source: branches/help/EDIT4/ED4_root.cxx

Last change on this file was 18463, checked in by westram, 5 years ago
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1// =============================================================== //
2//                                                                 //
3//   File      : ED4_root.cxx                                      //
4//   Purpose   :                                                   //
5//                                                                 //
6//   Institute of Microbiology (Technical University Munich)       //
7//   http://www.arb-home.de/                                       //
8//                                                                 //
9// =============================================================== //
10
11#include "ed4_class.hxx"
12#include "ed4_awars.hxx"
13#include "ed4_tools.hxx"
14#include "ed4_block.hxx"
15#include "ed4_dots.hxx"
16#include "ed4_nds.hxx"
17#include "ed4_list.hxx"
18#include "ed4_plugins.hxx"
19#include "ed4_visualizeSAI.hxx"
20#include "ed4_naligner.hxx"
21#include "ed4_ProteinViewer.hxx"
22#include "ed4_protein_2nd_structure.hxx"
23#include "graph_aligner_gui.hxx"
24#include "ed4_colStat.hxx"
25#include "ed4_seq_colors.hxx"
26#include "ed4_flags.hxx"
27
28#include <ed4_extern.hxx>
29#include <fast_aligner.hxx>
30
31#include <AW_helix.hxx>
32#include <gde.hxx>
33#include <awt.hxx>
34#include <awt_map_key.hxx>
35
36#include <aw_awars.hxx>
37#include <aw_preset.hxx>
38#include <aw_msg.hxx>
39#include <arb_progress.h>
40#include <aw_root.hxx>
41#include <aw_question.hxx>
42#include <aw_advice.hxx>
43#include <rootAsWin.h>
44#include "../WINDOW/aw_status.hxx" // @@@ hack - obsolete when EDIT4 status works like elsewhere
45
46#include <arb_version.h>
47#include <arb_file.h>
48#include <arb_defs.h>
49
50#include <arbdbt.h>
51#include <ad_cb.h>
52#include <macros.hxx>
53#include <st_window.hxx>
54
55#include <cctype>
56#include <map>
57
58ED4_WinContext ED4_WinContext::current_context;
59
60void ED4_folding_line::warn_illegal_dimension() {
61#if defined(DEBUG)
62    if (dimension<0.0) {
63        // e4_assert(0); // crashes gdb when called from scrollbar callback - so instead only dump backtrace
64        const char *msg = GBS_global_string("illegal dimension %f\n", dimension);
65        GBK_dump_backtrace(stderr, msg);
66    }
67#endif
68}
69
70void ED4_WinContext::warn_missing_context() const {
71    e4_assert(0);
72    GBK_dump_backtrace(stderr, "Missing context");
73    aw_message("Missing context - please send information from console to devel@arb-home.de");
74}
75
76static ARB_ERROR request_terminal_refresh(ED4_base *base, ED4_level lev) {
77    if (lev == LEV_NONE || (base->spec.level&lev) != 0) {
78        if (base->is_terminal()) base->request_refresh();
79    }
80    return NULp;
81}
82
83void ED4_root::request_refresh_for_all_terminals() {
84    main_manager->route_down_hierarchy(makeED4_route_cb(request_terminal_refresh, LEV_NONE)).expect_no_error();
85}
86
87void ED4_root::request_refresh_for_specific_terminals(ED4_level lev) {
88    main_manager->route_down_hierarchy(makeED4_route_cb(request_terminal_refresh, lev)).expect_no_error();
89}
90
91
92static ARB_ERROR request_sequence_refresh(ED4_base *base, bool consensi) {
93    ARB_ERROR error;
94    if (base->spec.level & LEV_SPECIES) {
95        if (base->is_consensus_manager() == consensi) {
96            error = base->to_manager()->route_down_hierarchy(makeED4_route_cb(request_terminal_refresh, LEV_SEQUENCE_STRING));
97        }
98    }
99    return error;
100}
101
102// if you want to refresh consensi AND sequences you may use request_refresh_for_specific_terminals(LEV_SEQUENCE_STRING)
103void ED4_root::request_refresh_for_consensus_terminals() {
104    main_manager->route_down_hierarchy(makeED4_route_cb(request_sequence_refresh, true)).expect_no_error();
105}
106void ED4_root::request_refresh_for_sequence_terminals() {
107    if (main_manager) {
108        main_manager->route_down_hierarchy(makeED4_route_cb(request_sequence_refresh, false)).expect_no_error();
109    }
110}
111
112void ED4_root::refresh_window_simple(bool redraw) {
113    // if 'redraw' -> update everything (ignoring refresh flag)
114    bool refresh_all = false;
115    if (redraw) {
116#if defined(TRACE_REFRESH)
117        fprintf(stderr, "- clear display (refresh_window_simple(redraw=true) called)\n"); fflush(stderr);
118#endif
119        main_manager->update_info.set_clear_at_refresh(1);
120        refresh_all = true;
121    }
122
123    main_manager->Show(refresh_all, false);
124    if (redraw) main_manager->update_info.set_clear_at_refresh(0);
125}
126
127void ED4_root::handle_update_requests(bool& redraw) {
128    if (main_manager->update_info.delete_requested) {
129#if defined(TRACE_REFRESH)
130        fprintf(stderr, "- handling requested deletes\n"); fflush(stderr);
131#endif
132        main_manager->delete_requested_children();
133        redraw = true;
134    }
135
136    if (main_manager->update_info.update_requested) {
137#if defined(TRACE_REFRESH)
138        fprintf(stderr, "- handling requested updates\n"); fflush(stderr);
139#endif
140        main_manager->update_requested_children();
141        redraw = true; // @@@ needed ?
142    }
143
144    while (main_manager->update_info.resize) {
145#if defined(TRACE_REFRESH)
146        fprintf(stderr, "- handling requested resizes\n"); fflush(stderr);
147#endif
148        main_manager->resize_requested_children();
149        redraw = true;
150    }
151
152    // make sure all update request have been handled:
153    e4_assert(!main_manager->update_info.delete_requested);
154    e4_assert(!main_manager->update_info.update_requested);
155    e4_assert(!main_manager->update_info.resize);
156}
157
158void ED4_root::special_window_refresh(bool handle_updates) {
159    // this function should only be used for window specific updates (e.g. cursor placement/deletion)
160    e4_assert(ED4_WinContext::have_context());
161
162    bool redraw = true;
163    if (handle_updates) handle_update_requests(redraw);
164    refresh_window_simple(redraw);
165    // do NOT clear_refresh_requests here!! this is no full refresh!
166}
167
168ED4_returncode ED4_root::refresh_all_windows(bool redraw) {
169    // if 'redraw' -> update everything (ignoring refresh flag)
170    GB_transaction ta(gb_main);
171
172    handle_update_requests(redraw);
173
174    ED4_window *window = first_window;
175    while (window) {
176        ED4_LocalWinContext uses(window);
177        refresh_window_simple(redraw);
178        window = window->next;
179    }
180
181    if (main_manager->update_info.refresh) main_manager->clear_refresh();
182
183    if (loadable_SAIs == LSAI_OUTDATED) {
184        GB_touch(GBT_get_SAI_data(gb_main)); // touch SAI data to force update of SAI selection list
185        loadable_SAIs = LSAI_UPTODATE;
186    }
187
188    return ED4_R_OK;
189}
190
191// --------------------------------------------------------------------------------
192
193#ifdef UNIT_TESTS
194#ifndef TEST_UNIT_H
195#include <test_unit.h>
196#endif
197
198static arb_test::match_expectation correct_win2world_calculation(ED4_foldable& foldable, int xwin_org, int ywin_org, int xwrld_expd, int ywrld_expd) {
199    using namespace arb_test;
200    match_expectation precondition(all().of(that(xwrld_expd).is_more_or_equal(xwin_org),
201                                            that(ywrld_expd).is_more_or_equal(ywin_org)));
202
203    AW_pos xwrld_calc = xwin_org;
204    AW_pos ywrld_calc = ywin_org;
205    foldable.win_to_world_coords(&xwrld_calc, &ywrld_calc);
206
207    match_expectation win_2_world_conversion(all().of(that(xwrld_calc).is_equal_to(xwrld_expd),
208                                                      that(ywrld_calc).is_equal_to(ywrld_expd)));
209
210    AW_pos xwin_back = xwrld_calc;
211    AW_pos ywin_back = ywrld_calc;
212    foldable.world_to_win_coords(&xwin_back, &ywin_back);
213
214    match_expectation world_back2_win_conversion(all().of(that(xwin_back).is_equal_to(xwin_org),
215                                                          that(ywin_back).is_equal_to(ywin_org)));
216
217    return all().of(precondition, win_2_world_conversion, world_back2_win_conversion);
218}
219
220static arb_test::match_expectation correct_world2win_calculation(ED4_foldable& foldable, int xwrld_org, int ywrld_org, int xwin_expd, int ywin_expd) {
221    using namespace arb_test;
222    match_expectation precondition(all().of(that(xwrld_org).is_more_or_equal(xwin_expd),
223                                            that(ywrld_org).is_more_or_equal(ywin_expd)));
224
225
226    AW_pos xwin_calc = xwrld_org;
227    AW_pos ywin_calc = ywrld_org;
228    foldable.world_to_win_coords(&xwin_calc, &ywin_calc);
229
230    match_expectation world_2_win_conversion(all().of(that(xwin_calc).is_equal_to(xwin_expd),
231                                                      that(ywin_calc).is_equal_to(ywin_expd)));
232
233    return all().of(precondition, world_2_win_conversion);
234}
235
236#define TEST_EXPECT_WIN_UNFOLDED(xwi,ywi)              TEST_EXPECTATION(correct_win2world_calculation(foldable, xwi, ywi, xwi, ywi))
237#define TEST_EXPECT_WIN_WORLD_FOLDING(xwi,ywi,fx,fy)   TEST_EXPECTATION(correct_win2world_calculation(foldable, xwi, ywi, (xwi)+(fx), (ywi)+(fy)))
238#define TEST_EXPECT_WORLD_WIN_FOLDING(xwo,ywo,xwi,ywi) TEST_EXPECTATION(correct_world2win_calculation(foldable, xwo, ywo, xwi, ywi))
239
240#define TEST_EXPECT_WIN_WORLD_FOLDING__BROKEN(xwi,ywi,fx,fy)        TEST_EXPECTATION__BROKEN(correct_win2world_calculation(foldable, xwi, ywi, (xwi)+(fx), (ywi)+(fy)))
241#define TEST_EXPECT_WIN_WORLD_FOLDING__BROKENIF(when,xwi,ywi,fx,fy) TEST_EXPECTATION__BROKENIF(when, correct_win2world_calculation(foldable, xwi, ywi, (xwi)+(fx), (ywi)+(fy)))
242
243void TEST_win_2_world() {
244    ED4_foldable foldable;
245
246    const int X1 = 200;
247    const int X2 = 300;
248    const int Y1 = 100;
249    const int Y2 = 200;
250
251    ED4_folding_line *hor100 = foldable.insert_folding_line(Y1, 0, PROP_HORIZONTAL);
252    ED4_folding_line *ver200 = foldable.insert_folding_line(X1, 0, PROP_VERTICAL);
253    ED4_folding_line *hor200 = foldable.insert_folding_line(Y2, 0, PROP_HORIZONTAL);
254    ED4_folding_line *ver300 = foldable.insert_folding_line(X2, 0, PROP_VERTICAL);
255
256    // nothing folded yet
257
258    const int x01 = X1/2;
259    const int x12 = (X1+X2)/2;
260    const int x23 = X2+x01;
261
262    const int y01 = Y1/2;
263    const int y12 = (Y1+Y2)/2;
264    const int y23 = Y2+y01;
265
266    TEST_EXPECT_WIN_UNFOLDED(x01, y01);
267    TEST_EXPECT_WIN_UNFOLDED(x12, y01);
268    TEST_EXPECT_WIN_UNFOLDED(x23, y01);
269
270    TEST_EXPECT_WIN_UNFOLDED(x01, y12);
271    TEST_EXPECT_WIN_UNFOLDED(x12, y12);
272    TEST_EXPECT_WIN_UNFOLDED(x23, y12);
273
274    TEST_EXPECT_WIN_UNFOLDED(x01, y23);
275    TEST_EXPECT_WIN_UNFOLDED(x12, y23);
276    TEST_EXPECT_WIN_UNFOLDED(x23, y23);
277
278    for (int FACTOR = 1; FACTOR <= 100; FACTOR += 7) {
279        TEST_ANNOTATE(GBS_global_string("FACTOR=%i", FACTOR));
280        int H1 = FACTOR* 10;
281        int H2 = FACTOR* 40;
282        int V1 = FACTOR* 20;
283        int V2 = FACTOR* 80;
284
285        hor100->set_dimension(H1);
286        hor200->set_dimension(H2);
287        ver200->set_dimension(V1);
288        ver300->set_dimension(V2);
289
290        TEST_EXPECT_WIN_UNFOLDED     (x01, y01); // always in unfolded range
291        TEST_EXPECT_WIN_WORLD_FOLDING(x12, y01, V1,    0);
292        TEST_EXPECT_WIN_WORLD_FOLDING(x23, y01, V1+V2, 0);
293
294        TEST_EXPECT_WIN_WORLD_FOLDING(x01, y12, 0,     H1);
295        TEST_EXPECT_WIN_WORLD_FOLDING(x12, y12, V1,    H1);
296        TEST_EXPECT_WIN_WORLD_FOLDING(x23, y12, V1+V2, H1);
297
298        TEST_EXPECT_WIN_WORLD_FOLDING(x01, y23, 0,     H1+H2);
299        TEST_EXPECT_WIN_WORLD_FOLDING(x12, y23, V1,    H1+H2);
300        TEST_EXPECT_WIN_WORLD_FOLDING(x23, y23, V1+V2, H1+H2);
301
302        // test "folded" world positions.
