source: branches/alilink/NTREE/NT_extern.cxx

Last change on this file was 18126, checked in by westram, 6 years ago
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1// =============================================================== //
2//                                                                 //
3//   File      : NT_extern.cxx                                     //
4//   Purpose   :                                                   //
5//                                                                 //
6//   Institute of Microbiology (Technical University Munich)       //
7//   http://www.arb-home.de/                                       //
8//                                                                 //
9// =============================================================== //
10
11#include "map_viewer.h"
12#include "NT_local.h"
13#include "ad_trees.h"
14#include "NT_group_search.h"
15
16#include <seq_quality.h>
17#include <multi_probe.hxx>
18#include <st_window.hxx>
19#include <GEN.hxx>
20#include <EXP.hxx>
21
22#include <TreeCallbacks.hxx>
23#include <AW_rename.hxx>
24#include <probe_gui.hxx>
25#include <primer_design.hxx>
26#include <gde.hxx>
27#include <awtc_submission.hxx>
28
29#include <macros.hxx>
30#include <nds.h>
31#include <db_query.h>
32#include <dbui.h>
33#include <refentries.h>
34#include <insdel.h>
35
36#include <awti_export.hxx>
37#include <awti_import.hxx>
38
39#include <awt.hxx>
40#include <awt_input_mask.hxx>
41#include <awt_sel_boxes.hxx>
42#include <awt_www.hxx>
43#include <awt_TreeAwars.hxx>
44#include <awt_misc.hxx>
45
46#include <aw_color_groups.hxx>
47#include <aw_advice.hxx>
48#include <aw_preset.hxx>
49#include <aw_awars.hxx>
50#include <aw_global_awars.hxx>
51#include <aw_file.hxx>
52#include <aw_msg.hxx>
53#include <arb_progress.h>
54#include <aw_root.hxx>
55#include <aw_question.hxx>
56#include <aw_select.hxx>
57#include <rootAsWin.h>
58
59#include <ad_cb.h>
60
61#include <arb_strbuf.h>
62#include <arb_file.h>
63#include <arb_version.h>
64
65#if defined(DEVEL_RALF)
66# define TRACE_GROUP_SELECTION
67#endif
68
69#define AWAR_EXPORT_NDS              "tmp/export_nds"
70#define AWAR_EXPORT_NDS_SEPARATOR    AWAR_EXPORT_NDS "/separator"
71#define AWAR_MARKED_SPECIES_COUNTER  "tmp/disp_marked_species"
72#define AWAR_NTREE_TITLE_MODE        "tmp/title_mode"
73
74void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
75
76void       create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
77AW_window *create_insertDeleteColumn_window(AW_root *root);
78AW_window *create_insertDeleteBySAI_window(AW_root *root, GBDATA *gb_main);
79
80AW_window *create_tree_window(AW_root *aw_root, AWT_graphic *awd);
81
82static void nt_changesecurity(AW_root *aw_root) {
83    int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
84    GB_push_transaction(GLOBAL.gb_main);
85    GB_change_my_security(GLOBAL.gb_main, level); // changes user security
86    GB_pop_transaction(GLOBAL.gb_main);
87}
88
89static void export_nds_cb(AW_window *aww, bool do_print) {
90    AW_root *aw_root = aww->get_root();
91    char    *name    = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
92    FILE    *out     = fopen(name, "w");
93
94    if (!out) {
95        aw_message("Error: Cannot open and write to file");
96    }
97    else {
98        GB_transaction ta(GLOBAL.gb_main);
99
100        make_node_text_init(GLOBAL.gb_main);
101        NDS_Type  nds_type  = (NDS_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
102        char     *tree_name = aw_root->awar(AWAR_TREE)->read_string();
103
104        for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
105             gb_species;
106             gb_species = GBT_next_marked_species(gb_species))
107        {
108            const char *buf = make_node_text_nds(GLOBAL.gb_main, gb_species, nds_type, NULp, tree_name);
109            fprintf(out, "%s\n", buf);
110        }
111        AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
112        fclose(out);
113        if (do_print) {
114            GB_ERROR error = GB_textprint(name);
115            if (error) aw_message(error);
116        }
117        free(tree_name);
118    }
119    free(name);
120}
121
122static AW_window *create_nds_export_window(AW_root *root) {
123    AW_window_simple *aws = new AW_window_simple;
124    aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
125    aws->load_xfig("sel_box_nds.fig");
126
127    aws->callback(AW_POPDOWN);
128    aws->at("close");
129    aws->create_button("CLOSE", "CLOSE", "C");
130
131    aws->callback(makeHelpCallback("arb_export_nds.hlp"));
132    aws->at("help");
133    aws->create_button("HELP", "HELP", "H");
134
135    aws->at("save");
136    aws->callback(makeWindowCallback(export_nds_cb, false));
137    aws->create_button("SAVE", "SAVE", "S");
138
139    aws->at("print");
140    aws->callback(makeWindowCallback(export_nds_cb, true));
141    aws->create_button("PRINT", "PRINT", "P");
142
143    aws->at("toggle1");
144    aws->label("Column output");
145    aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR, true);
146    aws->insert_default_option("Space padded",    "S", NDS_OUTPUT_SPACE_PADDED);
147    aws->insert_option        ("TAB separated",   "T", NDS_OUTPUT_TAB_SEPARATED);
148    aws->insert_option        ("Comma separated", "C", NDS_OUTPUT_COMMA_SEPARATED);
149    aws->update_option_menu();
150
151    AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS);
152
153    return aws;
154}
155
156static void create_export_nds_awars(AW_root *awr, AW_default def) {
157    AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds");
158    awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, NDS_OUTPUT_SPACE_PADDED, def);
159}
160
161static void selectedSpeciesChanged_cb(AW_root *awr) {
162    const char *value = awr->awar(AWAR_SPECIES_NAME)->read_char_pntr();
163    awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
164    if (value[0]) {
165        awr->awar(AWAR_GROUP)->write_pointer(NULp); // deselect group when species gets selected
166#if defined(TRACE_GROUP_SELECTION)
167        fputs("clear AWAR_GROUP (because species selected)\n", stderr);
168#endif
169    }
170}
171
172static void expert_mode_changed_cb(AW_root *aw_root) {
173    aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
174}
175
176static void NT_toggle_expert_mode(AW_window *aww) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
177static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
178
179static void nt_create_all_awars(AW_root *awr) {
180    // creates awars for all modules reachable from ARB_NT main window
181
182    awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT);
183    if (GB_read_clients(GLOBAL.gb_main)>=0) {
184        awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
185    }
186    else {
187        awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT);
188    }
189
190    awr->awar_string(AWAR_SPECIES_NAME, "",     GLOBAL.gb_main);
191    awr->awar_string(AWAR_SAI_NAME, "",     GLOBAL.gb_main);
192    awr->awar_string(AWAR_SAI_GLOBAL, "",     GLOBAL.gb_main);
193    awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown",    GLOBAL.gb_main);
194    awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info",    GLOBAL.gb_main);
195    awr->awar(AWAR_SPECIES_NAME)->add_callback(selectedSpeciesChanged_cb);
196    awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
197
198    awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
199
200    GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
201    EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
202#if defined(DEBUG)
203    AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT);
204#endif // DEBUG
205
206    AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
207
208    awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT);
209    awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
210#if defined(DEBUG) && 0
211    awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
212#endif // DEBUG
213
214    create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT);
215    create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
216    create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
217    create_trees_var(awr, AW_ROOT_DEFAULT);
218    DBUI::create_dbui_awars(awr);
219    AP_create_consensus_var(awr, AW_ROOT_DEFAULT);
220    {
221        GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, NULp, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT);
222        if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
223    }
224    NT_create_transpro_variables(awr, AW_ROOT_DEFAULT);
225    NT_create_resort_awars(awr, AW_ROOT_DEFAULT);
226    NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT);
227    NT_create_trackAliChanges_Awars(awr, GLOBAL.gb_main);
228
229    NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
230    NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
231    create_nds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, false);
232    create_export_nds_awars(awr, AW_ROOT_DEFAULT);
233    create_group_search_awars(awr, AW_ROOT_DEFAULT);
234    TREE_create_awars(awr, GLOBAL.gb_main);
235
236    awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
237    awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
238
239    AWTC_create_submission_variables(awr, GLOBAL.gb_main);
240    NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
241    NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar
242    SQ_create_awars(awr, AW_ROOT_DEFAULT);
243    RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT);
244
245    NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT);
246
247    GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
248    if (!error) {
249        AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
250        awar_expert->add_callback(expert_mode_changed_cb);
251        awar_expert->touch();
252
253        awt_create_aww_vars(awr, AW_ROOT_DEFAULT);
254    }
255
256    if (error) aw_message(error);
257}
258
259// --------------------------------------------------------------------------------
260
261static bool nt_disconnect_from_db(AW_root *aw_root, GBDATA*& gb_main_ref) {
262    // ask user if DB was not saved
263    // returns true if user allows to quit
264
265    // @@@ code here could as well be applied to both merge DBs
266    // - question about saving only with target DB!
