_EXP);
1529            {
1530                GDE_load_menu(awm, AWM_EXP, "Network");
1531            }
1532            awm->close_sub_menu();
1533            awm->sep______________();
1534
1535            awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1536            {
1537                GDE_load_menu(awm, AWM_EXP, NULL);
1538            }
1539            awm->close_sub_menu();
1540
1541            awm->sep______________();
1542            awm->insert_menu_topic("xterm",    "Start XTERM",     "X", "xterm.hlp",   AWM_ALL, AWT_console);
1543            awm->insert_menu_topic("viewlog",  "View ARB log",    "l", "console.hlp", AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_show_log.pl run",    XCMD_ASYNC_WAIT_ON_ERROR)); // ../SH/arb_show_log.pl
1544            awm->insert_menu_topic("viewserv", "View server log", "s", "console.hlp", AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_show_log.pl server", XCMD_ASYNC_WAIT_ON_ERROR));
1545            awm->sep______________();
1546            GDE_load_menu(awm, AWM_EXP, "User");
1547        }
1548        // --------------------
1549        //      Properties
1550
1551        awm->create_menu("Properties", "r", AWM_ALL);
1552        {
1553#if defined(ARB_MOTIF)
1554            awm->insert_menu_topic("props_menu",                 "Frame settings ...",          "F", "props_frame.hlp",      AWM_ALL, AW_preset_window);
1555#endif
1556            awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options",                "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1557            awm->insert_menu_topic("props_tree",                 "Tree colors & fonts",         "c", "color_props.hlp",      AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1558            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));
1559            awm->sep______________();
1560            awm->insert_menu_topic("!toggle_expert", "Toggle expert mode",         "x", 0, AWM_ALL, NT_toggle_expert_mode);
1561#if defined(ARB_MOTIF)
1562            awm->insert_menu_topic("!toggle_focus",  "Toggle focus follows mouse", "m", 0, AWM_ALL, NT_toggle_focus_policy);
1563#endif
1564            awm->sep______________();
1565            AW_insert_common_property_menu_entries(awm);
1566            awm->sep______________();
1567            awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1568        }
1569    }
1570
1571    awm->insert_help_topic("ARB_NT help",     "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1572
1573    // ----------------------
1574    //      mode buttons
1575    //
1576    // keep them synchronized as far as possible with those in ARB_PARSIMONY
1577    // see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1578
1579    awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1580    awm->create_mode("mode_mark.xpm",   "mode_mark.hlp",   AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1581    awm->create_mode("mode_group.xpm",  "mode_group.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1582    awm->create_mode("mode_zoom.xpm",   "mode_pzoom.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1583    awm->create_mode("mode_lzoom.xpm",  "mode_lzoom.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1584
1585    awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1586    awm->create_mode("mode_www.xpm",  "mode_www.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event,  ntw, AWT_MODE_WWW));
1587
1588    // topology-modification-modes
1589    awm->create_mode("mode_setroot.xpm",   "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1590    awm->create_mode("mode_swap.xpm",      "mode_swap.hlp",    AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1591    awm->create_mode("mode_move.xpm",      "mode_move.hlp",    AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1592    awm->create_mode("mode_length.xpm",    "mode_length.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1593    awm->create_mode("mode_multifurc.xpm", "mode_length.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1594
1595    // layout-modes
1596    awm->create_mode("mode_line.xpm",   "mode_width.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1597    awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1598    awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1599
1600    awm->set_info_area_height(250);
1601    awm->at(5, 2);
1602    awm->auto_space(-2, -2);
1603    awm->shadow_width(1);
1604
1605    // -------------------------
1606    //      create top area
1607
1608    int first_liney;
1609    int leftx;
1610    awm->get_at_position(&leftx, &first_liney);
1611
1612    // ---------------------
1613    //      quit + help
1614
1615    awm->button_length(0);
1616
1617    if (clone) {
1618        awm->callback(AW_POPDOWN);
1619        awm->create_button("CLOSE", "#close.xpm");
1620    }
1621    else {
1622        awm->callback(makeWindowCallback(NT_exit, EXIT_SUCCESS));
1623#if defined(ARB_GTK)
1624        awm->set_hide_on_close(false); //the main window should really close when closed
1625#endif
1626        awm->help_text("quit.hlp");
1627        awm->create_button("QUIT", "#quit.xpm");
1628#if defined(ARB_GTK)
1629        awm->set_close_action("QUIT");
1630#endif
1631    }
1632
1633    int db_pathx = awm->get_at_xposition();
1634
1635    // now fetch the yposition for the 2nd button line
1636    awm->at_newline();
1637    int second_liney = awm->get_at_yposition();
1638
1639    awm->callback(AW_help_entry_pressed);
1640    awm->help_text("arb_ntree.hlp");
1641    awm->create_button("?", "#help.xpm");
1642
1643    // --------------------------
1644    //      save + undo/redo
1645
1646    awm->callback(NT_save_quick_cb);
1647    awm->help_text("save.hlp");
1648    awm->create_button("SAVE", "#save.xpm");
1649
1650    awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1651    awm->help_text("save.hlp");
1652    awm->create_button("SAVE_AS", "#saveAs.xpm");
1653
1654    // undo/redo:
1655    awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1656    awm->help_text("undo.hlp");
1657    awm->create_button("UNDO", "#undo.xpm");
1658
1659    awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1660    awm->help_text("undo.hlp");
1661    awm->create_button("REDO", "#redo.xpm");
1662
1663    int db_pathx2 = awm->get_at_xposition();
1664
1665    // fetch position for mode help-line:
1666    awm->at_newline();
1667    int third_liney = awm->get_at_yposition();
1668
1669    awm->at(db_pathx, first_liney);
1670    // size of DB-name button is determined by buttons below:
1671    awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1672    awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1673    awm->help_text("save.hlp");
1674    awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1675
1676    // -----------------------------
1677    //      tree + tree display
1678
1679#define TREE_BUTTON_OVERSIZE 6
1680
1681    int db_treex      = awm->get_at_xposition();
1682    int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1683
1684    awm->at(db_treex, second_uppery);
1685    awm->button_length(0);
1686
1687    awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1688    awm->help_text("tr_type_radial.hlp");
1689    awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1690
1691    awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1692    awm->help_text("tr_type_list.hlp");
1693    awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1694
1695    awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1696    awm->help_text("tr_type_irs.hlp");
1697    awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1698
1699    awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1700    awm->help_text("tr_type_nds.hlp");
1701    awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1702
1703    int db_treex2 = awm->get_at_xposition();
1704
1705    awm->at(db_treex, first_liney);
1706    // size of tree-name button is determined by buttons below:
1707    awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1708    awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1709    awm->help_text("nt_tree_select.hlp");
1710    awm->create_button("SELECT_A_TREE", awar_tree);
1711
1712    // ---------------------------------------------------------------
1713    //      protection, alignment + editor (and maybe Genome Map)
1714
1715    int db_alignx = awm->get_at_xposition();
1716
1717    // editor and genemap buttons have to be 44x24 sized
1718#define EDIT_XSIZE 50
1719#define EDIT_YSIZE 30 // same as 'save as' buttons
1720
1721    // first draw protection:
1722    int protectx = db_alignx + 2*EDIT_XSIZE;
1723
1724    awm->at(protectx+2, first_liney+1);
1725    awm->button_length(0);
1726    awm->create_button(NULL, "#protect.xpm");
1727
1728    awm->at(protectx, second_liney+2);
1729    awm->create_option_menu(AWAR_SECURITY_LEVEL, true);
1730    awm->insert_option("0", 0, 0);
1731    awm->insert_option("1", 0, 1);
1732    awm->insert_option("2", 0, 2);
1733    awm->insert_option("3", 0, 3);
1734    awm->insert_option("4", 0, 4);
1735    awm->insert_option("5", 0, 5);
1736    awm->insert_default_option("6", 0, 6);
1737    awm->update_option_menu();
1738
1739    int db_searchx = awm->get_at_xposition() - 7;
1740
1741    // draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1742    awm->at(db_alignx, second_liney);
1743
1744    awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1745    awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1746    awm->help_text("arb_edit4.hlp");
1747    if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1748    else              awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1749
1750    if (is_genome_db) {
1751        awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1752        awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1753        awm->help_text("gene_map.hlp");
1754        awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1755    }
1756
1757    int db_alignx2 = awm->get_at_xposition();
1758
1759    awm->at(db_alignx, first_liney);
1760    awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1761    awm->callback(NT_create_select_alignment_window);
1762    awm->help_text("nt_align_select.hlp");
1763    awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1764
1765    // -------------------------------
1766    //      create mode-help line
1767
1768    awm->at(leftx, third_liney);
1769    awm->button_length(AWAR_FOOTER_MAX_LEN);
1770    awm->create_button(0, AWAR_FOOTER);
1771
1772    awm->at_newline();
1773    int bottomy = awm->get_at_yposition();
1774
1775    // ---------------------------------------
1776    //      Info / marked / Search / Jump
1777
1778    awm->button_length(7);
1779
1780    awm->at(db_searchx, first_liney);
1781    awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1782    awm->help_text("sp_search.hlp");
1783    awm->create_button("SEARCH",  "Search");
1784
1785    awm->at(db_searchx, second_uppery);
1786    awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1787    awm->help_text("tr_jump.hlp");
1788    awm->create_button("JUMP", "Jump");
1789
1790    int db_infox = awm->get_at_xposition();
1791
1792    awm->at(db_infox, first_liney);
1793    awm->button_length(13);
1794    awm->callback(popupinfo_wcb);
1795    awm->help_text("sp_search.hlp");
1796    awm->create_button("INFO",  AWAR_INFO_BUTTON_TEXT);
1797
1798    awm->at(db_infox, second_uppery);
1799    awm->button_length(13);
1800    awm->help_text("species_configs.hlp");
1801    awm->callback(makeWindowCallback(NT_popup_configuration_admin, ntw));
1802    awm->create_button("selection_admin2", AWAR_MARKED_SPECIES_COUNTER);
1803    {
1804        GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1805        GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(NT_update_marked_counter, static_cast<AW_window*>(awm)));
1806        NT_update_marked_counter(NULL, awm);
1807    }
1808
1809    // set height of top area:
1810    awm->set_info_area_height(bottomy+2);
1811    awm->set_bottom_area_height(0);
1812
1813    NT_activate_configMarkers_display(ntw);
1814
1815    // ------------------------------------
1816    //      Autostarts for development
1817
1818#if defined(DEVEL_RALF)
1819    // if (is_genome_db) GEN_map_first(awr)->show();
1820#endif // DEVEL_RALF
1821
1822    GB_pop_transaction(GLOBAL.gb_main);
1823
1824#if defined(DEBUG)
1825    AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1826#endif
1827
1828    return awm;
1829}
1830
1831TREE_canvas *NT_create_main_window(AW_root *aw_root) {
1832    GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1833    if (error) aw_message(error);
1834
1835    nt_create_all_awars(aw_root);
1836
1837    TREE_canvas *ntw = NULL;
1838    AW_window   *aww = popup_new_main_window(aw_root, 0, &ntw);
1839    NT_install_treeShader(ntw, GLOBAL.gb_main);
1840    aww->show();
1841
1842    error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1843    if (error) aw_message(error);
1844
1845    return ntw;
1846}
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