303        // they result in win positions lower than folding line!
304        TEST_EXPECT_WORLD_WIN_FOLDING(X1-1,    Y1-1,    X1-1,    Y1-1);    // left of/above folded range
305        TEST_EXPECT_WORLD_WIN_FOLDING(X1,      Y1,      X1-V1,   Y1-H1);   // left/upper end of folded range
306        TEST_EXPECT_WORLD_WIN_FOLDING(X1+5,    Y1+5,    X1+5-V1, Y1+5-H1); // in folded range
307        TEST_EXPECT_WORLD_WIN_FOLDING(X1+V1,   Y1+H1,   X1,      Y1);      // right/lower end of folded range
308        TEST_EXPECT_WORLD_WIN_FOLDING(X1+V1+1, Y1+H1+1, X1+1,    Y1+1);    // right of/below folded range
309    }
310}
311
312#endif // UNIT_TESTS
313
314// --------------------------------------------------------------------------------
315
316ED4_returncode ED4_root::deselect_all() {
317    ED4_multi_species_manager *main_multi_man = middle_area_man->get_multi_species_manager();
318    main_multi_man->deselect_all_species_and_SAI();
319
320    main_multi_man = top_area_man->get_multi_species_manager();
321    main_multi_man->deselect_all_species_and_SAI();
322
323    ED4_setBlocktype(ED4_BT_NOBLOCK);
324
325    return ED4_R_OK;
326}
327
328void ED4_root::remove_from_selected(ED4_species_name_terminal *name_term) { // @@@ change param to ED4_species_manager ?
329    if (name_term) {
330        if ((selected_objects->has_elem(name_term->selection_info))) {
331            selected_objects->remove_elem(name_term->selection_info);
332
333            delete name_term->selection_info;
334            name_term->selection_info    = NULp;
335            name_term->containing_species_manager()->set_selected(false);
336            name_term->dragged = false; // @@@ caller shall do this
337
338#ifdef DEBUG
339            GBDATA *gbd = name_term->get_species_pointer();
340
341            if (gbd) {
342                GB_transaction ta(gbd);
343                printf("removed term '%s'\n", GB_read_char_pntr(gbd));
344            }
345            else {
346                ED4_species_manager *spec_man = name_term->get_parent(LEV_SPECIES)->to_species_manager();
347
348                if (spec_man->is_consensus_manager()) {
349                    printf("removed consensus '%s'\n", name_term->id);
350                }
351                else {
352                    printf("removed unknown term '%s'\n", name_term->id ? name_term->id : "NULp");
353                }
354            }
355#endif
356
357            name_term->request_refresh();
358            ED4_sequence_terminal *seq_term = name_term->corresponding_sequence_terminal();
359            if (seq_term) seq_term->request_refresh();
360
361            // ProtView: Refresh corresponding orf terminals
362            if (alignment_type == GB_AT_DNA) {
363                PV_CallBackFunction(this->aw_root);
364            }
365
366            ED4_multi_species_manager *multi_man = name_term->get_parent(LEV_MULTI_SPECIES)->to_multi_species_manager();
367            multi_man->invalidate_species_counters();
368        }
369    }
370}
371
372void ED4_root::announce_useraction_in(AW_window *aww) {
373    for (ED4_window *win = first_window; win; win = win->next) {
374        if (win->aww == aww) {
375            most_recently_used_window = win;
376        }
377    }
378}
379
380ED4_returncode ED4_root::add_to_selected(ED4_species_name_terminal *name_term) { // @@@ change param to ED4_species_manager ?
381    if (!name_term || !name_term->has_property(PROP_SELECTABLE)) {   // check if object exists and may be selected
382        return ED4_R_IMPOSSIBLE;
383    }
384
385    if (!(selected_objects->has_elem(name_term->selection_info))) {     // object is really new to our list => calculate current extension and append it
386        ED4_selection_entry *sel_info = new ED4_selection_entry;
387        name_term->selection_info     = sel_info;
388
389        if (name_term->has_property(PROP_IS_HANDLE)) { // object is a handle for an object up in the hierarchy => search it
390            ED4_level  mlevel     = name_term->spec.handled_level;
391            ED4_base  *tmp_object = name_term;
392
393            while (tmp_object && !(tmp_object->spec.level & mlevel)) {
394                tmp_object = tmp_object->parent;
395            }
396
397            if (!tmp_object) return ED4_R_WARNING; // no target level found
398
399            sel_info->actual_width  = tmp_object->extension.size[WIDTH];
400            sel_info->actual_height = tmp_object->extension.size[HEIGHT];
401        }
402        else { // selected object is no handle => take it directly
403            sel_info->actual_width  = name_term->extension.size[WIDTH];
404            sel_info->actual_height = name_term->extension.size[HEIGHT];
405        }
406
407        sel_info->drag_old_x  = 0;
408        sel_info->drag_old_y  = 0;
409        sel_info->drag_off_x  = 0;
410        sel_info->drag_off_y  = 0;
411        sel_info->old_event_y = 0;
412
413        sel_info->object = name_term;
414
415        selected_objects->prepend_elem(sel_info);
416
417        name_term->containing_species_manager()->set_selected(true);
418
419#ifdef DEBUG
420        GBDATA *gbd = name_term->get_species_pointer();
421
422        if (gbd) {
423            printf("added term '%s'\n", GB_read_char_pntr(gbd));
424        }
425        else {
426            ED4_species_manager *spec_man = name_term->get_parent(LEV_SPECIES)->to_species_manager();
427            if (spec_man->is_consensus_manager()) {
428                printf("added consensus '%s'\n", name_term->id);
429            }
430            else {
431                printf("added unknown term '%s'\n", name_term->id ? name_term->id : "NULp");
432            }
433        }
434#endif
435
436        name_term->request_refresh();
437        ED4_sequence_terminal *seq_term = name_term->corresponding_sequence_terminal();
438        if (seq_term) seq_term->request_refresh();
439
440        // ProtView: Refresh corresponding orf terminals
441        if (alignment_type == GB_AT_DNA) {
442            PV_CallBackFunction(this->aw_root);
443        }
444
445        ED4_multi_species_manager *multi_man = name_term->get_parent(LEV_MULTI_SPECIES)->to_multi_species_manager();
446        multi_man->invalidate_species_counters();
447
448        return ED4_R_OK;
449    }
450
451    return ED4_R_IMPOSSIBLE;
452}
453
454void ED4_root::resize_all_requesting_childs() {
455    while (main_manager->update_info.resize) {
456        main_manager->resize_requested_children();
457    }
458}
459
460static ARB_ERROR change_char_table_length(ED4_base *base, int new_length) {
461    if (base->is_abstract_group_manager()) {
462        ED4_abstract_group_manager *group_man = base->to_abstract_group_manager();
463        group_man->table().change_table_length(new_length);
464    }
465    return NULp;
466}
467
468void ED4_alignment_length_changed(GBDATA *gb_alignment_len, GB_CB_TYPE IF_ASSERTION_USED(gbtype)) { // callback from database
469    e4_assert(gbtype==GB_CB_CHANGED);
470    int new_length = GB_read_int(gb_alignment_len);
471
472#if defined(DEBUG) && 1
473    printf("alignment_length_changed from %i to %i\n", MAXSEQUENCECHARACTERLENGTH, new_length);
474#endif
475
476    if (MAXSEQUENCECHARACTERLENGTH!=new_length) { // otherwise we already did this (i.e. we were called by changed_by_database)
477        bool was_increased = new_length>MAXSEQUENCECHARACTERLENGTH;
478
479        MAXSEQUENCECHARACTERLENGTH = new_length;
480
481        GBDATA *gb_main = ED4_ROOT->get_gb_main();
482        {
483            const char *err = ED4_ROOT->helix->init(gb_main); // reload helix
484            aw_message_if(err);
485        }
486        {
487            const char *err = ED4_ROOT->ecoli_ref->init(gb_main); // reload ecoli
488            aw_message_if(err);
489        }
490
491        if (ED4_ROOT->alignment_type == GB_AT_AA) {
492            // TODO: is this needed here?