267
268    if (gb_main_ref) {
269        if (GB_read_clients(gb_main_ref)>=0) {
270            if (GB_read_clock(gb_main_ref) > GB_last_saved_clock(gb_main_ref)) {
271                long secs;
272                secs = GB_last_saved_time(gb_main_ref);
273
274#if defined(DEBUG)
275                secs =  GB_time_of_day(); // simulate "just saved"
276#endif // DEBUG
277
278                const char *quit_buttons = "Quit ARB,Do NOT quit";
279                if (secs) {
280                    secs = GB_time_of_day() - secs;
281                    if (secs>10) {
282                        char *question = GBS_global_string_copy("You last saved your data %li:%li minutes ago\nSure to quit ?", secs/60, secs%60);
283                        int   dontQuit = aw_question("quit_arb", question, quit_buttons);
284                        free(question);
285                        if (dontQuit) {
286                            return false;
287                        }
288                    }
289                }
290                else {
291                    if (aw_question("quit_arb", "You never saved any data\nSure to quit ???", quit_buttons)) {
292                        return false;
293                    }
294                }
295            }
296        }
297
298        GBCMS_shutdown(gb_main_ref);
299
300        GBDATA *gb_main = gb_main_ref;
301        gb_main_ref     = NULp;                  // avoid further usage
302
303        nt_assert(aw_root);
304#if defined(WARN_TODO)
305#warning instead of directly calling the following functions, try to add them as GB_atclose_callback
306#endif
307        aw_root->unlink_awars_from_DB(gb_main);
308        AWT_destroy_input_masks();
309#if defined(DEBUG)
310        AWT_browser_forget_db(gb_main);
311#endif // DEBUG
312
313        GB_close(gb_main);
314    }
315    return true;
316}
317
318static void nt_run(const char *command) {
319    GB_ERROR error = GBK_system(command);
320    if (error) {
321        fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
322#if defined(DEBUG)
323        GBK_dump_backtrace(stderr, "nt_run-error");
324#endif
325    }
326}
327
328void NT_start(const char *arb_ntree_args, bool restart_with_new_ARB_PID) {
329    char *command = GBS_global_string_copy("arb_launcher --async %s %s", restart_with_new_ARB_PID ? "arb" : "arb_ntree", arb_ntree_args);
330    nt_run(command);
331    free(command);
332}
333
334__ATTR__NORETURN static void really_exit(int exitcode, bool kill_my_clients) {
335    if (kill_my_clients) {
336        nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
337    }
338    exit(exitcode);
339}
340
341void NT_exit(AW_window *aws, int exitcode) {
342    AW_root *aw_root = aws->get_root();
343    AWTI_cleanup_importer();
344    shutdown_macro_recording(aw_root);
345    bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
346    if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
347        really_exit(exitcode, is_server_and_has_clients);
348    }
349}
350void NT_restart(AW_root *aw_root, const char *arb_ntree_args) {
351    // restarts arb_ntree (with new ARB_PID)
352    bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
353    if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main))  {
354        NT_start(arb_ntree_args, true);
355        really_exit(EXIT_SUCCESS, is_server_and_has_clients);
356    }
357}
358
359static void nt_start_2nd_arb(AW_window *aww, bool quit) {
360    // start 2nd arb with intro window
361    AW_root *aw_root = aww->get_root();
362    char    *dir4intro;
363    GB_split_full_path(aw_root->awar(AWAR_DB_PATH)->read_char_pntr(), &dir4intro, NULp, NULp, NULp);
364    if (!dir4intro) {
365        dir4intro = ARB_strdup(".");
366    }
367
368    if (quit) {
369        NT_restart(aw_root, dir4intro);
370    }
371    else {
372        NT_start(dir4intro, true);
373    }
374    free(dir4intro);
375}
376
377// --------------------------------------------------------------------------------
378
379static void NT_save_quick_cb(AW_window *aww) {
380    AW_root *awr      = aww->get_root();
381    char    *filename = awr->awar(AWAR_DB_PATH)->read_string();
382
383    awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
384
385    GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
386    free( filename);
387    if (error) aw_message(error);
388    else       AW_refresh_fileselection(awr, AWAR_DBBASE);
389}
390
391
392static void NT_save_quick_as_cb(AW_window *aww) {
393    AW_root  *awr      = aww->get_root();
394    char     *filename = awr->awar(AWAR_DB_PATH)->read_string();
395    GB_ERROR  error    = GB_save_quick_as(GLOBAL.gb_main, filename);
396    if (!error) AW_refresh_fileselection(awr, AWAR_DBBASE);
397    aww->hide_or_notify(error);
398
399    free(filename);
400}
401
402#define AWAR_DB_TYPE          AWAR_DBBASE "/type"      // created by AWT_insert_DBsaveType_selector
403#define AWAR_DB_COMPRESSION   AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector
404#define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name"
405
406static void NT_save_as_cb(AW_window *aww) {
407    AW_root    *awr      = aww->get_root();
408    char       *filename = awr->awar(AWAR_DB_PATH)->read_string();
409    const char *atype    = awr->awar(AWAR_DB_TYPE)->read_char_pntr();
410    const char *ctype    = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr();
411    char       *savetype = GBS_global_string_copy("%s%s", atype, ctype);
412
413    awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
414    GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype);
415    if (!error) AW_refresh_fileselection(awr, AWAR_DBBASE);
416    aww->hide_or_notify(error);
417
418    free(savetype);
419    free(filename);
420}
421
422static AW_window *NT_create_save_quick_as_window(AW_root *aw_root, const char *base_name) {
423    static AW_window_simple *aws = NULp;
424    if (!aws) {
425        aws = new AW_window_simple;
426        aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as");
427        aws->load_xfig("save_as.fig");
428
429        aws->at("close");
430        aws->callback(AW_POPDOWN);
431        aws->create_button("CLOSE", "CLOSE", "C");
432
433        aws->callback(makeHelpCallback("save.hlp"));
434        aws->at("help");
435        aws->create_button("HELP", "HELP", "H");
436
437        AW_create_standard_fileselection(aws, base_name);
438
439        aws->at("comment");
440        aws->create_text_field(AWAR_DB_COMMENT);
441
442        aws->at("save");
443        aws->callback(NT_save_quick_as_cb);
444        aws->create_button("SAVE", "SAVE", "S");
445    }
446    return aws;
447}
448
449static void NT_database_optimization(AW_window *aww) {
450    arb_progress        progress("Optimizing database compression", 2L);
451    GB_topSecurityLevel unsecured(GLOBAL.gb_main);
452
453    GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
454    if (!error) {
455        ConstStrArray ali_names;
456        GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
457
458        arb_progress ali_progress("Optimizing sequence data", ali_names.size());
459        ali_progress.allow_title_reuse();
460
461        error = GBT_check_data(GLOBAL.gb_main, NULp);
462        error = GB_end_transaction(GLOBAL.gb_main, error);
463
464        if (!error) {
465            char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string();
466            for (int i = 0; ali_names[i]; ++i) {
467                error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
468                ali_progress.inc_and_check_user_abort(error);
469            }
470            free(tree_name);
471        }
472    }
473    progress.inc_and_check_user_abort(error);
474
475    if (!error) {
476        error = GB_optimize(GLOBAL.gb_main);
477        progress.inc_and_check_user_abort(error);
478    }
479    aww->hide_or_notify(error);
480}
481
482static AW_window *NT_create_database_optimization_window(AW_root *aw_root) {
483    static AW_window_simple *aws = NULp;
484    if (aws) return aws;
485    GB_transaction ta(GLOBAL.gb_main);
486
487    const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
488    aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree);
489
490    aws = new AW_window_simple;
491    aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression");
492    aws->load_xfig("optimize.fig");
493
494    aws->at("trees");
495    awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME, true);
496
497    aws->at("close");
498    aws->callback(AW_POPDOWN);
499    aws->create_button("CLOSE", "CLOSE", "C");
500
501    aws->callback(makeHelpCallback("optimize.hlp"));
502    aws->at("help");
503    aws->create_button("HELP", "HELP", "H");
504
505    aws->at("go");
506    aws->callback(NT_database_optimization);
507    aws->create_button("GO", "GO");
508    return aws;
509}
510
511static AW_window *NT_create_save_as(AW_root *aw_root, const char *base_name) {
512    static AW_window_simple *aws = NULp;
513    if (aws) return aws;
514
515    aws = new AW_window_simple;
516    aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
517    aws->load_xfig("save_as.fig");
518
519    aws->at("close");
520    aws->callback(AW_POPDOWN);
521    aws->create_button("CLOSE", "CLOSE", "C");
522
523    aws->at("help");
524    aws->callback(makeHelpCallback("save.hlp"));
525    aws->create_button("HELP", "HELP", "H");
526
527    AW_create_standard_fileselection(aws, base_name);
528
529    aws->at("type");
530    AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE);
531
532    aws->at("compression");
533    AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION);
534
535    aws->at("optimize");
536    aws->callback(NT_create_database_optimization_window);
537    aws->help_text("optimize.hlp");
538    aws->create_autosize_button("OPTIMIZE", "Optimize database compression");
539
540    aws->at("save");
541    aws->callback(NT_save_as_cb);
542    aws->create_button("SAVE", "SAVE", "S");
543
544    aws->at("comment");
545    aws->create_text_field(AWAR_DB_COMMENT);
546
547    return aws;
548}
549
550static void NT_undo_cb(AW_window*, GB_UNDO_TYPE undo_type, TREE_canvas *ntw) {
551    GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type);
552    if (error) aw_message(error);
553    else {
554        GB_transaction ta(GLOBAL.gb_main);
555        AWT_auto_refresh allowed_on(ntw);
556        ntw->request_refresh();
557    }
558}
559
560enum streamSource { FROM_PIPE, FROM_FILE };
561static char *stream2str(streamSource source, const char *commandOrFile) {
562    char *output = NULp;
563    FILE *in     = NULp;
564
565    switch (source) {
566        case FROM_PIPE: in = popen(commandOrFile, "r"); break;
567        case FROM_FILE: in = fopen(commandOrFile, "rt"); break;
568    }
569
570    if (in) {
571        GBS_strstruct *out = GBS_stropen(2000);
572        int c;
573
574        while (EOF != (c = fgetc(in))) GBS_chrcat(out, c);
575
576        switch (source) {
577            case FROM_PIPE: pclose(in); break;
578            case FROM_FILE: fclose(in); break;
579        }
580
581        // skip trailing linefeeds
582        long offset = GBS_memoffset(out);
583        while (offset>0 && GBS_mempntr(out)[offset-1] == '\n') {
584            GBS_str_cut_tail(out, 1);
585            offset--;
586        }
587
588        output = GBS_strclose(out);
589    }
590    return output;
591}
592
593inline void removeTrailingNewlines(char *str) {
594    char *eos = strchr(str, 0)-1;
595    while (eos >= str && eos[0] == '\n') *eos-- = 0;
596}
597
598inline void append_named_value(GBS_strstruct *out, const char *prefix, const char *value) {
599    GBS_strcat(out, GBS_global_string("%-*s: %s\n", 12, prefix, value));
600}
601inline void append_command_output(GBS_strstruct *out, const char *prefix, const char *command) {
602    char *output = stream2str(FROM_PIPE, command);
603    if (output) {
604        removeTrailingNewlines(output);
605        if (strcmp(output, "unknown") != 0) append_named_value(out, prefix, output);
606        free(output);
607    }
608}
609
610static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) {
611    DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
612    nt_mode_event(NULp, canvas, mode);
613}
614
615static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) {
616    AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
617    if (tree_root) {
618        AWT_auto_refresh allowed_on(ntw);
619        GB_transaction   ta(ntw->gb_main);
620
621        NT_mark_all_cb(NULp, ntw, 0); // unmark all
622        tree_root->mark_duplicates();
623        ntw->request_structure_update();
624    }
625}
626
627static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) {
628    GB_transaction  ta(ntw->gb_main);
629    AP_tree        *tree_root = AWT_TREE(ntw)->get_root_node();
630
631    if (tree_root) {
632        AWT_auto_refresh allowed_on(ntw);
633        tree_root->justify_branch_lenghs(ntw->gb_main);
634        ntw->request_save_and_zoom_reset();
635    }
636}
637
638#if defined(DEBUG)
639static void NT_fix_database(AW_window *) {
640    GB_ERROR err = NULp;
641    err = GB_fix_database(GLOBAL.gb_main);
642    if (err) aw_message(err);
643}
644#endif
645
646static void relink_pseudo_species_to_organisms(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash) {
647    if (ref_gb_node) {
648        if (GEN_is_pseudo_gene_species(ref_gb_node)) {
649            GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
650
651            if (gb_organism) {
652                char *name = GBT_read_string(gb_organism, "name");
653
654                if (name) {
655                    freeset(ref_name, name);
656                    ref_gb_node = gb_organism;
657                }
658            }
659        }
660    }
661}
662
663static void NT_pseudo_species_to_organism(AW_window *, TREE_canvas *ntw) {
664    GB_transaction  ta(ntw->gb_main);
665    AP_tree        *tree_root = AWT_TREE(ntw)->get_root_node();
666
667    if (tree_root) {
668        AWT_auto_refresh allowed_on(ntw);
669
670        GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
671        tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
672        GBS_free_hash(organism_hash);
673        ntw->request_save();
674    }
675}
676
677
678// #########################################
679// #########################################
680// ###                                   ###
681// ##          user mask section          ##
682// ###                                   ###
683// #########################################
684// #########################################
685
686struct nt_item_type_species_selector FINAL_TYPE : public awt_item_type_selector {
687    nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
688    ~nt_item_type_species_selector() OVERRIDE {}
689
690    const char *get_self_awar() const OVERRIDE {
691        return AWAR_SPECIES_NAME;
692    }
693    size_t get_self_awar_content_length() const OVERRIDE {
694        return 12; // should be enough for "nnaammee.999"
695    }
696    GBDATA *current(AW_root *root, GBDATA *gb_main) const OVERRIDE { // give the current item
697        char           *species_name = root->awar(get_self_awar())->read_string();
698        GBDATA         *gb_species   = NULp;
699
700        if (species_name[0]) {
701            GB_transaction ta(gb_main);
702            gb_species = GBT_find_species(gb_main, species_name);
703        }
704
705        free(species_name);
706        return gb_species;
707    }
708    const char *getKeyPath() const OVERRIDE { // give the keypath for items
709        return CHANGE_KEY_PATH;
710    }
711};
712
713static nt_item_type_species_selector item_type_species;
714
715static void NT_open_mask_window(AW_window *aww, int id, GBDATA *gb_main) {
716    const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
717    nt_assert(descriptor);
718    if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
719}
720
721static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
722    AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
723}
724static AW_window *create_colorize_species_window(AW_root *aw_root) {
725    return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
726}
727
728static void NT_update_marked_counter(GBDATA*, AW_window* aww) {
729    /*! Updates marked counter and issues redraw on tree if number of marked species changes.