493            const char *err = ED4_pfold_set_SAI(&ED4_ROOT->protstruct, gb_main, ED4_ROOT->alignment_name, &ED4_ROOT->protstruct_len); // reload protstruct
494            aw_message_if(err);
495        }
496
497        if (was_increased) {
498            ED4_ROOT->main_manager->route_down_hierarchy(makeED4_route_cb(change_char_table_length, new_length)).expect_no_error();
499            ED4_ROOT->root_group_man->remap()->mark_compile_needed_force();
500        }
501    }
502}
503
504ARB_ERROR ED4_root::init_alignment() {
505    GB_transaction ta(gb_main);
506
507    alignment_name = GBT_get_default_alignment(gb_main);
508    alignment_type = GBT_get_alignment_type(gb_main, alignment_name);
509    if (alignment_type==GB_AT_UNKNOWN) {
510        return GBS_global_string("You have to select a valid alignment before you can start ARB_EDIT4\n(%s)", GB_await_error());
511    }
512
513    GBDATA *gb_alignment = GBT_get_alignment(gb_main, alignment_name);
514    if (!gb_alignment) {
515        return GBS_global_string("You can't edit without an existing alignment\n(%s)", GB_await_error());
516    }
517
518    GBDATA *gb_alignment_len = GB_search(gb_alignment, "alignment_len", GB_FIND);
519    int alignment_length = GB_read_int(gb_alignment_len);
520    MAXSEQUENCECHARACTERLENGTH = alignment_length;
521
522    GB_add_callback(gb_alignment_len, GB_CB_CHANGED, makeDatabaseCallback(ED4_alignment_length_changed));
523
524    aw_root->awar_string(AWAR_EDITOR_ALIGNMENT, alignment_name);
525
526    return NULp;
527}
528
529void ED4_root::recalc_font_group() {
530    int font_GC[] = {
531        ED4_G_SEQUENCES,
532        ED4_G_STANDARD,
533        ED4_G_FLAG_INFO,
534    };
535
536    font_group.unregisterAll();
537    for (unsigned i = 0; i<ARRAY_ELEMS(font_GC); ++i) {
538        ED4_MostRecentWinContext context;
539        font_group.registerFont(current_device(), font_GC[i]);
540    }
541}
542
543static ARB_ERROR force_group_update(ED4_base *base) {
544    if (base->is_multi_species_manager()) {
545        base->to_multi_species_manager()->update_requested_by_child();
546    }
547    return NULp;
548}
549
550ED4_returncode ED4_root::create_hierarchy(const char *area_string_middle, const char *area_string_top) {
551    // creates internal hierarchy of editor
552
553    long total_no_of_groups  = 0;
554    long total_no_of_species = 0;
555    {
556        // count species and related info (e.g. helix) displayed in the top region (a == 0)
557        // count no of species and sais including groups in middle region (a == 1)
558
559        const char *area_string[2] = { area_string_top, area_string_middle };
560        for (int a = 0; a<2; ++a) {
561            long group_count;
562            long species_count;
563
564            EDB_root_bact::calc_no_of_all(area_string[a], &group_count, &species_count);
565
566            total_no_of_groups  += group_count;
567            total_no_of_species += species_count;
568        }
569    }
570
571    SmartPtr<arb_progress> startup_progress = new arb_progress("EDIT4 startup");
572
573    GB_push_transaction(gb_main);
574
575    ecoli_ref = new BI_ecoli_ref;
576    ecoli_ref->init(gb_main);
577
578    // [former position of ali-init-code]
579
580    main_manager   = new ED4_main_manager("Main_Manager", 0, 0, NULp); // build a test hierarchy
581    root_group_man = new ED4_root_group_manager("Root_Group_Manager", 0, 0, main_manager);
582
583    main_manager->append_member(root_group_man);
584
585    ED4_device_manager *device_manager = new ED4_device_manager("Device_Manager", 0, 0, root_group_man);
586    root_group_man->append_member(device_manager);
587
588    {
589        int col_stat_term_height = 50; // @@@ Hoehe des ColumnStatistics Terminals ausrechnen
590
591        ref_terminals.init(
592            new ED4_sequence_info_terminal("Reference_Sequence_Info_Terminal",         MAXINFO_WIDTH, TERMINAL_HEIGHT,       NULp),
593            new ED4_sequence_terminal     ("Reference_Sequence_Terminal",              300,           TERMINAL_HEIGHT,       NULp, false),
594            new ED4_sequence_info_terminal("Reference_ColumnStatistics_Info_Terminal", MAXINFO_WIDTH, col_stat_term_height, NULp),
595            new ED4_columnStat_terminal   ("Reference_ColumnStatistics_Terminal",      300,           col_stat_term_height, NULp)
596            );
597    }
598
599    {
600        arb_progress species_progress("Loading species", total_no_of_species);
601
602        // ********** Top Area beginning **********
603
604        ED4_multi_species_manager *top_multi_species_manager;
605        ED4_spacer_terminal       *top_spacer_terminal;
606        ED4_spacer_terminal       *top_mid_spacer_terminal;
607        ED4_spacer_terminal       *top_multi_spacer_terminal_beg;
608        ED4_line_terminal         *top_mid_line_terminal;
609        {
610            ED4_area_manager *top_area_manager = new ED4_area_manager("Top_Area_Manager", 0, 0, device_manager);
611            device_manager->append_member(top_area_manager);
612            top_area_man = top_area_manager;
613
614            top_spacer_terminal = new ED4_spacer_terminal("Top_Spacer", false, 100, 10, top_area_manager);
615            top_area_manager->append_member(top_spacer_terminal);
616
617            top_multi_species_manager = new ED4_multi_species_manager("Top_MultiSpecies_Manager", 0, 0, top_area_manager);
618            top_area_manager->append_member(top_multi_species_manager);
619
620            top_multi_spacer_terminal_beg = new ED4_spacer_terminal("Top_Left_Spacer", false, 0, 3, top_multi_species_manager);
621            top_multi_species_manager->append_member(top_multi_spacer_terminal_beg);
622
623            reference = new ED4_reference;
624
625            int index = 0;
626            EDB_root_bact::scan_string(top_multi_species_manager, ref_terminals, area_string_top, &index, species_progress);
627            GB_pop_transaction(gb_main);
628
629            const int TOP_MID_LINE_HEIGHT   = 3;
630            int       TOP_MID_SPACER_HEIGHT = font_group.get_max_height()-TOP_MID_LINE_HEIGHT;
631
632            top_mid_line_terminal = new ED4_line_terminal("Top_Mid_Line_Terminal", 0, TOP_MID_LINE_HEIGHT, device_manager);    // width will be set below
633            device_manager->append_member(top_mid_line_terminal);
634
635            top_mid_spacer_terminal = new ED4_spacer_terminal("Top_Middle_Spacer", true, 880, TOP_MID_SPACER_HEIGHT, device_manager);
636            device_manager->append_member(top_mid_spacer_terminal);
637
638            // needed to avoid text-clipping problems:
639            main_manager->set_top_middle_spacer_terminal(top_mid_spacer_terminal);
640            main_manager->set_top_middle_line_terminal(top_mid_line_terminal);
641        }
642
643        // ********** Middle Area beginning **********
644
645        ED4_area_manager          *middle_area_manager;
646        ED4_tree_terminal         *tree_terminal;
647        ED4_multi_species_manager *mid_multi_species_manager;
648        ED4_spacer_terminal       *mid_multi_spacer_terminal_beg;
649        ED4_line_terminal         *mid_bot_line_terminal;
650        ED4_spacer_terminal       *total_bottom_spacer;
651        {
652            middle_area_manager = new ED4_area_manager("Middle_Area_Manager", 0, 0, device_manager);
653            device_manager->append_member(middle_area_manager);
654            middle_area_man = middle_area_manager;
655
656            tree_terminal = new ED4_tree_terminal("Tree", 2, 0, middle_area_manager);
657            middle_area_manager->append_member(tree_terminal);
658
659            mid_multi_species_manager = new ED4_multi_species_manager("Middle_MultiSpecies_Manager", 0, 0, middle_area_manager);
660            middle_area_manager->append_member(mid_multi_species_manager);
661
662            mid_multi_spacer_terminal_beg = new ED4_spacer_terminal("Mid_Multi_Spacer_Terminal_Beg", false, 0, 3, mid_multi_species_manager);
663            mid_multi_species_manager->append_member(mid_multi_spacer_terminal_beg);
664
665            scroll_links.link_for_ver_slider = middle_area_manager;
666
667            {
668                GB_transaction ta(gb_main);
669                int index  = 0;
670                EDB_root_bact::scan_string(mid_multi_species_manager, ref_terminals, area_string_middle, &index, species_progress);
671            }
672
673            {
674                ED4_spacer_terminal *mid_bot_spacer_terminal = new ED4_spacer_terminal("Middle_Bot_Spacer_Terminal", false, 880, 10, device_manager);
675                device_manager->append_member(mid_bot_spacer_terminal);
676            }
677
678            mid_bot_line_terminal = new ED4_line_terminal("Mid_Bot_Line_Terminal", 0, 3, device_manager);    // width will be set below
679            device_manager->append_member(mid_bot_line_terminal);
680
681            total_bottom_spacer = new ED4_spacer_terminal("Total_Bottom_Spacer_terminal", false, 0, 10000, device_manager);
682            total_bottom_spacer->clr_property(PROP_DYNA_RESIZE);
683            device_manager->append_member(total_bottom_spacer);
684        }
685
686        if (scroll_links.link_for_hor_slider) {
687            const long ext_width    = long(scroll_links.link_for_hor_slider->extension.size[WIDTH]);
688            const long spacer_width = ext_width + MAXNAME_WIDTH + SEQUENCE_INFO_WIDTH;
689            const long line_width   = spacer_width + TREE_TERMINAL_WIDTH;
690
691            top_multi_spacer_terminal_beg->extension.size[WIDTH] = spacer_width;
692            mid_multi_spacer_terminal_beg->extension.size[WIDTH] = spacer_width;
693            total_bottom_spacer->extension.size[WIDTH]           = spacer_width;
694
695            top_mid_line_terminal->extension.size[WIDTH] = line_width;
696            mid_bot_line_terminal->extension.size[WIDTH] = line_width;
697
698        }
699
700        tree_terminal->set_links(NULp, mid_multi_species_manager);                          // set links
701        top_spacer_terminal->set_links(tree_terminal, top_multi_species_manager);
702        top_mid_spacer_terminal->set_links(middle_area_manager, NULp);
703        total_bottom_spacer->set_links(mid_bot_line_terminal, NULp);
704
705        species_progress.done();
706    }
707
708    first_window->update_window_coords();
709    resize_all_requesting_childs();
710
711    main_manager->route_down_hierarchy(makeED4_route_cb(force_group_update)).expect_no_error();
712
713    if (!scroll_links.link_for_hor_slider) { // happens when no species AND no SAI has data
714        startup_progress->done();
715        startup_progress.setNull(); // make progress disappear (otherwise prompter below is often behind progress window)
716        GB_pop_transaction(gb_main);
717
718        aw_popup_ok(GBS_global_string("No species/SAI contains data in '%s'\nARB_EDIT4 will terminate", alignment_name));
719        ED4_exit();
720    }
721
722    // build consensi
723    {
724        arb_progress consensi_progress("Initializing consensi", total_no_of_species+total_no_of_groups+1); // 1 is root_group_man
725
726        root_group_man->create_consensus(root_group_man, &consensi_progress);
727        e4_assert(root_group_man->table().ok());
728        consensi_progress.done(); // if there is a "top"-group, progress increment is one to low
729    }
730
731    root_group_man->remap()->mark_compile_needed_force();
732    root_group_man->update_remap();
733
734    // calc size and display:
735
736    resize_all_requesting_childs();
737
738    e4_assert(main_manager);
739
740    {
741        ED4_base *x_link      = scroll_links.link_for_hor_slider;
742        ED4_base *y_link      = scroll_links.link_for_ver_slider;
743        ED4_base *width_link  = x_link;
744        ED4_base *height_link = y_link;
745
746        ED4_window *win = first_window;
747        while (win) {
748            win->set_scrolled_rectangle(x_link, y_link, width_link, height_link);
749            win->aww->show();
750            win->update_scrolled_rectangle();
751            win = win->next;
752        }
753    }
754
755    ED4_request_relayout();
756    ED4_finish_and_show_notFoundMessage();
757
758#if defined(DEBUG) && 0
759    // dump created hierarchy:
760    puts("---------------------------------------- [main_manager dump start]");
761    main_manager->dump(1);
762    puts("---------------------------------------- [main_manager dump end]");
763#endif
764
765    return ED4_R_OK;
766}
767
768ED4_returncode ED4_root::get_area_rectangle(AW_screen_area *rect, AW_pos x, AW_pos y) {
769    // returns win-coordinates of area (defined by folding lines) which contains position x/y
770    int                    x1, x2, y1, y2;
771    const AW_screen_area&  area_rect = current_device()->get_area_size();
772
773    x1 = area_rect.l;
774    for (const ED4_folding_line *flv=current_ed4w()->get_vertical_folding(); ; flv = flv->get_next()) {
775        if (flv) {
776            x2 = int(flv->get_pos()); // @@@ use AW_INT ?
777        }
778        else {
779            x2 = area_rect.r;
780            if (x1==x2) {
781                break;
782            }
783        }
784
785        y1 = area_rect.t;
786        for (const ED4_folding_line *flh=current_ed4w()->get_horizontal_folding(); ; flh = flh->get_next()) {
787            if (flh) {
788                y2 = int(flh->get_pos()); // @@@ use AW_INT ?