730     * Called on any change of species_information container.
731     */
732    long        count   = GBT_count_marked_species(GLOBAL.gb_main);
733    const char *buffer  = count ? GBS_global_string("%li marked", count) : "";
734    AW_awar    *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
735    char       *oldval  = counter->read_string();
736    if (strcmp(oldval, buffer)) {
737        counter->write_string(buffer);
738        aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
739    }
740    free(oldval);
741}
742
743// --------------------------------------------------------------------------------------------------
744
745static void NT_alltree_remove_leafs(AW_window *, GBT_TreeRemoveType mode, GBDATA *gb_main) {
746    GB_ERROR       error = NULp;
747    GB_transaction ta(gb_main);
748
749    ConstStrArray tree_names;
750    GBT_get_tree_names(tree_names, gb_main, false);
751
752    if (!tree_names.empty()) {
753        long treeCount = tree_names.size();
754
755        const char *whats_removed = NULp;
756        switch (mode) {
757            case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
758            case GBT_REMOVE_MARKED:  whats_removed = "marked";  break;
759            default: nt_assert(0); break;
760        }
761
762        const char *task = GBS_global_string("Deleting %s from %li trees", whats_removed, treeCount);
763
764        arb_progress  progress(task, treeCount);
765        GB_HASH      *species_hash = GBT_create_species_hash(gb_main);
766
767        int modified = 0;
768
769        for (int t = 0; t<treeCount && !error; t++) {
770            progress.subtitle(tree_names[t]);
771            TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
772            if (!tree) {
773                aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
774            }
775            else {
776                int removed        = 0;
777                int groups_removed = 0;
778
779                tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
780
781                nt_assert(removed >= groups_removed);
782
783                if (!tree) {
784                    aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
785                }
786                else {
787                    if (removed>0) {
788                        error = GBT_write_tree(gb_main, tree_names[t], tree);
789                        if (error) {
790                            aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
791                        }
792                        else {
793                            if (groups_removed>0) {
794                                aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
795                            }
796                            else {
797                                aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
798                            }
799                            modified++;
800                        }
801                    }
802                    UNCOVERED();
803                    destroy(tree);
804                }
805            }
806            progress.inc_and_check_user_abort(error);
807        }
808
809        if (modified) {
810            aw_message(GBS_global_string("Changed %i of %li trees.", modified, treeCount));
811        }
812        else {
813            aw_message("No tree modified");
814        }
815
816        GBS_free_hash(species_hash);
817    }
818
819    aw_message_if(ta.close(error));
820}
821
822TreeNode *NT_get_tree_root_of_canvas(TREE_canvas *ntw) {
823    AWT_graphic_tree *tree = AWT_TREE(ntw);
824    if (tree) {
825        AP_tree *root = tree->get_root_node();
826        if (root) return root;
827    }
828    return NULp;
829}
830
831// --------------------------------------------------------------------------------------------------
832
833static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
834    GB_transaction ta(gb_main);
835    GBT_mark_all(gb_main, 0);
836
837    DBItemSetIter end = referred.end();
838    for (DBItemSetIter s = referred.begin(); s != end; ++s) {
839        GB_write_flag(*s, 1);
840    }
841    return ARB_ERROR();
842}
843
844static AW_window *create_mark_by_refentries_window(AW_root *awr, GBDATA *gbmain) {
845    static AW_window *aws = NULp;
846    if (!aws) {
847        static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
848        aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULp, "Mark referenced", mark_referred_species);
849    }
850    return aws;
851}
852
853// --------------------------------------------------------------------------------------------------
854
855static void merge_from_to(AW_root *awr, const char *db_awar_name, bool merge_to) {
856    const char *db_name  = awr->awar(db_awar_name)->read_char_pntr();
857    char       *quotedDB = GBK_singlequote(db_name);
858
859    AWT_system_cb(
860        GBS_global_string(
861            merge_to
862            ? "arb_ntree : %s &"
863            : "arb_ntree %s : &",
864            quotedDB)
865        );
866
867    free(quotedDB);
868}
869
870static void merge_from_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, false); }
871static void merge_into_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, true); }
872
873static AW_window *NT_create_merge_from_window(AW_root *awr) {
874    static char *awar_name = NULp; // do not free, bound to callback
875    AW_window *aw_from     =
876        awt_create_load_box(awr, "Merge data from", "other ARB database",
877                            ".", ".arb", &awar_name,
878                            makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
879    return aw_from;
880}
881static AW_window *NT_create_merge_to_window(AW_root *awr) {
882    static char *awar_name = NULp; // do not free, bound to callback
883    AW_window *aw_to       =
884        awt_create_load_box(awr, "Merge data to", "other ARB database",
885                            ".", ".arb", &awar_name,
886                            makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
887                            makeWindowCallback(AW_POPDOWN), NULp);
888    return aw_to;
889}
890
891// --------------------------------------------------------------------------------------------------
892
893static void update_main_window_title(AW_root* awr, AW_window_menu_modes* aww, int clone) {
894    const char* filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
895    if (clone) {
896        aww->set_window_title(GBS_global_string("%s - ARB (%i)",  filename, clone));
897    }
898    else {
899        aww->set_window_title(GBS_global_string("%s - ARB", filename));
900    }
901}
902
903static void canvas_tree_awar_changed_cb(AW_awar *, bool, TREE_canvas *ntw) {
904    NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
905    AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
906    TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_TREE);
907}
908
909class TREE_canvas_registry {
910    int          count;
911    TREE_canvas *canvas[MAX_NT_WINDOWS];
912
913    static TREE_canvas_registry *SINGLETON;
914
915    TREE_canvas_registry() : count(0) {
916        AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
917    }
918
919public:
920    static TREE_canvas_registry& instance() {
921        if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
922        return *SINGLETON;
923    }
924
925    void register_canvas(TREE_canvas *ntw) {
926        nt_assert(count<MAX_NT_WINDOWS);
927        nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
928        canvas[count++] = ntw;
929        ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
930    }
931
932    int get_count() const  { return count; }
933
934    TREE_canvas *get_canvas(int idx) const {
935        if (idx<0 || idx>=count) return NULp;
936        return canvas[idx];
937    }
938};
939
940TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULp;
941
942TREE_canvas *NT_get_canvas_by_index(int idx) {
943    /*! return canvas with index 'idx' [0...MAX_NT_WINDOWS-1] */
944    nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
945    return TREE_canvas_registry::instance().get_canvas(idx);
946}
947
948#if defined(TRACE_GROUP_SELECTION)
949static TREE_canvas *find_canvas_showing(AWT_graphic_tree *agt) {
950    // look for (registered) canvas showing given AWT_graphic_tree
951    // returns NULp if none found
952    const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
953
954    int maxIdx = reg.get_count();
955    for (int32_t i = 0; i<maxIdx; ++i) {
956        TREE_canvas *ntw = reg.get_canvas(i);
957        if (ntw->gfx == agt) return ntw;
958    }
959    return NULp;
960}
961#endif
962
963void NT_fill_canvas_selection_list(class AW_selection_list *sellst, TREE_canvas *to_skip) {
964    /*! insert canvases into selection list (using canvas-indices as values)
965     */
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 && ntw != to_skip) {
972            nt_assert(ntw->get_awar_tree());
973            const char *treename    = ntw->get_awar_tree()->read_char_pntr();
974            const char *description = i
975                ? GBS_global_string("ARB (%i):  %s", i, treename)
976                : GBS_global_string("ARB main: %s", treename);
977            sellst->insert(description, i);
978        }
979    }
980}
981
982// ----------------------------------
983//      group-selection handlers
984
985void NT_deselect_group(AW_root *awr) {
986    awr->awar(AWAR_GROUP)->write_pointer(NULp);
987}
988
989static bool track_group_selection_by_canvas = true;
990
991static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) {
992    const Group& group = gfx->get_selected_group();
993
994#if defined(TRACE_GROUP_SELECTION)
995    fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track");
996    TREE_canvas *ntw = find_canvas_showing(gfx);
997    if (group.is_valid()) {
998        fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name());
999    }
1000    else {
1001        fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index());
1002    }
1003#endif
1004
1005    if (track_group_selection_by_canvas) {
1006        // set group-awar:
1007        gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULp if !group.is_valid()
1008    }
1009}
1010
1011static void group_awar_changed_cb(AW_root *awr) {
1012    AW_awar *awar_group      = awr->awar(AWAR_GROUP);
1013    GBDATA  *gb_wanted_group = awar_group->read_pointer();
1014
1015    GBDATA *gb_wanted_tree = NULp;
1016    {
1017        if (gb_wanted_group) {
1018            GB_transaction ta(gb_wanted_group);
1019            gb_wanted_tree = GB_get_father(gb_wanted_group);
1020            awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected
1021#if defined(TRACE_GROUP_SELECTION)
1022            fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr);
1023#endif
1024        }
1025#if defined(TRACE_GROUP_SELECTION)
1026        const char *group_name = NULp;
1027        if (gb_wanted_group) {
1028            GB_transaction  ta(gb_wanted_group);
1029            GBDATA         *gb_name = GB_entry(gb_wanted_group, "group_name");
1030            if (gb_name) group_name = GB_read_char_pntr(gb_name);
1031        }
1032        fprintf(stderr, "group awar changed to %p", gb_wanted_group);
1033        if (group_name) fprintf(stderr, " (='%s')", group_name);
1034        fputc('\n', stderr);
1035#endif
1036    }
1037
1038    LocallyModify<bool> ignore_group_selection_by_canvas(track_group_selection_by_canvas, false);
1039
1040    {
1041        const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1042
1043        int maxIdx = reg.get_count();
1044        for (int32_t i = 0; i<maxIdx; ++i) {
1045            TREE_canvas      *ntw        = reg.get_canvas(i);
1046            AWT_graphic_tree *agt        = AWT_TREE(ntw);
1047            const Group&      curr_group = agt->get_selected_group();
1048
1049            GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree();
1050            if (gb_curr_tree == gb_wanted_tree) {
1051                AWT_auto_refresh allowed_on(ntw);
1052                if (!curr_group.is_valid() ||                       // no group selected
1053                    curr_group.get_group_data() != gb_wanted_group) // wrong group selected
1054                {
1055                    agt->select_group(gb_wanted_group);
1056                    ntw->request_refresh();
1057                }
1058                // perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group)
1059                TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_GROUP);
1060            }
1061            else {
1062                if (curr_group.is_valid()) {
1063                    AWT_auto_refresh allowed_on(ntw);
1064                    agt->deselect_group();
1065                    ntw->request_refresh();
1066                }
1067            }
1068        }
1069    }
1070}
1071
1072// ----------------------------
1073//      create main window
1074
1075static AW_window *popup_new_main_window(AW_root *awr, int clone, TREE_canvas **result_ntw) {
1076    /*! create ARB_NTREE main window
1077     * @param awr application root
1078     * @param clone == 0 -> first window (full functionality); >0 -> additional tree views (restricted functionality)
1079     * @param result_ntw is set to the created TREE_canvas (passed pointer may be NULp if result is not needed)
1080     */
1081    GB_push_transaction(GLOBAL.gb_main);
1082
1083    char        window_title[256];
1084    const char *awar_tree = NULp;
1085
1086    if (clone) {
1087        awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
1088        sprintf(window_title, "ARB_NT_%i", clone);
1089    }
1090    else {
1091        awar_tree = AWAR_TREE;
1092        sprintf(window_title, "ARB_NT");
1093    }
1094    AW_window_menu_modes *awm = new AW_window_menu_modes;
1095    awm->init(awr, window_title, window_title, 0, 0);
1096
1097    awr->awar(AWAR_DB_NAME)
1098       ->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1099       ->update();
1100
1101    awm->button_length(5);
1102
1103    if (!clone) AW_init_color_group_defaults("arb_ntree");
1104
1105    AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1106
1107    if (!clone) { // while creating initial window
1108        AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb));
1109        awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb);
1110    }
1111
1112    TREE_canvas *ntw;
1113    {
1114        AW_awar *tree_awar = awr->awar_string(awar_tree);
1115        {
1116            AP_tree_display_style prev_style = tree->get_tree_style();
1117            tree->set_tree_style(AP_LIST_SIMPLE, NULp); // avoid NDS warnings during startup
1118
1119            ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1120            tree->set_tree_style(prev_style, ntw);
1121            ntw->set_mode(AWT_MODE_SELECT);
1122        }
1123
1124        if (result_ntw) *result_ntw = ntw;
1125
1126        {
1127            const char *tree_name          = tree_awar->read_char_pntr();
1128            const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1129
1130            if (existing_tree_name) {
1131                tree_awar->write_string(existing_tree_name);
1132                NT_reload_tree_event(awr, ntw, true); // load first tree
1133            }
1134            else {
1135                AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, NULp, "no_tree.hlp");
1136                tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list
1137            }
1138
1139            TREE_canvas_registry::instance().register_canvas(ntw);
1140            AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1141        }
1142    }
1143
1144    TREE_install_update_callbacks(ntw);
1145
1146    bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); //  is this a genome database ? (default = 0 = not a genom db)
1147
1148    WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1149
1150    // --------------
1151    //      File
1152
1153#if defined(DEBUG)
1154    AWT_create_debug_menu(awm);
1155#endif // DEBUG
1156
1157    bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1158
1159    if (clone) {
1160        awm->create_menu("File", "F", AWM_ALL);
1161        if (allow_new_window) {
1162            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));
1163        }
1164        awm->insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN);
1165    }
1166    else {
1167#if defined(DEBUG)
1168        // add more to debug-menu
1169        awm->sep______________();
1170        awm->insert_menu_topic("fix_db",      "Fix database",            "F", NULp, AWM_ALL, NT_fix_database);
1171        awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", NULp, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1172        awm->insert_menu_topic("test_compr",  "Test compression",        "T", NULp, AWM_ALL, makeWindowCallback(GBT_compression_test,       GLOBAL.gb_main));
1173#endif // DEBUG
1174
1175        awm->create_menu("File", "F", AWM_ALL);
1176        {
1177            // keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1178            awm->insert_menu_topic("save_changes", "Quicksave changes",          "s", "save.hlp",      AWM_ALL, NT_save_quick_cb);
1179            awm->insert_menu_topic("save_all_as",  "Save whole database as ...", "w", "save.hlp",      AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1180            if (allow_new_window) {
1181                awm->sep______________();
1182                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));
1183            }
1184            awm->sep______________();
1185            awm->insert_menu_topic("optimize_db",  "Optimize database compression", "O", "optimize.hlp",  AWM_ALL, NT_create_database_optimization_window);
1186            awm->sep______________();
1187
1188            awm->insert_sub_menu("Import",      "I");
1189            {
1190                awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1191                awm->insert_menu_topic("import_seq", "Import from external format",   "I", "arb_import.hlp",     AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1192                GDE_load_menu(awm, AWM_EXP, "Import");
1193            }
1194            awm->close_sub_menu();
1195
1196            awm->insert_sub_menu("Export",      "E");
1197            {
1198                awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1199                awm->insert_menu_topic("export_seqs",   "Export to external format",   "f", "arb_export.hlp",      AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1200                GDE_load_menu(awm, AWM_ALL, "Export");
1201                awm->insert_menu_topic("export_nds",    "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp",  AWM_ALL, create_nds_export_window);
1202            }
1203            awm->close_sub_menu();
1204            awm->sep______________();
1205
1206            insert_macro_menu_entry(awm, false);
1207
1208            awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1209            {
1210                awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback  ("version.hlp"));
1211                awm->insert_menu_topic("bug_report",   "Report bug",                              "b", NULp,          AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1212                awm->insert_menu_topic("mailing_list", "Mailing list",                            "M", NULp,          AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1213            }
1214            awm->close_sub_menu();
1215            awm->sep______________();
1216
1217            awm->insert_menu_topic("new_arb",     "Start second database",      "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1218            awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1219            awm->insert_menu_topic("quit",        "Quit",                       "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_exit, EXIT_SUCCESS));