789            }
790            else {
791                y2 = area_rect.b;
792                if (y1==y2) {
793                    break;
794                }
795            }
796
797            if (x1<=x && x<=x2 && y1<=y && y<=y2) {
798                rect->t = y1;
799                rect->b = y2;
800                rect->l = x1;
801                rect->r = x2;
802                return ED4_R_OK;
803            }
804            y1 = y2;
805            if (!flh) break;
806        }
807        x1 = x2;
808        if (!flv) break;
809    }
810    return ED4_R_IMPOSSIBLE; // no area contains x/y :-(
811}
812
813void ED4_root::copy_window_struct(ED4_window *source, ED4_window *destination) {
814    destination->slider_pos_horizontal  = source->slider_pos_horizontal;
815    destination->slider_pos_vertical    = source->slider_pos_vertical;
816    destination->coords         = source->coords;
817}
818
819
820static void reload_helix_cb() {
821    const char *err = ED4_ROOT->helix->init(ED4_ROOT->get_gb_main());
822    if (err) aw_message(err);
823    ED4_request_full_refresh();
824}
825
826
827static void reload_ecoli_cb() {
828    const char *err = ED4_ROOT->ecoli_ref->init(ED4_ROOT->get_gb_main());
829    if (err) aw_message(err);
830    ED4_request_full_refresh();
831}
832
833// ---------------------------------------
834//      recursion through all species
835
836DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_Species_Callback, ARB_ERROR, GBDATA *); // generates makeED4_Species_Callback
837
838static ARB_ERROR do_sth_with_species(ED4_base *base, const ED4_Species_Callback *cb) {
839    ARB_ERROR error = NULp;
840
841    if (base->is_species_manager()) {
842        ED4_species_manager       *species_manager       = base->to_species_manager();
843        ED4_species_name_terminal *species_name_terminal = species_manager->search_spec_child_rek(LEV_SPECIES_NAME)->to_species_name_terminal();
844
845        if (species_name_terminal->get_species_pointer()) {
846            char *species_name = GB_read_as_string(species_name_terminal->get_species_pointer());
847
848            e4_assert(species_name);
849            GBDATA *species = GBT_find_species(ED4_ROOT->get_gb_main(), species_name);
850
851            error = species
852                ? (*cb)(species)
853                : GB_append_exportedError(GBS_global_string("can't find species '%s'", species_name));
854
855            free(species_name);
856        }
857    }
858
859    return error;
860}
861
862
863static ARB_ERROR ED4_with_all_loaded_species(const ED4_Species_Callback& cb) {
864    return ED4_ROOT->root_group_man->route_down_hierarchy(makeED4_route_cb(do_sth_with_species, &cb));
865}
866
867static bool is_named(ED4_base *base, const char *wanted_name) {
868    ED4_species_name_terminal *name_term = base->to_species_name_terminal();
869    GBDATA                    *gbd       = name_term->get_species_pointer();
870    if (gbd) {
871        const char *name = GB_read_char_pntr(gbd);
872        e4_assert(name);
873
874        return strcmp(name, wanted_name) == 0;
875    }
876    return false;
877}
878
879static bool is_species_named(ED4_base *base, const char *species_name) {
880    return base->inside_species_seq_manager() && is_named(base, species_name);
881}
882
883static bool is_SAI_named(ED4_base *base, const char *sai_name) {
884    return base->inside_SAI_manager() && is_named(base, sai_name);
885}
886
887ED4_species_name_terminal *ED4_find_species_or_SAI_name_terminal(const char *species_name) {
888    ED4_base *base = ED4_ROOT->root_group_man->find_first_that(LEV_SPECIES_NAME, makeED4_basePredicate(is_species_named, species_name));
889    return base ? base->to_species_name_terminal() : NULp;
890}
891ED4_species_name_terminal *ED4_find_species_name_terminal(const char *species_name) {
892    ED4_base *base = ED4_ROOT->root_group_man->find_first_that(LEV_SPECIES_NAME, makeED4_basePredicate(is_species_named, species_name));
893    return base ? base->to_species_name_terminal() : NULp;
894}
895ED4_species_name_terminal *ED4_find_SAI_name_terminal(const char *sai_name) {
896    ED4_base *base = ED4_ROOT->root_group_man->find_first_that(LEV_SPECIES_NAME, makeED4_basePredicate(is_SAI_named, sai_name));
897    return base ? base->to_species_name_terminal() : NULp;
898}
899
900static char *get_group_consensus(const char *species_name, PosRange range) {
901    ED4_species_name_terminal *name_term = ED4_find_species_name_terminal(species_name);
902    char *consensus = NULp;
903
904    if (name_term) {
905        ED4_abstract_group_manager *group_man = name_term->get_parent(ED4_level(LEV_GROUP|LEV_ROOTGROUP))->to_abstract_group_manager();
906        if (group_man) {
907            consensus = group_man->build_consensus_string(range);
908        }
909    }
910
911    return consensus;
912}
913
914static bool get_selected_range(PosRange& range) {
915    ED4_selected_elem *listElem = ED4_ROOT->selected_objects->head();
916    if (listElem) {
917        ED4_sequence_terminal *seqTerm = listElem->elem()->object->corresponding_sequence_terminal();
918        return ED4_get_selected_range(seqTerm, range);
919    }
920    return false;
921}
922
923static ED4_selected_elem *curr_aligner_elem = NULp;
924
925static GBDATA *get_next_selected_species() {
926    if (!curr_aligner_elem) return NULp;
927
928    ED4_species_manager *specMan = curr_aligner_elem->elem()->object->containing_species_manager();
929    curr_aligner_elem = curr_aligner_elem->next();
930    return specMan->get_species_pointer();
931}
932
933static GBDATA *get_first_selected_species(int *total_no_of_selected_species) {
934    int selected = ED4_ROOT->selected_objects->size();
935
936    if (total_no_of_selected_species) {
937        *total_no_of_selected_species = selected;
938    }
939
940    if (selected) {
941        curr_aligner_elem = ED4_ROOT->selected_objects->head();
942    }
943    else {
944        curr_aligner_elem = NULp;
945    }
946
947    return get_next_selected_species();
948}
949
950static ARB_ERROR ED4_delete_temp_entries(GBDATA *species, GB_CSTR alignment_name) {
951    return FastAligner_delete_temp_entries(species, alignment_name);
952}
953
954static void ED4_remove_faligner_entries() {
955    GBDATA    *gb_main = ED4_ROOT->get_gb_main();
956    ARB_ERROR  error   = GB_begin_transaction(gb_main);
957    if (!error) error  = ED4_with_all_loaded_species(makeED4_Species_Callback(ED4_delete_temp_entries, ED4_ROOT->alignment_name));
958    GB_end_transaction_show_error(gb_main, error, aw_message);
959}
960
961static void toggle_helix_for_SAI(AW_window *aww) {
962    ED4_LocalWinContext  uses(aww);
963    ED4_cursor          *cursor = &current_cursor();
964
965    if (cursor->in_SAI_terminal()) {
966        ED4_sequence_terminal      *sai_term      = cursor->owner_of_cursor->to_sequence_terminal();
967        ED4_sequence_info_terminal *sai_info_term = sai_term->parent->search_spec_child_rek(LEV_SEQUENCE_INFO)->to_sequence_info_terminal();
968
969        GBDATA         *gb_sai_data = sai_info_term->data();
970        GB_transaction  ta(gb_sai_data);
971
972        GBDATA *gb_sai      = GB_get_grandfather(gb_sai_data);
973        GBDATA *gb_disp_sec = GB_searchOrCreate_int(gb_sai, "showsec", 0);
974
975        bool show_sec = 1-bool(GB_read_int(gb_disp_sec));
976        GB_ERROR error = GB_write_int(gb_disp_sec, show_sec);
977        if (!error) {
978            sai_term->set_secstruct_display(show_sec);
979            sai_term->request_refresh();
980        }
981        if (error) aw_message(error);
982    }
983    else {
984        aw_message("Please select an SAI");
985    }
986}
987
988static void title_mode_changed(AW_root *aw_root, AW_window *aww) {
989    int title_mode = aw_root->awar(AWAR_EDIT_TITLE_MODE)->read_int();
990
991    if (title_mode==0) {
992        aww->set_info_area_height(57);
993    }
994    else {
995        aww->set_info_area_height(170);
996    }
997}
998
999static void ED4_undo_redo(AW_window *aww, GB_UNDO_TYPE undo_type) {
1000    ED4_LocalWinContext uses(aww);
1001
1002    GBDATA   *gb_main = ED4_ROOT->get_gb_main();
1003    GB_ERROR  error   = GB_undo(gb_main, undo_type);
1004
1005    if (error) {
1006        aw_message(error);
1007    }
1008    else {
1009        GB_begin_transaction(gb_main);
1010        GB_commit_transaction(gb_main);
1011        ED4_cursor *cursor = &current_cursor();
1012        if (cursor->owner_of_cursor) cursor->owner_of_cursor->request_refresh();
1013    }
1014}
1015
1016static AW_window *ED4_zoom_message_window(AW_root *root) {
1017    AW_window_simple *aws = new AW_window_simple;
1018
1019    aws->init(root, "ZOOM_ERR_MSG", "Errors and warnings");
1020    aws->load_xfig("edit4/message.fig");
1021
1022    aws->callback(AW_POPDOWN);
1023    aws->at("hide");
1024    aws->create_button("HIDE", "HIDE");
1025
1026    aws->callback(aw_clear_message_cb);
1027    aws->at("clear");
1028    aws->create_button("CLEAR", "CLEAR");
1029
1030    aws->at("errortext");
1031    aws->create_text_field(AWAR_ERROR_MESSAGES);
1032
1033    return aws;
1034}
1035
1036
1037static char *cat(char *toBuf, const char *s1, const char *s2) {
1038    char *buf = toBuf;
1039
1040    while ((*buf++=*s1++)!=0) ;
1041    buf--;
1042    while ((*buf++=*s2++)!=0) ;
1043
1044    return toBuf;
1045}
1046
1047static void insert_search_fields(AW_window_menu_modes *awmm,
1048                                 const char *label_prefix, const char *macro_prefix,
1049                                 const char *pattern_awar_name, const char *show_awar_name,
1050                                 int short_form, ED4_SearchPositionType type, ED4_window *ed4w)
1051{
1052    char buf[200];
1053
1054    if (!short_form) {
1055        awmm->at(cat(buf, label_prefix, "search"));
1056        awmm->create_input_field(pattern_awar_name, 30);
1057    }
1058
1059    awmm->at(cat(buf, label_prefix, "n"));
1060    awmm->help_text("e4_search.hlp");
1061    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(+1, type), ed4w));
1062    awmm->create_button(cat(buf, macro_prefix, "_SEARCH_NEXT"), "#edit/next.xpm");
1063
1064    awmm->at(cat(buf, label_prefix, "l"));
1065    awmm->help_text("e4_search.hlp");
1066    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(-1, type), ed4w));
1067    awmm->create_button(cat(buf, macro_prefix, "_SEARCH_LAST"), "#edit/last.xpm");
1068
1069    awmm->at(cat(buf, label_prefix, "d"));
1070    awmm->help_text("e4_search.hlp");
1071    awmm->callback(makeWindowCallback(ED4_popup_search_window, type));
1072    awmm->create_button(cat(buf, macro_prefix, "_SEARCH_DETAIL"), "#edit/detail.xpm");
1073
1074    awmm->at(cat(buf, label_prefix, "s"));
1075    awmm->create_toggle(show_awar_name);
1076}
1077
1078static void ED4_set_protection(AW_window *aww, int wanted_protection) {
1079    ED4_LocalWinContext uses(aww);
1080    ED4_cursor *cursor = &current_cursor();
1081    GB_ERROR    error  = NULp;
1082
1083    if (cursor->owner_of_cursor) {
1084        ED4_sequence_terminal      *seq_term      = cursor->owner_of_cursor->to_sequence_terminal();
1085        ED4_sequence_info_terminal *seq_info_term = seq_term->parent->search_spec_child_rek(LEV_SEQUENCE_INFO)->to_sequence_info_terminal();
1086        GBDATA                     *gbd           = seq_info_term->data();
1087
1088        GB_transaction      ta(gbd);
1089        GB_topSecurityLevel unsecured(gbd);
1090
1091        error = GB_write_security_write(gbd, wanted_protection);
1092        error = ta.close(error);
1093    }
1094    else {
1095        error = "No species selected";
1096    }
1097
1098    if (error) aw_message(error);
1099}
1100
1101enum MenuSelectType { // @@@ rename -> MenuHighlightType
1102    ED4_MS_NONE,
1103    ED4_MS_ALL,
1104    ED4_MS_INVERT,
1105    ED4_MS_INVERT_GROUP,
1106    ED4_MS_UNMARK_ALL,
1107    ED4_MS_MARK_SELECTED,
1108    ED4_MS_UNMARK_SELECTED,
1109    ED4_MS_SELECT_MARKED,
1110    ED4_MS_DESELECT_MARKED,
1111    ED4_MS_TOGGLE_BLOCKTYPE
1112};
1113
1114static void ED4_menu_highlight(AW_window *aww, MenuSelectType select) { // @@@ rename select -> hilight
1115    GBDATA         *gb_main = ED4_ROOT->get_gb_main();
1116    GB_transaction  ta(gb_main);
1117
1118    ED4_multi_species_manager *middle_multi_man = ED4_ROOT->middle_area_man->get_multi_species_manager();
1119
1120    e4_assert(middle_multi_man);
1121
1122    switch (select) {
1123        case ED4_MS_NONE: {
1124            if (ED4_getBlocktype()!=ED4_BT_NOBLOCK) {
1125                ED4_ROOT->deselect_all();
1126            }
1127            break;
1128        }
1129        case ED4_MS_ALL: {
1130            middle_multi_man->select_all(true); // only species
1131            ED4_correctBlocktypeAfterSelection();
1132            break;
1133        }
1134        case ED4_MS_INVERT: {
1135            middle_multi_man->invert_selection_of_all_species();
1136            ED4_correctBlocktypeAfterSelection();
1137            break;
1138        }
1139        case ED4_MS_SELECT_MARKED: {
1140            middle_multi_man->marked_species_select(true);
1141            ED4_correctBlocktypeAfterSelection();
1142            break;
1143        }
1144        case ED4_MS_DESELECT_MARKED: {
1145            middle_multi_man->marked_species_select(false);
1146            ED4_correctBlocktypeAfterSelection();
1147            break;
1148        }
1149        case ED4_MS_UNMARK_ALL: {
1150            GBT_mark_all(gb_main, 0);
1151            break;
1152        }
1153        case ED4_MS_MARK_SELECTED: {
1154            middle_multi_man->selected_species_mark(true);
1155            ED4_correctBlocktypeAfterSelection();
1156            break;
1157        }
1158        case ED4_MS_UNMARK_SELECTED: {
1159            middle_multi_man->selected_species_mark(false);
1160            ED4_correctBlocktypeAfterSelection();
1161            break;
1162        }
1163        case ED4_MS_INVERT_GROUP: {
1164            ED4_cursor *cursor = &ED4_ROOT->first_window->get_matching_ed4w(aww)->cursor;
1165            int done = 0;
1166
1167            if (cursor->owner_of_cursor) {
1168                ED4_multi_species_manager *multi_man = cursor->owner_of_cursor->get_parent(LEV_MULTI_SPECIES)->to_multi_species_manager();
1169
1170                multi_man->invert_selection_of_all_species();
1171                ED4_correctBlocktypeAfterSelection();
1172                done = 1;
1173            }
1174
1175            if (!done) {
1176                aw_message("Place cursor into group");
1177            }
1178            break;
1179        }
1180        case ED4_MS_TOGGLE_BLOCKTYPE: {
1181            ED4_toggle_block_type();
1182            break;
1183        }
1184        default: {
1185            e4_assert(0);
1186            break;
1187        }
1188    }
1189
1190    ED4_request_full_refresh();
1191}
1192
1193static void ED4_menu_perform_block_operation(AW_window *, ED4_blockoperation_type type) {
1194    ED4_perform_block_operation(type);
1195}
1196
1197static void modes_cb(AW_window*, ED4_species_mode smode) {
1198    ED4_ROOT->species_mode = smode;
1199    for (ED4_window *win = ED4_ROOT->first_window; win; win = win->next) {
1200        win->aww->select_mode(smode);
1201    }
1202    if (smode == ED4_SM_INFO) {
1203        AWT_trigger_remote_action(NULp, ED4_ROOT->get_gb_main(), "ARB_NT:species_info");
1204    }
1205}
1206
1207void ED4_no_dangerous_modes() {
1208    if (ED4_ROOT->species_mode == ED4_SM_KILL) {
1209        modes_cb(NULp, ED4_SM_MOVE);
1210    }
1211}
1212
1213static char *get_helix_string(GBDATA *gb_main, const char *alignment_name) {
1214    GB_transaction ta(gb_main);
1215
1216    char   *helix_string = NULp;
1217    char   *helix_name   = GBT_get_default_helix(gb_main);
1218    GBDATA *gb_helix_con = GBT_find_SAI(gb_main, helix_name);
1219    if (gb_helix_con) {
1220        GBDATA *gb_helix = GBT_find_sequence(gb_helix_con, alignment_name);
1221        if (gb_helix) helix_string = GB_read_string(gb_helix);
1222    }
1223    free(helix_name);
1224
1225    return helix_string;
1226}
1227
1228const AlignDataAccess *ED4_get_aligner_data_access() {
1229    static SmartPtr<AlignDataAccess> aliDataAccess;
1230
1231    if (aliDataAccess.isNull()) {
1232        aliDataAccess = new AlignDataAccess(ED4_ROOT->get_gb_main(),
1233                                            ED4_ROOT->alignment_name,
1234                                            true, ED4_trigger_instant_refresh, // perform refresh
1235                                            get_group_consensus,               // aligner fetches consensus of group of species via this function
1236                                            get_selected_range,                // aligner fetches column range of selection via this function
1237                                            get_first_selected_species,        // aligner fetches first and..
1238                                            get_next_selected_species,         // .. following selected species via these functions
1239                                            get_helix_string);                 // used by island_hopping (if configured to use sec-structure)
1240    }
1241
1242    return aliDataAccess.content();
1243}
1244
1245static AW_window *ED4_create_faligner_window(AW_root *awr, const AlignDataAccess *data_access) {
1246#if defined(DEBUG)
1247    static const AlignDataAccess *last_data_access = NULp;
1248
1249    e4_assert(!last_data_access || (last_data_access == data_access)); // there shall be only one AlignDataAccess
1250    last_data_access = data_access;
1251#endif
1252
1253    static AW_window *aws = NULp;
1254    if (!aws) aws = FastAligner_create_window(awr, data_access);
1255    return aws;
1256}
1257
1258static const char *propertyName(GBDATA *gb_main, int mode) {
1259    // mode == 0 -> alignment specific          (e.g. "edit4_ali_16s.arb")
1260    // mode == 1 -> alignment-type specific     (e.g. "edit4_rna.arb")
1261    // mode == 2 -> unspecific (normal)         (always "edit4.arb")
1262    //
1263    // Note : result is only valid until next call
1264
1265    e4_assert(mode >= 0 && mode <= 2);
1266
1267    const char *result;
1268    if (mode == 2) {
1269        result = "edit4.arb";
1270    }
1271    else {
1272        static char *ali_name    = NULp;
1273        static char *ali_type    = NULp;
1274        static char *result_copy = NULp;
1275
1276        if (!ali_name) {
1277            GB_transaction ta(gb_main);
1278
1279            ali_name    = GBT_get_default_alignment(gb_main);
1280            ali_type    = GBT_get_alignment_type_string(gb_main, ali_name);
1281            result_copy = new char[21+strlen(ali_name)];
1282        }
1283
1284        sprintf(result_copy, "edit4_%s.arb", mode == 0 ? ali_name : ali_type);
1285        result = result_copy;
1286    }
1287
1288    return result;
1289}
1290
1291static void ED4_save_properties(AW_window *aw, int mode) {
1292    AW_save_specific_properties(aw, propertyName(ED4_ROOT->get_gb_main(), mode));
1293}
1294
1295void ED4_popup_gc_window(AW_window *awp, AW_gc_manager *gcman) {
1296    typedef std::map<AW_gc_manager*, AW_window*> gcwin;
1297    static gcwin win;
1298
1299    gcwin::iterator found = win.find(gcman);
1300
1301    AW_window *aww = NULp;
1302    if (found == win.end()) {
1303        aww        = AW_create_gc_window(awp->get_root(), gcman);
1304        win[gcman] = aww;
1305    }
1306    else {
1307        aww = win[gcman];
1308    }
1309    aww->activate();
1310}
1311
1312static void gc_change_cb(GcChange whatChanged) {
1313    if (whatChanged == GC_FONT_CHANGED) {
1314        ED4_resize_all_extensions();
1315    }
1316    ED4_request_full_instant_refresh();
1317}
1318
1319ED4_returncode ED4_root::generate_window(AW_device **device, ED4_window **new_window) {
1320    {
1321        ED4_window *ed4w = first_window;
1322
1323        while (ed4w) { // before creating a window look for a hidden window
1324            if (ed4w->is_hidden) {
1325                ed4w->aww->show();
1326                ed4w->is_hidden = false;
1327                return ED4_R_BREAK;
1328            }
1329            ed4w = ed4w->next;
1330        }
1331    }
1332
1333    if (ED4_window::no_of_windows == MAXWINDOWS) { // no more than 5 windows allowed
1334        aw_message(GBS_global_string("Restricted to %i windows", MAXWINDOWS));
1335        return ED4_R_BREAK;
1336    }
1337
1338    AW_window_menu_modes *awmm = new AW_window_menu_modes;
1339    {
1340        int   winNum   = ED4_window::no_of_windows+1;
1341        char *winName  = winNum>1 ? GBS_global_string_copy("ARB_EDIT4_%i", winNum) : ARB_strdup("ARB_EDIT4");
1342        char *winTitle = GBS_global_string_copy("ARB_EDIT4 *%d* [%s]", winNum, alignment_name);
1343
1344        awmm->init(aw_root, winName, winTitle, 800, 450);
1345
1346        free(winTitle);
1347        free(winName);
1348    }
1349
1350    *device     = awmm->get_device(AW_MIDDLE_AREA); // points to Middle Area device
1351    *new_window = ED4_window::insert_window(awmm);   // append to window list
1352
1353    e4_assert(ED4_window::no_of_windows >= 1);
1354    bool clone = ED4_window::no_of_windows>1;
1355    if (!clone) {                                   // this is the first window
1356        AW_init_color_group_defaults("arb_edit4");
1357    }
1358    else { // additional edit windows
1359        copy_window_struct(first_window, *new_window);
1360    }
1361
1362    ED4_LocalWinContext uses(*new_window);
1363
1364    // each window has its own gc-manager
1365    gc_manager = AW_manage_GC(awmm,
1366                              "ARB_EDIT4",                   // but all gc-managers use the same colors
1367                              *device,
1368                              ED4_G_DRAG,
1369                              AW_GCM_DATA_AREA,
1370                              makeGcChangedCallback(gc_change_cb), // callback triggering refresh on gc-change
1371
1372                              "#f8f8f8",
1373                              "STANDARD$black",              // standard color showing species/group info (name, ...)