1220        }
1221
1222        // -----------------
1223        //      Species
1224
1225        awm->create_menu("Species", "c", AWM_ALL);
1226        {
1227            awm->insert_menu_topic("species_search", "Search and query",    "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1228            awm->insert_menu_topic("species_info",   "Species information", "i", "sp_info.hlp",   AWM_ALL, popupinfo_wcb);
1229
1230            awm->sep______________();
1231
1232            NT_insert_mark_submenus(awm, ntw, 1);
1233            awm->insert_menu_topic("mark_by_ref",     "Mark by reference..", "r", "markbyref.hlp",       AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1234            awm->insert_menu_topic("species_colors",  "Colors ...",          "l", "colorize.hlp",        AWM_ALL, create_colorize_species_window);
1235            awm->insert_menu_topic("selection_admin", "Selections ...",      "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1236
1237            awm->sep______________();
1238
1239            awm->insert_sub_menu("Database fields admin", "f");
1240            DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1241            awm->close_sub_menu();
1242            NT_create_mask_submenu(awm);
1243
1244            awm->sep______________();
1245
1246            awm->insert_menu_topic("del_marked",    "Delete Marked Species",    "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1247
1248            awm->insert_sub_menu("Sort Species",         "s");
1249            {
1250                awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp",  AWM_ALL, NT_create_resort_window);
1251                awm->insert_menu_topic("$sort_by_tree",  "According to Phylogeny",        "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1252            }
1253            awm->close_sub_menu();
1254
1255            awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1256            {
1257                awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1258                awm->insert_menu_topic("join_marked",   "Join Marked Species",                        "J", "species_join.hlp",  AWM_EXP, NT_create_species_join_window);
1259            }
1260            awm->close_sub_menu();
1261
1262            awm->sep______________();
1263
1264            awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1265
1266            awm->sep______________();
1267
1268            awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1269
1270            awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1271            {
1272                awm->insert_menu_topic("imp_names",    "Import names from file", "I", "vn_import.hlp",  AWM_EXP, NT_importValidNames);
1273                awm->insert_menu_topic("del_names",    "Delete names from DB",   "D", "vn_delete.hlp",  AWM_EXP, NT_deleteValidNames);
1274                awm->insert_menu_topic("sug_names",    "Suggest valid names",    "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1275                awm->insert_menu_topic("search_names", "Search manually",        "m", "vn_search.hlp",  AWM_EXP, NT_create_searchManuallyNames_window);
1276            }
1277            awm->close_sub_menu();
1278        }
1279
1280        // ----------------------------
1281        //      Genes + Experiment
1282
1283        if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1284
1285        // ------------------
1286        //      Sequence
1287
1288        awm->create_menu("Sequence", "S", AWM_ALL);
1289        {
1290            awm->insert_menu_topic("seq_admin",   "Sequence/Alignment Admin", "A", "ad_align.hlp",   AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)NULp));
1291            awm->insert_sub_menu("Insert/delete", "I");
1292            {
1293                awm->insert_menu_topic("ins_del_col", ".. column",     "c", "insdel.hlp",     AWM_ALL, create_insertDeleteColumn_window);
1294                awm->insert_menu_topic("ins_del_sai", ".. using SAI",  "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window,  GLOBAL.gb_main));
1295            }
1296            awm->close_sub_menu();
1297            awm->sep______________();
1298
1299            awm->insert_sub_menu("Edit Sequences", "E");
1300            {
1301                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));
1302                awm->insert_menu_topic("new2_arb_edit4", "... plus relatives",            "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1303                awm->insert_menu_topic("old_arb_edit4",  "Using earlier configuration",   "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1304            }
1305            awm->close_sub_menu();
1306
1307            awm->sep______________();
1308
1309            awm->insert_sub_menu("Align Sequences",  "S");
1310            {
1311                awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1312                GDE_load_menu(awm, AWM_ALL, "Align");
1313            }
1314            awm->close_sub_menu();
1315            awm->insert_menu_topic("seq_concat",    "Concatenate Sequences/Alignments", "C", "concatenate.hlp",       AWM_ALL, NT_createConcatenationWindow);
1316            awm->insert_menu_topic("track_changes", "Track alignment changes",          "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1317            awm->sep______________();
1318
1319            awm->insert_menu_topic("dna_2_pro", "Perform translation",      "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1320            awm->insert_menu_topic("arb_dist",  "Distance Matrix + ARB NJ", "D", "dist.hlp",                AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1321            awm->sep______________();
1322
1323            awm->insert_menu_topic("seq_quality",   "Check Sequence Quality", "Q", "seq_quality.hlp",   AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1324            awm->insert_menu_topic("chimera_check", "Chimera Check",          "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1325
1326            awm->sep______________();
1327
1328            GDE_load_menu(awm, AWM_ALL, "Print");
1329        }
1330
1331        // -------------
1332        //      SAI
1333
1334        awm->create_menu("SAI", "A", AWM_ALL);
1335        {
1336            awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1337            awm->insert_sub_menu("Create SAI using ...", "C");
1338            {
1339                awm->insert_menu_topic("sai_max_freq",  "Max. Frequency",                                               "M", "max_freq.hlp",     AWM_EXP, AP_create_max_freq_window);
1340                awm->insert_menu_topic("sai_consensus", "Consensus",                                                    "C", "consensus.hlp",    AWM_ALL, AP_create_con_expert_window);
1341                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);
1342                awm->insert_menu_topic("arb_phyl",      "Filter by base frequency",                                     "F", "phylo.hlp",        AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_phylo &"));
1343                awm->insert_menu_topic("sai_pfold",     "Protein secondary structure (field \"sec_struct\")",           "P", "pfold.hlp",        AWM_EXP, NT_create_sai_from_pfold);
1344
1345                GDE_load_menu(awm, AWM_EXP, "SAI");
1346            }
1347            awm->close_sub_menu();
1348
1349            awm->insert_sub_menu("Other functions", "O");
1350            {
1351                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));
1352                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));
1353                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);
1354            }
1355            awm->close_sub_menu();
1356        }
1357
1358        // ----------------
1359        //      Probes
1360
1361        awm->create_menu("Probes", "P", AWM_ALL);
1362        {
1363            awm->insert_menu_topic("probe_design", "Design Probes",          "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1364            awm->insert_menu_topic("probe_multi",  "Calculate Multi-Probes", "u", "multiprobe.hlp",  AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1365            awm->insert_menu_topic("probe_match",  "Match Probes",           "M", "probematch.hlp",  AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1366            awm->sep______________();
1367            awm->insert_menu_topic("probe_match_sp",   "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window,    ntw));
1368            awm->sep______________();
1369            awm->insert_menu_topic("primer_design_new", "Design Primers",            "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1370            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));
1371            awm->sep______________();
1372            awm->insert_menu_topic("pt_server_admin",   "PT_SERVER Admin",           "A", "probeadmin.hlp",  AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1373        }
1374
1375    }
1376
1377    // --------------
1378    //      Tree
1379
1380    awm->create_menu("Tree", "T", AWM_ALL);
1381    {
1382        if (!clone) {
1383            awm->insert_sub_menu("Add Species to Existing Tree", "A");
1384            {
1385                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 &"));
1386                awm->insert_menu_topic("arb_pars",       "ARB Parsimony interactive",        "i", "pars.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_pars &"));
1387                GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1388            }
1389            awm->close_sub_menu();
1390        }
1391
1392        awm->insert_sub_menu("Remove Species from Tree",     "R");
1393        {
1394            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));
1395            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));
1396            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));