1374                              "FlagInfo$#DDD",
1375                              "#SEQUENCES (0)$#505050",      // default color for sequences (color 0)
1376
1377                              "+-HELIX (1)$#8E0000",  "+-COLOR 2$#0000dd",    "-COLOR 3$#00AA55",
1378                              "+-COLOR 4$#80f",       "+-COLOR 5$#c0a020",    "-COLOR 6$grey",
1379                              "+-COLOR 7$#ff0000",    "+-COLOR 8$#44aaff",    "-COLOR 9$#ffaa00",
1380
1381                              "+-CURSOR$#FF0080",     "+-MARKED$#f4f8e0",     "-SELECTED$#FFFF80",
1382
1383                              "+-RANGE 0$#FFFFFF",    "+-RANGE 1$#F0F0F0",    "-RANGE 2$#E0E0E0",
1384                              "+-RANGE 3$#D8D8D8",    "+-RANGE 4$#D0D0D0",    "-RANGE 5$#C8C8C8",
1385                              "+-RANGE 6$#C0C0C0",    "+-RANGE 7$#B8B8B8",    "-RANGE 8$#B0B0B0",
1386                              "-RANGE 9$#A0A0A0",
1387
1388                              // colors used to Paint search patterns
1389                              // (do not change the names of these gcs)
1390                              "+-User1$#B8E2F8",      "+-User2$#B8E2F8",      "-Probe$#B8E2F8", // see also SEC_graphic::init_devices
1391                              "+-Primer(l)$#A9FE54",  "+-Primer(r)$#A9FE54",  "-Primer(g)$#A9FE54",
1392                              "+-Sig(l)$#DBB0FF",     "+-Sig(r)$#DBB0FF",     "-Sig(g)$#DBB0FF",
1393
1394                              "+-MISMATCHES$#FF9AFF", "+-Flag$#7c7ce3",       "-FlagFill$#aacef1",
1395
1396                              "&color_groups", // use color groups
1397
1398                              NULp);
1399
1400    // since the gc-managers of all EDIT4-windows point to the same window properties,
1401    // changing fonts and colors is always done on first gc-manager
1402    static AW_gc_manager *first_gc_manager = NULp;
1403    if (!first_gc_manager) first_gc_manager = gc_manager;
1404
1405    // --------------
1406    //      File
1407
1408#if defined(DEBUG)
1409    AWT_create_debug_menu(awmm);
1410#endif // DEBUG
1411
1412    awmm->create_menu("File", "F", AWM_ALL);
1413
1414    awmm->insert_menu_topic("new_win", "New Editor Window", "N", NULp, AWM_ALL, ED4_new_editor_window);
1415    awmm->sep______________();
1416    awmm->insert_menu_topic("save_config",                    "Save configuration",        "S", "species_configs_saveload.hlp", AWM_ALL, makeWindowCallback(ED4_saveConfiguration, false));
1417    awmm->insert_menu_topic(awmm->local_id("save_config_as"), "Save configuration as ...", "a", "species_configs_saveload.hlp", AWM_ALL, ED4_create_saveConfigurationAs_window);
1418    awmm->insert_menu_topic(awmm->local_id("load_config"),    "Load configuration ...",    "L", "species_configs_saveload.hlp", AWM_ALL, ED4_create_loadConfiguration_window);
1419    awmm->insert_menu_topic("reload_config",                  "Reload configuration",      "R", "species_configs_saveload.hlp", AWM_ALL, ED4_reloadConfiguration);
1420    insert_macro_menu_entry(awmm, true);
1421    awmm->sep______________();
1422    // keep the following entries in sync with ../NTREE/NT_extern.cxx@common_save_menu_entries
1423    awmm->insert_menu_topic("save_changes", "Quicksave changes",          "c", "save.hlp", AWM_ALL, makeWindowCallback(AWT_trigger_remote_action, gb_main, "ARB_NT:save_changes"));
1424    awmm->insert_menu_topic("save_all_as",  "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeWindowCallback(AWT_trigger_remote_action, gb_main, "ARB_NT:save_all_as"));
1425#if defined(DEBUG)
1426    awmm->sep______________();
1427    awmm->insert_menu_topic("deb1", "[DEBUG] remote: invalid app", "D", NULp, AWM_ALL, makeWindowCallback(AWT_trigger_remote_action, gb_main, "ARB_NTREE:aljdlaisjdlad"));
1428    awmm->insert_menu_topic("deb2", "[DEBUG] remote: invalid cmd", "E", NULp, AWM_ALL, makeWindowCallback(AWT_trigger_remote_action, gb_main, "ARB_NT:aljdlaisjdlad"));
1429#endif
1430    awmm->sep______________();
1431    GDE_load_menu(awmm, AWM_ALL, "Print");
1432    awmm->sep______________();
1433
1434    if (clone) awmm->insert_menu_topic("close", "CLOSE", "C", NULp, AWM_ALL, ED4_quit_editor);
1435    else       awmm->insert_menu_topic("quit",  "QUIT",  "Q", NULp, AWM_ALL, ED4_quit_editor);
1436
1437    // ----------------
1438    //      Create
1439
1440    awmm->create_menu("Create", "C", AWM_ALL);
1441    awmm->insert_menu_topic(awmm->local_id("create_species"),                "Create new species",                "n", NULp, AWM_ALL, makeCreateWindowCallback(ED4_create_new_seq_window, CREATE_NEW_SPECIES));
1442    awmm->insert_menu_topic(awmm->local_id("create_species_from_consensus"), "Create new species from consensus", "u", NULp, AWM_ALL, makeCreateWindowCallback(ED4_create_new_seq_window, CREATE_FROM_CONSENSUS));
1443    awmm->insert_menu_topic(awmm->local_id("copy_species"),                  "Copy current species",              "C", NULp, AWM_ALL, makeCreateWindowCallback(ED4_create_new_seq_window, COPY_SPECIES));
1444    awmm->sep______________();
1445    awmm->insert_menu_topic("create_group",           "Create new Group (from selected)", "G", NULp, AWM_ALL, makeWindowCallback(group_species_cb, false));
1446    awmm->insert_menu_topic("create_groups_by_field", "Create new groups using Field",    "F", NULp, AWM_ALL, makeWindowCallback(group_species_cb, true));
1447
1448    // --------------
1449    //      Edit
1450
1451    awmm->create_menu("Edit", "E", AWM_ALL);
1452    awmm->insert_menu_topic("refresh",                  "Refresh [Ctrl-L]",           "f", NULp,                 AWM_ALL, makeWindowCallback(ED4_request_full_refresh));
1453    awmm->insert_menu_topic("load_current",             "Load current species [GET]", "G", "e4_get_species.hlp", AWM_ALL, makeWindowCallback(ED4_get_and_jump_to_current));
1454    awmm->insert_menu_topic("load_marked",              "Load marked species",        "m", "e4_get_species.hlp", AWM_ALL, makeWindowCallback(ED4_get_marked_from_menu));
1455    awmm->insert_menu_topic(awmm->local_id("load_SAI"), "Load SAI ...",               "L", "e4_get_species.hlp", AWM_ALL, ED4_create_loadSAI_window);
1456    awmm->sep______________();
1457    awmm->insert_menu_topic("refresh_ecoli",       "Reload Ecoli sequence",        "E", "ecoliref.hlp", AWM_ALL, makeWindowCallback(reload_ecoli_cb));
1458    awmm->insert_menu_topic("refresh_helix",       "Reload Helix",                 "H", "helix.hlp",    AWM_ALL, makeWindowCallback(reload_helix_cb));
1459    awmm->insert_menu_topic("helix_jump_opposite", "Jump helix opposite [Ctrl-J]", "J", NULp,           AWM_ALL, ED4_helix_jump_opposite);
1460    awmm->sep______________();
1461
1462    awmm->insert_sub_menu("Set protection of current ", "p");
1463    {
1464        char macro[] = "to_0",
1465            topic[] = ".. to 0",
1466            hotkey[] = "0";
1467
1468        for (char i='0'; i<='6'; i++) {
1469            macro[3] = topic[6] = hotkey[0] = i;
1470            awmm->insert_menu_topic(macro, topic, hotkey, "security.hlp", AWM_ALL, makeWindowCallback(ED4_set_protection, i-'0'));
1471        }
1472    }
1473    awmm->close_sub_menu();
1474
1475    awmm->sep______________();
1476    awmm->insert_menu_topic(awmm->local_id("fast_aligner"),   INTEGRATED_ALIGNERS_TITLE,            "I", "faligner.hlp",     AWM_ALL,            makeCreateWindowCallback(ED4_create_faligner_window, ED4_get_aligner_data_access()));
1477    awmm->insert_menu_topic("fast_align_set_ref",             "Set aligner reference [Ctrl-R]",     "R", "faligner.hlp",     AWM_ALL,            RootAsWindowCallback::simple(FastAligner_set_reference_species));
1478    awmm->insert_menu_topic(awmm->local_id("align_sequence"), "Old aligner from ARB_EDIT [broken]", "O", "ne_align_seq.hlp", AWM_DISABLED,       makeCreateWindowCallback(create_naligner_window, get_gb_main()));
1479    awmm->insert_menu_topic("sina",                           "SINA (SILVA Incremental Aligner)",   "S", "sina_main.hlp",    sina_mask(aw_root), makeWindowCallback(show_sina_window, ED4_get_aligner_data_access()));
1480    awmm->insert_menu_topic("del_ali_tmp",                    "Remove all aligner Entries",         "v", NULp,               AWM_ALL,            makeWindowCallback(ED4_remove_faligner_entries));
1481    awmm->sep______________();
1482    awmm->insert_menu_topic("missing_bases", "Dot potentially missing bases", "D", "missbase.hlp", AWM_EXP, ED4_popup_dot_missing_bases_window);
1483
1484    if (alignment_type == GB_AT_RNA) { // if the database contains valid alignment of rRNA sequences
1485        awmm->sep______________();
1486        awmm->insert_menu_topic("sec_edit", "Edit secondary structure", "c", "arb_secedit.hlp", AWM_ALL, makeWindowCallback(ED4_start_plugin, gb_main, "SECEDIT"));
1487#if defined(ARB_OPENGL)
1488        awmm->insert_menu_topic("rna3d", "View 3D molecule", "3", "rna3d_general.hlp", AWM_ALL, makeWindowCallback(ED4_start_plugin, gb_main, "RNA3D"));
1489#endif // ARB_OPENGL
1490#if defined(DEBUG)
1491        awmm->insert_menu_topic("noplugin", "DEBUG: call unknown plugin", "u", NULp, AWM_ALL, makeWindowCallback(ED4_start_plugin, gb_main, "testplugin"));
1492#endif // DEBUG
1493    }
1494
1495    // --------------
1496    //      View
1497
1498    awmm->create_menu("View", "V", AWM_ALL);
1499    awmm->insert_sub_menu("Search", "S");
1500    {
1501        int         s;
1502        const char *hotkeys  = "12Poiclrg";
1503        char        hotkey[] = "_";
1504
1505        e4_assert(strlen(hotkeys) == SEARCH_PATTERNS);
1506
1507        for (s=0; s<SEARCH_PATTERNS; s++) {
1508            ED4_SearchPositionType type = ED4_SearchPositionType(s);
1509            const char *id = ED4_SearchPositionTypeId[type];
1510            int len = strlen(id);
1511            char *macro_name = GB_give_buffer(2*(len+8));
1512            char *menu_entry_name = macro_name+(len+8);
1513
1514#ifndef NDEBUG
1515            memset(macro_name, 0, 2*(len+8)); // to avoid memchk-warning
1516#endif
1517            sprintf(macro_name, "%s_SEARCH", id);
1518            char *p = macro_name;
1519            while (1) {
1520                char c = *p++;
1521                if (!c) break;
1522                p[-1] = toupper(c);
1523            }
1524            sprintf(menu_entry_name, "%s Search", id);
1525
1526            hotkey[0] = hotkeys[s];
1527            awmm->insert_menu_topic(awmm->local_id(macro_name), menu_entry_name, hotkey, "e4_search.hlp", AWM_ALL, makeWindowCallback(ED4_popup_search_window, type));
1528        }
1529    }
1530    awmm->close_sub_menu();
1531    awmm->sep______________();
1532    awmm->insert_sub_menu("Cursor position ", "p");
1533    awmm->insert_menu_topic("store_curpos",   "Store cursor position",    "S", NULp, AWM_ALL, ED4_store_curpos);
1534    awmm->insert_menu_topic("restore_curpos", "Restore cursor position ", "R", NULp, AWM_ALL, ED4_restore_curpos);
1535    awmm->insert_menu_topic("clear_curpos",   "Clear stored positions",   "C", NULp, AWM_ALL, makeWindowCallback(ED4_clear_stored_curpos));
1536    awmm->close_sub_menu();
1537
1538    awmm->sep______________();
1539    awmm->insert_menu_topic("change_cursor",             "Change cursor type",   "t", NULp,           AWM_ALL, ED4_change_cursor);
1540    awmm->insert_menu_topic(awmm->local_id("view_diff"), "View differences ...", "V", "viewdiff.hlp", AWM_ALL, ED4_create_viewDifferences_window);
1541    awmm->sep______________();
1542    awmm->insert_menu_topic("enable_col_stat",  "Activate column statistics", "A", "st_ml.hlp", AWM_EXP, ED4_activate_col_stat);
1543    awmm->insert_menu_topic("disable_col_stat", "Disable column statistics",  "i", "st_ml.hlp", AWM_EXP, ED4_disable_col_stat);
1544    awmm->insert_menu_topic("detail_col_stat",  "Toggle detailed Col.-Stat.", "C", "st_ml.hlp", AWM_EXP, ED4_toggle_detailed_column_stats);
1545    awmm->insert_menu_topic("dcs_threshold",    "Set threshold for D.c.s.",   "f", "st_ml.hlp", AWM_EXP, makeWindowCallback(ED4_set_col_stat_threshold));
1546    awmm->sep______________();
1547    awmm->insert_menu_topic(awmm->local_id("visualize_SAI"), "Visualize SAIs",                "z", "visualizeSAI.hlp",   AWM_ALL, ED4_createVisualizeSAI_window);
1548    awmm->insert_menu_topic("toggle_saisec",                 "Toggle secondary info for SAI", "o", "toggle_secinfo.hlp", AWM_ALL, toggle_helix_for_SAI);
1549
1550    // Enable ProteinViewer only for DNA sequence type
1551    if (alignment_type == GB_AT_DNA) {
1552        awmm->insert_menu_topic(awmm->local_id("Protein_Viewer"), "Protein Viewer", "w", "proteinViewer.hlp", AWM_ALL, ED4_CreateProteinViewer_window);
1553    }
1554
1555    // ---------------
1556    //      Block
1557
1558    awmm->create_menu("Block", "B", AWM_ALL);
1559
1560    awmm->insert_menu_topic("select_marked",   "Highlight marked species",    "e", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_SELECT_MARKED));
1561    awmm->insert_menu_topic("deselect_marked", "De-highlight marked species", "k", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_DESELECT_MARKED));
1562    awmm->insert_menu_topic("select_all",      "Highlight all species",       "s", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_ALL));
1563    awmm->insert_menu_topic("deselect_all",    "De-highlight all species",    "D", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_NONE));
1564    awmm->sep______________();
1565    awmm->insert_menu_topic("mark_selected",   "Mark highlighted species",   "M", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_MARK_SELECTED));
1566    awmm->insert_menu_topic("unmark_selected", "Unmark highlighted species", "n", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_UNMARK_SELECTED));
1567    awmm->insert_menu_topic("unmark_all",      "Unmark all species",         "U", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_UNMARK_ALL));
1568    awmm->sep______________();
1569    awmm->insert_menu_topic("invert_all",   "Invert highlighted species", "I", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_INVERT));
1570    awmm->insert_menu_topic("invert_group", "Invert group",               "g", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_INVERT_GROUP));
1571    awmm->sep______________();
1572    awmm->insert_menu_topic("lowcase", "Change to lower case ", "w", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_LOWER_CASE));
1573    awmm->insert_menu_topic("upcase",  "Change to upper case",  "p", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_UPPER_CASE));
1574    awmm->sep______________();
1575    awmm->insert_menu_topic("reverse",            "Reverse highlighted ",    "v", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_REVERSE));
1576    awmm->insert_menu_topic("complement",         "Complement highlighted ", "o", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_COMPLEMENT));
1577    awmm->insert_menu_topic("reverse_complement", "Reverse complement",      "t", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_REVERSE_COMPLEMENT));
1578    awmm->sep______________();
1579    awmm->insert_menu_topic("unalignBlockLeft",   "Unalign block left",   "a", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_UNALIGN_LEFT));
1580    awmm->insert_menu_topic("unalignBlockCenter", "Unalign block center", "c", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_UNALIGN_CENTER));
1581    awmm->insert_menu_topic("unalignBlockRight",  "Unalign block right",  "b", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_UNALIGN_RIGHT));
1582    awmm->sep______________();
1583    awmm->insert_menu_topic(awmm->local_id("replace"), "Search & Replace ", "h", "e4_replace.hlp", AWM_ALL, ED4_create_replace_window);
1584    awmm->insert_menu_topic(awmm->local_id("setsai"),  "Modify SAI ",       "y", "e4_modsai.hlp",  AWM_ALL, ED4_create_modsai_window);
1585    awmm->sep______________();
1586    awmm->insert_menu_topic("toggle_block_type", "Exchange: Line<->Column", "x", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_TOGGLE_BLOCKTYPE));
1587    awmm->insert_menu_topic("shift_left",        "Shift block left ",       "l", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_SHIFT_LEFT));
1588    awmm->insert_menu_topic("shift_right",       "Shift block right",       "r", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_SHIFT_RIGHT));
1589
1590    // --------------------
1591    //      Properties
1592
1593    awmm->create_menu("Properties", "P", AWM_ALL);
1594
1595    awmm->insert_menu_topic(awmm->local_id("props_frame"),     "Frame settings ...",    "g", NULp,               AWM_ALL, AW_preset_window);
1596    awmm->insert_menu_topic(awmm->local_id("props_options"),   "Editor Options ",       "O", "e4_options.hlp",   AWM_ALL, ED4_create_editor_options_window);
1597    awmm->insert_menu_topic(awmm->local_id("props_consensus"), "Consensus Definition ", "u", "e4_consensus.hlp", AWM_ALL, ED4_create_consensus_definition_window);
1598    awmm->sep______________();
1599
1600    awmm->insert_menu_topic("props_data",                       "Change Colors & Fonts ", "C", NULp,                  AWM_ALL, makeWindowCallback      (ED4_popup_gc_window,          first_gc_manager));
1601    awmm->insert_menu_topic(awmm->local_id("props_seq_colors"), "Sequence color mapping", "S", "sequence_colors.hlp", AWM_ALL, makeCreateWindowCallback(ED4_create_seq_colors_window, sequence_colors));
1602
1603    awmm->sep______________();
1604
1605    awmm->insert_menu_topic(awmm->local_id("props_nds"),     "Select visible info (NDS) ", "D", "ed4_nds.hlp",   AWM_ALL, ED4_create_nds_window);
1606    awmm->insert_menu_topic(awmm->local_id("props_flags"),   "Select species flags",       "f", "ed4_flags.hlp", AWM_ALL, makeCreateWindowCallback(ED4_configure_species_flags, gb_main));
1607    {
1608        static WindowCallback reqRelCb = makeWindowCallback(ED4_request_relayout);
1609        if (alignment_type == GB_AT_AA) awmm->insert_menu_topic(awmm->local_id("props_pfold"),     "Protein Match Settings ", "P", "pfold_props.hlp", AWM_ALL, makeCreateWindowCallback(ED4_pfold_create_props_window, &reqRelCb));
1610        else                            awmm->insert_menu_topic(awmm->local_id("props_helix_sym"), "Helix Settings ",         "H", "helixsym.hlp",    AWM_ALL, makeCreateWindowCallback(create_helix_props_window,     &reqRelCb));
1611    }
1612    awmm->insert_menu_topic(awmm->local_id("props_key_map"), "Key Mappings ",              "K", "nekey_map.hlp", AWM_ALL, create_key_map_window);
1613
1614    awmm->sep______________();
1615    AW_insert_common_property_menu_entries(awmm);
1616    awmm->sep______________();
1617    awmm->insert_sub_menu("Save properties ...", "a");
1618    {
1619        static const char * const tag[] = { "save_alispecific_props", "save_alitype_props", "save_props" };
1620        static const char * const entry_type[] = { "alignment specific ", "ali-type specific ", "" };
1621
1622        // check what is the default mode
1623        int default_mode = -1;
1624        for (int mode = 0; mode <= 2; ++mode) {
1625            if (strcmp(GB_path_in_arbprop(propertyName(gb_main, mode)), db_name) == 0) {
1626                default_mode = mode;
1627                break;
1628            }
1629        }
1630        if (default_mode == -1) default_mode = 2; // no properties yet -> use 'edit4.arb'
1631
1632        const char *entry = GBS_global_string("Save loaded Properties (%s)", propertyName(gb_main, default_mode));
1633        awmm->insert_menu_topic("save_loaded_props", entry, "l", "e4_defaults.hlp", AWM_ALL, makeWindowCallback(ED4_save_properties, default_mode));
1634        awmm->sep______________();
1635
1636        for (int mode = 2; mode >= 0; --mode) {
1637            char hotkey[] = "x";
1638            hotkey[0]     = "Pta"[mode];
1639            entry         = GBS_global_string("Save %sProperties (%s)", entry_type[mode], propertyName(gb_main, mode));
1640            awmm->insert_menu_topic(tag[mode], entry, hotkey, "e4_defaults.hlp", AWM_ALL, makeWindowCallback(ED4_save_properties, mode));
1641        }
1642    }
1643    awmm->close_sub_menu();
1644
1645    awmm->insert_help_topic("ARB_EDIT4 help",     "E", "e4.hlp", AWM_ALL, makeHelpCallback("e4.hlp"));
1646
1647    // ----------------------------------------------------------------------------------------------------
1648
1649    aw_root->awar_int(AWAR_EDIT_TITLE_MODE)->add_callback(makeRootCallback(title_mode_changed, static_cast<AW_window*>(awmm)));
1650    awmm->set_bottom_area_height(0);   // No bottom area
1651
1652    awmm->auto_space(5, -2);
1653    awmm->shadow_width(3);
1654
1655    int db_pathx, db_pathy;
1656    awmm->get_at_position(&db_pathx, &db_pathy);
1657
1658    awmm->shadow_width(1);
1659    awmm->load_xfig("edit4/editmenu.fig", false);
1660
1661    // --------------------------
1662    //      help /quit /fold
1663
1664    awmm->button_length(0);
1665
1666    awmm->at("quit");
1667    awmm->callback(ED4_quit_editor);
1668    awmm->help_text("quit.hlp");
1669
1670    if (clone) awmm->create_button("CLOSE", "#close.xpm");
1671    else       awmm->create_button("QUIT",  "#quit.xpm");
1672
1673    awmm->at("help");
1674    awmm->callback(AW_help_entry_pressed);
1675    awmm->help_text("e4.hlp");
1676    awmm->create_button("HELP", "#help.xpm");
1677
1678    awmm->at("fold");
1679    awmm->help_text("e4.hlp");
1680    awmm->create_toggle(AWAR_EDIT_TITLE_MODE, "#more.xpm", "#less.xpm");
1681
1682    // -------------------
1683    //      positions
1684
1685    awmm->button_length(0);
1686
1687    awmm->at("posTxt");     awmm->create_button(NULp, "Position");
1688
1689    awmm->button_length(6+1);
1690
1691    awmm->at("ecoliTxt");   awmm->create_button(NULp, ED4_AWAR_NDS_ECOLI_NAME, NULp, "+");
1692
1693    awmm->button_length(0);
1694
1695    awmm->at("baseTxt");    awmm->create_button(NULp, "Base");
1696    awmm->at("iupacTxt");   awmm->create_button(NULp, "IUPAC");
1697    awmm->at("helixnrTxt"); awmm->create_button(NULp, "Helix#");
1698
1699    awmm->at("pos");
1700    awmm->callback(makeWindowCallback(ED4_jump_to_cursor_position, current_ed4w()->awar_path_for_cursor, ED4_POS_SEQUENCE)); // @@@ used as INPUTFIELD_CB (see #559)
1701    awmm->create_input_field(current_ed4w()->awar_path_for_cursor, 7);
1702
1703    awmm->at("ecoli");
1704    awmm->callback(makeWindowCallback(ED4_jump_to_cursor_position, current_ed4w()->awar_path_for_Ecoli, ED4_POS_ECOLI)); // @@@ used as INPUTFIELD_CB (see #559)
1705    awmm->create_input_field(current_ed4w()->awar_path_for_Ecoli, 6);
1706
1707    awmm->at("base");
1708    awmm->callback(makeWindowCallback(ED4_jump_to_cursor_position, current_ed4w()->awar_path_for_basePos, ED4_POS_BASE)); // @@@ used as INPUTFIELD_CB (see #559)
1709    awmm->create_input_field(current_ed4w()->awar_path_for_basePos, 6);
1710
1711    awmm->at("iupac");
1712    awmm->callback(makeWindowCallback(ED4_set_iupac, current_ed4w()->awar_path_for_IUPAC)); // @@@ used as INPUTFIELD_CB (see #559)
1713    awmm->create_input_field(current_ed4w()->awar_path_for_IUPAC, 4);
1714
1715    awmm->at("helixnr");
1716    awmm->callback(makeWindowCallback(ED4_set_helixnr, current_ed4w()->awar_path_for_helixNr)); // @@@ used as INPUTFIELD_CB (see #559)
1717    awmm->create_input_field(current_ed4w()->awar_path_for_helixNr, 5);
1718
1719    // ----------------------------
1720    //      jump/get/undo/redo
1721
1722    awmm->button_length(4);
1723
1724    awmm->at("jump");
1725    awmm->callback(ED4_jump_to_current_species);
1726    awmm->help_text("e4_get_species.hlp");
1727    awmm->create_button("JUMP", "Jump");
1728
1729    awmm->at("get");
1730    awmm->callback(makeWindowCallback(ED4_get_and_jump_to_current));
1731    awmm->help_text("e4_get_species.hlp");
1732    awmm->create_button("GET", "Get");
1733
1734    awmm->button_length(0);
1735
1736    awmm->at("undo");
1737    awmm->callback(makeWindowCallback(ED4_undo_redo, GB_UNDO_UNDO));
1738    awmm->help_text("undo.hlp");
1739    awmm->create_button("UNDO", "#undo.xpm");
1740
1741    awmm->at("redo");
1742    awmm->callback(makeWindowCallback(ED4_undo_redo, GB_UNDO_REDO));
1743    awmm->help_text("undo.hlp");
1744    awmm->create_button("REDO", "#redo.xpm");
1745
1746    // --------------------------
1747    //      aligner / SAIviz
1748
1749    awmm->button_length(7);
1750
1751    awmm->at("aligner");
1752    awmm->callback(makeCreateWindowCallback(ED4_create_faligner_window, ED4_get_aligner_data_access()));
1753    awmm->help_text("faligner.hlp");
1754    awmm->create_button("ALIGNER", "Aligner");
1755
1756    awmm->at("saiviz");
1757    awmm->callback(ED4_createVisualizeSAI_window);
1758    awmm->help_text("visualizeSAI.hlp");
1759    awmm->create_button("SAIVIZ", "SAIviz");
1760
1761    // -------------------------------------------
1762    //      align/insert/protection/direction
1763
1764    awmm->button_length(0);
1765
1766    awmm->at("protect");
1767    awmm->create_option_menu(AWAR_EDIT_SECURITY_LEVEL, true);
1768    awmm->insert_option        ("0", NULp, 0);
1769    awmm->insert_option        ("1", NULp, 1);
1770    awmm->insert_option        ("2", NULp, 2);
1771    awmm->insert_option        ("3", NULp, 3);
1772    awmm->insert_option        ("4", NULp, 4);
1773    awmm->insert_option        ("5", NULp, 5);
1774    awmm->insert_default_option("6", NULp, 6);
1775    awmm->update_option_menu();
1776
1777    // draw protection icon AFTER protection!!