1397            awm->sep______________();
1398            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));
1399            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));
1400        }
1401        awm->close_sub_menu();
1402
1403        if (!clone) {
1404            awm->insert_sub_menu("Build tree from sequence data",    "B");
1405            {
1406                awm->insert_sub_menu("Distance matrix methods", "D");
1407                awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1408                GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1409                awm->close_sub_menu();
1410
1411                awm->insert_sub_menu("Maximum Parsimony methods", "P");
1412                GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1413                awm->close_sub_menu();
1414
1415                awm->insert_sub_menu("Maximum Likelihood methods", "L");
1416                GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1417                GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1418                awm->close_sub_menu();
1419
1420                awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1421                GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1422                awm->close_sub_menu();
1423            }
1424            awm->close_sub_menu();
1425        }
1426
1427        awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1428
1429        awm->sep______________();
1430
1431        awm->insert_sub_menu("Reset zoom",         "z");
1432        {
1433            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));
1434            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));
1435        }
1436        awm->close_sub_menu();
1437
1438        awm->sep______________();
1439
1440        // taxonomic groups
1441        NT_insert_collapse_submenu(awm, ntw);
1442        if (!clone) {
1443            awm->insert_menu_topic("group_search",     "Search groups...",    "g", "group_search.hlp",     AWM_ALL, makeWindowCallback      (popup_group_search_window,         GLOBAL.gb_main));
1444            awm->insert_menu_topic("compare_taxonomy", "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1445            awm->insert_menu_topic("move_groups",      "Move groups...",      "n", "move_groups.hlp",      AWM_ALL, makeCreateWindowCallback(NT_create_moveGroupInfo_window));
1446        }
1447
1448        awm->sep______________();
1449
1450        if (!clone) {
1451            awm->insert_menu_topic("compare_topology", "Compare topology...", "p", "compare_topo.hlp",     AWM_ALL, makeCreateWindowCallback(NT_create_compareTopologies_window));
1452        }
1453
1454        awm->insert_sub_menu("Modify branches", "M");
1455        {
1456            awm->insert_menu_topic(awm->local_id("tree_remove_remark"),     "Remove bootstraps",      "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap,    ntw));
1457            awm->sep______________();
1458            awm->insert_menu_topic(awm->local_id("tree_reset_lengths"),     "Reset branchlengths",   "R", "tbl_reset.hlp",   AWM_ALL, makeWindowCallback(NT_reset_branchlengths,   ntw));
1459            awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1460            awm->insert_menu_topic(awm->local_id("tree_scale_lengths"),     "Scale Branchlengths",   "S", "tbl_scale.hlp",   AWM_ALL, makeWindowCallback(NT_scale_tree,            ntw));
1461            awm->sep______________();
1462            awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1463            awm->sep______________();
1464            awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1465            awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1466
1467        }
1468        awm->close_sub_menu();
1469        awm->insert_sub_menu("Beautify tree", "e");
1470        {
1471            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));
1472            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));
1473            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));
1474            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));
1475            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));
1476            awm->sep______________();
1477            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));
1478        }
1479        awm->close_sub_menu();
1480
1481        awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "h", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1482        awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "u", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback(NT_mark_duplicates, ntw));
1483
1484        awm->sep______________();
1485
1486        awm->insert_menu_topic(awm->local_id("shade"),            "Tree shading...",       "s", "tree_shading.hlp",     AWM_ALL, makeWindowCallback      (NT_configure_treeShader));
1487        awm->insert_menu_topic(awm->local_id("syncscroll"),       "Sync tree scrolling..", "o", "syncscroll.hlp",       AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1488
1489        awm->sep______________();
1490
1491        awm->insert_menu_topic(awm->local_id("tree_select"),        "Select Tree",      "T", NULp, AWM_ALL, makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1492        awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", NULp, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1493
1494        if (!clone) {
1495            awm->sep______________();
1496            awm->insert_menu_topic("tree_admin", "Tree admin",               "i", "treeadm.hlp",   AWM_ALL, popup_tree_admin_window);
1497            awm->insert_menu_topic("nds",        "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_nds_window, GLOBAL.gb_main));
1498        }
1499
1500        awm->sep______________();
1501        awm->insert_menu_topic("transversion",       "Transversion analysis",   "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1502
1503        if (!clone) {
1504            awm->sep______________();
1505            awm->insert_menu_topic("print_tree",  "Print tree",          "P", "tree2prt.hlp",  AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1506            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)));
1507        }
1508
1509        if (is_genome_db) {
1510            awm->sep______________();
1511            awm->insert_sub_menu("Other..",  "O", AWM_EXP);
1512            {
1513                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));
1514            }
1515            awm->close_sub_menu();
1516        }
1517    }
1518
1519    if (!clone) {
1520        // ---------------
1521        //      Tools
1522
1523        awm->create_menu("Tools", "o", AWM_ALL);
1524        {
1525            awm->insert_menu_topic("names_admin",      "Name server admin (IDs)",    "s", "namesadmin.hlp",  AWM_ALL, makeCreateWindowCallback(AW_create_namesadmin_window, GLOBAL.gb_main));
1526            awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1527            {
1528                awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1529            }
1530            awm->close_sub_menu();
1531            awm->insert_sub_menu("Network", "N", AWM_EXP);
1532            {
1533                GDE_load_menu(awm, AWM_EXP, "Network");
1534            }
1535            awm->close_sub_menu();
1536            awm->sep______________();
1537
1538            awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1539            {
1540                GDE_load_menu(awm, AWM_EXP, NULp);
1541            }
1542            awm->close_sub_menu();
1543
1544            awm->sep______________();
1545            awm->insert_menu_topic("xterm",    "Start XTERM",     "X", "xterm.hlp",   AWM_ALL, AWT_console);
1546            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
1547            awm->insert_menu_topic("viewserv", "View server log", "V", "console.hlp", AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_show_log.pl server", XCMD_ASYNC_WAIT_ON_ERROR));
1548            awm->sep______________();
1549            GDE_load_menu(awm, AWM_EXP, "User");
1550        }
1551        // --------------------
1552        //      Properties
1553
1554        awm->create_menu("Properties", "r", AWM_ALL);
1555        {
1556            awm->insert_menu_topic("props_menu",                 "Frame settings ...",          "F", "props_frame.hlp",      AWM_ALL, AW_preset_window);
1557            awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options",                "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1558            awm->insert_menu_topic("props_tree",                 "Tree colors & fonts",         "c", "color_props.hlp",      AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1559            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));
1560            awm->sep______________();
1561            awm->insert_menu_topic("!toggle_expert", "Toggle expert mode",         "x", NULp, AWM_ALL, NT_toggle_expert_mode);
1562            awm->insert_menu_topic("!toggle_focus",  "Toggle focus follows mouse", "m", NULp, AWM_ALL, NT_toggle_focus_policy);
1563            awm->sep______________();
1564            AW_insert_common_property_menu_entries(awm);
1565            awm->sep______________();
1566            awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1567        }
1568    }
1569
1570    awm->insert_help_topic("ARB_NT help",     "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1571
1572    // ----------------------
1573    //      mode buttons
1574    //
1575    // keep them synchronized as far as possible with those in ARB_PARSIMONY
1576    // see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1577
1578    awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1579    awm->create_mode("mode_mark.xpm",   "mode_mark.hlp",   AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1580    awm->create_mode("mode_group.xpm",  "mode_group.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1581    awm->create_mode("mode_zoom.xpm",   "mode_pzoom.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1582    awm->create_mode("mode_lzoom.xpm",  "mode_lzoom.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1583
1584    awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1585    awm->create_mode("mode_www.xpm",  "mode_www.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event,  ntw, AWT_MODE_WWW));
1586
1587    // topology-modification-modes
1588    awm->create_mode("mode_setroot.xpm",   "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1589    awm->create_mode("mode_swap.xpm",      "mode_swap.hlp",    AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1590    awm->create_mode("mode_move.xpm",      "mode_move.hlp",    AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1591    awm->create_mode("mode_length.xpm",    "mode_length.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1592    awm->create_mode("mode_multifurc.xpm", "mode_length.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1593
1594    // layout-modes
1595    awm->create_mode("mode_line.xpm",   "mode_width.hlp",  AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1596    awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1597    awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1598
1599    awm->set_info_area_height(250);
1600    awm->at(5, 2);
1601    awm->auto_space(-2, -2);
1602    awm->shadow_width(1);
1603
1604    // -------------------------
1605    //      create top area
1606
1607    int first_liney;
1608    int leftx;
1609    awm->get_at_position(&leftx, &first_liney);
1610
1611    // ---------------------
1612    //      quit + help
1613
1614    awm->button_length(0);
1615
1616    if (clone) {
1617        awm->callback(AW_POPDOWN);
1618        awm->create_button("CLOSE", "#close.xpm");
1619    }
1620    else {
1621        awm->callback(makeWindowCallback(NT_exit, EXIT_SUCCESS));
1622        awm->help_text("quit.hlp");
1623        awm->create_button("QUIT", "#quit.xpm");
1624    }
1625
1626    int db_pathx = awm->get_at_xposition();
1627
1628    // now fetch the yposition for the 2nd button line
1629    awm->at_newline();
1630    int second_liney = awm->get_at_yposition();
1631
1632    awm->callback(AW_help_entry_pressed);
1633    awm->help_text("arb_ntree.hlp");
1634    awm->create_button("?", "#help.xpm");
1635
1636    // --------------------------
1637    //      save + undo/redo
1638
1639    awm->callback(NT_save_quick_cb);
1640    awm->help_text("save.hlp");
1641    awm->create_button("SAVE", "#save.xpm");
1642
1643    awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1644    awm->help_text("save.hlp");
1645    awm->create_button("SAVE_AS", "#saveAs.xpm");
1646
1647    // undo/redo:
1648    awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1649    awm->help_text("undo.hlp");
1650    awm->create_button("UNDO", "#undo.xpm");
1651
1652    awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1653    awm->help_text("undo.hlp");
1654    awm->create_button("REDO", "#redo.xpm");
1655
1656    int db_pathx2 = awm->get_at_xposition();
1657
1658    // fetch position for mode help-line:
1659    awm->at_newline();
1660    int third_liney = awm->get_at_yposition();
1661
1662    awm->at(db_pathx, first_liney);
1663    // size of DB-name button is determined by buttons below:
1664    awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1665    awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1666    awm->help_text("save.hlp");
1667    awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1668
1669    // -----------------------------
1670    //      tree + tree display
1671
1672#define TREE_BUTTON_OVERSIZE 6
1673
1674    int db_treex      = awm->get_at_xposition();
1675    int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1676
1677    awm->at(db_treex, second_uppery);
1678    awm->button_length(0);
1679
1680    awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1681    awm->help_text("tr_type_radial.hlp");
1682    awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1683
1684    awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1685    awm->help_text("tr_type_list.hlp");
1686    awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1687
1688    awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1689    awm->help_text("tr_type_irs.hlp");
1690    awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1691
1692    awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1693    awm->help_text("tr_type_nds.hlp");
1694    awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1695
1696    int db_treex2 = awm->get_at_xposition();
1697
1698    awm->at(db_treex, first_liney);
1699    // size of tree-name button is determined by buttons below:
1700    awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1701    awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1702    awm->help_text("nt_tree_select.hlp");
1703    awm->create_button("SELECT_A_TREE", awar_tree);
1704
1705    // ---------------------------------------------------------------
1706    //      protection, alignment + editor (and maybe Genome Map)
1707
1708    int db_alignx = awm->get_at_xposition();
1709
1710    // editor and genemap buttons have to be 44x24 sized
1711#define EDIT_XSIZE 50
1712#define EDIT_YSIZE 30 // same as 'save as' buttons
1713
1714    // first draw protection:
1715    int protectx = db_alignx + 2*EDIT_XSIZE;
1716
1717    awm->at(protectx+2, first_liney+1);
1718    awm->button_length(0);
1719    awm->create_button(NULp, "#protect.xpm");
1720
1721    awm->at(protectx, second_liney+2);
1722    awm->create_option_menu(AWAR_SECURITY_LEVEL, true);
1723    awm->insert_option        ("0", NULp, 0);
1724    awm->insert_option        ("1", NULp, 1);
1725    awm->insert_option        ("2", NULp, 2);
1726    awm->insert_option        ("3", NULp, 3);
1727    awm->insert_option        ("4", NULp, 4);
1728    awm->insert_option        ("5", NULp, 5);
1729    awm->insert_default_option("6", NULp, 6);
1730    awm->update_option_menu();
1731
1732    int db_searchx = awm->get_at_xposition() - 7;
1733
1734    // draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1735    awm->at(db_alignx, second_liney);
1736
1737    awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1738    awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1739    awm->help_text("arb_edit4.hlp");
1740    if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1741    else              awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1742
1743    if (is_genome_db) {
1744        awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1745        awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1746        awm->help_text("gene_map.hlp");
1747        awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1748    }
1749
1750    int db_alignx2 = awm->get_at_xposition();
1751
1752    awm->at(db_alignx, first_liney);
1753    awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1754    awm->callback(NT_create_select_alignment_window);
1755    awm->help_text("nt_align_select.hlp");
1756    awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1757
1758    // -------------------------------
1759    //      create mode-help line
1760
1761    awm->at(leftx, third_liney);
1762    awm->button_length(AWAR_FOOTER_MAX_LEN);
1763    awm->create_button(NULp, AWAR_FOOTER);
1764
1765    awm->at_newline();
1766    int bottomy = awm->get_at_yposition();
1767
1768    // ---------------------------------------
1769    //      Info / marked / Search / Jump
1770
1771    awm->button_length(7);
1772
1773    awm->at(db_searchx, first_liney);
1774    awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1775    awm->help_text("sp_search.hlp");
1776    awm->create_button("SEARCH",  "Search");
1777
1778    awm->at(db_searchx, second_uppery);
1779    awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1780    awm->help_text("tr_jump.hlp");
1781    awm->create_button("JUMP", "Jump");
1782
1783    int db_infox = awm->get_at_xposition();
1784
1785    awm->at(db_infox, first_liney);
1786    awm->button_length(13);
1787    awm->callback(popupinfo_wcb);
1788    awm->help_text("sp_search.hlp");
1789    awm->create_button("INFO",  AWAR_INFO_BUTTON_TEXT);
1790
1791    awm->at(db_infox, second_uppery);
1792    awm->button_length(13);
1793    awm->help_text("species_configs.hlp");
1794    awm->callback(makeWindowCallback(NT_popup_configuration_admin, ntw));
1795    awm->create_button("selection_admin2", AWAR_MARKED_SPECIES_COUNTER);
1796    {
1797        GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1798        GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(NT_update_marked_counter, static_cast<AW_window*>(awm)));
1799        NT_update_marked_counter(NULp, awm);
1800    }
1801
1802    // set height of top area:
1803    awm->set_info_area_height(bottomy+2);
1804    awm->set_bottom_area_height(0);
1805
1806    NT_activate_configMarkers_display(ntw);
1807
1808    // ------------------------------------
1809    //      Autostarts for development
1810
1811#if defined(DEVEL_RALF)
1812    // if (is_genome_db) GEN_map_first(awr)->show();
1813#endif // DEVEL_RALF
1814
1815    GB_pop_transaction(GLOBAL.gb_main);
1816
1817#if defined(DEBUG)
1818    AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1819#endif
1820
1821    return awm;
1822}
1823
1824TREE_canvas *NT_create_main_window(AW_root *aw_root) {
1825    GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1826    if (error) aw_message(error);
1827
1828    nt_create_all_awars(aw_root);
1829
1830    TREE_canvas *ntw = NULp;
1831    AW_window   *aww = popup_new_main_window(aw_root, 0, &ntw);
1832    NT_install_treeShader(ntw, GLOBAL.gb_main);
1833    aww->show();
1834
1835    error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1836    if (error) aw_message(error);
1837
1838    return ntw;
1839}
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