1778    awmm->at("pico");
1779    awmm->create_button(NULp, "#protect.xpm");
1780
1781    // draw align/edit-button AFTER protection!!
1782    awmm->at("edit");
1783    awmm->create_toggle(AWAR_EDIT_MODE, "#edit/align.xpm", "#edit/editseq.xpm", 7);
1784
1785    awmm->at("insert");
1786    awmm->create_text_toggle(AWAR_INSERT_MODE, "Replace", "Insert", 7);
1787
1788    awmm->at("direct");
1789    awmm->create_toggle(AWAR_EDIT_RIGHTWARD, "#edit/3to5.xpm", "#edit/5to3.xpm", 7);
1790
1791    // -------------------------
1792    //      secedit / rna3d
1793
1794    int xoffset = 0;
1795
1796    if (alignment_type == GB_AT_RNA) { // if the database contains valid alignment of rRNA sequences
1797        // add buttons for RNA3D and SECEDIT plugins
1798
1799        awmm->button_length(0);
1800
1801        awmm->at("secedit");
1802        awmm->callback(makeWindowCallback(ED4_start_plugin, gb_main, "SECEDIT"));
1803        awmm->help_text("arb_secedit.hlp");
1804        awmm->create_button("SECEDIT", "#edit/secedit.xpm");
1805
1806#if defined(ARB_OPENGL)
1807        awmm->at("rna3d");
1808        awmm->callback(makeWindowCallback(ED4_start_plugin, gb_main, "RNA3D"));
1809        awmm->help_text("rna3d_general.hlp");
1810        awmm->create_button("RNA3D", "#edit/rna3d.xpm");
1811#endif // ARB_OPENGL
1812    }
1813    else {
1814        awmm->at("secedit");
1815        int xsecedit = awmm->get_at_xposition();
1816        awmm->at("zoom");
1817        int xzoom    = awmm->get_at_xposition();
1818        xoffset      = xsecedit-xzoom; // shift message stuff to the left by xoffset
1819    }
1820
1821    {
1822        int x, y;
1823
1824        awmm->at("zoom");
1825        if (xoffset) { awmm->get_at_position(&x, &y); awmm->at(x+xoffset, y); }
1826        awmm->callback(ED4_zoom_message_window);
1827        awmm->create_button("ZOOM", "#edit/zoom.xpm");
1828
1829        awmm->at("clear");
1830        if (xoffset) { awmm->get_at_position(&x, &y); awmm->at(x+xoffset, y); }
1831        awmm->callback(aw_clear_message_cb);
1832        awmm->create_button("CLEAR", "#edit/clear.xpm");
1833
1834        awmm->at("errortext");
1835        if (xoffset) { awmm->get_at_position(&x, &y); awmm->at(x+xoffset, y); }
1836        aw_root->awar_string(AWAR_ERROR_MESSAGES, "This is ARB Edit4 [Build " ARB_VERSION "]");
1837        awmm->create_text_field(AWAR_ERROR_MESSAGES);
1838        aw_set_local_message();
1839    }
1840
1841    // ---------------------
1842    //      'more' area
1843
1844    awmm->at("cons");
1845    awmm->create_toggle(ED4_AWAR_CONSENSUS_SHOW, "#edit/nocons.xpm", "#edit/cons.xpm");
1846
1847    awmm->at("num");
1848    awmm->create_toggle(ED4_AWAR_DIGITS_AS_REPEAT, "#edit/norepeat.xpm", "#edit/repeat.xpm");
1849
1850    awmm->at("key");
1851    awmm->create_toggle("key_mapping/enable", "#edit/nokeymap.xpm", "#edit/keymap.xpm");
1852
1853    // search
1854
1855    awmm->button_length(0);
1856#define INSERT_SEARCH_FIELDS(Short, label_prefix, prefix)       \
1857    insert_search_fields(awmm,                                  \
1858                         #label_prefix,                         \
1859                         #prefix,                               \
1860                         ED4_AWAR_##prefix##_SEARCH_PATTERN,    \
1861                         ED4_AWAR_##prefix##_SEARCH_SHOW,       \
1862                         Short,                                 \
1863                         ED4_##prefix##_PATTERN,                \
1864                         current_ed4w()                         \
1865        )
1866
1867    INSERT_SEARCH_FIELDS(0, u1, USER1);
1868    INSERT_SEARCH_FIELDS(0, u2, USER2);
1869    INSERT_SEARCH_FIELDS(0, pro, PROBE);
1870    INSERT_SEARCH_FIELDS(1, pri1, PRIMER1);
1871    INSERT_SEARCH_FIELDS(1, pri2, PRIMER2);
1872    INSERT_SEARCH_FIELDS(1, pri3, PRIMER3);
1873    INSERT_SEARCH_FIELDS(1, sig1, SIG1);
1874    INSERT_SEARCH_FIELDS(1, sig2, SIG2);
1875    INSERT_SEARCH_FIELDS(1, sig3, SIG3);
1876
1877#undef INSERT_SEARCH_FIELDS
1878
1879    awmm->at("alast");
1880    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(-1, ED4_ANY_PATTERN), current_ed4w()));
1881    awmm->create_button("ALL_SEARCH_LAST", "#edit/last.xpm");
1882
1883    awmm->at("anext");
1884    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(+1, ED4_ANY_PATTERN), current_ed4w()));
1885    awmm->create_button("ALL_SEARCH_NEXT", "#edit/next.xpm");
1886
1887    title_mode_changed(aw_root, awmm);
1888
1889    // Buttons at left window border
1890
1891    awmm->create_mode("edit/arrow.xpm", "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_MOVE));
1892    awmm->create_mode("edit/kill.xpm",  "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_KILL));
1893    awmm->create_mode("edit/mark.xpm",  "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_MARK));
1894    awmm->create_mode("mode_info.xpm",  "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_INFO));
1895
1896    FastAligner_create_variables(awmm->get_root(), props_db);
1897
1898#if defined(DEBUG)
1899    AWT_check_action_ids(awmm->get_root(), "");
1900#endif
1901
1902    announce_useraction_in(awmm);
1903
1904    return ED4_R_OK;
1905}
1906
1907AW_window *ED4_root::create_first_window() {
1908    // Note: other windows are generated by generate_window
1909    AW_device  *device     = NULp;
1910    ED4_window *new_window = NULp;
1911
1912    generate_window(&device, &new_window);
1913
1914    ED4_LocalWinContext uses(new_window);
1915
1916    ED4_calc_terminal_extentions(); // (Note: done again later, but otherwise variables are used uninitialized);
1917
1918    DRAW                    = 1;
1919    move_cursor             = 0;
1920    max_seq_terminal_length = 0;
1921
1922    ED4_init_notFoundMessage();
1923
1924    return new_window->aww;
1925}
1926
1927ED4_index ED4_root::pixel2pos(AW_pos click_x) {
1928    // 'click_x' is the x-offset into the terminal in pixels
1929    // returns the x-offset into the terminal in base positions (clipped to max. allowed position)
1930
1931    int       length_of_char = font_group.get_width(ED4_G_SEQUENCES);
1932    ED4_index scr_pos        = int((click_x-CHARACTEROFFSET) / length_of_char);
1933    int       max_scrpos     = root_group_man->remap()->get_max_screen_pos();
1934
1935    if (scr_pos>max_scrpos) scr_pos = max_scrpos;
1936
1937    return scr_pos;
1938}
1939
1940inline char *detectProperties(GBDATA *gb_main) {
1941    char *propname = NULp;
1942
1943    // check if edit4_?na.arb / edit4_ali_???.arb exist in $ARB_PROP
1944    for (int mode = 0; !propname && mode <= 1; ++mode) {
1945        const char *fullprop = GB_path_in_arbprop(propertyName(gb_main, mode));
1946        if (GB_is_regularfile(fullprop)) {
1947            freedup(propname, fullprop);
1948        }
1949    }
1950
1951    // if not, use 'mode 2', i.e. "edit4.arb"
1952    // (no full path, we want to load default from arb_defaults)
1953    if (!propname) propname = ARB_strdup(propertyName(gb_main, 2));
1954
1955    return propname;
1956}
1957
1958ED4_root::ED4_root(GBDATA *gb_main_)
1959    : most_recently_used_window(NULp),
1960      cons_param(NULp),
1961      gb_main(gb_main_),
1962      db_name(detectProperties(gb_main)),
1963      aw_root(AWT_create_root(db_name, "ARB_EDIT4", need_macro_ability())),
1964      props_db(AW_ROOT_DEFAULT),
1965      first_window(NULp),
1966      main_manager(NULp),
1967      middle_area_man(NULp),
1968      top_area_man(NULp),
1969      root_group_man(NULp),
1970      selected_objects(new ED4_selected_list),
1971      folding_action(false),
1972      species_mode(ED4_SM_MOVE),
1973      ecoli_ref(NULp),
1974      alignment_name(NULp),
1975      alignment_type(GB_AT_UNKNOWN),
1976      reference(NULp),
1977      sequence_colors(NULp),
1978      gc_manager(NULp),
1979      st_ml(NULp),
1980      helix(NULp),
1981      helix_spacing(0),
1982      helix_add_spacing(0),
1983      terminal_add_spacing(0),
1984      protstruct(NULp),
1985      protstruct_len(0),
1986      edk(NULp),
1987      column_stat_activated(false),
1988      column_stat_initialized(false),
1989      visualizeSAI(false),
1990      visualizeSAI_allSpecies(false),
1991      loadable_SAIs(LSAI_UNUSED),
1992      temp_gc(0)
1993{}
1994
1995
1996ED4_root::~ED4_root() {
1997    delete aw_root;
1998    delete first_window;
1999    delete reference; // needs to be deleted before main_manager (to ensure reference callbacks are removed)
2000    delete main_manager; // also deletes middle_area_man + top_area_man
2001    delete ecoli_ref;
2002    delete selected_objects;
2003    delete helix;
2004    delete sequence_colors;
2005    delete edk;
2006    STAT_destroy_ST_ML(st_ml);
2007
2008    free(protstruct);
2009    free(db_name);
2010    free(alignment_name);
2011}
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